1
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de Freitas Pereira M, Cohen D, Auer L, Aubry N, Bogeat-Triboulot MB, Buré C, Engle NL, Jolivet Y, Kohler A, Novák O, Pavlović I, Priault P, Tschaplinski TJ, Hummel I, Vaultier MN, Veneault-Fourrey C. Ectomycorrhizal symbiosis prepares its host locally and systemically for abiotic cue signaling. Plant J 2023; 116:1784-1803. [PMID: 37715981 DOI: 10.1111/tpj.16465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 08/31/2023] [Accepted: 09/05/2023] [Indexed: 09/18/2023]
Abstract
Tree growth and survival are dependent on their ability to perceive signals, integrate them, and trigger timely and fitted molecular and growth responses. While ectomycorrhizal symbiosis is a predominant tree-microbe interaction in forest ecosystems, little is known about how and to what extent it helps trees cope with environmental changes. We hypothesized that the presence of Laccaria bicolor influences abiotic cue perception by Populus trichocarpa and the ensuing signaling cascade. We submitted ectomycorrhizal or non-ectomycorrhizal P. trichocarpa cuttings to short-term cessation of watering or ozone fumigation to focus on signaling networks before the onset of any physiological damage. Poplar gene expression, metabolite levels, and hormone levels were measured in several organs (roots, leaves, mycorrhizas) and integrated into networks. We discriminated the signal responses modified or maintained by ectomycorrhization. Ectomycorrhizas buffered hormonal changes in response to short-term environmental variations systemically prepared the root system for further fungal colonization and alleviated part of the root abscisic acid (ABA) signaling. The presence of ectomycorrhizas in the roots also modified the leaf multi-omics landscape and ozone responses, most likely through rewiring of the molecular drivers of photosynthesis and the calcium signaling pathway. In conclusion, P. trichocarpa-L. bicolor symbiosis results in a systemic remodeling of the host's signaling networks in response to abiotic changes. In addition, ectomycorrhizal, hormonal, metabolic, and transcriptomic blueprints are maintained in response to abiotic cues, suggesting that ectomycorrhizas are less responsive than non-mycorrhizal roots to abiotic challenges.
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Affiliation(s)
| | - David Cohen
- Université de Lorraine, AgroParisTech, INRAE, UMR Silva, F-54000, Nancy, France
| | - Lucas Auer
- Université de Lorraine, INRAE, Laboratory of Excellence ARBRE, UMR Interactions Arbres/Microorganismes, F-54000, Nancy, France
| | - Nathalie Aubry
- Université de Lorraine, AgroParisTech, INRAE, UMR Silva, F-54000, Nancy, France
| | | | - Cyril Buré
- Université de Lorraine, AgroParisTech, INRAE, UMR Silva, F-54000, Nancy, France
| | - Nancy L Engle
- Plant Systems Biology Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831, USA
| | - Yves Jolivet
- Université de Lorraine, AgroParisTech, INRAE, UMR Silva, F-54000, Nancy, France
| | - Annegret Kohler
- Université de Lorraine, INRAE, Laboratory of Excellence ARBRE, UMR Interactions Arbres/Microorganismes, F-54000, Nancy, France
| | - Ondřej Novák
- Laboratory of Growth Regulators, Faculty of Science of Palacký University & Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 27, 78371, Olomouc, Czech Republic
| | - Iva Pavlović
- Laboratory of Growth Regulators, Faculty of Science of Palacký University & Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 27, 78371, Olomouc, Czech Republic
| | - Pierrick Priault
- Université de Lorraine, AgroParisTech, INRAE, UMR Silva, F-54000, Nancy, France
| | - Timothy J Tschaplinski
- Plant Systems Biology Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831, USA
| | - Irène Hummel
- Université de Lorraine, AgroParisTech, INRAE, UMR Silva, F-54000, Nancy, France
| | | | - Claire Veneault-Fourrey
- Université de Lorraine, INRAE, Laboratory of Excellence ARBRE, UMR Interactions Arbres/Microorganismes, F-54000, Nancy, France
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2
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Yao T, Zhang J, Yates TB, Shrestha HK, Engle NL, Ployet R, John C, Feng K, Bewg WP, Chen MSS, Lu H, Harding SA, Qiao Z, Jawdy SS, Shu M, Yuan W, Mozaffari K, Harman-Ware AE, Happs RM, York LM, Binder BM, Yoshinaga Y, Daum C, Tschaplinski TJ, Abraham PE, Tsai CJ, Barry K, Lipzen A, Schmutz J, Tuskan GA, Chen JG, Muchero W. Expression quantitative trait loci mapping identified PtrXB38 as a key hub gene in adventitious root development in Populus. New Phytol 2023; 239:2248-2264. [PMID: 37488708 DOI: 10.1111/nph.19126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 06/13/2023] [Indexed: 07/26/2023]
Abstract
Plant establishment requires the formation and development of an extensive root system with architecture modulated by complex genetic networks. Here, we report the identification of the PtrXB38 gene as an expression quantitative trait loci (eQTL) hotspot, mapped using 390 leaf and 444 xylem Populus trichocarpa transcriptomes. Among predicted targets of this trans-eQTL were genes involved in plant hormone responses and root development. Overexpression of PtrXB38 in Populus led to significant increases in callusing and formation of both stem-born roots and base-born adventitious roots. Omics studies revealed that genes and proteins controlling auxin transport and signaling were involved in PtrXB38-mediated adventitious root formation. Protein-protein interaction assays indicated that PtrXB38 interacts with components of endosomal sorting complexes required for transport machinery, implying that PtrXB38-regulated root development may be mediated by regulating endocytosis pathway. Taken together, this work identified a crucial root development regulator and sheds light on the discovery of other plant developmental regulators through combining eQTL mapping and omics approaches.
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Affiliation(s)
- Tao Yao
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Jin Zhang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, 311300, China
| | - Timothy B Yates
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Bredesen Center for Interdisciplinary Research, University of Tennessee, Knoxville, TN, 37996, USA
| | - Him K Shrestha
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Nancy L Engle
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Raphael Ployet
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Cai John
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Bredesen Center for Interdisciplinary Research, University of Tennessee, Knoxville, TN, 37996, USA
| | - Kai Feng
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - William Patrick Bewg
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA, 30602, USA
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Margot S S Chen
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA, 30602, USA
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Haiwei Lu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Department of Academic Education, Central Community College - Hastings, Hastings, NE, 68902, USA
| | - Scott A Harding
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA, 30602, USA
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Zhenzhen Qiao
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Sara S Jawdy
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Mengjun Shu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Wenya Yuan
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, 311300, China
| | - Khadijeh Mozaffari
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA, 30602, USA
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Anne E Harman-Ware
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Renee M Happs
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Larry M York
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Brad M Binder
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Yuko Yoshinaga
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Christopher Daum
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Timothy J Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Paul E Abraham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Chung-Jui Tsai
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, 311300, China
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jeremy Schmutz
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
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3
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Rasor BJ, Chirania P, Rybnicky GA, Giannone RJ, Engle NL, Tschaplinski TJ, Karim AS, Hettich RL, Jewett MC. Mechanistic Insights into Cell-Free Gene Expression through an Integrated -Omics Analysis of Extract Processing Methods. ACS Synth Biol 2023; 12:405-418. [PMID: 36700560 DOI: 10.1021/acssynbio.2c00339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Cell-free systems derived from crude cell extracts have developed into tools for gene expression, with applications in prototyping, biosensing, and protein production. Key to the development of these systems is optimization of cell extract preparation methods. However, the applied nature of these optimizations often limits investigation into the complex nature of the extracts themselves, which contain thousands of proteins and reaction networks with hundreds of metabolites. Here, we sought to uncover the black box of proteins and metabolites in Escherichia coli cell-free reactions based on different extract preparation methods. We assess changes in transcription and translation activity from σ70 promoters in extracts prepared with acetate or glutamate buffer and the common post-lysis processing steps of a runoff incubation and dialysis. We then utilize proteomic and metabolomic analyses to uncover potential mechanisms behind these changes in gene expression, highlighting the impact of cold shock-like proteins and the role of buffer composition.
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Affiliation(s)
- Blake J Rasor
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States.,Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States.,Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Payal Chirania
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States.,Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Grant A Rybnicky
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States.,Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States.,Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, Illinois 60208, United States
| | - Richard J Giannone
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Nancy L Engle
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Timothy J Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Ashty S Karim
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States.,Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States.,Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Robert L Hettich
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States.,Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States.,Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois 60611, United States.,Simpson Querrey Institute, Northwestern University, Chicago, Illinois 60611, United States
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4
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Dahal S, Hurst GB, Chourey K, Engle NL, Burdick LH, Morrell-Falvey JL, Tschaplinski TJ, Doktycz MJ, Pelletier DA. Mechanism for Utilization of the Populus-Derived Metabolite Salicin by a Pseudomonas- Rahnella Co-Culture. Metabolites 2023; 13:metabo13020140. [PMID: 36837758 PMCID: PMC9959693 DOI: 10.3390/metabo13020140] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 12/30/2022] [Accepted: 01/10/2023] [Indexed: 01/18/2023] Open
Abstract
Pseudomonas fluorescens GM16 associates with Populus, a model plant in biofuel production. Populus releases abundant phenolic glycosides such as salicin, but P. fluorescens GM16 cannot utilize salicin, whereas Pseudomonas strains are known to utilize compounds similar to the aglycone moiety of salicin-salicyl alcohol. We propose that the association of Pseudomonas to Populus is mediated by another organism (such as Rahnella aquatilis OV744) that degrades the glucosyl group of salicin. In this study, we demonstrate that in the Rahnella-Pseudomonas salicin co-culture model, Rahnella grows by degrading salicin to glucose 6-phosphate and salicyl alcohol which is secreted out and is subsequently utilized by P. fluorescens GM16 for its growth. Using various quantitative approaches, we elucidate the individual pathways for salicin and salicyl alcohol metabolism present in Rahnella and Pseudomonas, respectively. Furthermore, we were able to establish that the salicyl alcohol cross-feeding interaction between the two strains on salicin medium is carried out through the combination of their respective individual pathways. The research presents one of the potential advantages of salicyl alcohol release by strains such as Rahnella, and how phenolic glycosides could be involved in attracting multiple types of bacteria into the Populus microbiome.
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Affiliation(s)
- Sanjeev Dahal
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
- Genome Science and Technology Program, University of Tennessee, Knoxville, TN 37996, USA
- Department of Chemical Engineering, Queen’s University, Kingston, ON K7L 3N6, Canada
| | - Gregory B. Hurst
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Karuna Chourey
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Nancy L. Engle
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Leah H. Burdick
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | | | | | - Mitchel J. Doktycz
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Dale A. Pelletier
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
- Correspondence:
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5
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Shrestha HK, Fichman Y, Engle NL, Tschaplinski TJ, Mittler R, Dixon RA, Hettich RL, Barros J, Abraham PE. Multi-omic characterization of bifunctional peroxidase 4-coumarate 3-hydroxylase knockdown in Brachypodium distachyon provides insights into lignin modification-associated pleiotropic effects. Front Plant Sci 2022; 13:908649. [PMID: 36247563 PMCID: PMC9554711 DOI: 10.3389/fpls.2022.908649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 09/09/2022] [Indexed: 06/16/2023]
Abstract
A bifunctional peroxidase enzyme, 4-coumarate 3-hydroxylase (C3H/APX), provides a parallel route to the shikimate shunt pathway for the conversion of 4-coumarate to caffeate in the early steps of lignin biosynthesis. Knockdown of C3H/APX (C3H/APX-KD) expression has been shown to reduce the lignin content in Brachypodium distachyon. However, like many other lignin-modified plants, C3H/APX-KDs show unpredictable pleiotropic phenotypes, including stunted growth, delayed senescence, and reduced seed yield. A system-wide level understanding of altered biological processes in lignin-modified plants can help pinpoint the lignin-modification associated growth defects to benefit future studies aiming to negate the yield penalty. Here, a multi-omic approach was used to characterize molecular changes resulting from C3H/APX-KD associated lignin modification and negative growth phenotype in Brachypodium distachyon. Our findings demonstrate that C3H/APX knockdown in Brachypodium stems substantially alters the abundance of enzymes implicated in the phenylpropanoid biosynthetic pathway and disrupt cellular redox homeostasis. Moreover, it elicits plant defense responses associated with intracellular kinases and phytohormone-based signaling to facilitate growth-defense trade-offs. A deeper understanding along with potential targets to mitigate the pleiotropic phenotypes identified in this study could aid to increase the economic feasibility of lignocellulosic biofuel production.
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Affiliation(s)
- Him K. Shrestha
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Genome Science and Technology, University of Tennessee-Knoxville, Knoxville, TN, United States
| | - Yosef Fichman
- Division of Plant Sciences and Interdisciplinary Plant Group, University of Missouri, Columbia, MO, United States
| | - Nancy L. Engle
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | | | - Ron Mittler
- Division of Plant Sciences and Interdisciplinary Plant Group, University of Missouri, Columbia, MO, United States
| | - Richard A. Dixon
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX, United States
| | - Robert L. Hettich
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Jaime Barros
- Division of Plant Sciences and Interdisciplinary Plant Group, University of Missouri, Columbia, MO, United States
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX, United States
| | - Paul E. Abraham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
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6
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Barros J, Shrestha HK, Serrani-Yarce JC, Engle NL, Abraham PE, Tschaplinski TJ, Hettich RL, Dixon RA. Proteomic and metabolic disturbances in lignin-modified Brachypodium distachyon. Plant Cell 2022; 34:3339-3363. [PMID: 35670759 PMCID: PMC9421481 DOI: 10.1093/plcell/koac171] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 05/23/2022] [Indexed: 05/30/2023]
Abstract
Lignin biosynthesis begins with the deamination of phenylalanine and tyrosine (Tyr) as a key branch point between primary and secondary metabolism in land plants. Here, we used a systems biology approach to investigate the global metabolic responses to lignin pathway perturbations in the model grass Brachypodium distachyon. We identified the lignin biosynthetic protein families and found that ammonia-lyases (ALs) are among the most abundant proteins in lignifying tissues in grasses. Integrated metabolomic and proteomic data support a link between lignin biosynthesis and primary metabolism mediated by the ammonia released from ALs that is recycled for the synthesis of amino acids via glutamine. RNA interference knockdown of lignin genes confirmed that the route of the canonical pathway using shikimate ester intermediates is not essential for lignin formation in Brachypodium, and there is an alternative pathway from Tyr via sinapic acid for the synthesis of syringyl lignin involving yet uncharacterized enzymatic steps. Our findings support a model in which plant ALs play a central role in coordinating the allocation of carbon for lignin synthesis and the nitrogen available for plant growth. Collectively, these data also emphasize the value of integrative multiomic analyses to advance our understanding of plant metabolism.
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Affiliation(s)
| | - Him K Shrestha
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
- Genome Science and Technology, University of Tennessee, Knoxville, Tennessee 37916, USA
| | - Juan C Serrani-Yarce
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, Texas 76201, USA
| | - Nancy L Engle
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, Texas 76201, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
| | - Paul E Abraham
- Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
| | - Timothy J Tschaplinski
- Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
| | - Robert L Hettich
- Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
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7
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Bewg WP, Harding SA, Engle NL, Vaidya BN, Zhou R, Reeves J, Horn TW, Joshee N, Jenkins JW, Shu S, Barry KW, Yoshinaga Y, Grimwood J, Schmitz RJ, Schmutz J, Tschaplinski TJ, Tsai CJ. Multiplex knockout of trichome-regulating MYB duplicates in hybrid poplar using a single gRNA. Plant Physiol 2022; 189:516-526. [PMID: 35298644 PMCID: PMC9157173 DOI: 10.1093/plphys/kiac128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 02/24/2022] [Indexed: 05/13/2023]
Abstract
As the focus for CRISPR/Cas-edited plants moves from proof-of-concept to real-world applications, precise gene manipulation will increasingly require concurrent multiplex editing for polygenic traits. A common approach for editing across multiple sites is to design one guide RNA (gRNA) per target; however, this complicates construct assembly and increases the possibility of off-target mutations. In this study, we utilized one gRNA to target MYB186, a known positive trichome regulator, as well as its paralogs MYB138 and MYB38 at a consensus site for mutagenesis in hybrid poplar (Populus tremula × P. alba INRA 717-1B4). Unexpected duplications of MYB186 and MYB138 resulted in eight alleles for the three targeted genes in the hybrid poplar. Deep sequencing and polymerase chain reaction analyses confirmed editing across all eight targets in nearly all of the resultant glabrous mutants, ranging from small indels to large genomic dropouts, with no off-target activity detected at four potential sites. This highlights the effectiveness of a single gRNA targeting conserved exonic regions for multiplex editing. Additionally, cuticular wax and whole-leaf analyses showed a complete absence of triterpenes in the trichomeless mutants, hinting at a previously undescribed role for the nonglandular trichomes of poplar.
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Affiliation(s)
- William P Bewg
- School of Forestry and Natural Resources, University of Georgia, Athens, Georgia 30602, USA
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602, USA
| | - Scott A Harding
- School of Forestry and Natural Resources, University of Georgia, Athens, Georgia 30602, USA
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602, USA
| | - Nancy L Engle
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
| | - Brajesh N Vaidya
- Department of Plant Science, Fort Valley State University, Georgia, 31030, USA
| | - Ran Zhou
- School of Forestry and Natural Resources, University of Georgia, Athens, Georgia 30602, USA
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602, USA
| | - Jacob Reeves
- Department of Computer Science, University of Georgia, Athens, Georgia 30602, USA
| | - Thomas W Horn
- Department of Computer Science, University of Georgia, Athens, Georgia 30602, USA
| | - Nirmal Joshee
- Department of Plant Science, Fort Valley State University, Georgia, 31030, USA
| | - Jerry W Jenkins
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
- U.S. Department of Energy Joint Genome Institute, Berkeley, California 94720, USA
| | - Shengqiang Shu
- U.S. Department of Energy Joint Genome Institute, Berkeley, California 94720, USA
| | - Kerrie W Barry
- U.S. Department of Energy Joint Genome Institute, Berkeley, California 94720, USA
| | - Yuko Yoshinaga
- U.S. Department of Energy Joint Genome Institute, Berkeley, California 94720, USA
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
- U.S. Department of Energy Joint Genome Institute, Berkeley, California 94720, USA
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
- U.S. Department of Energy Joint Genome Institute, Berkeley, California 94720, USA
| | | | - Chung-Jui Tsai
- School of Forestry and Natural Resources, University of Georgia, Athens, Georgia 30602, USA
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602, USA
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8
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Zhuo C, Wang X, Docampo-Palacios M, Sanders BC, Engle NL, Tschaplinski TJ, Hendry JI, Maranas CD, Chen F, Dixon RA. Developmental changes in lignin composition are driven by both monolignol supply and laccase specificity. Sci Adv 2022; 8:eabm8145. [PMID: 35263134 PMCID: PMC8906750 DOI: 10.1126/sciadv.abm8145] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 01/17/2022] [Indexed: 05/25/2023]
Abstract
The factors controlling lignin composition remain unclear. Catechyl (C)-lignin is a homopolymer of caffeyl alcohol with unique properties as a biomaterial and precursor of industrial chemicals. The lignin synthesized in the seed coat of Cleome hassleriana switches from guaiacyl (G)- to C-lignin at around 12 to 14 days after pollination (DAP), associated with a rerouting of the monolignol pathway. Lack of synthesis of caffeyl alcohol limits C-lignin formation before around 12 DAP, but coniferyl alcohol is still synthesized and highly accumulated after 14 DAP. We propose a model in which, during C-lignin biosynthesis, caffeyl alcohol noncompetitively inhibits oxidation of coniferyl alcohol by cell wall laccases, a process that might limit movement of coniferyl alcohol to the apoplast. Developmental changes in both substrate availability and laccase specificity together account for the metabolic fates of G- and C-monolignols in the Cleome seed coat.
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Affiliation(s)
- Chunliu Zhuo
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, 1155 Union Circle #311428, Denton, TX 76203, USA
- Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Xin Wang
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, 1155 Union Circle #311428, Denton, TX 76203, USA
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Maite Docampo-Palacios
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, 1155 Union Circle #311428, Denton, TX 76203, USA
| | - Brian C. Sanders
- Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Nancy L. Engle
- Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Timothy J. Tschaplinski
- Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - John I. Hendry
- Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Costas D. Maranas
- Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Fang Chen
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, 1155 Union Circle #311428, Denton, TX 76203, USA
- Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Richard A. Dixon
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, 1155 Union Circle #311428, Denton, TX 76203, USA
- Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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9
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Villalobos Solis MI, Engle NL, Spangler MK, Cottaz S, Fort S, Maeda J, Ané JM, Tschaplinski TJ, Labbé JL, Hettich RL, Abraham PE, Rush TA. Expanding the Biological Role of Lipo-Chitooligosaccharides and Chitooligosaccharides in Laccaria bicolor Growth and Development. Front Fungal Biol 2022; 3:808578. [PMID: 37746234 PMCID: PMC10512320 DOI: 10.3389/ffunb.2022.808578] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 01/10/2022] [Indexed: 09/26/2023]
Abstract
The role of lipo-chitooligosaccharides (LCOs) as signaling molecules that mediate the establishment of symbiotic relationships between fungi and plants is being redefined. New evidence suggests that the production of these molecular signals may be more of a common trait in fungi than what was previously thought. LCOs affect different aspects of growth and development in fungi. For the ectomycorrhizal forming fungi, Laccaria bicolor, the production and effects of LCOs have always been studied with a symbiotic plant partner; however, there is still no scientific evidence describing the effects that these molecules have on this organism. Here, we explored the physiological, molecular, and metabolomic changes in L. bicolor when grown in the presence of exogenous sulfated and non-sulfated LCOs, as well as the chitooligomers, chitotetraose (CO4), and chitooctaose (CO8). Physiological data from 21 days post-induction showed reduced fungal growth in response to CO and LCO treatments compared to solvent controls. The underlying molecular changes were interrogated by proteomics, which revealed substantial alterations to biological processes related to growth and development. Moreover, metabolite data showed that LCOs and COs caused a downregulation of organic acids, sugars, and fatty acids. At the same time, exposure to LCOs resulted in the overproduction of lactic acid in L. bicolor. Altogether, these results suggest that these signals might be fungistatic compounds and contribute to current research efforts investigating the emerging impacts of these molecules on fungal growth and development.
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Affiliation(s)
| | - Nancy L. Engle
- Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Margaret K. Spangler
- Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Sylvain Cottaz
- Université Grenoble Alpes, CNRS, CERMAV, Grenoble, France
| | - Sébastien Fort
- Université Grenoble Alpes, CNRS, CERMAV, Grenoble, France
| | - Junko Maeda
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States
- Department of Agronomy, University of Wisconsin-Madison, Madison, WI, United States
| | - Jean-Michel Ané
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States
- Department of Agronomy, University of Wisconsin-Madison, Madison, WI, United States
| | | | - Jesse L. Labbé
- Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Robert L. Hettich
- Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Paul E. Abraham
- Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Tomás A. Rush
- Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
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10
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Sacko O, Engle NL, Tschaplinski TJ, Kumar S, Lee JW. Ozonized biochar filtrate effects on the growth of Pseudomonas putida and cyanobacteria Synechococcus elongatus PCC 7942. BIORESOUR BIOPROCESS 2022; 9:2. [PMID: 38647802 PMCID: PMC10991886 DOI: 10.1186/s40643-021-00491-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 12/27/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Biochar ozonization was previously shown to dramatically increase its cation exchange capacity, thus improving its nutrient retention capacity. The potential soil application of ozonized biochar warrants the need for a toxicity study that investigates its effects on microorganisms. RESULTS In the study presented here, we found that the filtrates collected from ozonized pine 400 biochar and ozonized rogue biochar did not have any inhibitory effects on the soil environmental bacteria Pseudomonas putida, even at high dissolved organic carbon (DOC) concentrations of 300 ppm. However, the growth of Synechococcus elongatus PCC 7942 was inhibited by the ozonized biochar filtrates at DOC concentrations greater than 75 ppm. Further tests showed the presence of some potential inhibitory compounds (terephthalic acid and p-toluic acid) in the filtrate of non-ozonized pine 400 biochar; these compounds were greatly reduced upon wet-ozonization of the biochar material. Nutrient detection tests also showed that dry-ozonization of rogue biochar enhanced the availability of nitrate and phosphate in its filtrate, a property that may be desirable for soil application. CONCLUSION Ozonized biochar substances can support soil environmental bacterium Pseudomonas putida growth, since ozonization detoxifies the potential inhibitory aromatic molecules.
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Affiliation(s)
- Oumar Sacko
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA, 23529, USA
| | - Nancy L Engle
- Oak Ridge National Laboratory, PO Box 2008, Oak Ridge, TN, 37831, USA
| | | | - Sandeep Kumar
- Department of Civil and Environmental Engineering, Old Dominion University, Norfolk, VA, 23529, USA
| | - James Weifu Lee
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA, 23529, USA.
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11
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Qiao Z, Yates TB, Shrestha HK, Engle NL, Flanagan A, Morrell‐Falvey JL, Sun Y, Tschaplinski TJ, Abraham PE, Labbé J, Wang Z, Hettich RL, Tuskan GA, Muchero W, Chen J. Towards engineering ectomycorrhization into switchgrass bioenergy crops via a lectin receptor-like kinase. Plant Biotechnol J 2021; 19:2454-2468. [PMID: 34272801 PMCID: PMC8633507 DOI: 10.1111/pbi.13671] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 06/24/2021] [Accepted: 07/09/2021] [Indexed: 05/22/2023]
Abstract
Soil-borne microbes can establish compatible relationships with host plants, providing a large variety of nutritive and protective compounds in exchange for photosynthesized sugars. However, the molecular mechanisms mediating the establishment of these beneficial relationships remain unclear. Our previous genetic mapping and whole-genome resequencing studies identified a gene deletion event of a Populus trichocarpa lectin receptor-like kinase gene PtLecRLK1 in Populus deltoides that was associated with poor-root colonization by the ectomycorrhizal fungus Laccaria bicolor. By introducing PtLecRLK1 into a perennial grass known to be a non-host of L. bicolor, switchgrass (Panicum virgatum L.), we found that L. bicolor colonizes ZmUbipro-PtLecRLK1 transgenic switchgrass roots, which illustrates that the introduction of PtLecRLK1 has the potential to convert a non-host to a host of L. bicolor. Furthermore, transcriptomic and proteomic analyses on inoculated-transgenic switchgrass roots revealed genes/proteins overrepresented in the compatible interaction and underrepresented in the pathogenic defence pathway, consistent with the view that pathogenic defence response is down-regulated during compatible interaction. Metabolomic profiling revealed that root colonization in the transgenic switchgrass was associated with an increase in N-containing metabolites and a decrease in organic acids, sugars, and aromatic hydroxycinnamate conjugates, which are often seen in the early steps of establishing compatible interactions. These studies illustrate that PtLecRLK1 is able to render a plant susceptible to colonization by the ectomycorrhizal fungus L. bicolor and shed light on engineering mycorrhizal symbiosis into a non-host to enhance plant productivity and fitness on marginal lands.
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Affiliation(s)
- Zhenzhen Qiao
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
| | - Timothy B. Yates
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
- Bredesen Center for Interdisciplinary Research and Graduate EducationUniversity of TennesseeKnoxvilleTNUSA
| | - Him K. Shrestha
- Genome Science and TechnologyUniversity of TennesseeKnoxvilleTNUSA
- Chemical Science DivisionOak Ridge National LaboratoryOak RidgeTNUSA
| | - Nancy L. Engle
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
| | | | | | - Yali Sun
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
| | | | - Paul E. Abraham
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
- Chemical Science DivisionOak Ridge National LaboratoryOak RidgeTNUSA
| | - Jessy Labbé
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
| | | | - Robert L. Hettich
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
- Chemical Science DivisionOak Ridge National LaboratoryOak RidgeTNUSA
| | | | | | - Jin‐Gui Chen
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
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12
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Jiang SC, Engle NL, Banday ZZ, Cecchini NM, Jung HW, Tschaplinski TJ, Greenberg JT. ALD1 accumulation in Arabidopsis epidermal plastids confers local and non-autonomous disease resistance. J Exp Bot 2021; 72:2710-2726. [PMID: 33463678 PMCID: PMC8006555 DOI: 10.1093/jxb/eraa609] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 12/24/2020] [Indexed: 05/10/2023]
Abstract
The Arabidopsis plastid-localized ALD1 protein acts in the lysine catabolic pathway that produces infection-induced pipecolic acid (Pip), Pip derivatives, and basal non-Pip metabolite(s). ALD1 is indispensable for disease resistance associated with Pseudomonas syringae infections of naïve plants as well as those previously immunized by a local infection, a phenomenon called systemic acquired resistance (SAR). Pseudomonas syringae is known to associate with mesophyll as well as epidermal cells. To probe the importance of epidermal cells in conferring bacterial disease resistance, we studied plants in which ALD1 was only detectable in the epidermal cells of specific leaves. Local disease resistance and many features of SAR were restored when ALD1 preferentially accumulated in the epidermal plastids at immunization sites. Interestingly, SAR restoration occurred without appreciable accumulation of Pip or known Pip derivatives in secondary distal leaves. Our findings establish that ALD1 has a non-autonomous effect on pathogen growth and defense activation. We propose that ALD1 is sufficient in the epidermis of the immunized leaves to activate SAR, but basal ALD1 and possibly a non-Pip metabolite(s) are also needed at all infection sites to fully suppress bacterial growth. Thus, epidermal plastids that contain ALD1 play a key role in local and whole-plant immune signaling.
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Affiliation(s)
- Shang-Chuan Jiang
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL, USA
| | | | - Zeeshan Zahoor Banday
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL, USA
| | - Nicolás M Cecchini
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL, USA
| | - Ho Won Jung
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL, USA
| | | | - Jean T Greenberg
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL, USA
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13
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Veach AM, Morris R, Yip DZ, Yang ZK, Engle NL, Cregger MA, Tschaplinski TJ, Schadt CW. Correction to: Rhizosphere microbiomes diverge among Populus trichocarpa plant-host genotypes and chemotypes, but it depends on soil origin. Microbiome 2021; 9:21. [PMID: 33482901 PMCID: PMC7825163 DOI: 10.1186/s40168-021-01003-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
An amendment to this paper has been published and can be accessed via the original article.
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Affiliation(s)
- Allison M Veach
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN, 37831-6038, USA
| | - Reese Morris
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN, 37831-6038, USA
| | - Daniel Z Yip
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN, 37831-6038, USA
| | - Zamin K Yang
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN, 37831-6038, USA
| | - Nancy L Engle
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN, 37831-6038, USA
| | - Melissa A Cregger
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN, 37831-6038, USA
| | - Timothy J Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN, 37831-6038, USA
| | - Christopher W Schadt
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN, 37831-6038, USA.
- Department of Microbiology, University of Tennessee, Knoxville, TN, 37996, USA.
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14
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Saint-Vincent PMB, Ridout M, Engle NL, Lawrence TJ, Yeary ML, Tschaplinski TJ, Newcombe G, Pelletier DA. Isolation, Characterization, and Pathogenicity of Two Pseudomonas syringae Pathovars from Populus trichocarpa Seeds. Microorganisms 2020; 8:microorganisms8081137. [PMID: 32731357 PMCID: PMC7465253 DOI: 10.3390/microorganisms8081137] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 07/21/2020] [Accepted: 07/23/2020] [Indexed: 11/16/2022] Open
Abstract
Pseudomonas syringae is a ubiquitous plant pathogen, infecting both woody and herbaceous plants and resulting in devastating agricultural crop losses. Characterized by a remarkable specificity for plant hosts, P. syringae pathovars utilize a number of virulence factors including the type III secretion system and effector proteins to elicit disease in a particular host species. Here, two Pseudomonas syringae strains were isolated from diseased Populustrichocarpa seeds. The pathovars were capable of inhibiting poplar seed germination and were selective for the Populus genus. Sequencing of the newly described organisms revealed similarity to phylogroup II pathogens and genomic regions associated with woody host-associated plant pathogens, as well as genes for specific virulence factors. The host response to infection, as revealed through metabolomics, is the induction of the stress response through the accumulation of higher-order salicylates. Combined with necrosis on leaf surfaces, the plant appears to quickly respond by isolating infected tissues and mounting an anti-inflammatory defense. This study improves our understanding of the initial host response to epiphytic pathogens in Populus and provides a new model system for studying the effects of a bacterial pathogen on a woody host plant in which both organisms are fully genetically sequenced.
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Affiliation(s)
- Patricia MB Saint-Vincent
- Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; (P.M.S.-V.); (N.L.E.); (T.J.L.); (M.L.Y.); (T.J.T.)
- Geologic and Environmental Systems Directorate, National Energy Technology Laboratory, Pittsburgh, PA 15236, USA
| | - Mary Ridout
- Department of Forest, Rangeland and Fire Sciences, University of Idaho, Moscow, ID 83844, USA; (M.R.); (G.N.)
| | - Nancy L. Engle
- Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; (P.M.S.-V.); (N.L.E.); (T.J.L.); (M.L.Y.); (T.J.T.)
| | - Travis J. Lawrence
- Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; (P.M.S.-V.); (N.L.E.); (T.J.L.); (M.L.Y.); (T.J.T.)
| | - Meredith L. Yeary
- Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; (P.M.S.-V.); (N.L.E.); (T.J.L.); (M.L.Y.); (T.J.T.)
| | - Timothy J. Tschaplinski
- Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; (P.M.S.-V.); (N.L.E.); (T.J.L.); (M.L.Y.); (T.J.T.)
| | - George Newcombe
- Department of Forest, Rangeland and Fire Sciences, University of Idaho, Moscow, ID 83844, USA; (M.R.); (G.N.)
| | - Dale A. Pelletier
- Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; (P.M.S.-V.); (N.L.E.); (T.J.L.); (M.L.Y.); (T.J.T.)
- Correspondence:
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15
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Zhang J, Xie M, Li M, Ding J, Pu Y, Bryan AC, Rottmann W, Winkeler KA, Collins CM, Singan V, Lindquist EA, Jawdy SS, Gunter LE, Engle NL, Yang X, Barry K, Tschaplinski TJ, Schmutz J, Tuskan GA, Muchero W, Chen J. Overexpression of a Prefoldin β subunit gene reduces biomass recalcitrance in the bioenergy crop Populus. Plant Biotechnol J 2020; 18:859-871. [PMID: 31498543 PMCID: PMC7004918 DOI: 10.1111/pbi.13254] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 08/21/2019] [Accepted: 09/02/2019] [Indexed: 05/06/2023]
Abstract
Prefoldin (PFD) is a group II chaperonin that is ubiquitously present in the eukaryotic kingdom. Six subunits (PFD1-6) form a jellyfish-like heterohexameric PFD complex and function in protein folding and cytoskeleton organization. However, little is known about its function in plant cell wall-related processes. Here, we report the functional characterization of a PFD gene from Populus deltoides, designated as PdPFD2.2. There are two copies of PFD2 in Populus, and PdPFD2.2 was ubiquitously expressed with high transcript abundance in the cambial region. PdPFD2.2 can physically interact with DELLA protein RGA1_8g, and its subcellular localization is affected by the interaction. In P. deltoides transgenic plants overexpressing PdPFD2.2, the lignin syringyl/guaiacyl ratio was increased, but cellulose content and crystallinity index were unchanged. In addition, the total released sugar (glucose and xylose) amounts were increased by 7.6% and 6.1%, respectively, in two transgenic lines. Transcriptomic and metabolomic analyses revealed that secondary metabolic pathways, including lignin and flavonoid biosynthesis, were affected by overexpressing PdPFD2.2. A total of eight hub transcription factors (TFs) were identified based on TF binding sites of differentially expressed genes in Populus transgenic plants overexpressing PdPFD2.2. In addition, several known cell wall-related TFs, such as MYB3, MYB4, MYB7, TT8 and XND1, were affected by overexpression of PdPFD2.2. These results suggest that overexpression of PdPFD2.2 can reduce biomass recalcitrance and PdPFD2.2 is a promising target for genetic engineering to improve feedstock characteristics to enhance biofuel conversion and reduce the cost of lignocellulosic biofuel production.
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Affiliation(s)
- Jin Zhang
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
- Center for Bioenergy InnovationOak Ridge National LaboratoryOak RidgeTNUSA
| | - Meng Xie
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
- Center for Bioenergy InnovationOak Ridge National LaboratoryOak RidgeTNUSA
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
| | - Mi Li
- Chemical & Biomolecular EngineeringUniversity of TennesseeKnoxvilleTNUSA
| | - Jinhua Ding
- Chemical & Biomolecular EngineeringUniversity of TennesseeKnoxvilleTNUSA
- College of TextilesDonghua UniversityShanghaiChina
| | - Yunqiao Pu
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
- Center for Bioenergy InnovationOak Ridge National LaboratoryOak RidgeTNUSA
| | | | | | | | | | - Vasanth Singan
- U.S. Department of Energy Joint Genome InstituteWalnut CreekCAUSA
| | | | - Sara S. Jawdy
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
- Center for Bioenergy InnovationOak Ridge National LaboratoryOak RidgeTNUSA
| | - Lee E. Gunter
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
- Center for Bioenergy InnovationOak Ridge National LaboratoryOak RidgeTNUSA
| | - Nancy L. Engle
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
- Center for Bioenergy InnovationOak Ridge National LaboratoryOak RidgeTNUSA
| | - Xiaohan Yang
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
- Center for Bioenergy InnovationOak Ridge National LaboratoryOak RidgeTNUSA
| | - Kerrie Barry
- U.S. Department of Energy Joint Genome InstituteWalnut CreekCAUSA
| | - Timothy J. Tschaplinski
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
- Center for Bioenergy InnovationOak Ridge National LaboratoryOak RidgeTNUSA
| | - Jeremy Schmutz
- U.S. Department of Energy Joint Genome InstituteWalnut CreekCAUSA
- HudsonAlpha Institute for BiotechnologyHuntsvilleALUSA
| | - Gerald A. Tuskan
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
- Center for Bioenergy InnovationOak Ridge National LaboratoryOak RidgeTNUSA
| | - Wellington Muchero
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
- Center for Bioenergy InnovationOak Ridge National LaboratoryOak RidgeTNUSA
| | - Jin‐Gui Chen
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
- Center for Bioenergy InnovationOak Ridge National LaboratoryOak RidgeTNUSA
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16
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Tschaplinski TJ, Abraham PE, Jawdy SS, Gunter LE, Martin MZ, Engle NL, Yang X, Tuskan GA. The nature of the progression of drought stress drives differential metabolomic responses in Populus deltoides. Ann Bot 2019; 124:617-626. [PMID: 30689716 PMCID: PMC6821281 DOI: 10.1093/aob/mcz002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 01/01/2019] [Indexed: 05/08/2023]
Abstract
BACKGROUND AND AIMS The use of woody crops for Quad-level (approx. 1 × 1018 J) energy production will require marginal agricultural lands that experience recurrent periods of water stress. Populus species have the capacity to increase dehydration tolerance by lowering osmotic potential via osmotic adjustment. The aim of this study was to investigate how the inherent genetic potential of a Populus clone to respond to drought interacts with the nature of the drought to determine the degree of biochemical response. METHODS A greenhouse drought stress study was conducted on Populus deltoides 'WV94' and the resulting metabolite profiles of leaves were determined by gas chromatography-mass spectrometry following trimethylsilylation for plants subjected to cyclic mild (-0.5 MPa pre-dawn leaf water potential) drought vs. cyclic severe (-1.26 MPa) drought in contrast to well-watered controls (-0.1 MPa) after two or four drought cycles, and in contrast to plants subjected to acute drought, where plants were desiccated for up to 8 d. KEY RESULTS The nature of drought (cyclic vs. acute), frequency of drought (number of cycles) and the severity of drought (mild vs. severe) all dictated the degree of osmotic adjustment and the nature of the organic solutes that accumulated. Whereas cyclic drought induced the largest responses in primary metabolism (soluble sugars, organic acids and amino acids), acute onset of prolonged drought induced the greatest osmotic adjustment and largest responses in secondary metabolism, especially populosides (hydroxycinnamic acid conjugates of salicin). CONCLUSIONS The differential adaptive metabolite responses in cyclic vs. acute drought suggest that stress acclimation occurs via primary metabolism in response to cyclic drought, whereas expanded metabolic plasticity occurs via secondary metabolism following severe, acute drought. The shift in carbon partitioning to aromatic metabolism with the production of a diverse suite of higher order salicylates lowers osmotic potential and increases the probability of post-stress recovery.
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Affiliation(s)
| | | | - Sara S Jawdy
- Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Lee E Gunter
- Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | | | | | - Xiaohan Yang
- Oak Ridge National Laboratory, Oak Ridge, TN, USA
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17
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Uehling JK, Entler MR, Meredith HR, Millet LJ, Timm CM, Aufrecht JA, Bonito GM, Engle NL, Labbé JL, Doktycz MJ, Retterer ST, Spatafora JW, Stajich JE, Tschaplinski TJ, Vilgalys RJ. Microfluidics and Metabolomics Reveal Symbiotic Bacterial-Fungal Interactions Between Mortierella elongata and Burkholderia Include Metabolite Exchange. Front Microbiol 2019; 10:2163. [PMID: 31632357 PMCID: PMC6779839 DOI: 10.3389/fmicb.2019.02163] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 09/03/2019] [Indexed: 01/12/2023] Open
Abstract
We identified two poplar (Populus sp.)-associated microbes, the fungus, Mortierella elongata strain AG77, and the bacterium, Burkholderia strain BT03, that mutually promote each other’s growth. Using culture assays in concert with a novel microfluidic device to generate time-lapse videos, we found growth specific media differing in pH and pre-conditioned by microbial growth led to increased fungal and bacterial growth rates. Coupling microfluidics and comparative metabolomics data results indicated that observed microbial growth stimulation involves metabolic exchange during two ordered events. The first is an emission of fungal metabolites, including organic acids used or modified by bacteria. A second signal of unknown nature is produced by bacteria which increases fungal growth rates. We find this symbiosis is initiated in part by metabolic exchange involving fungal organic acids.
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Affiliation(s)
- Jessie K Uehling
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States.,Department of Biology, Duke University, Durham, NC, United States
| | - Matthew R Entler
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Hannah R Meredith
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States.,Department of Biomedical Engineering, Duke University, Durham, NC, United States
| | - Larry J Millet
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,The Bredesen Center, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Collin M Timm
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Jayde A Aufrecht
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Gregory M Bonito
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
| | - Nancy L Engle
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Jessy L Labbé
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,Genome Science & Technology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Mitchel J Doktycz
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,Genome Science & Technology, The University of Tennessee, Knoxville, Knoxville, TN, United States.,Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Scott T Retterer
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Joseph W Spatafora
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA, United States
| | | | - Rytas J Vilgalys
- Department of Biology, Duke University, Durham, NC, United States
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18
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Man Ha C, Fine D, Bhatia A, Rao X, Martin MZ, Engle NL, Wherritt DJ, Tschaplinski TJ, Sumner LW, Dixon RA. Ectopic Defense Gene Expression Is Associated with Growth Defects in Medicago truncatula Lignin Pathway Mutants. Plant Physiol 2019; 181:63-84. [PMID: 31289215 PMCID: PMC6716239 DOI: 10.1104/pp.19.00533] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 06/26/2019] [Indexed: 05/04/2023]
Abstract
Lignin provides essential mechanical support for plant cell walls but decreases the digestibility of forage crops and increases the recalcitrance of biofuel crops. Attempts to modify lignin content and/or composition by genetic modification often result in negative growth effects. Although several studies have attempted to address the basis for such effects in individual transgenic lines, no common mechanism linking lignin modification with perturbations in plant growth and development has yet been identified. To address whether a common mechanism exists, we have analyzed transposon insertion mutants resulting in independent loss of function of five enzymes of the monolignol pathway, as well as one double mutant, in the model legume Medicago truncatula These plants exhibit growth phenotypes from essentially wild type to severely retarded. Extensive phenotypic, transcriptomic, and metabolomics analyses, including structural characterization of differentially expressed compounds, revealed diverse phenotypic consequences of lignin pathway perturbation that were perceived early in plant development but were not predicted by lignin content or composition alone. Notable phenotypes among the mutants with severe growth impairment were increased trichome numbers, accumulation of a variety of triterpene saponins, and extensive but differential ectopic expression of defense response genes. No currently proposed model explains the observed phenotypes across all lines. We propose that reallocation of resources into defense pathways is linked to the severity of the final growth phenotype in monolignol pathway mutants of M. truncatula, although it remains unclear whether this is a cause or an effect of the growth impairment.
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Affiliation(s)
- Chan Man Ha
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, Texas 76201
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Dennis Fine
- Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401
| | - Anil Bhatia
- Department of Biochemistry and MU Metabolomics Center, University of Missouri, Columbia, Missouri 65201
| | - Xiaolan Rao
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, Texas 76201
- Bioenergy Sciences Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Madhavi Z Martin
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
- Bioenergy Sciences Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
- BioSciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Nancy L Engle
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
- Bioenergy Sciences Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
- BioSciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Daniel J Wherritt
- Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401
- University of Texas at San Antonio, San Antonio, Texas 78249
| | - Timothy J Tschaplinski
- Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401
- University of Texas at San Antonio, San Antonio, Texas 78249
| | - Lloyd W Sumner
- Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401
- Department of Biochemistry and MU Metabolomics Center, University of Missouri, Columbia, Missouri 65201
| | - Richard A Dixon
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, Texas 76201
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
- Bioenergy Sciences Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
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19
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Ray P, Abraham PE, Guo Y, Giannone RJ, Engle NL, Yang ZK, Jacobson D, Hettich RL, Tschaplinski TJ, Craven KD. Scavenging organic nitrogen and remodelling lipid metabolism are key survival strategies adopted by the endophytic fungi, Serendipita vermifera and Serendipita bescii to alleviate nitrogen and phosphorous starvation in vitro. Environ Microbiol Rep 2019; 11:548-557. [PMID: 30970176 PMCID: PMC6850091 DOI: 10.1111/1758-2229.12757] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 04/08/2019] [Accepted: 04/08/2019] [Indexed: 05/02/2023]
Abstract
Serendipitaceae represents a diverse fungal group in the Basidiomycota that includes endophytes and lineages that repeatedly evolved ericoid, orchid and ectomycorrhizal lifestyle. Plants rely upon both nitrogen and phosphorous, for essential growth processes, and are often provided by mycorrhizal fungi. In this study, we investigated the cellular proteome of Serendipita vermifera MAFF305830 and closely related Serendipita vermifera subsp. bescii NFPB0129 grown in vitro under (N) ammonium and (P) phosphate starvation conditions. Mycelial growth pattern was documented under these conditions to correlate growth-specific responses to nutrient starvation. We found that N-starvation accelerated hyphal radial growth, whereas P-starvation accelerated hyphal branching. Additionally, P-starvation triggers an integrated starvation response leading to remodelling of lipid metabolism. Higher abundance of an ammonium transporter known to serve as both an ammonium sensor and stimulator of hyphal growth was detected under N-starvation. Additionally, N-starvation led to strong up-regulation of nitrate, amino acid, peptide, and urea transporters, along with several proteins predicted to have peptidase activity. Taken together, our finding suggests S. bescii and S. vermifera have the metabolic capacity for nitrogen assimilation from organic forms of N compounds. We hypothesize that the nitrogen metabolite repression is a key regulator of such organic N assimilation.
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Affiliation(s)
- Prasun Ray
- Noble Research Institute, LLCArdmoreOK 73401USA
| | - Paul E. Abraham
- Chemical Sciences Division, Oak Ridge National LaboratoryOak RidgeTN 37831USA
| | | | - Richard J. Giannone
- Chemical Sciences Division, Oak Ridge National LaboratoryOak RidgeTN 37831USA
| | - Nancy L. Engle
- Biosciences Division, Oak Ridge National LaboratoryOak RidgeTN 37831USA
| | - Zamin K. Yang
- Biosciences Division, Oak Ridge National LaboratoryOak RidgeTN 37831USA
| | - Daniel Jacobson
- Biosciences Division, Oak Ridge National LaboratoryOak RidgeTN 37831USA
| | - Robert L. Hettich
- Chemical Sciences Division, Oak Ridge National LaboratoryOak RidgeTN 37831USA
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20
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Veach AM, Morris R, Yip DZ, Yang ZK, Engle NL, Cregger MA, Tschaplinski TJ, Schadt CW. Rhizosphere microbiomes diverge among Populus trichocarpa plant-host genotypes and chemotypes, but it depends on soil origin. Microbiome 2019; 7:76. [PMID: 31103040 PMCID: PMC6525979 DOI: 10.1186/s40168-019-0668-8] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 03/20/2019] [Indexed: 05/19/2023]
Abstract
BACKGROUND Plants have developed defense strategies for phytopathogen and herbivore protection via coordinated metabolic mechanisms. Low-molecular weight metabolites produced within plant tissues, such as salicylic acid, represent one such mechanism which likely mediates plant - microbe interactions above and below ground. Salicylic acid is a ubiquitous phytohormone at low levels in most plants, yet are concentrated defense compounds in Populus, likely acting as a selective filter for rhizosphere microbiomes. We propagated twelve Populus trichocarpa genotypes which varied an order of magnitude in salicylic acid (SA)-related secondary metabolites, in contrasting soils from two different origins. After four months of growth, plant properties (leaf growth, chlorophyll content, and net photosynthetic rate) and plant root metabolomics specifically targeting SA metabolites were measured via GC-MS. In addition, rhizosphere microbiome composition was measured via Illumina MiSeq sequencing of 16S and ITS2 rRNA-genes. RESULTS Soil origin was the primary filter causing divergence in bacterial/archaeal and fungal communities with plant genotype secondarily influential. Both bacterial/archaeal and fungal evenness varied between soil origins and bacterial/archaeal diversity and evenness correlated with at least one SA metabolite (diversity: populin; evenness: total phenolics). The production of individual salicylic acid derivatives that varied by host genotype resulted in compositional differences for bacteria /archaea (tremuloidin) and fungi (salicylic acid) within one soil origin (Clatskanie) whereas soils from Corvallis did not illicit microbial compositional changes due to salicylic acid derivatives. Several dominant bacterial (e.g., Betaproteobacteria, Acidobacteria, Verrucomicrobia, Chloroflexi, Gemmatimonadete, Firmicutes) and one fungal phyla (Mortierellomycota) also correlated with specific SA secondary metabolites; bacterial phyla exhibited more negative interactions (declining abundance with increasing metabolite concentration) than positive interactions. CONCLUSIONS These results indicate microbial communities diverge most among soil origin. However, within a soil origin, bacterial/archaeal communities are responsive to plant SA production within greenhouse-based rhizosphere microbiomes. Fungal microbiomes are impacted by root SA-metabolites, but overall to a lesser degree within this experimental context. These results suggest plant defense strategies, such as SA and its secondary metabolites, may partially drive patterns of both bacterial/archaeal and fungal taxa-specific colonization and assembly.
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Affiliation(s)
- Allison M. Veach
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN 37831-6038 USA
| | - Reese Morris
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN 37831-6038 USA
| | - Daniel Z. Yip
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN 37831-6038 USA
| | - Zamin K. Yang
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN 37831-6038 USA
| | - Nancy L. Engle
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN 37831-6038 USA
| | - Melissa A. Cregger
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN 37831-6038 USA
| | - Timothy J. Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN 37831-6038 USA
| | - Christopher W. Schadt
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN 37831-6038 USA
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996 USA
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21
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Xie H, Engle NL, Venketachalam S, Yoo CG, Barros J, Lecoultre M, Howard N, Li G, Sun L, Srivastava AC, Pattathil S, Pu Y, Hahn MG, Ragauskas AJ, Nelson RS, Dixon RA, Tschaplinski TJ, Blancaflor EB, Tang Y. Combining loss of function of FOLYLPOLYGLUTAMATE SYNTHETASE1 and CAFFEOYL- COA 3- O- METHYLTRANSFERASE1 for lignin reduction and improved saccharification efficiency in Arabidopsis thaliana. Biotechnol Biofuels 2019; 12:108. [PMID: 31073332 PMCID: PMC6498598 DOI: 10.1186/s13068-019-1446-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 04/20/2019] [Indexed: 05/07/2023]
Abstract
BACKGROUND Downregulation of genes involved in lignin biosynthesis and related biochemical pathways has been used as a strategy to improve biofuel production. Plant C1 metabolism provides the methyl units used for the methylation reactions carried out by two methyltransferases in the lignin biosynthetic pathway: caffeic acid 3-O-methyltransferase (COMT) and caffeoyl-CoA 3-O-methyltransferase (CCoAOMT). Mutations in these genes resulted in lower lignin levels and altered lignin compositions. Reduced lignin levels can also be achieved by mutations in the C1 pathway gene, folylpolyglutamate synthetase1 (FPGS1), in both monocotyledons and dicotyledons, indicating a link between the C1 and lignin biosynthetic pathways. To test if lignin content can be further reduced by combining genetic mutations in C1 metabolism and the lignin biosynthetic pathway, fpgs1ccoaomt1 double mutants were generated and functionally characterized. RESULTS Double fpgs1ccoaomt1 mutants had lower thioacidolysis lignin monomer yield and acetyl bromide lignin content than the ccoaomt1 or fpgs1 mutants and the plants themselves displayed no obvious long-term negative growth phenotypes. Moreover, extracts from the double mutants had dramatically improved enzymatic polysaccharide hydrolysis efficiencies than the single mutants: 15.1% and 20.7% higher than ccoaomt1 and fpgs1, respectively. The reduced lignin and improved sugar release of fpgs1ccoaomt1 was coupled with changes in cell-wall composition, metabolite profiles, and changes in expression of genes involved in cell-wall and lignin biosynthesis. CONCLUSION Our observations demonstrate that additional reduction in lignin content and improved sugar release can be achieved by simultaneous downregulation of a gene in the C1 (FPGS1) and lignin biosynthetic (CCOAOMT) pathways. These improvements in sugar accessibility were achieved without introducing unwanted long-term plant growth and developmental defects.
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Affiliation(s)
- Hongli Xie
- Noble Research Institute, LLC, 2510 Sam Noble Parkway, Ardmore, OK 73401 USA
- BioEnergy Science Center, United States Department of Energy, Oak Ridge, TN 37831 USA
| | - Nancy L. Engle
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- BioEnergy Science Center, United States Department of Energy, Oak Ridge, TN 37831 USA
- The Center for Bioenergy Innovation, United States Department of Energy, Oak Ridge, TN 37831 USA
| | - Sivasankari Venketachalam
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602 USA
- BioEnergy Science Center, United States Department of Energy, Oak Ridge, TN 37831 USA
- The Center for Bioenergy Innovation, United States Department of Energy, Oak Ridge, TN 37831 USA
| | - Chang Geun Yoo
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- BioEnergy Science Center, United States Department of Energy, Oak Ridge, TN 37831 USA
- The Center for Bioenergy Innovation, United States Department of Energy, Oak Ridge, TN 37831 USA
| | - Jaime Barros
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX 76203 USA
- BioEnergy Science Center, United States Department of Energy, Oak Ridge, TN 37831 USA
- The Center for Bioenergy Innovation, United States Department of Energy, Oak Ridge, TN 37831 USA
| | - Mitch Lecoultre
- Noble Research Institute, LLC, 2510 Sam Noble Parkway, Ardmore, OK 73401 USA
- BioEnergy Science Center, United States Department of Energy, Oak Ridge, TN 37831 USA
| | - Nikki Howard
- Noble Research Institute, LLC, 2510 Sam Noble Parkway, Ardmore, OK 73401 USA
- BioEnergy Science Center, United States Department of Energy, Oak Ridge, TN 37831 USA
| | - Guifen Li
- Noble Research Institute, LLC, 2510 Sam Noble Parkway, Ardmore, OK 73401 USA
| | - Liang Sun
- Noble Research Institute, LLC, 2510 Sam Noble Parkway, Ardmore, OK 73401 USA
| | - Avinash C. Srivastava
- Noble Research Institute, LLC, 2510 Sam Noble Parkway, Ardmore, OK 73401 USA
- BioEnergy Science Center, United States Department of Energy, Oak Ridge, TN 37831 USA
| | - Sivakumar Pattathil
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602 USA
- BioEnergy Science Center, United States Department of Energy, Oak Ridge, TN 37831 USA
| | - Yunqiao Pu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- BioEnergy Science Center, United States Department of Energy, Oak Ridge, TN 37831 USA
- The Center for Bioenergy Innovation, United States Department of Energy, Oak Ridge, TN 37831 USA
| | - Michael G. Hahn
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602 USA
- BioEnergy Science Center, United States Department of Energy, Oak Ridge, TN 37831 USA
- The Center for Bioenergy Innovation, United States Department of Energy, Oak Ridge, TN 37831 USA
| | - Arthur J. Ragauskas
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- BioEnergy Science Center, United States Department of Energy, Oak Ridge, TN 37831 USA
- The Center for Bioenergy Innovation, United States Department of Energy, Oak Ridge, TN 37831 USA
| | - Richard S. Nelson
- Noble Research Institute, LLC, 2510 Sam Noble Parkway, Ardmore, OK 73401 USA
- BioEnergy Science Center, United States Department of Energy, Oak Ridge, TN 37831 USA
| | - Richard A. Dixon
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX 76203 USA
- BioEnergy Science Center, United States Department of Energy, Oak Ridge, TN 37831 USA
- The Center for Bioenergy Innovation, United States Department of Energy, Oak Ridge, TN 37831 USA
| | - Timothy J. Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- BioEnergy Science Center, United States Department of Energy, Oak Ridge, TN 37831 USA
- The Center for Bioenergy Innovation, United States Department of Energy, Oak Ridge, TN 37831 USA
| | - Elison B. Blancaflor
- Noble Research Institute, LLC, 2510 Sam Noble Parkway, Ardmore, OK 73401 USA
- BioEnergy Science Center, United States Department of Energy, Oak Ridge, TN 37831 USA
| | - Yuhong Tang
- Noble Research Institute, LLC, 2510 Sam Noble Parkway, Ardmore, OK 73401 USA
- BioEnergy Science Center, United States Department of Energy, Oak Ridge, TN 37831 USA
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22
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Sander K, Chung D, Hyatt D, Westpheling J, Klingeman DM, Rodriguez M, Engle NL, Tschaplinski TJ, Davison BH, Brown SD. Rex in Caldicellulosiruptor bescii: Novel regulon members and its effect on the production of ethanol and overflow metabolites. Microbiologyopen 2019; 8:e00639. [PMID: 29797457 PMCID: PMC6391272 DOI: 10.1002/mbo3.639] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 03/03/2018] [Accepted: 03/05/2018] [Indexed: 11/23/2022] Open
Abstract
Rex is a global redox-sensing transcription factor that senses and responds to the intracellular [NADH]/[NAD+ ] ratio to regulate genes for central metabolism, and a variety of metabolic processes in Gram-positive bacteria. We decipher and validate four new members of the Rex regulon in Caldicellulosiruptor bescii; a gene encoding a class V aminotransferase, the HydG FeFe Hydrogenase maturation protein, an oxidoreductase, and a gene encoding a hypothetical protein. Structural genes for the NiFe and FeFe hydrogenases, pyruvate:ferredoxin oxidoreductase, as well as the rex gene itself are also members of this regulon, as has been predicted previously in different organisms. A C. bescii rex deletion strain constructed in an ethanol-producing strain made 54% more ethanol (0.16 mmol/L) than its genetic parent after 36 hr of fermentation, though only under nitrogen limited conditions. Metabolomic interrogation shows this rex-deficient ethanol-producing strain synthesizes other reduced overflow metabolism products likely in response to more reduced intracellular redox conditions and the accumulation of pyruvate. These results suggest ethanol production is strongly dependent on the native intracellular redox state in C. bescii, and highlight the combined promise of using this gene and manipulation of culture conditions to yield strains capable of producing ethanol at higher yields and final titer.
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Affiliation(s)
- Kyle Sander
- Department of Chemical and Biomolecular EngineeringUniversity of TennesseeKnoxvilleTennessee
- Bredesen Center for Interdisciplinary Graduate Research and EducationUniversity of TennesseeKnoxvilleTennessee
- BioEnergy Sciences CenterOak Ridge National LaboratoryOak RidgeTennessee
| | - Daehwan Chung
- BioEnergy Sciences CenterOak Ridge National LaboratoryOak RidgeTennessee
- Department of GeneticsUniversity of GeorgiaAthensGeorgia
- Present address:
National Renewable Energy LaboratoryGoldenCO
| | - Doug Hyatt
- BioEnergy Sciences CenterOak Ridge National LaboratoryOak RidgeTennessee
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTennessee
| | - Janet Westpheling
- BioEnergy Sciences CenterOak Ridge National LaboratoryOak RidgeTennessee
- Department of GeneticsUniversity of GeorgiaAthensGeorgia
| | - Dawn M. Klingeman
- BioEnergy Sciences CenterOak Ridge National LaboratoryOak RidgeTennessee
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTennessee
| | - Miguel Rodriguez
- BioEnergy Sciences CenterOak Ridge National LaboratoryOak RidgeTennessee
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTennessee
| | - Nancy L. Engle
- BioEnergy Sciences CenterOak Ridge National LaboratoryOak RidgeTennessee
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTennessee
| | - Timothy J. Tschaplinski
- BioEnergy Sciences CenterOak Ridge National LaboratoryOak RidgeTennessee
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTennessee
| | - Brian H. Davison
- Department of Chemical and Biomolecular EngineeringUniversity of TennesseeKnoxvilleTennessee
- Bredesen Center for Interdisciplinary Graduate Research and EducationUniversity of TennesseeKnoxvilleTennessee
- BioEnergy Sciences CenterOak Ridge National LaboratoryOak RidgeTennessee
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTennessee
| | - Steven D. Brown
- Bredesen Center for Interdisciplinary Graduate Research and EducationUniversity of TennesseeKnoxvilleTennessee
- BioEnergy Sciences CenterOak Ridge National LaboratoryOak RidgeTennessee
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTennessee
- Present address:
LanzaTechSkokieIL
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23
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Cecchini NM, Roychoudhry S, Speed DJ, Steffes K, Tambe A, Zodrow K, Konstantinoff K, Jung HW, Engle NL, Tschaplinski TJ, Greenberg JT. Underground Azelaic Acid-Conferred Resistance to Pseudomonas syringae in Arabidopsis. Mol Plant Microbe Interact 2019; 32:86-94. [PMID: 30156481 DOI: 10.1094/mpmi-07-18-0185-r] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Local interactions between individual plant organs and diverse microorganisms can lead to whole plant immunity via the mobilization of defense signals. One such signal is the plastid lipid-derived oxylipin azelaic acid (AZA). Arabidopsis lacking AZI1 or EARLI1, related lipid transfer family proteins, exhibit reduced AZA transport among leaves and cannot mount systemic immunity. AZA has been detected in roots as well as leaves. Therefore, the present study addresses the effects on plants of AZA application to roots. AZA but not the structurally related suberic acid inhibits root growth when directly in contact with roots. Treatment of roots with AZA also induces resistance to Pseudomonas syringae in aerial tissues. These effects of AZA on root growth and disease resistance depend, at least partially, on AZI1 and EARLI1. AZI1 in roots localizes to plastids, similar to its known location in leaves. Interestingly, kinases previously shown to modify AZI1 in vitro, MPK3 and MPK6, are also needed for AZA-induced root-growth inhibition and aboveground immunity. Finally, deuterium-labeled AZA applied to the roots does not move to aerial tissues. Thus, AZA application to roots triggers systemic immunity through an AZI1/EARLI1/MPK3/MPK6-dependent pathway and AZA effects may involve one or more additional mobile signals.
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Affiliation(s)
- Nicolás M Cecchini
- 1 Department of Molecular Genetics and Cell Biology, The University of Chicago, 929 East 57th Street GCIS 524W, Chicago, IL 60637, U.S.A
| | - Suruchi Roychoudhry
- 1 Department of Molecular Genetics and Cell Biology, The University of Chicago, 929 East 57th Street GCIS 524W, Chicago, IL 60637, U.S.A
| | - DeQuantarius J Speed
- 1 Department of Molecular Genetics and Cell Biology, The University of Chicago, 929 East 57th Street GCIS 524W, Chicago, IL 60637, U.S.A
| | - Kevin Steffes
- 1 Department of Molecular Genetics and Cell Biology, The University of Chicago, 929 East 57th Street GCIS 524W, Chicago, IL 60637, U.S.A
| | - Arjun Tambe
- 1 Department of Molecular Genetics and Cell Biology, The University of Chicago, 929 East 57th Street GCIS 524W, Chicago, IL 60637, U.S.A
| | - Kristin Zodrow
- 1 Department of Molecular Genetics and Cell Biology, The University of Chicago, 929 East 57th Street GCIS 524W, Chicago, IL 60637, U.S.A
| | - Katerina Konstantinoff
- 1 Department of Molecular Genetics and Cell Biology, The University of Chicago, 929 East 57th Street GCIS 524W, Chicago, IL 60637, U.S.A
| | - Ho Won Jung
- 2 Department of Molecular Genetics, Dong-A University, 37 Nakdong-Daero 550beon-gil, Saha-gu, Busan 49315, Korea; and
| | - Nancy L Engle
- 3 Oak Ridge National Laboratory, PO Box 2008, Oak Ridge, TN 37831, U.S.A
| | | | - Jean T Greenberg
- 1 Department of Molecular Genetics and Cell Biology, The University of Chicago, 929 East 57th Street GCIS 524W, Chicago, IL 60637, U.S.A
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Faraji M, Fonseca LL, Escamilla-Treviño L, Barros-Rios J, Engle NL, Yang ZK, Tschaplinski TJ, Dixon RA, Voit EO. A dynamic model of lignin biosynthesis in Brachypodium distachyon. Biotechnol Biofuels 2018; 11:253. [PMID: 30250505 PMCID: PMC6145374 DOI: 10.1186/s13068-018-1241-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 08/27/2018] [Indexed: 05/31/2023]
Abstract
BACKGROUND Lignin is a crucial molecule for terrestrial plants, as it offers structural support and permits the transport of water over long distances. The hardness of lignin reduces plant digestibility by cattle and sheep; it also makes inedible plant materials recalcitrant toward the enzymatic fermentation of cellulose, which is a potentially valuable substrate for sustainable biofuels. Targeted attempts to change the amount or composition of lignin in relevant plant species have been hampered by the fact that the lignin biosynthetic pathway is difficult to understand, because it uses several enzymes for the same substrates, is regulated in an ill-characterized manner, may operate in different locations within cells, and contains metabolic channels, which the plant may use to funnel initial substrates into specific monolignols. RESULTS We propose a dynamic mathematical model that integrates various datasets and other information regarding the lignin pathway in Brachypodium distachyon and permits explanations for some counterintuitive observations. The model predicts the lignin composition and label distribution in a BdPTAL knockdown strain, with results that are quite similar to experimental data. CONCLUSION Given the present scarcity of available data, the model resulting from our analysis is presumably not final. However, it offers proof of concept for how one may design integrative pathway models of this type, which are necessary tools for predicting the consequences of genomic or other alterations toward plants with lignin features that are more desirable than in their wild-type counterparts.
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Affiliation(s)
- Mojdeh Faraji
- The Wallace H. Coulter, Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 950 Atlantic Drive, Atlanta, GA 30332-2000 USA
- BioEnergy Sciences Center (BESC), Oak Ridge National Lab, Oak Ridge, TN USA
| | - Luis L. Fonseca
- The Wallace H. Coulter, Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 950 Atlantic Drive, Atlanta, GA 30332-2000 USA
- BioEnergy Sciences Center (BESC), Oak Ridge National Lab, Oak Ridge, TN USA
| | - Luis Escamilla-Treviño
- BioEnergy Sciences Center (BESC), Oak Ridge National Lab, Oak Ridge, TN USA
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, 1155 Union Circle #305220, Denton, TX 76203-5017 USA
| | - Jaime Barros-Rios
- BioEnergy Sciences Center (BESC), Oak Ridge National Lab, Oak Ridge, TN USA
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, 1155 Union Circle #305220, Denton, TX 76203-5017 USA
| | - Nancy L. Engle
- BioEnergy Sciences Center (BESC), Oak Ridge National Lab, Oak Ridge, TN USA
- Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN 37831 USA
| | - Zamin K. Yang
- BioEnergy Sciences Center (BESC), Oak Ridge National Lab, Oak Ridge, TN USA
- Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN 37831 USA
| | - Timothy J. Tschaplinski
- BioEnergy Sciences Center (BESC), Oak Ridge National Lab, Oak Ridge, TN USA
- Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN 37831 USA
| | - Richard A. Dixon
- BioEnergy Sciences Center (BESC), Oak Ridge National Lab, Oak Ridge, TN USA
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, 1155 Union Circle #305220, Denton, TX 76203-5017 USA
| | - Eberhard O. Voit
- The Wallace H. Coulter, Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 950 Atlantic Drive, Atlanta, GA 30332-2000 USA
- BioEnergy Sciences Center (BESC), Oak Ridge National Lab, Oak Ridge, TN USA
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25
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Song Y, Johnson D, Peng R, Hensley DK, Bonnesen PV, Liang L, Huang J, Yang F, Zhang F, Qiao R, Baddorf AP, Tschaplinski TJ, Engle NL, Hatzell MC, Wu Z, Cullen DA, Meyer HM, Sumpter BG, Rondinone AJ. A physical catalyst for the electrolysis of nitrogen to ammonia. Sci Adv 2018; 4:e1700336. [PMID: 29719860 PMCID: PMC5922794 DOI: 10.1126/sciadv.1700336] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 03/12/2018] [Indexed: 05/10/2023]
Abstract
Ammonia synthesis consumes 3 to 5% of the world's natural gas, making it a significant contributor to greenhouse gas emissions. Strategies for synthesizing ammonia that are not dependent on the energy-intensive and methane-based Haber-Bosch process are critically important for reducing global energy consumption and minimizing climate change. Motivated by a need to investigate novel nitrogen fixation mechanisms, we herein describe a highly textured physical catalyst, composed of N-doped carbon nanospikes, that electrochemically reduces dissolved N2 gas to ammonia in an aqueous electrolyte under ambient conditions. The Faradaic efficiency (FE) achieves 11.56 ± 0.85% at -1.19 V versus the reversible hydrogen electrode, and the maximum production rate is 97.18 ± 7.13 μg hour-1 cm-2. The catalyst contains no noble or rare metals but rather has a surface composed of sharp spikes, which concentrates the electric field at the tips, thereby promoting the electroreduction of dissolved N2 molecules near the electrode. The choice of electrolyte is also critically important because the reaction rate is dependent on the counterion type, suggesting a role in enhancing the electric field at the sharp spikes and increasing N2 concentration within the Stern layer. The energy efficiency of the reaction is estimated to be 5.25% at the current FE of 11.56%.
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Affiliation(s)
- Yang Song
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Daniel Johnson
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Rui Peng
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Dale K. Hensley
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Peter V. Bonnesen
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Liangbo Liang
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Jingsong Huang
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Fengchang Yang
- Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Fei Zhang
- Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Rui Qiao
- Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Arthur P. Baddorf
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | | | - Nancy L. Engle
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Marta C. Hatzell
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Zili Wu
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - David A. Cullen
- Materials Science and Technology Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Harry M. Meyer
- Materials Science and Technology Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Bobby G. Sumpter
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Adam J. Rondinone
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Corresponding author.
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26
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Whitham JM, Moon JW, Rodriguez M, Engle NL, Klingeman DM, Rydzak T, Abel MM, Tschaplinski TJ, Guss AM, Brown SD. Clostridium thermocellum LL1210 pH homeostasis mechanisms informed by transcriptomics and metabolomics. Biotechnol Biofuels 2018; 11:98. [PMID: 29632556 PMCID: PMC5887222 DOI: 10.1186/s13068-018-1095-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Accepted: 03/24/2018] [Indexed: 05/21/2023]
Abstract
BACKGROUND Clostridium (Ruminiclostridium) thermocellum is a model fermentative anaerobic thermophile being studied and engineered for consolidated bioprocessing of lignocellulosic feedstocks into fuels and chemicals. Engineering efforts have resulted in significant improvements in ethanol yields and titers although further advances are required to make the bacterium industry-ready. For instance, fermentations at lower pH could enable co-culturing with microbes that have lower pH optima, augment productivity, and reduce buffering cost. C. thermocellum is typically grown at neutral pH, and little is known about its pH limits or pH homeostasis mechanisms. To better understand C. thermocellum pH homeostasis we grew strain LL1210 (C. thermocellum DSM1313 Δhpt ΔhydG Δldh Δpfl Δpta-ack), currently the highest ethanol producing strain of C. thermocellum, at different pH values in chemostat culture and applied systems biology tools. RESULTS Clostridium thermocellum LL1210 was found to be growth-limited below pH 6.24 at a dilution rate of 0.1 h-1. F1F0-ATPase gene expression was upregulated while many ATP-utilizing enzymes and pathways were downregulated at pH 6.24. These included most flagella biosynthesis genes, genes for chemotaxis, and other motility-related genes (> 50) as well as sulfate transport and reduction, nitrate transport and nitrogen fixation, and fatty acid biosynthesis genes. Clustering and enrichment of differentially expressed genes at pH values 6.48, pH 6.24 and pH 6.12 (washout conditions) compared to pH 6.98 showed inverse differential expression patterns between the F1F0-ATPase and genes for other ATP-utilizing enzymes. At and below pH 6.24, amino acids including glutamate and valine; long-chain fatty acids, their iso-counterparts and glycerol conjugates; glycolysis intermediates 3-phosphoglycerate, glucose 6-phosphate, and glucose accumulated intracellularly. Glutamate was 267 times more abundant in cells at pH 6.24 compared to pH 6.98, and intercellular concentration reached 1.8 μmol/g pellet at pH 5.80 (stopped flow). CONCLUSIONS Clostridium thermocellum LL1210 can grow under slightly acidic conditions, similar to limits reported for other strains. This foundational study provides a detailed characterization of a relatively acid-intolerant bacterium and provides genetic targets for strain improvement. Future studies should examine adding gene functions used by more acid-tolerant bacteria for improved pH homeostasis at acidic pH values.
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Affiliation(s)
- Jason M. Whitham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
- BioEnergy Science Center, National Laboratory, Oak Ridge, TN USA
| | - Ji-Won Moon
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Miguel Rodriguez
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
- BioEnergy Science Center, National Laboratory, Oak Ridge, TN USA
| | - Nancy L. Engle
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
- BioEnergy Science Center, National Laboratory, Oak Ridge, TN USA
| | - Dawn M. Klingeman
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
- BioEnergy Science Center, National Laboratory, Oak Ridge, TN USA
| | - Thomas Rydzak
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
- BioEnergy Science Center, National Laboratory, Oak Ridge, TN USA
- Present Address: Department of Biological Science, University of Calgary, Calgary, AB T2N 1N4 Canada
| | - Malaney M. Abel
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
- BioEnergy Science Center, National Laboratory, Oak Ridge, TN USA
| | - Timothy J. Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
- BioEnergy Science Center, National Laboratory, Oak Ridge, TN USA
| | - Adam M. Guss
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
- BioEnergy Science Center, National Laboratory, Oak Ridge, TN USA
| | - Steven D. Brown
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
- BioEnergy Science Center, National Laboratory, Oak Ridge, TN USA
- Present Address: LanzaTech, Inc., Skokie, IL USA
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27
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Verbeke TJ, Giannone RJ, Klingeman DM, Engle NL, Rydzak T, Guss AM, Tschaplinski TJ, Brown SD, Hettich RL, Elkins JG. Erratum: Corrigendum: Pentose sugars inhibit metabolism and increase expression of an AgrD-type cyclic pentapeptide in Clostridium thermocellum. Sci Rep 2017; 7:46875. [PMID: 28749932 PMCID: PMC5532492 DOI: 10.1038/srep46875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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28
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Verbeke TJ, Giannone RJ, Klingeman DM, Engle NL, Rydzak T, Guss AM, Tschaplinski TJ, Brown SD, Hettich RL, Elkins JG. Pentose sugars inhibit metabolism and increase expression of an AgrD-type cyclic pentapeptide in Clostridium thermocellum. Sci Rep 2017; 7:43355. [PMID: 28230109 PMCID: PMC5322536 DOI: 10.1038/srep43355] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 01/18/2017] [Indexed: 12/22/2022] Open
Abstract
Clostridium thermocellum could potentially be used as a microbial biocatalyst to produce renewable fuels directly from lignocellulosic biomass due to its ability to rapidly solubilize plant cell walls. While the organism readily ferments sugars derived from cellulose, pentose sugars from xylan are not metabolized. Here, we show that non-fermentable pentoses inhibit growth and end-product formation during fermentation of cellulose-derived sugars. Metabolomic experiments confirmed that xylose is transported intracellularly and reduced to the dead-end metabolite xylitol. Comparative RNA-seq analysis of xylose-inhibited cultures revealed several up-regulated genes potentially involved in pentose transport and metabolism, which were targeted for disruption. Deletion of the ATP-dependent transporter, CbpD partially alleviated xylose inhibition. A putative xylitol dehydrogenase, encoded by Clo1313_0076, was also deleted resulting in decreased total xylitol production and yield by 41% and 46%, respectively. Finally, xylose-induced inhibition corresponds with the up-regulation and biogenesis of a cyclical AgrD-type, pentapeptide. Medium supplementation with the mature cyclical pentapeptide also inhibits bacterial growth. Together, these findings provide new foundational insights needed for engineering improved pentose utilizing strains of C. thermocellum and reveal the first functional Agr-type cyclic peptide to be produced by a thermophilic member of the Firmicutes.
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Affiliation(s)
- Tobin J Verbeke
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Richard J Giannone
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Dawn M Klingeman
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Nancy L Engle
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Thomas Rydzak
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Adam M Guss
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Timothy J Tschaplinski
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Steven D Brown
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Robert L Hettich
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - James G Elkins
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
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29
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Li M, Pu Y, Yoo CG, Gjersing E, Decker SR, Doeppke C, Shollenberger T, Tschaplinski TJ, Engle NL, Sykes RW, Davis MF, Baxter HL, Mazarei M, Fu C, Dixon RA, Wang ZY, Neal Stewart C, Ragauskas AJ. Study of traits and recalcitrance reduction of field-grown COMT down-regulated switchgrass. Biotechnol Biofuels 2017; 10:12. [PMID: 28053668 PMCID: PMC5209956 DOI: 10.1186/s13068-016-0695-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 12/23/2016] [Indexed: 05/22/2023]
Abstract
BACKGROUND The native recalcitrance of plants hinders the biomass conversion process using current biorefinery techniques. Down-regulation of the caffeic acid O-methyltransferase (COMT) gene in the lignin biosynthesis pathway of switchgrass reduced the thermochemical and biochemical conversion recalcitrance of biomass. Due to potential environmental influences on lignin biosynthesis and deposition, studying the consequences of physicochemical changes in field-grown plants without pretreatment is essential to evaluate the performance of lignin-altered plants. We determined the chemical composition, cellulose crystallinity and the degree of its polymerization, molecular weight of hemicellulose, and cellulose accessibility of cell walls in order to better understand the fundamental features of why biomass is recalcitrant to conversion without pretreatment. The most important is to investigate whether traits and features are stable in the dynamics of field environmental effects over multiple years. RESULTS Field-grown COMT down-regulated plants maintained both reduced cell wall recalcitrance and lignin content compared with the non-transgenic controls for at least 3 seasons. The transgenic switchgrass yielded 35-84% higher total sugar release (enzymatic digestibility or saccharification) from a 72-h enzymatic hydrolysis without pretreatment and also had a 25-32% increase in enzymatic sugar release after hydrothermal pretreatment. The COMT-silenced switchgrass lines had consistently lower lignin content, e.g., 12 and 14% reduction for year 2 and year 3 growing season, respectively, than the control plants. By contrast, the transgenic lines had 7-8% more xylan and galactan contents than the wild-type controls. Gel permeation chromatographic results revealed that the weight-average molecular weights of hemicellulose were 7-11% lower in the transgenic than in the control lines. In addition, we found that silencing of COMT in switchgrass led to 20-22% increased cellulose accessibility as measured by the Simons' stain protocol. No significant changes were observed on the arabinan and glucan contents, cellulose crystallinity, and cellulose degree of polymerization between the transgenic and control plants. With the 2-year comparative analysis, both the control and transgenic lines had significant increases in lignin and glucan contents and hemicellulose molecular weight across the growing seasons. CONCLUSIONS The down-regulation of COMT in switchgrass resulting in a reduced lignin content and biomass recalcitrance is stable in a field-grown trial for at least three seasons. Among the determined affecting factors, the reduced biomass recalcitrance of the COMT-silenced switchgrass, grown in the field conditions for two and three seasons, was likely related to the decreased lignin content and increased biomass accessibility, whereas the cellulose crystallinity and degree of its polymerization and hemicellulose molecular weights did not contribute to the reduction of recalcitrance significantly. This finding suggests that lignin down-regulation in lignocellulosic feedstock confers improved saccharification that translates from greenhouse to field trial and that lignin content and biomass accessibility are two significant factors for developing a reduced recalcitrance feedstock by genetic modification.
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Affiliation(s)
- Mi Li
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory (ORNL), Oak Ridge, TN USA
- BioSciences Division, ORNL, Oak Ridge, TN USA
- UT-ORNL Joint Institute for Biological Sciences, Oak Ridge, TN USA
| | - Yunqiao Pu
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory (ORNL), Oak Ridge, TN USA
- BioSciences Division, ORNL, Oak Ridge, TN USA
- UT-ORNL Joint Institute for Biological Sciences, Oak Ridge, TN USA
| | - Chang Geun Yoo
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory (ORNL), Oak Ridge, TN USA
- BioSciences Division, ORNL, Oak Ridge, TN USA
- UT-ORNL Joint Institute for Biological Sciences, Oak Ridge, TN USA
| | - Erica Gjersing
- Biosciences Center, National Renewable Energy Laboratory (NREL), Golden, CO USA
| | - Stephen R. Decker
- Biosciences Center, National Renewable Energy Laboratory (NREL), Golden, CO USA
| | - Crissa Doeppke
- Biosciences Center, National Renewable Energy Laboratory (NREL), Golden, CO USA
| | - Todd Shollenberger
- Biosciences Center, National Renewable Energy Laboratory (NREL), Golden, CO USA
| | - Timothy J. Tschaplinski
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory (ORNL), Oak Ridge, TN USA
- BioSciences Division, ORNL, Oak Ridge, TN USA
- UT-ORNL Joint Institute for Biological Sciences, Oak Ridge, TN USA
| | - Nancy L. Engle
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory (ORNL), Oak Ridge, TN USA
- BioSciences Division, ORNL, Oak Ridge, TN USA
- UT-ORNL Joint Institute for Biological Sciences, Oak Ridge, TN USA
| | | | | | - Holly L. Baxter
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory (ORNL), Oak Ridge, TN USA
- Department of Plant Sciences, University of Tennessee, Knoxville, TN USA
| | - Mitra Mazarei
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory (ORNL), Oak Ridge, TN USA
- Department of Plant Sciences, University of Tennessee, Knoxville, TN USA
| | - Chunxiang Fu
- Forage Improvement Division, The Samuel Roberts Noble Foundation, Ardmore, OK USA
| | - Richard A. Dixon
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory (ORNL), Oak Ridge, TN USA
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX USA
| | - Zeng-Yu Wang
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory (ORNL), Oak Ridge, TN USA
- Forage Improvement Division, The Samuel Roberts Noble Foundation, Ardmore, OK USA
| | - C. Neal Stewart
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory (ORNL), Oak Ridge, TN USA
- Department of Plant Sciences, University of Tennessee, Knoxville, TN USA
| | - Arthur J. Ragauskas
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory (ORNL), Oak Ridge, TN USA
- BioSciences Division, ORNL, Oak Ridge, TN USA
- UT-ORNL Joint Institute for Biological Sciences, Oak Ridge, TN USA
- Department of Chemical and Biomolecular Engineering & Department of Forestry, Wildlife and Fisheries, University of Tennessee, Knoxville, TN USA
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30
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Poudel S, Giannone RJ, Rodriguez M, Raman B, Martin MZ, Engle NL, Mielenz JR, Nookaew I, Brown SD, Tschaplinski TJ, Ussery D, Hettich RL. Integrated omics analyses reveal the details of metabolic adaptation of Clostridium thermocellum to lignocellulose-derived growth inhibitors released during the deconstruction of switchgrass. Biotechnol Biofuels 2017; 10:14. [PMID: 28077967 PMCID: PMC5223564 DOI: 10.1186/s13068-016-0697-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 12/24/2016] [Indexed: 05/03/2023]
Abstract
BACKGROUND Clostridium thermocellum is capable of solubilizing and converting lignocellulosic biomass into ethanol. Although much of the work-to-date has centered on characterizing this microbe's growth on model cellulosic substrates, such as cellobiose, Avicel, or filter paper, it is vitally important to understand its metabolism on more complex, lignocellulosic substrates to identify relevant industrial bottlenecks that could undermine efficient biofuel production. To this end, we have examined a time course progression of C. thermocellum grown on switchgrass to assess the metabolic and protein changes that occur during the conversion of plant biomass to ethanol. RESULTS The most striking feature of the metabolome was the observed accumulation of long-chain, branched fatty acids over time, implying an adaptive restructuring of C. thermocellum's cellular membrane as the culture progresses. This is undoubtedly a response to the gradual accumulation of lignocellulose-derived inhibitory compounds as the organism deconstructs the switchgrass to access the embedded cellulose. Corroborating the metabolomics data, proteomic analysis revealed a corresponding time-dependent increase in various enzymes, including those involved in the interconversion of branched amino acids valine, leucine, and isoleucine to iso- and anteiso-fatty acid precursors. Additionally, the metabolic accumulation of hemicellulose-derived sugars and sugar alcohols concomitant with increased abundance of enzymes involved in C5 sugar metabolism/pentose phosphate pathway indicates that C. thermocellum shifts glycolytic intermediates to alternate pathways to modulate overall carbon flux in response to C5 sugar metabolites that increase during lignocellulose deconstruction. CONCLUSIONS Integrated omic platforms provided complementary systems biological information that highlight C. thermocellum's specific response to cytotoxic inhibitors released during the deconstruction and utilization of switchgrass. These additional viewpoints allowed us to fully realize the level to which the organism adapts to an increasingly challenging culture environment-information that will prove critical to C. thermocellum's industrial efficacy.
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Affiliation(s)
- Suresh Poudel
- Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN 37831 USA
- Department of Genome Science and Technology, University of Tennessee, Knoxville, TN 37996 USA
| | | | - Miguel Rodriguez
- Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN 37831 USA
| | - Babu Raman
- Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN 37831 USA
- Dow AgroSciences, 9330 Zionsville Road, Indianapolis, IN 46268 USA
| | - Madhavi Z. Martin
- Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN 37831 USA
| | - Nancy L. Engle
- Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN 37831 USA
| | | | - Intawat Nookaew
- Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN 37831 USA
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR 72205 USA
| | - Steven D. Brown
- Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN 37831 USA
- Department of Genome Science and Technology, University of Tennessee, Knoxville, TN 37996 USA
| | | | - David Ussery
- Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN 37831 USA
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR 72205 USA
| | - Robert L. Hettich
- Chemical Sciences Division, Oak Ridge National Lab, Oak Ridge, TN 37831 USA
- Department of Genome Science and Technology, University of Tennessee, Knoxville, TN 37996 USA
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31
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Yang Y, Yoo CG, Winkeler KA, Collins CM, Hinchee MAW, Jawdy SS, Gunter LE, Engle NL, Pu Y, Yang X, Tschaplinski TJ, Ragauskas AJ, Tuskan GA, Chen JG. Overexpression of a Domain of Unknown Function 231-containing protein increases O-xylan acetylation and cellulose biosynthesis in Populus. Biotechnol Biofuels 2017; 10:311. [PMID: 29299061 PMCID: PMC5744390 DOI: 10.1186/s13068-017-0998-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 12/14/2017] [Indexed: 05/02/2023]
Abstract
BACKGROUND Domain of Unknown Function 231-containing proteins (DUF231) are plant specific and their function is largely unknown. Studies in the model plants Arabidopsis and rice suggested that some DUF231 proteins act in the process of O-acetyl substitution of hemicellulose and esterification of pectin. However, little is known about the function of DUF231 proteins in woody plant species. RESULTS This study provides evidence supporting that one member of DUF231 family proteins in the woody perennial plant Populus deltoides (genotype WV94), PdDUF231A, has a role in the acetylation of xylan and affects cellulose biosynthesis. A total of 52 DUF231-containing proteins were identified in the Populus genome. In P. deltoides transgenic lines overexpressing PdDUF231A (OXPdDUF231A), glucose and cellulose contents were increased. Consistent with these results, the transcript levels of cellulose biosynthesis-related genes were increased in the OXPdDUF231A transgenic lines. Furthermore, the relative content of total acetylated xylan was increased in the OXPdDUF231A transgenic lines. Enzymatic saccharification assays revealed that the rate of glucose release increased in OXPdDUF231A transgenic lines. Plant biomass productivity was also increased in OXPdDUF231A transgenic lines. CONCLUSIONS These results suggest that PdDUF231A affects cellulose biosynthesis and plays a role in the acetylation of xylan. PdDUF231A is a promising target for genetic modification for biofuel production because biomass productivity and compositional quality can be simultaneously improved through overexpression.
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Affiliation(s)
- Yongil Yang
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Chang Geun Yoo
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- UT-ORNL Joint Institute for Biological Science, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | | | | | | | - Sara S. Jawdy
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Lee E. Gunter
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Nancy L. Engle
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Yunqiao Pu
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- UT-ORNL Joint Institute for Biological Science, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Xiaohan Yang
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Timothy J. Tschaplinski
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Arthur J. Ragauskas
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- UT-ORNL Joint Institute for Biological Science, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN 37996 USA
- Department of Forestry, Wildlife, and Fisheries, University of Tennessee, Knoxville, TN 37996 USA
| | - Gerald A. Tuskan
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Jin-Gui Chen
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
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Bible AN, Fletcher SJ, Pelletier DA, Schadt CW, Jawdy SS, Weston DJ, Engle NL, Tschaplinski T, Masyuko R, Polisetti S, Bohn PW, Coutinho TA, Doktycz MJ, Morrell-Falvey JL. A Carotenoid-Deficient Mutant in Pantoea sp. YR343, a Bacteria Isolated from the Rhizosphere of Populus deltoides, Is Defective in Root Colonization. Front Microbiol 2016; 7:491. [PMID: 27148182 PMCID: PMC4834302 DOI: 10.3389/fmicb.2016.00491] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 03/24/2016] [Indexed: 11/13/2022] Open
Abstract
The complex interactions between plants and their microbiome can have a profound effect on the health and productivity of the plant host. A better understanding of the microbial mechanisms that promote plant health and stress tolerance will enable strategies for improving the productivity of economically important plants. Pantoea sp. YR343 is a motile, rod-shaped bacterium isolated from the roots of Populus deltoides that possesses the ability to solubilize phosphate and produce the phytohormone indole-3-acetic acid (IAA). Pantoea sp. YR343 readily colonizes plant roots and does not appear to be pathogenic when applied to the leaves or roots of selected plant hosts. To better understand the molecular mechanisms involved in plant association and rhizosphere survival by Pantoea sp. YR343, we constructed a mutant in which the crtB gene encoding phytoene synthase was deleted. Phytoene synthase is responsible for converting geranylgeranyl pyrophosphate to phytoene, an important precursor to the production of carotenoids. As predicted, the ΔcrtB mutant is defective in carotenoid production, and shows increased sensitivity to oxidative stress. Moreover, we find that the ΔcrtB mutant is impaired in biofilm formation and production of IAA. Finally we demonstrate that the ΔcrtB mutant shows reduced colonization of plant roots. Taken together, these data suggest that carotenoids are important for plant association and/or rhizosphere survival in Pantoea sp. YR343.
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Affiliation(s)
- Amber N. Bible
- Biosciences Division, Oak Ridge National LaboratoryOak Ridge, TN, USA
| | - Sarah J. Fletcher
- Biosciences Division, Oak Ridge National LaboratoryOak Ridge, TN, USA
| | - Dale A. Pelletier
- Biosciences Division, Oak Ridge National LaboratoryOak Ridge, TN, USA
| | | | - Sara S. Jawdy
- Biosciences Division, Oak Ridge National LaboratoryOak Ridge, TN, USA
| | - David J. Weston
- Biosciences Division, Oak Ridge National LaboratoryOak Ridge, TN, USA
| | - Nancy L. Engle
- Biosciences Division, Oak Ridge National LaboratoryOak Ridge, TN, USA
| | | | - Rachel Masyuko
- Department of Chemical and Biomolecular Engineering, University of Notre DameNotre Dame, IN, USA
| | - Sneha Polisetti
- Department of Chemical and Biomolecular Engineering, University of Notre DameNotre Dame, IN, USA
| | - Paul W. Bohn
- Department of Chemical and Biomolecular Engineering, University of Notre DameNotre Dame, IN, USA
| | - Teresa A. Coutinho
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of PretoriaPretoria, South Africa
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Dumitrache A, Akinosho H, Rodriguez M, Meng X, Yoo CG, Natzke J, Engle NL, Sykes RW, Tschaplinski TJ, Muchero W, Ragauskas AJ, Davison BH, Brown SD. Consolidated bioprocessing of Populus using Clostridium (Ruminiclostridium) thermocellum: a case study on the impact of lignin composition and structure. Biotechnol Biofuels 2016; 9:31. [PMID: 26855670 PMCID: PMC4743434 DOI: 10.1186/s13068-016-0445-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 01/20/2016] [Indexed: 05/04/2023]
Abstract
BACKGROUND Higher ratios of syringyl-to-guaiacyl (S/G) lignin components of Populus were shown to improve sugar release by enzymatic hydrolysis using commercial blends. Cellulolytic microbes are often robust biomass hydrolyzers and may offer cost advantages; however, it is unknown whether their activity can also be significantly influenced by the ratio of different monolignol types in Populus biomass. Hydrolysis and fermentation of autoclaved, but otherwise not pretreated Populus trichocarpa by Clostridium thermocellum ATCC 27405 was compared using feedstocks that had similar carbohydrate and total lignin contents but differed in S/G ratios. RESULTS Populus with an S/G ratio of 2.1 was converted more rapidly and to a greater extent compared to similar biomass that had a ratio of 1.2. For either microbes or commercial enzymes, an approximate 50 % relative difference in total solids solubilization was measured for both biomasses, which suggests that the differences and limitations in the microbial breakdown of lignocellulose may be largely from the enzymatic hydrolytic process. Surprisingly, the reduction in glucan content per gram solid in the residual microbially processed biomass was similar (17-18 %) irrespective of S/G ratio, pointing to a similar mechanism of solubilization that proceeded at different rates. Fermentation metabolome testing did not reveal the release of known biomass-derived alcohol and aldehyde inhibitors that could explain observed differences in microbial hydrolytic activity. Biomass-derived p-hydroxybenzoic acid was up to nine-fold higher in low S/G ratio biomass fermentations, but was not found to be inhibitory in subsequent test fermentations. Cellulose crystallinity and degree of polymerization did not vary between Populus lines and had minor changes after fermentation. However, lignin molecular weights and cellulose accessibility determined by Simons' staining were positively correlated to the S/G content. CONCLUSIONS Higher S/G ratios in Populus biomass lead to longer and more linear lignin chains and greater access to surface cellulosic content by microbe-bound enzymatic complexes. Substrate access limitation is suggested as a primary bottleneck in solubilization of minimally processed Populus, which has important implications for microbial deconstruction of lignocellulose biomass. Our findings will allow others to examine different Populus lines and to test if similar observations are possible for other plant species.
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Affiliation(s)
- Alexandru Dumitrache
- />Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- />BioEnergy Sciences Center, Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
| | - Hannah Akinosho
- />Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- />BioEnergy Sciences Center, Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
- />Renewable Bioproducts Institute, Georgia Institute of Technology, Atlanta, GA 30332 USA
- />UT-ORNL Joint Institute for Biological Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Miguel Rodriguez
- />Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- />BioEnergy Sciences Center, Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
| | - Xianzhi Meng
- />BioEnergy Sciences Center, Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
- />Renewable Bioproducts Institute, Georgia Institute of Technology, Atlanta, GA 30332 USA
- />School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332 USA
| | - Chang Geun Yoo
- />Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- />BioEnergy Sciences Center, Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
- />UT-ORNL Joint Institute for Biological Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Jace Natzke
- />Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- />BioEnergy Sciences Center, Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
| | - Nancy L. Engle
- />Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- />BioEnergy Sciences Center, Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
| | - Robert W. Sykes
- />National Renewable Energy Laboratory, US Department of Energy, Golden, CO 80401 USA
| | - Timothy J. Tschaplinski
- />Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- />BioEnergy Sciences Center, Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
| | - Wellington Muchero
- />Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- />BioEnergy Sciences Center, Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
| | - Arthur J. Ragauskas
- />Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- />BioEnergy Sciences Center, Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
- />UT-ORNL Joint Institute for Biological Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- />Department of Chemical and Biomolecular Engineering, Department of Forestry, Wildlife, and Fisheries, University of Tennessee, Knoxville, TN 37996 USA
| | - Brian H. Davison
- />Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- />BioEnergy Sciences Center, Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
| | - Steven D. Brown
- />Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- />BioEnergy Sciences Center, Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
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Currie DH, Raman B, Gowen CM, Tschaplinski TJ, Land ML, Brown SD, Covalla SF, Klingeman DM, Yang ZK, Engle NL, Johnson CM, Rodriguez M, Shaw AJ, Kenealy WR, Lynd LR, Fong SS, Mielenz JR, Davison BH, Hogsett DA, Herring CD. Genome-scale resources for Thermoanaerobacterium saccharolyticum. BMC Syst Biol 2015; 9:30. [PMID: 26111937 PMCID: PMC4518999 DOI: 10.1186/s12918-015-0159-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 03/09/2015] [Indexed: 01/12/2023]
Abstract
Background Thermoanaerobacterium saccharolyticum is a hemicellulose-degrading thermophilic anaerobe that was previously engineered to produce ethanol at high yield. A major project was undertaken to develop this organism into an industrial biocatalyst, but the lack of genome information and resources were recognized early on as a key limitation. Results Here we present a set of genome-scale resources to enable the systems level investigation and development of this potentially important industrial organism. Resources include a complete genome sequence for strain JW/SL-YS485, a genome-scale reconstruction of metabolism, tiled microarray data showing transcription units, mRNA expression data from 71 different growth conditions or timepoints and GC/MS-based metabolite analysis data from 42 different conditions or timepoints. Growth conditions include hemicellulose hydrolysate, the inhibitors HMF, furfural, diamide, and ethanol, as well as high levels of cellulose, xylose, cellobiose or maltodextrin. The genome consists of a 2.7 Mbp chromosome and a 110 Kbp megaplasmid. An active prophage was also detected, and the expression levels of CRISPR genes were observed to increase in association with those of the phage. Hemicellulose hydrolysate elicited a response of carbohydrate transport and catabolism genes, as well as poorly characterized genes suggesting a redox challenge. In some conditions, a time series of combined transcription and metabolite measurements were made to allow careful study of microbial physiology under process conditions. As a demonstration of the potential utility of the metabolic reconstruction, the OptKnock algorithm was used to predict a set of gene knockouts that maximize growth-coupled ethanol production. The predictions validated intuitive strain designs and matched previous experimental results. Conclusion These data will be a useful asset for efforts to develop T. saccharolyticum for efficient industrial production of biofuels. The resources presented herein may also be useful on a comparative basis for development of other lignocellulose degrading microbes, such as Clostridium thermocellum. Electronic supplementary material The online version of this article (doi:10.1186/s12918-015-0159-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Devin H Currie
- Mascoma Corporation, 67 Etna Rd, 03766, Lebanon, NH, USA.
| | - Babu Raman
- BioEnergy Science Center, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN, 37831, USA. .,Dow AgroSciences, 9330 Zionsville Road, Indianapolis, IN, 46268, USA.
| | - Christopher M Gowen
- Chemical and Life Science Engineering, Virginia Commonwealth University, P.O. Box 843028, Richmond, Virginia, 23284, USA. .,Centre for Applied Bioscience and Bioengineering, Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada.
| | - Timothy J Tschaplinski
- BioEnergy Science Center, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN, 37831, USA.
| | - Miriam L Land
- BioEnergy Science Center, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN, 37831, USA.
| | - Steven D Brown
- BioEnergy Science Center, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN, 37831, USA.
| | - Sean F Covalla
- Mascoma Corporation, 67 Etna Rd, 03766, Lebanon, NH, USA.
| | - Dawn M Klingeman
- BioEnergy Science Center, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN, 37831, USA.
| | - Zamin K Yang
- BioEnergy Science Center, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN, 37831, USA.
| | - Nancy L Engle
- BioEnergy Science Center, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN, 37831, USA.
| | - Courtney M Johnson
- BioEnergy Science Center, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN, 37831, USA.
| | - Miguel Rodriguez
- BioEnergy Science Center, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN, 37831, USA.
| | - A Joe Shaw
- Mascoma Corporation, 67 Etna Rd, 03766, Lebanon, NH, USA. .,Novogy Inc, Cambridge, MA, 02138, USA.
| | | | - Lee R Lynd
- Mascoma Corporation, 67 Etna Rd, 03766, Lebanon, NH, USA. .,Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH, 03755, USA.
| | - Stephen S Fong
- Chemical and Life Science Engineering, Virginia Commonwealth University, P.O. Box 843028, Richmond, Virginia, 23284, USA.
| | - Jonathan R Mielenz
- BioEnergy Science Center, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN, 37831, USA.
| | - Brian H Davison
- BioEnergy Science Center, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN, 37831, USA.
| | | | - Christopher D Herring
- Mascoma Corporation, 67 Etna Rd, 03766, Lebanon, NH, USA. .,Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH, 03755, USA.
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Weston DJ, Rogers A, Tschaplinski TJ, Gunter LE, Jawdy SA, Engle NL, Heady LE, Tuskan GA, Wullschleger SD. Scaling nitrogen and carbon interactions: what are the consequences of biological buffering? Ecol Evol 2015; 5:2839-50. [PMID: 26306170 PMCID: PMC4541989 DOI: 10.1002/ece3.1565] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 05/26/2015] [Indexed: 11/27/2022] Open
Abstract
Understanding the consequences of elevated CO2 (eCO2; 800 ppm) on terrestrial ecosystems is a central theme in global change biology, but relatively little is known about how altered plant C and N metabolism influences higher levels of biological organization. Here, we investigate the consequences of C and N interactions by genetically modifying the N-assimilation pathway in Arabidopsis and initiating growth chamber and mesocosm competition studies at current CO2 (cCO2; 400 ppm) and eCO2 over multiple generations. Using a suite of ecological, physiological, and molecular genomic tools, we show that a single-gene mutant of a key enzyme (nia2) elicited a highly orchestrated buffering response starting with a fivefold increase in the expression of a gene paralog (nia1) and a 63% increase in the expression of gene network module enriched for N-assimilation genes. The genetic perturbation reduced amino acids, protein, and TCA-cycle intermediate concentrations in the nia2 mutant compared to the wild-type, while eCO2 mainly increased carbohydrate concentrations. The mutant had reduced net photosynthetic rates due to a 27% decrease in carboxylation capacity and an 18% decrease in electron transport rates. The expression of these buffering mechanisms resulted in a penalty that negatively correlated with fitness and population dynamics yet showed only minor alterations in our estimates of population function, including total per unit area biomass, ground cover, and leaf area index. This study provides insight into the consequences of buffering mechanisms that occur post-genetic perturbations in the N pathway and the associated outcomes these buffering systems have on plant populations relative to eCO2.
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Affiliation(s)
- David J Weston
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, Tennessee, 37831-6407
| | - Alistair Rogers
- Biological, Environmental & Climate Sciences Department, Brookhaven National Laboratory Upton, New York, 11973-5000
| | | | - Lee E Gunter
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, Tennessee, 37831-6407
| | - Sara A Jawdy
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, Tennessee, 37831-6407
| | - Nancy L Engle
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, Tennessee, 37831-6407
| | - Lindsey E Heady
- Biological, Environmental & Climate Sciences Department, Brookhaven National Laboratory Upton, New York, 11973-5000
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, Tennessee, 37831-6407
| | - Stan D Wullschleger
- Environmental Sciences Division, Oak Ridge National Laboratory Oak Ridge, Tennessee, 37831-6301
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Zhao Q, Zeng Y, Yin Y, Pu Y, Jackson LA, Engle NL, Martin MZ, Tschaplinski TJ, Ding SY, Ragauskas AJ, Dixon RA. Pinoresinol reductase 1 impacts lignin distribution during secondary cell wall biosynthesis in Arabidopsis. Phytochemistry 2015; 112:170-8. [PMID: 25107662 DOI: 10.1016/j.phytochem.2014.07.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2014] [Revised: 03/30/2014] [Accepted: 07/07/2014] [Indexed: 05/24/2023]
Abstract
Pinoresinol reductase (PrR) catalyzes the conversion of the lignan (-)-pinoresinol to (-)-lariciresinol in Arabidopsis thaliana, where it is encoded by two genes, PrR1 and PrR2, that appear to act redundantly. PrR1 is highly expressed in lignified inflorescence stem tissue, whereas PrR2 expression is barely detectable in stems. Co-expression analysis has indicated that PrR1 is co-expressed with many characterized genes involved in secondary cell wall biosynthesis, whereas PrR2 expression clusters with a different set of genes. The promoter of the PrR1 gene is regulated by the secondary cell wall related transcription factors SND1 and MYB46. The loss-of-function mutant of PrR1 shows, in addition to elevated levels of pinoresinol, significantly decreased lignin content and a slightly altered lignin structure with lower abundance of cinnamyl alcohol end groups. Stimulated Raman scattering (SRS) microscopy analysis indicated that the lignin content of the prr1-1 loss-of-function mutant is similar to that of wild-type plants in xylem cells, which exhibit a normal phenotype, but is reduced in the fiber cells. Together, these data suggest an association of the lignan biosynthetic enzyme encoded by PrR1 with secondary cell wall biosynthesis in fiber cells.
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Affiliation(s)
- Qiao Zhao
- Plant Biology Division, Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA
| | - Yining Zeng
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA; BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Yanbin Yin
- Department of Biological Sciences, Northern Illinois University, DeKalb, IL 60115, USA
| | - Yunqiao Pu
- Institute of Paper Science and Technology, Georgia Institute of Technology, Atlanta, GA, USA; BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Lisa A Jackson
- Plant Biology Division, Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA; BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Nancy L Engle
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Madhavi Z Martin
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Timothy J Tschaplinski
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Shi-You Ding
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA; BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Arthur J Ragauskas
- Institute of Paper Science and Technology, Georgia Institute of Technology, Atlanta, GA, USA; BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Richard A Dixon
- Plant Biology Division, Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA; BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; Department of Biological Sciences, University of North Texas, Denton, TX 76203, USA.
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Cecchini NM, Jung HW, Engle NL, Tschaplinski TJ, Greenberg JT. ALD1 Regulates Basal Immune Components and Early Inducible Defense Responses in Arabidopsis. Mol Plant Microbe Interact 2015; 28:455-66. [PMID: 25372120 DOI: 10.1094/mpmi-06-14-0187-r] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Robust immunity requires basal defense machinery to mediate timely responses and feedback cycles to amplify defenses against potentially spreading infections. AGD2-LIKE DEFENSE RESPONSE PROTEIN 1 (ALD1) is needed for the accumulation of the plant defense signal salicylic acid (SA) during the first hours after infection with the pathogen Pseudomonas syringae and is also upregulated by infection and SA. ALD1 is an aminotransferase with multiple substrates and products in vitro. Pipecolic acid (Pip) is an ALD1-dependent bioactive product induced by P. syringae. Here, we addressed roles of ALD1 in mediating defense amplification as well as the levels and responses of basal defense machinery. ALD1 needs immune components PAD4 and ICS1 (an SA synthesis enzyme) to confer disease resistance, possibly through a transcriptional amplification loop between them. Furthermore, ALD1 affects basal defense by controlling microbial-associated molecular pattern (MAMP) receptor levels and responsiveness. Vascular exudates from uninfected ALD1-overexpressing plants confer local immunity to the wild type and ald1 mutants yet are not enriched for Pip. We infer that, in addition to affecting Pip accumulation, ALD1 produces non-Pip metabolites that play roles in immunity. Thus, distinct metabolite signals controlled by the same enzyme affect basal and early defenses versus later defense responses, respectively.
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Affiliation(s)
- Nicolás M Cecchini
- 1 Department of Molecular Genetics and Cell Biology, The University of Chicago, 929 East 57th Street GCIS 524W, Chicago 60637, U.S.A
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Tschaplinski TJ, Plett JM, Engle NL, Deveau A, Cushman KC, Martin MZ, Doktycz MJ, Tuskan GA, Brun A, Kohler A, Martin F. Populus trichocarpa and Populus deltoides exhibit different metabolomic responses to colonization by the symbiotic fungus Laccaria bicolor. Mol Plant Microbe Interact 2014; 27:546-56. [PMID: 24548064 DOI: 10.1094/mpmi-09-13-0286-r] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Within boreal and temperate forest ecosystems, the majority of trees and shrubs form beneficial relationships with mutualistic ectomycorrhizal (ECM) fungi that support plant health through increased access to nutrients as well as aiding in stress and pest tolerance. The intimate interaction between fungal hyphae and plant roots results in a new symbiotic "organ" called the ECM root tip. Little is understood concerning the metabolic reprogramming that favors the formation of this hybrid tissue in compatible interactions and what prevents the formation of ECM root tips in incompatible interactions. We show here that the metabolic changes during favorable colonization between the ECM fungus Laccaria bicolor and its compatible host, Populus trichocarpa, are characterized by shifts in aromatic acid, organic acid, and fatty acid metabolism. We demonstrate that this extensive metabolic reprogramming is repressed in incompatible interactions and that more defensive compounds are produced or retained. We also demonstrate that L. bicolor can metabolize a number of secreted defensive compounds and that the degradation of some of these compounds produces immune response metabolites (e.g., salicylic acid from salicin). Therefore, our results suggest that the metabolic responsiveness of plant roots to L. bicolor is a determinant factor in fungus-host interactions.
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Li Y, Xu T, Tschaplinski TJ, Engle NL, Yang Y, Graham DE, He Z, Zhou J. Improvement of cellulose catabolism in Clostridium cellulolyticum by sporulation abolishment and carbon alleviation. Biotechnol Biofuels 2014; 7:25. [PMID: 24555718 PMCID: PMC3936895 DOI: 10.1186/1754-6834-7-25] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2013] [Accepted: 02/06/2014] [Indexed: 05/23/2023]
Abstract
BACKGROUND Clostridium cellulolyticum can degrade lignocellulosic biomass, and ferment the soluble sugars to produce valuable chemicals such as lactate, acetate, ethanol and hydrogen. However, the cellulose utilization efficiency of C. cellulolyticum still remains very low, impeding its application in consolidated bioprocessing for biofuels production. In this study, two metabolic engineering strategies were exploited to improve cellulose utilization efficiency, including sporulation abolishment and carbon overload alleviation. RESULTS The spo0A gene at locus Ccel_1894, which encodes a master sporulation regulator was inactivated. The spo0A mutant abolished the sporulation ability. In a high concentration of cellulose (50 g/l), the performance of the spo0A mutant increased dramatically in terms of maximum growth, final concentrations of three major metabolic products, and cellulose catabolism. The microarray and gas chromatography-mass spectrometry (GC-MS) analyses showed that the valine, leucine and isoleucine biosynthesis pathways were up-regulated in the spo0A mutant. Based on this information, a partial isobutanol producing pathway modified from valine biosynthesis was introduced into C. cellulolyticum strains to further increase cellulose consumption by alleviating excessive carbon load. The introduction of this synthetic pathway to the wild-type strain improved cellulose consumption from 17.6 g/l to 28.7 g/l with a production of 0.42 g/l isobutanol in the 50 g/l cellulose medium. However, the spo0A mutant strain did not appreciably benefit from introduction of this synthetic pathway and the cellulose utilization efficiency did not further increase. A technical highlight in this study was that an in vivo promoter strength evaluation protocol was developed using anaerobic fluorescent protein and flow cytometry for C. cellulolyticum. CONCLUSIONS In this study, we inactivated the spo0A gene and introduced a heterologous synthetic pathway to manipulate the stress response to heavy carbon load and accumulation of metabolic products. These findings provide new perspectives to enhance the ability of cellulolytic bacteria to produce biofuels and biocommodities with high efficiency and at low cost directly from lignocellulosic biomass.
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Affiliation(s)
- Yongchao Li
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, 101 David L. Boren Boulevard, Norman, OK 73019, USA
| | - Tao Xu
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, 101 David L. Boren Boulevard, Norman, OK 73019, USA
| | - Timothy J Tschaplinski
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Nancy L Engle
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - David E Graham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Zhili He
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, 101 David L. Boren Boulevard, Norman, OK 73019, USA
| | - Jizhong Zhou
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, 101 David L. Boren Boulevard, Norman, OK 73019, USA
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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Clarkson SM, Hamilton-Brehm SD, Giannone RJ, Engle NL, Tschaplinski TJ, Hettich RL, Elkins JG. A comparative multidimensional LC-MS proteomic analysis reveals mechanisms for furan aldehyde detoxification in Thermoanaerobacter pseudethanolicus 39E. Biotechnol Biofuels 2014; 7:165. [PMID: 25506391 PMCID: PMC4265447 DOI: 10.1186/s13068-014-0165-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 11/07/2014] [Indexed: 05/07/2023]
Abstract
BACKGROUND Chemical and physical pretreatment of lignocellulosic biomass improves substrate reactivity for increased microbial biofuel production, but also restricts growth via the release of furan aldehydes, such as furfural and 5-hydroxymethylfurfural (5-HMF). The physiological effects of these inhibitors on thermophilic, fermentative bacteria are important to understand; especially as cellulolytic strains are being developed for consolidated bioprocessing (CBP) of lignocellulosic feedstocks. Identifying mechanisms for detoxification of aldehydes in naturally resistant strains, such as Thermoanaerobacter spp., may also enable improvements in candidate CBP microorganisms. RESULTS Thermoanaerobacter pseudethanolicus 39E, an anaerobic, saccharolytic thermophile, was found to grow readily in the presence of 30 mM furfural and 20 mM 5-HMF and reduce these aldehydes to their respective alcohols in situ. The proteomes of T. pseudethanolicus 39E grown in the presence or absence of 15 mM furfural were compared to identify upregulated enzymes potentially responsible for the observed reduction. A total of 225 proteins were differentially regulated in response to the 15 mM furfural treatment with 152 upregulated versus 73 downregulated. Only 87 proteins exhibited a twofold or greater change in abundance in either direction. Of these, 54 were upregulated in the presence of furfural and 33 were downregulated. Two oxidoreductases were upregulated at least twofold by furfural and were targeted for further investigation. Teth39_1597 encodes a predicted butanol dehydrogenase (BdhA) and Teth39_1598, a predicted aldo/keto reductase (AKR). Both genes were cloned from T. pseudethanolicus 39E, with the respective enzymes overexpressed in E. coli and specific activities determined against a variety of aldehydes. Overexpressed BdhA showed significant activity with all aldehydes tested, including furfural and 5-HMF, using NADPH as the cofactor. Cell extracts with AKR also showed activity with NADPH, but only with four-carbon butyraldehyde and isobutyraldehyde. CONCLUSIONS T. pseudethanolicus 39E displays intrinsic tolerance to the common pretreatment inhibitors furfural and 5-HMF. Multidimensional proteomic analysis was used as an effective tool to identify putative mechanisms for detoxification of furfural and 5-HMF. T. pseudethanolicus was found to upregulate an NADPH-dependent alcohol dehydrogenase 6.8-fold in response to furfural. In vitro enzyme assays confirmed the reduction of furfural and 5-HMF to their respective alcohols.
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Affiliation(s)
- Sonya M Clarkson
- />BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6341 USA
- />Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6341 USA
| | - Scott D Hamilton-Brehm
- />BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6341 USA
- />Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6341 USA
- />Current address: Division of Earth and Ecosystem Sciences, Desert Research Institute, Las Vegas, NV USA
| | - Richard J Giannone
- />BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6341 USA
- />Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6341 USA
| | - Nancy L Engle
- />BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6341 USA
- />Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6341 USA
| | - Timothy J Tschaplinski
- />BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6341 USA
- />Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6341 USA
| | - Robert L Hettich
- />BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6341 USA
- />Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6341 USA
| | - James G Elkins
- />BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6341 USA
- />Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6341 USA
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Holwerda EK, Thorne PG, Olson DG, Amador-Noguez D, Engle NL, Tschaplinski TJ, van Dijken JP, Lynd LR. The exometabolome of Clostridium thermocellum reveals overflow metabolism at high cellulose loading. Biotechnol Biofuels 2014; 7:155. [PMID: 25379055 PMCID: PMC4207885 DOI: 10.1186/s13068-014-0155-1] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2014] [Accepted: 10/03/2014] [Indexed: 05/18/2023]
Abstract
BACKGROUND Clostridium thermocellum is a model thermophilic organism for the production of biofuels from lignocellulosic substrates. The majority of publications studying the physiology of this organism use substrate concentrations of ≤10 g/L. However, industrially relevant concentrations of substrate start at 100 g/L carbohydrate, which corresponds to approximately 150 g/L solids. To gain insight into the physiology of fermentation of high substrate concentrations, we studied the growth on, and utilization of high concentrations of crystalline cellulose varying from 50 to 100 g/L by C. thermocellum. RESULTS Using a defined medium, batch cultures of C. thermocellum achieved 93% conversion of cellulose (Avicel) initially present at 100 g/L. The maximum rate of substrate utilization increased with increasing substrate loading. During fermentation of 100 g/L cellulose, growth ceased when about half of the substrate had been solubilized. However, fermentation continued in an uncoupled mode until substrate utilization was almost complete. In addition to commonly reported fermentation products, amino acids - predominantly L-valine and L-alanine - were secreted at concentrations up to 7.5 g/L. Uncoupled metabolism was also accompanied by products not documented previously for C. thermocellum, including isobutanol, meso- and RR/SS-2,3-butanediol and trace amounts of 3-methyl-1-butanol, 2-methyl-1-butanol and 1-propanol. We hypothesize that C. thermocellum uses overflow metabolism to balance its metabolism around the pyruvate node in glycolysis. CONCLUSIONS C. thermocellum is able to utilize industrially relevant concentrations of cellulose, up to 93 g/L. We report here one of the highest degrees of crystalline cellulose utilization observed thus far for a pure culture of C. thermocellum, the highest maximum substrate utilization rate and the highest amount of isobutanol produced by a wild-type organism.
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Affiliation(s)
- Evert K Holwerda
- />Thayer School of Engineering, Dartmouth College, Hanover, NH 03755 USA
- />BioEnergy Science Center, Oak Ridge, TN 37830 USA
| | | | - Daniel G Olson
- />Thayer School of Engineering, Dartmouth College, Hanover, NH 03755 USA
- />BioEnergy Science Center, Oak Ridge, TN 37830 USA
| | - Daniel Amador-Noguez
- />Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Nancy L Engle
- />BioEnergy Science Center, Oak Ridge, TN 37830 USA
- />Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
| | - Timothy J Tschaplinski
- />BioEnergy Science Center, Oak Ridge, TN 37830 USA
- />Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
| | - Johannes P van Dijken
- />Emeritus Industrial Biotechnology of Delft University of Technology, Delft, BC 2628 The Netherlands
| | - Lee R Lynd
- />Thayer School of Engineering, Dartmouth College, Hanover, NH 03755 USA
- />BioEnergy Science Center, Oak Ridge, TN 37830 USA
- />Mascoma Corporation, Lebanon, NH 03766 USA
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Linville JL, Rodriguez M, Land M, Syed MH, Engle NL, Tschaplinski TJ, Mielenz JR, Cox CD. Industrial robustness: understanding the mechanism of tolerance for the Populus hydrolysate-tolerant mutant strain of Clostridium thermocellum. PLoS One 2013; 8:e78829. [PMID: 24205326 PMCID: PMC3804516 DOI: 10.1371/journal.pone.0078829] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 09/16/2013] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND An industrially robust microorganism that can efficiently degrade and convert lignocellulosic biomass into ethanol and next-generation fuels is required to economically produce future sustainable liquid transportation fuels. The anaerobic, thermophilic, cellulolytic bacterium Clostridium thermocellum is a candidate microorganism for such conversions but it, like many bacteria, is sensitive to potential toxic inhibitors developed in the liquid hydrolysate produced during biomass processing. Microbial processes leading to tolerance of these inhibitory compounds found in the pretreated biomass hydrolysate are likely complex and involve multiple genes. METHODOLOGY/PRINCIPAL FINDINGS In this study, we developed a 17.5% v/v Populus hydrolysate tolerant mutant strain of C. thermocellum by directed evolution. The genome of the wild type strain, six intermediate population samples and seven single colony isolates were sequenced to elucidate the mechanism of tolerance. Analysis of the 224 putative mutations revealed 73 high confidence mutations. A longitudinal analysis of the intermediate population samples, a pan-genomic analysis of the isolates, and a hotspot analysis revealed 24 core genes common to all seven isolates and 8 hotspots. Genetic mutations were matched with the observed phenotype through comparison of RNA expression levels during fermentation by the wild type strain and mutant isolate 6 in various concentrations of Populus hydrolysate (0%, 10%, and 17.5% v/v). CONCLUSION/SIGNIFICANCE The findings suggest that there are multiple mutations responsible for the Populus hydrolysate tolerant phenotype resulting in several simultaneous mechanisms of action, including increases in cellular repair, and altered energy metabolism. To date, this study provides the most comprehensive elucidation of the mechanism of tolerance to a pretreated biomass hydrolysate by C. thermocellum. These findings make important contributions to the development of industrially robust strains of consolidated bioprocessing microorganisms.
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Affiliation(s)
- Jessica L Linville
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee, United States of America ; Bioenergy Science Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
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Trajano HL, Engle NL, Foston M, Ragauskas AJ, Tschaplinski TJ, Wyman CE. The fate of lignin during hydrothermal pretreatment. Biotechnol Biofuels 2013; 6:110. [PMID: 23902789 PMCID: PMC3751430 DOI: 10.1186/1754-6834-6-110] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 07/26/2013] [Indexed: 05/02/2023]
Abstract
BACKGROUND Effective enzymatic hydrolysis of lignocellulosic biomass benefits from lignin removal, relocation, and/or modification during hydrothermal pretreatment. Phase transition, depolymerization/repolymerization, and solubility effects may all influence these lignin changes. To better understand how lignin is altered, Populus trichocarpa x P. deltoides wood samples and cellulolytic enzyme lignin (CEL) isolated from P. trichocarpa x P. deltoides were subjected to batch and flowthrough pretreatments. The residual solids and liquid hydrolysate were characterized by gel permeation chromatography, heteronuclear single quantum coherence NMR, compositional analysis, and gas chromatography-mass spectrometry. RESULTS Changes in the structure of the solids recovered after the pretreatment of CEL and the production of aromatic monomers point strongly to depolymerization and condensation being primary mechanisms for lignin extraction and redeposition. The differences in lignin removal and phenolic compound production from native P. trichocarpa x P. deltoides and CEL suggested that lignin-carbohydrate interactions increased lignin extraction and the extractability of syringyl groups relative to guaiacyl groups. CONCLUSIONS These insights into delignification during hydrothermal pretreatment point to desirable pretreatment strategies and plant modifications. Because depolymerization followed by repolymerization appears to be the dominant mode of lignin modification, limiting the residence time of depolymerized lignin moieties in the bulk liquid phase should reduce lignin content in pretreated biomass. In addition, the increase in lignin removal in the presence of polysaccharides suggests that increasing lignin-carbohydrate cross-links in biomass would increase delignification during pretreatment.
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Affiliation(s)
- Heather L Trajano
- Department of Chemical and Environmental Engineering and Center for Environmental Research and Technology, Bourns College of Engineering, University of California Riverside, 1084 Columbia Ave, Riverside, CA 92507, USA
- Current address: Department of Chemical and Biological Engineering, The University of British Columbia, 2360 East Mall, Vancouver, British Columbia V6T 1Z3, Canada
- BioEnergy Science Center, Oak Ridge National Laboratory, PO Box 2008 MS6341, Oak Ridge, TN 37831, USA
| | - Nancy L Engle
- Biosciences Division, Oak Ridge National Laboratory, PO Box 2008 MS6341, Oak Ridge, TN 37831, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, PO Box 2008 MS6341, Oak Ridge, TN 37831, USA
| | - Marcus Foston
- School of Chemistry and Biochemistry, Institute of Paper Science and Technology, Georgia Institute of Technology, 500 10th Street N.W., Atlanta, GA 30332, USA
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, 1 Brookings Drive, Saint Louis, MO 63130, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, PO Box 2008 MS6341, Oak Ridge, TN 37831, USA
| | - Arthur J Ragauskas
- School of Chemistry and Biochemistry, Institute of Paper Science and Technology, Georgia Institute of Technology, 500 10th Street N.W., Atlanta, GA 30332, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, PO Box 2008 MS6341, Oak Ridge, TN 37831, USA
| | - Timothy J Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, PO Box 2008 MS6341, Oak Ridge, TN 37831, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, PO Box 2008 MS6341, Oak Ridge, TN 37831, USA
| | - Charles E Wyman
- Department of Chemical and Environmental Engineering and Center for Environmental Research and Technology, Bourns College of Engineering, University of California Riverside, 1084 Columbia Ave, Riverside, CA 92507, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, PO Box 2008 MS6341, Oak Ridge, TN 37831, USA
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Shen H, Poovaiah CR, Ziebell A, Tschaplinski TJ, Pattathil S, Gjersing E, Engle NL, Katahira R, Pu Y, Sykes R, Chen F, Ragauskas AJ, Mielenz JR, Hahn MG, Davis M, Stewart CN, Dixon RA. Enhanced characteristics of genetically modified switchgrass (Panicum virgatum L.) for high biofuel production. Biotechnol Biofuels 2013; 6:71. [PMID: 23651942 PMCID: PMC3652750 DOI: 10.1186/1754-6834-6-71] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Accepted: 04/30/2013] [Indexed: 05/18/2023]
Abstract
BACKGROUND Lignocellulosic biomass is one of the most promising renewable and clean energy resources to reduce greenhouse gas emissions and dependence on fossil fuels. However, the resistance to accessibility of sugars embedded in plant cell walls (so-called recalcitrance) is a major barrier to economically viable cellulosic ethanol production. A recent report from the US National Academy of Sciences indicated that, "absent technological breakthroughs", it was unlikely that the US would meet the congressionally mandated renewable fuel standard of 35 billion gallons of ethanol-equivalent biofuels plus 1 billion gallons of biodiesel by 2022. We here describe the properties of switchgrass (Panicum virgatum) biomass that has been genetically engineered to increase the cellulosic ethanol yield by more than 2-fold. RESULTS We have increased the cellulosic ethanol yield from switchgrass by 2.6-fold through overexpression of the transcription factor PvMYB4. This strategy reduces carbon deposition into lignin and phenolic fermentation inhibitors while maintaining the availability of potentially fermentable soluble sugars and pectic polysaccharides. Detailed biomass characterization analyses revealed that the levels and nature of phenolic acids embedded in the cell-wall, the lignin content and polymer size, lignin internal linkage levels, linkages between lignin and xylans/pectins, and levels of wall-bound fucose are all altered in PvMYB4-OX lines. Genetically engineered PvMYB4-OX switchgrass therefore provides a novel system for further understanding cell wall recalcitrance. CONCLUSIONS Our results have demonstrated that overexpression of PvMYB4, a general transcriptional repressor of the phenylpropanoid/lignin biosynthesis pathway, can lead to very high yield ethanol production through dramatic reduction of recalcitrance. MYB4-OX switchgrass is an excellent model system for understanding recalcitrance, and provides new germplasm for developing switchgrass cultivars as biomass feedstocks for biofuel production.
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Affiliation(s)
- Hui Shen
- Plant Biology Division, Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Charleson R Poovaiah
- Department of Plant Sciences, University of Tennessee, 2431 Joe Johnson Dr., Knoxville, TN, 37996, USA
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Angela Ziebell
- National Renewable Energy Laboratory, 1617 Cole Blvd., Golden, CO, 80401, USA
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Timothy J Tschaplinski
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Sivakumar Pattathil
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd., Athens, GA, 30602, USA
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Erica Gjersing
- National Renewable Energy Laboratory, 1617 Cole Blvd., Golden, CO, 80401, USA
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Nancy L Engle
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Rui Katahira
- National Renewable Energy Laboratory, 1617 Cole Blvd., Golden, CO, 80401, USA
- Present address: Department of Biological Sciences, University of North Texas, 1155 Union Circle, Denton, TX 76203, USA
| | - Yunqiao Pu
- National Renewable Energy Laboratory, 1617 Cole Blvd., Golden, CO, 80401, USA
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Robert Sykes
- National Renewable Energy Laboratory, 1617 Cole Blvd., Golden, CO, 80401, USA
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Fang Chen
- Plant Biology Division, Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Arthur J Ragauskas
- School of Chemistry & Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive, 30332, Atlanta, GA, USA
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Jonathan R Mielenz
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Michael G Hahn
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd., Athens, GA, 30602, USA
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Mark Davis
- National Renewable Energy Laboratory, 1617 Cole Blvd., Golden, CO, 80401, USA
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - C Neal Stewart
- Department of Plant Sciences, University of Tennessee, 2431 Joe Johnson Dr., Knoxville, TN, 37996, USA
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Richard A Dixon
- Plant Biology Division, Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Present address: Department of Biological Sciences, University of North Texas, 1155 Union Circle, Denton, TX 76203, USA
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van der Veen D, Lo J, Brown SD, Johnson CM, Tschaplinski TJ, Martin M, Engle NL, van den Berg RA, Argyros AD, Caiazza NC, Guss AM, Lynd LR. Characterization of Clostridium thermocellum strains with disrupted fermentation end-product pathways. J Ind Microbiol Biotechnol 2013; 40:725-34. [PMID: 23645383 DOI: 10.1007/s10295-013-1275-5] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Accepted: 04/15/2013] [Indexed: 10/26/2022]
Abstract
Clostridium thermocellum is a thermophilic, cellulolytic anaerobe that is a candidate microorganism for industrial biofuels production. Strains with mutations in genes associated with production of L-lactate (Δldh) and/or acetate (Δpta) were characterized to gain insight into the intracellular processes that convert cellobiose to ethanol and other fermentation end-products. Cellobiose-grown cultures of the Δldh strain had identical biomass accumulation, fermentation end-products, transcription profile, and intracellular metabolite concentrations compared to its parent strain (DSM1313 Δhpt Δspo0A). The Δpta-deficient strain grew slower and had 30 % lower final biomass concentration compared to the parent strain, yet produced 75 % more ethanol. A Δldh Δpta double-mutant strain evolved for faster growth had a growth rate and ethanol yield comparable to the parent strain, whereas its biomass accumulation was comparable to Δpta. Free amino acids were secreted by all examined strains, with both Δpta strains secreting higher amounts of alanine, valine, isoleucine, proline, glutamine, and threonine. Valine concentration for Δldh Δpta reached 5 mM by the end of growth, or 2.7 % of the substrate carbon utilized. These secreted amino acid concentrations correlate with increased intracellular pyruvate concentrations, up to sixfold in the Δpta and 16-fold in the Δldh Δpta strain. We hypothesize that the deletions in fermentation end-product pathways result in an intracellular redox imbalance, which the organism attempts to relieve, in part by recycling NADP⁺ through increased production of amino acids.
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Kridelbaugh DM, Nelson J, Engle NL, Tschaplinski TJ, Graham DE. Nitrogen and sulfur requirements for Clostridium thermocellum and Caldicellulosiruptor bescii on cellulosic substrates in minimal nutrient media. Bioresour Technol 2013; 130:125-35. [PMID: 23306120 DOI: 10.1016/j.biortech.2012.12.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Revised: 10/08/2012] [Accepted: 12/01/2012] [Indexed: 05/04/2023]
Abstract
Growth media for cellulolytic Clostridium thermocellum ATCC 27405 and Caldicellulosiruptor bescii bacteria usually contain excess nutrients that would increase costs for consolidated bioprocessing for biofuel production and create a waste stream with nitrogen, sulfur and phosphate. C. thermocellum was grown on crystalline cellulose with varying concentrations of nitrogen and sulfur compounds, and growth rate and ethanol production response curves were determined. Both bacteria assimilated sulfate in the presence of ascorbate reductant, increasing the ratio of oxidized to reduced fermentation products. From these results, a low ionic strength, defined minimal nutrient medium with decreased nitrogen, sulfur, phosphate and vitamin supplements was developed for the fermentation of cellobiose, cellulose and acid-pretreated Populus. Carbon and electron balance calculations indicate the unidentified residual fermentation products must include highly reduced molecules. Both bacterial populations were maintained in co-cultures with substrates containing cellulose and xylan in defined medium with sulfate and basal vitamin supplements.
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Affiliation(s)
- Donna M Kridelbaugh
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6038, United States
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Yee KL, Rodriguez Jr M, Tschaplinski TJ, Engle NL, Martin MZ, Fu C, Wang ZY, Hamilton-Brehm SD, Mielenz JR. Evaluation of the bioconversion of genetically modified switchgrass using simultaneous saccharification and fermentation and a consolidated bioprocessing approach. Biotechnol Biofuels 2012; 5:81. [PMID: 23146305 PMCID: PMC3503607 DOI: 10.1186/1754-6834-5-81] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Accepted: 10/31/2012] [Indexed: 05/02/2023]
Abstract
BACKGROUND The inherent recalcitrance of lignocellulosic biomass is one of the major economic hurdles for the production of fuels and chemicals from biomass. Additionally, lignin is recognized as having a negative impact on enzymatic hydrolysis of biomass, and as a result much interest has been placed on modifying the lignin pathway to improve bioconversion of lignocellulosic feedstocks. RESULTS Down-regulation of the caffeic acid 3-O-methyltransferase (COMT) gene in the lignin pathway yielded switchgrass (Panicum virgatum) that was more susceptible to bioconversion after dilute acid pretreatment. Here we examined the response of these plant lines to milder pretreatment conditions with yeast-based simultaneous saccharification and fermentation and a consolidated bioprocessing approach using Clostridium thermocellum, Caldicellulosiruptor bescii and Caldicellulosiruptor obsidiansis. Unlike the S. cerevisiae SSF conversions, fermentations of pretreated transgenic switchgrass with C. thermocellum showed an apparent inhibition of fermentation not observed in the wild-type switchgrass. This inhibition can be eliminated by hot water extraction of the pretreated biomass, which resulted in superior conversion yield with transgenic versus wild-type switchgrass for C. thermocellum, exceeding the yeast-based SSF yield. Further fermentation evaluation of the transgenic switchgrass indicated differential inhibition for the Caldicellulosiruptor sp. strains, which could not be rectified by additional processing conditions. Gas chromatography-mass spectrometry (GC-MS) metabolite profiling was used to examine the fermentation broth to elucidate the relative abundance of lignin derived aromatic compounds. The types and abundance of fermentation-derived-lignin constituents varied between C. thermocellum and each of the Caldicellulosiruptor sp. strains. CONCLUSIONS The down-regulation of the COMT gene improves the bioconversion of switchgrass relative to the wild-type regardless of the pretreatment condition or fermentation microorganism. However, bacterial fermentations demonstrated strain-dependent sensitivity to the COMT transgenic biomass, likely due to additional soluble lignin pathway-derived constituents resulting from the COMT gene disruption. Removal of these inhibitory constituents permitted completion of fermentation by C. thermocellum, but not by the Caldicellulosiruptor sp. strains. The reason for this difference in performance is currently unknown.
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Affiliation(s)
- Kelsey L Yee
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6226, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6226, USA
| | - Miguel Rodriguez Jr
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6226, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6226, USA
| | - Timothy J Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6226, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6226, USA
| | - Nancy L Engle
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6226, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6226, USA
| | - Madhavi Z Martin
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6226, USA
| | - Chunxiang Fu
- Forage Improvement Division, The Samuel Roberts Noble Foundation, Ardmore, OK, 73401, USA
| | - Zeng-Yu Wang
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6226, USA
- Forage Improvement Division, The Samuel Roberts Noble Foundation, Ardmore, OK, 73401, USA
| | - Scott D Hamilton-Brehm
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6226, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6226, USA
| | - Jonathan R Mielenz
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6226, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6226, USA
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Tschaplinski TJ, Standaert RF, Engle NL, Martin MZ, Sangha AK, Parks JM, Smith JC, Samuel R, Jiang N, Pu Y, Ragauskas AJ, Hamilton CY, Fu C, Wang ZY, Davison BH, Dixon RA, Mielenz JR. Down-regulation of the caffeic acid O-methyltransferase gene in switchgrass reveals a novel monolignol analog. Biotechnol Biofuels 2012; 5:71. [PMID: 22998926 PMCID: PMC3524654 DOI: 10.1186/1754-6834-5-71] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Accepted: 09/05/2012] [Indexed: 05/02/2023]
Abstract
UNLABELLED BACKGROUND Down-regulation of the caffeic acid 3-O-methyltransferase EC 2.1.1.68 (COMT) gene in the lignin biosynthetic pathway of switchgrass (Panicum virgatum) resulted in cell walls of transgenic plants releasing more constituent sugars after pretreatment by dilute acid and treatment with glycosyl hydrolases from an added enzyme preparation and from Clostridium thermocellum. Fermentation of both wild-type and transgenic switchgrass after milder hot water pretreatment with no water washing showed that only the transgenic switchgrass inhibited C. thermocellum. Gas chromatography-mass spectrometry (GCMS)-based metabolomics were undertaken on cell wall aqueous extracts to determine the nature of the microbial inhibitors. RESULTS GCMS confirmed the increased concentration of a number of phenolic acids and aldehydes that are known inhibitors of microbial fermentation. Metabolomic analyses of the transgenic biomass additionally revealed the presence of a novel monolignol-like metabolite, identified as trans-3, 4-dimethoxy-5-hydroxycinnamyl alcohol (iso-sinapyl alcohol) in both non-pretreated, as well as hot water pretreated samples. iso-Sinapyl alcohol and its glucoside were subsequently generated by organic synthesis and the identity of natural and synthetic materials were confirmed by mass spectrometric and NMR analyses. The additional novel presence of iso-sinapic acid, iso-sinapyl aldehyde, and iso-syringin suggest the increased activity of a para-methyltransferase, concomitant with the reduced COMT activity, a strict meta-methyltransferase. Quantum chemical calculations were used to predict the most likely homodimeric lignans generated from dehydration reactions, but these products were not evident in plant samples. CONCLUSIONS Down-regulation of COMT activity in switchgrass resulted in the accumulation of previously undetected metabolites resembling sinapyl alcohol and its related metabolites, but that are derived from para-methylation of 5-hydroxyconiferyl alcohol, and related precursors and products; the accumulation of which suggests altered metabolism of 5-hydroxyconiferyl alcohol in switchgrass. Given that there was no indication that iso-sinapyl alcohol was integrated in cell walls, it is considered a monolignol analog. Diversion of substrates from sinapyl alcohol to free iso-sinapyl alcohol, its glucoside, and associated upstream lignin pathway changes, including increased phenolic aldehydes and acids, are together associated with more facile cell wall deconstruction, and to the observed inhibitory effect on microbial growth. However, iso-sinapyl alcohol and iso-sinapic acid, added separately to media, were not inhibitory to C. thermocellum cultures.
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Affiliation(s)
- Timothy J Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6341, USA
- BioEnergy Science Center, Oak Ridge, TN 38731, USA
| | - Robert F Standaert
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6341, USA
- BioEnergy Science Center, Oak Ridge, TN 38731, USA
- Department of Biochemistry and Molecular & Cellular Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Nancy L Engle
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6341, USA
- BioEnergy Science Center, Oak Ridge, TN 38731, USA
| | - Madhavi Z Martin
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6341, USA
- BioEnergy Science Center, Oak Ridge, TN 38731, USA
| | - Amandeep K Sangha
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6341, USA
- BioEnergy Science Center, Oak Ridge, TN 38731, USA
- Department of Biochemistry and Molecular & Cellular Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Jerry M Parks
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6341, USA
- BioEnergy Science Center, Oak Ridge, TN 38731, USA
| | - Jeremy C Smith
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6341, USA
- BioEnergy Science Center, Oak Ridge, TN 38731, USA
- Department of Biochemistry and Molecular & Cellular Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Reichel Samuel
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- BioEnergy Science Center, Oak Ridge, TN 38731, USA
| | - Nan Jiang
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- BioEnergy Science Center, Oak Ridge, TN 38731, USA
| | - Yunqiao Pu
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- BioEnergy Science Center, Oak Ridge, TN 38731, USA
| | - Arthur J Ragauskas
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- BioEnergy Science Center, Oak Ridge, TN 38731, USA
| | - Choo Y Hamilton
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6341, USA
- BioEnergy Science Center, Oak Ridge, TN 38731, USA
| | - Chunxiang Fu
- Forage Improvement Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
- BioEnergy Science Center, Oak Ridge, TN 38731, USA
| | - Zeng-Yu Wang
- Forage Improvement Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
- BioEnergy Science Center, Oak Ridge, TN 38731, USA
| | - Brian H Davison
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6341, USA
- BioEnergy Science Center, Oak Ridge, TN 38731, USA
| | - Richard A Dixon
- Plant Biology Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
- BioEnergy Science Center, Oak Ridge, TN 38731, USA
| | - Jonathan R Mielenz
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6341, USA
- BioEnergy Science Center, Oak Ridge, TN 38731, USA
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Yang S, Giannone RJ, Dice L, Yang ZK, Engle NL, Tschaplinski TJ, Hettich RL, Brown SD. Clostridium thermocellum ATCC27405 transcriptomic, metabolomic and proteomic profiles after ethanol stress. BMC Genomics 2012; 13:336. [PMID: 22823947 PMCID: PMC3478167 DOI: 10.1186/1471-2164-13-336] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Accepted: 07/01/2012] [Indexed: 01/12/2023] Open
Abstract
Background Clostridium thermocellum is a candidate consolidated bioprocessing biocatalyst, which is a microorganism that expresses enzymes for both cellulose hydrolysis and its fermentation to produce fuels such as lignocellulosic ethanol. However, C. thermocellum is relatively sensitive to ethanol compared to ethanologenic microorganisms such as yeast and Zymomonas mobilis that are used in industrial fermentations but do not possess native enzymes for industrial cellulose hydrolysis. Results In this study, C. thermocellum was grown to mid-exponential phase and then treated with ethanol to a final concentration of 3.9 g/L to investigate its physiological and regulatory responses to ethanol stress. Samples were taken pre-shock and 2, 12, 30, 60, 120, and 240 min post-shock, and from untreated control fermentations for systems biology analyses. Cell growth was arrested by ethanol supplementation with intracellular accumulation of carbon sources such as cellobiose, and sugar phosphates, including fructose-6-phosphate and glucose-6-phosphate. The largest response of C. thermocellum to ethanol shock treatment was in genes and proteins related to nitrogen uptake and metabolism, which is likely important for redirecting the cells physiology to overcome inhibition and allow growth to resume. Conclusion This study suggests possible avenues for metabolic engineering and provides comprehensive, integrated systems biology datasets that will be useful for future metabolic modeling and strain development endeavors.
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Affiliation(s)
- Shihui Yang
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, USA
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50
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Li Y, Tschaplinski TJ, Engle NL, Hamilton CY, Rodriguez M, Liao JC, Schadt CW, Guss AM, Yang Y, Graham DE. Combined inactivation of the Clostridium cellulolyticum lactate and malate dehydrogenase genes substantially increases ethanol yield from cellulose and switchgrass fermentations. Biotechnol Biofuels 2012; 5:2. [PMID: 22214220 PMCID: PMC3268733 DOI: 10.1186/1754-6834-5-2] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Accepted: 01/04/2012] [Indexed: 05/03/2023]
Abstract
BACKGROUND The model bacterium Clostridium cellulolyticum efficiently degrades crystalline cellulose and hemicellulose, using cellulosomes to degrade lignocellulosic biomass. Although it imports and ferments both pentose and hexose sugars to produce a mixture of ethanol, acetate, lactate, H2 and CO2, the proportion of ethanol is low, which impedes its use in consolidated bioprocessing for biofuels production. Therefore genetic engineering will likely be required to improve the ethanol yield. Plasmid transformation, random mutagenesis and heterologous expression systems have previously been developed for C. cellulolyticum, but targeted mutagenesis has not been reported for this organism, hindering genetic engineering. RESULTS The first targeted gene inactivation system was developed for C. cellulolyticum, based on a mobile group II intron originating from the Lactococcus lactis L1.LtrB intron. This markerless mutagenesis system was used to disrupt both the paralogous L-lactate dehydrogenase (Ccel_2485; ldh) and L-malate dehydrogenase (Ccel_0137; mdh) genes, distinguishing the overlapping substrate specificities of these enzymes. Both mutations were then combined in a single strain, resulting in a substantial shift in fermentation toward ethanol production. This double mutant produced 8.5-times more ethanol than wild-type cells growing on crystalline cellulose. Ethanol constituted 93% of the major fermentation products, corresponding to a molar ratio of ethanol to organic acids of 15, versus 0.18 in wild-type cells. During growth on acid-pretreated switchgrass, the double mutant also produced four times as much ethanol as wild-type cells. Detailed metabolomic analyses identified increased flux through the oxidative branch of the mutant's tricarboxylic acid pathway. CONCLUSIONS The efficient intron-based gene inactivation system produced the first non-random, targeted mutations in C. cellulolyticum. As a key component of the genetic toolbox for this bacterium, markerless targeted mutagenesis enables functional genomic research in C. cellulolyticum and rapid genetic engineering to significantly alter the mixture of fermentation products. The initial application of this system successfully engineered a strain with high ethanol productivity from cellobiose, cellulose and switchgrass.
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Affiliation(s)
- Yongchao Li
- Biosciences Division, Oak Ridge National Laboratory, PO Box 2008, MS-6038, Oak Ridge, TN 37831-6038, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Timothy J Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, PO Box 2008, MS-6038, Oak Ridge, TN 37831-6038, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Nancy L Engle
- Biosciences Division, Oak Ridge National Laboratory, PO Box 2008, MS-6038, Oak Ridge, TN 37831-6038, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Choo Y Hamilton
- Biosciences Division, Oak Ridge National Laboratory, PO Box 2008, MS-6038, Oak Ridge, TN 37831-6038, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Miguel Rodriguez
- Biosciences Division, Oak Ridge National Laboratory, PO Box 2008, MS-6038, Oak Ridge, TN 37831-6038, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - James C Liao
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Christopher W Schadt
- Biosciences Division, Oak Ridge National Laboratory, PO Box 2008, MS-6038, Oak Ridge, TN 37831-6038, USA
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996-0845, USA
| | - Adam M Guss
- Biosciences Division, Oak Ridge National Laboratory, PO Box 2008, MS-6038, Oak Ridge, TN 37831-6038, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Yunfeng Yang
- Biosciences Division, Oak Ridge National Laboratory, PO Box 2008, MS-6038, Oak Ridge, TN 37831-6038, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - David E Graham
- Biosciences Division, Oak Ridge National Laboratory, PO Box 2008, MS-6038, Oak Ridge, TN 37831-6038, USA
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996-0845, USA
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