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Wang H, Le Y, Sun J. Light-driven bio-decolorization of triphenylmethane dyes by a Clostridium thermocellum-CdS biohybrid. JOURNAL OF HAZARDOUS MATERIALS 2022; 431:128596. [PMID: 35248959 DOI: 10.1016/j.jhazmat.2022.128596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 02/18/2022] [Accepted: 02/24/2022] [Indexed: 06/14/2023]
Abstract
Widespread application of synthetic dyes could generate colored wastewaters causing a range of serious environmental problems. Due to the complex nature of effluents from textile industries, it is difficult to obtain satisfactory treatment of dyes-contaminated wastewater using one single method. Biohybrids coupling of photocatalysts and biocatalysts have great potential in environmental purification. However, how to select suitable organisms and enhance the hybrid's catalytic activities remain challenging. Here, a novel biohybrid system (Clostridium thermocellum-CdS), created for light-driven biodecolorization under thermophilic treatment by using non-photosynthetic microorganism C. thermocellum self-photosensitized with CdS nanoparticles was established. The biohybrids exhibited remarkable decolorization effects on triphenylmethane dyes. The highest decolorization rate was 0.206 min-1. More importantly, enhanced catalytic activities of cadmium sulfide (CdS)-based biohybrids by controlling the particle sizes of semiconductors were demonstrated. Biohybrids systems (Clostridium thermocellum-CdS) through the self-precipitation of CdS with different particle sizes not only showed dramatic changes in the optical properties but also exhibited a very different decolorization rate. This work can not only further broaden targeted applications of CdS-based biohybrids but also demonstrate a promising route for improving biohybrids corresponding photocatalytic capabilities through in situ precipitation CdS with different particle sizes.
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Affiliation(s)
- Huilei Wang
- Biofuels institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, PR China
| | - Yilin Le
- Biofuels institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, PR China.
| | - Jianzhong Sun
- Biofuels institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, PR China.
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2
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Wang Y, Li L, Xia Y, Zhang T. Reliable and Scalable Identification and Prioritization of Putative Cellulolytic Anaerobes With Large Genome Data. FRONTIERS IN BIOINFORMATICS 2022; 2:813771. [PMID: 36304268 PMCID: PMC9580877 DOI: 10.3389/fbinf.2022.813771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 02/18/2022] [Indexed: 11/23/2022] Open
Abstract
In the era of high-throughput sequencing, genetic information that is inherently whispering hints of the microbes’ functional niches is becoming easily accessible; however, properly identifying and characterizing these genetic hints to infer the microbes’ functional niches remains a challenge. Regarding genome-centric interpretation on the specific functional niche of cellulose hydrolysis for anaerobes, often encountered in practice is a lack of confidence in predicting the anaerobes’ real cellulolytic competency based solely on abundances of the varying carbohydrate-active enzyme modules annotated or on their taxonomy affiliation. Recognition of the synergy machineries that include but not limited to the cellulosome gene clusters is equally important as the annotation of individual carbohydrate-active modules or genes. In the interpretation of complete genomes of 2,768 microbe strains whose phenotypes have been well documented, with the incorporation of an automatic recognition of synergy among the carbohydrate active elements annotated, an explicit genotype–phenotype correlation was evidenced to be feasible for cellulolytic anaerobes, and a bioinformatic pipeline was developed accordingly. This genome-centric pipeline would categorize putative cellulolytic anaerobes into six genotype groups based on differential cellulose-hydrolyzing capacity and varying synergy mechanisms. Suggested in this genotype–phenotype correlation analysis was a finer categorization of the cellulosome gene clusters: although cellulosome complexes, by their nature, could enable the assembly of a number of carbohydrate-active units, they do not certainly guarantee the formation of the cellulose–enzyme–microbe complex or the cellulose-hydrolyzing activity of the corresponding anaerobe strains, for example, the well-known Clostridium acetobutylicum strains. Also, recognized in this genotype-phenotype correlation analysis was the genetic foundation of a previously unrecognized machinery that may mediate the microbe–cellulose adhesion, to be specific, enzymes encoded by genes harboring both the surface layer homology and cellulose-binding CBM modules. Applicability of this pipeline on scalable annotation of large genome datasets was further tested with the annotation of 7,902 reference genomes downloaded from NCBI, from which 14 genomes of putative paradigm cellulose-hydrolyzing anaerobes were identified. We believe the pipeline developed in this study would be a good add as a bioinformatic tool for genome-centric interpretation of uncultivated anaerobes, specifically on their functional niche of cellulose hydrolysis.
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Affiliation(s)
- Yubo Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, The University of Hong Kong, Pokfulam, China
| | - Liguan Li
- Environmental Microbiome Engineering and Biotechnology Laboratory, The University of Hong Kong, Pokfulam, China
| | - Yu Xia
- Environmental Microbiome Engineering and Biotechnology Laboratory, The University of Hong Kong, Pokfulam, China
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, The University of Hong Kong, Pokfulam, China
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, China
- Shenzhen Bay Laboratory, Shenzhen, China
- *Correspondence: Tong Zhang,
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3
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Gardner JG, Schreier HJ. Unifying themes and distinct features of carbon and nitrogen assimilation by polysaccharide-degrading bacteria: a summary of four model systems. Appl Microbiol Biotechnol 2021; 105:8109-8127. [PMID: 34611726 DOI: 10.1007/s00253-021-11614-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/20/2021] [Accepted: 09/21/2021] [Indexed: 11/24/2022]
Abstract
Our current understanding of enzymatic polysaccharide degradation has come from a huge number of in vitro studies with purified enzymes. While this vast body of work has been invaluable in identifying and characterizing novel mechanisms of action and engineering desirable traits into these enzymes, a comprehensive picture of how these enzymes work as part of a native in vivo system is less clear. Recently, several model bacteria have emerged with genetic systems that allow for a more nuanced study of carbohydrate active enzymes (CAZymes) and how their activity affects bacterial carbon metabolism. With these bacterial model systems, it is now possible to not only study a single nutrient system in isolation (i.e., carbohydrate degradation and carbon metabolism), but also how multiple systems are integrated. Given that most environmental polysaccharides are carbon rich but nitrogen poor (e.g., lignocellulose), the interplay between carbon and nitrogen metabolism in polysaccharide-degrading bacteria can now be studied in a physiologically relevant manner. Therefore, in this review, we have summarized what has been experimentally determined for CAZyme regulation, production, and export in relation to nitrogen metabolism for two Gram-positive (Caldicellulosiruptor bescii and Clostridium thermocellum) and two Gram-negative (Bacteroides thetaiotaomicron and Cellvibrio japonicus) polysaccharide-degrading bacteria. By comparing and contrasting these four bacteria, we have highlighted the shared and unique features of each, with a focus on in vivo studies, in regard to carbon and nitrogen assimilation. We conclude with what we believe are two important questions that can act as guideposts for future work to better understand the integration of carbon and nitrogen metabolism in polysaccharide-degrading bacteria. KEY POINTS: • Regardless of CAZyme deployment system, the generation of a local pool of oligosaccharides is a common strategy among Gram-negative and Gram-positive polysaccharide degraders as a means to maximally recoup the energy expenditure of CAZyme production and export. • Due to the nitrogen deficiency of insoluble polysaccharide-containing substrates, Gram-negative and Gram-positive polysaccharide degraders have a diverse set of strategies for supplementation and assimilation. • Future work needs to precisely characterize the energetic expenditures of CAZyme deployment and bolster our understanding of how carbon and nitrogen metabolism are integrated in both Gram-negative and Gram-positive polysaccharide-degrading bacteria, as both of these will significantly influence a given bacterium's suitability for biotechnology applications.
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Affiliation(s)
- Jeffrey G Gardner
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD, USA.
| | - Harold J Schreier
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD, USA.,Department of Marine Biotechnology, Institute of Marine and Environmental Technology, University of Maryland, Baltimore County, Baltimore, MD, USA
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4
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Wu C, Cano M, Gao X, Lo J, Maness P, Xiong W. A quantitative lens on anaerobic life: leveraging the state-of-the-art fluxomics approach to explore clostridial metabolism. Curr Opin Biotechnol 2020; 64:47-54. [DOI: 10.1016/j.copbio.2019.09.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 09/02/2019] [Accepted: 09/12/2019] [Indexed: 10/25/2022]
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Mazzoli R, Olson D. Clostridium thermocellum: A microbial platform for high-value chemical production from lignocellulose. ADVANCES IN APPLIED MICROBIOLOGY 2020; 113:111-161. [PMID: 32948265 DOI: 10.1016/bs.aambs.2020.07.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Second generation biorefining, namely fermentation processes based on lignocellulosic feedstocks, has attracted tremendous interest (owing to the large availability and low cost of this biomass) as a strategy to produce biofuels and commodity chemicals that is an alternative to oil refining. However, the innate recalcitrance of lignocellulose has slowed progress toward economically viable processes. Consolidated bioprocessing (CBP), i.e., single-step fermentation of lignocellulose may dramatically reduce the current costs of 2nd generation biorefining. Metabolic engineering has been used as a tool to develop improved microbial strains supporting CBP. Clostridium thermocellum is among the most efficient cellulose degraders isolated so far and one of the most promising host organisms for application of CBP. The development of efficient and reliable genetic tools has allowed significant progress in metabolic engineering of this strain aimed at expanding the panel of growth substrates and improving the production of a number of commodity chemicals of industrial interest such as ethanol, butanol, isobutanol, isobutyl acetate and lactic acid. The present review aims to summarize recent developments in metabolic engineering of this organism which currently represents a reference model for the development of biocatalysts for 2nd generation biorefining.
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6
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Jay ZJ, Hunt KA, Chou KJ, Schut GJ, Maness PC, Adams MWW, Carlson RP. Integrated thermodynamic analysis of electron bifurcating [FeFe]-hydrogenase to inform anaerobic metabolism and H 2 production. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1861:148087. [PMID: 31669490 DOI: 10.1016/j.bbabio.2019.148087] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 09/14/2019] [Accepted: 10/18/2019] [Indexed: 12/27/2022]
Abstract
Electron bifurcating, [FeFe]-hydrogenases are recently described members of the hydrogenase family and catalyze a combination of exergonic and endergonic electron exchanges between three carriers (2 ferredoxinred- + NAD(P)H + 3 H+ = 2 ferredoxinox + NAD(P)+ + 2 H2). A thermodynamic analysis of the bifurcating, [FeFe]-hydrogenase reaction, using electron path-independent variables, quantified potential biological roles of the reaction without requiring enzyme details. The bifurcating [FeFe]-hydrogenase reaction, like all bifurcating reactions, can be written as a sum of two non-bifurcating reactions. Therefore, the thermodynamic properties of the bifurcating reaction can never exceed the properties of the individual, non-bifurcating, reactions. The bifurcating [FeFe]-hydrogenase reaction has three competitive properties: 1) enabling NAD(P)H-driven proton reduction at pH2 higher than the concurrent operation of the two, non-bifurcating reactions, 2) oxidation of NAD(P)H and ferredoxin simultaneously in a 1:1 ratio, both are produced during typical glucose fermentations, and 3) enhanced energy conservation (~10 kJ mol-1 H2) relative to concurrent operation of the two, non-bifurcating reactions. Our analysis demonstrated ferredoxin E°' largely determines the sensitivity of the bifurcating reaction to pH2, modulation of the reduced/oxidized electron carrier ratios contributed less to equilibria shifts. Hydrogenase thermodynamics data were integrated with typical and non-typical glycolysis pathways to evaluate achieving the 'Thauer limit' (4 H2 per glucose) as a function of temperature and pH2. For instance, the bifurcating [FeFe]-hydrogenase reaction permits the Thauer limit at 60 °C if pH 2 ≤ ~10 mbar. The results also predict Archaea, expressing a non-typical glycolysis pathway, would not benefit from a bifurcating [FeFe]-hydrogenase reaction; interestingly, no Archaea have been observed experimentally with a [FeFe]-hydrogenase enzyme.
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Affiliation(s)
- Zackary J Jay
- Department of Chemical and Biological Engineering, Center for Biofilm Engineering,Thermal Biology Institute, Montana State University, Bozeman, MT 59717, USA
| | - Kristopher A Hunt
- Department of Chemical and Biological Engineering, Center for Biofilm Engineering,Thermal Biology Institute, Montana State University, Bozeman, MT 59717, USA
| | - Katherine J Chou
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Gerrit J Schut
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Pin-Ching Maness
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Ross P Carlson
- Department of Chemical and Biological Engineering, Center for Biofilm Engineering,Thermal Biology Institute, Montana State University, Bozeman, MT 59717, USA.
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7
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Nakazono-Nagaoka E, Fujikawa T, Shikata A, Tachaapaikoon C, Waeonukul R, Pason P, Ratanakhanokchai K, Kosugi A. Draft genome sequence data of Clostridium thermocellum PAL5 possessing high cellulose-degradation ability. Data Brief 2019; 25:104274. [PMID: 31406903 PMCID: PMC6685675 DOI: 10.1016/j.dib.2019.104274] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 07/09/2019] [Accepted: 07/09/2019] [Indexed: 12/25/2022] Open
Abstract
Clostridium thermocellum is a potent cellulolytic bacterium. C. thermocellum strain PAL5, was derived from strain S14 that was isolated from bagasse paper sludge, possesses higher cellulose-degradation ability than representative strains ATCC27405 and DSM1313. In this work, we determined the draft genome sequence of C. thermocellum PAL5. Genomic DNA was used for whole-genome sequencing using the Illumina HiSeq 2500. We obtained 215 contigs of >200 bp (N50, 78,366 bp; mean length, 17,378 bp). The assembled data were subjected to the National Center for Biotechnology Information (NCBI) Prokaryotic Genome Annotation Pipeline, and 3198 protein-coding sequences, 53 tRNA genes, and 4 rRNA genes were identified. The data are accessible at NCBI (the accession number SBHL00000000). Our data resource will facilitate further studies of efficient cellulose-degradation using C. thermocellum.
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Affiliation(s)
- Eiko Nakazono-Nagaoka
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Japan
| | - Takashi Fujikawa
- Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization (NARO), Japan
| | - Ayumi Shikata
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Japan
| | - Chakrit Tachaapaikoon
- Pilot Plant Development and Training Institute (PDTI), King Mongkut's University of Technology Thonburi (KMUTT), Thailand
| | - Rattiya Waeonukul
- Pilot Plant Development and Training Institute (PDTI), King Mongkut's University of Technology Thonburi (KMUTT), Thailand
| | - Patthra Pason
- Pilot Plant Development and Training Institute (PDTI), King Mongkut's University of Technology Thonburi (KMUTT), Thailand
| | - Khanok Ratanakhanokchai
- Enzyme Technology Laboratory, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT), Thailand
| | - Akihiko Kosugi
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Japan
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8
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Sahoo K, Sahoo RK, Gaur M, Subudhi E. Cellulolytic thermophilic microorganisms in white biotechnology: a review. Folia Microbiol (Praha) 2019; 65:25-43. [DOI: 10.1007/s12223-019-00710-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 04/15/2019] [Indexed: 10/26/2022]
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9
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Papanek B, O’Dell KB, Manga P, Giannone RJ, Klingeman DM, Hettich RL, Brown SD, Guss AM. Transcriptomic and proteomic changes from medium supplementation and strain evolution in high-yielding Clostridium thermocellum strains. ACTA ACUST UNITED AC 2018; 45:1007-1015. [DOI: 10.1007/s10295-018-2073-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Accepted: 08/18/2018] [Indexed: 01/05/2023]
Abstract
Abstract
Clostridium thermocellum is a potentially useful organism for the production of lignocellulosic biofuels because of its ability to directly deconstruct cellulose and convert it into ethanol. Previously engineered C. thermocellum strains have achieved higher yields and titers of ethanol. These strains often initially grow more poorly than the wild type. Adaptive laboratory evolution and medium supplementation have been used to improve growth, but the mechanism(s) by which growth improves remain(s) unclear. Here, we studied (1) wild-type C. thermocellum, (2) the slow-growing and high-ethanol-yielding mutant AG553, and (3) the faster-growing evolved mutant AG601, each grown with and without added formate. We used a combination of transcriptomics and proteomics to understand the physiological impact of the metabolic engineering, evolution, and medium supplementation. Medium supplementation with formate improved growth in both AG553 and AG601. Expression of C1 metabolism genes varied with formate addition, supporting the hypothesis that the primary benefit of added formate is the supply of C1 units for biosynthesis. Expression of stress response genes such as those involved in the sporulation cascade was dramatically over-represented in AG553, even after the addition of formate, suggesting that the source of the stress may be other issues such as redox imbalances. The sporulation response is absent in evolved strain AG601, suggesting that sporulation limits the growth of engineered strain AG553. A better understanding of the stress response and mechanisms of improved growth hold promise for informing rational improvement of C. thermocellum for lignocellulosic biofuel production.
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Affiliation(s)
- Beth Papanek
- 0000 0004 0446 2659 grid.135519.a Biosciences Division Oak Ridge National Laboratory Oak Ridge TN USA
- 0000 0001 2315 1184 grid.411461.7 Bredesen Center for Interdisciplinary Research and Graduate Education University of Tennessee-Knoxville Knoxville TN USA
- 0000 0004 1936 9991 grid.35403.31 Integrated Bioprocessing Research Laboratory University of Illinois-Urbana-Champaign Urbana IL USA
| | - Kaela B O’Dell
- 0000 0004 0446 2659 grid.135519.a Biosciences Division Oak Ridge National Laboratory Oak Ridge TN USA
| | - Punita Manga
- 0000 0004 0446 2659 grid.135519.a Biosciences Division Oak Ridge National Laboratory Oak Ridge TN USA
- 0000 0001 2315 1184 grid.411461.7 The Graduate School of Genome Science and Technology University of Tennessee-Knoxville Knoxville TN USA
| | - Richard J Giannone
- 0000 0004 0446 2659 grid.135519.a Biosciences Division Oak Ridge National Laboratory Oak Ridge TN USA
| | - Dawn M Klingeman
- 0000 0004 0446 2659 grid.135519.a Biosciences Division Oak Ridge National Laboratory Oak Ridge TN USA
| | - Robert L Hettich
- 0000 0004 0446 2659 grid.135519.a Biosciences Division Oak Ridge National Laboratory Oak Ridge TN USA
| | - Steven D Brown
- 0000 0004 0446 2659 grid.135519.a Biosciences Division Oak Ridge National Laboratory Oak Ridge TN USA
- 0000 0001 2315 1184 grid.411461.7 The Graduate School of Genome Science and Technology University of Tennessee-Knoxville Knoxville TN USA
- LanzaTech Inc 8045 Lamon Ave, Suite 400 60077 Skokie IL USA
| | - Adam M Guss
- 0000 0004 0446 2659 grid.135519.a Biosciences Division Oak Ridge National Laboratory Oak Ridge TN USA
- 0000 0001 2315 1184 grid.411461.7 Bredesen Center for Interdisciplinary Research and Graduate Education University of Tennessee-Knoxville Knoxville TN USA
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Schwarz WH, Brunecky R, Broeker J, Liebl W, Zverlov VV. Handling gene and protein names in the age of bioinformatics: the special challenge of secreted multimodular bacterial enzymes such as the cbhA/cbh9A gene of Clostridium thermocellum. World J Microbiol Biotechnol 2018; 34:42. [PMID: 29480332 DOI: 10.1007/s11274-018-2424-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Accepted: 02/20/2018] [Indexed: 01/11/2023]
Abstract
An increasing number of researchers working in biology, biochemistry, biotechnology, bioengineering, bioinformatics and other related fields of science are using biological molecules. As the scientific background of the members of different scientific communities is more diverse than ever before, the number of scientists not familiar with the rules for non-ambiguous designation of genetic elements is increasing. However, with biological molecules gaining importance through biotechnology, their functional and unambiguous designation is vital. Unfortunately, naming genes and proteins is not an easy task. In addition, the traditional concepts of bioinformatics are challenged with the appearance of proteins comprising different modules with a respective function in each module. This article highlights basic rules and novel solutions in designation recently used within the community of bacterial geneticists, and we discuss the present-day handling of gene and protein designations. As an example we will utilize a recent mischaracterization of gene nomenclature. We make suggestions for better handling of names in future literature as well as in databases and annotation projects. Our methodology emphasizes the hydrolytic function of multi-modular genes and extracellular proteins from bacteria.
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Affiliation(s)
- Wolfgang H Schwarz
- Department of Microbiology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Emil‑Ramann‑Str. 4, 85354, Freising, Germany.
| | - Roman Brunecky
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
| | - Jannis Broeker
- Department of Microbiology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Emil‑Ramann‑Str. 4, 85354, Freising, Germany
| | - Wolfgang Liebl
- Department of Microbiology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Emil‑Ramann‑Str. 4, 85354, Freising, Germany
| | - Vladimir V Zverlov
- Department of Microbiology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Emil‑Ramann‑Str. 4, 85354, Freising, Germany. .,Institute of Molecular Genetics, Russian Academy of Science, Kurchatov Sq. 2, 123182, Moscow, Russia.
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11
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Singh N, Mathur AS, Gupta RP, Barrow CJ, Tuli D, Puri M. Enhanced cellulosic ethanol production via consolidated bioprocessing by Clostridium thermocellum ATCC 31924☆. BIORESOURCE TECHNOLOGY 2018; 250:860-867. [PMID: 30001594 DOI: 10.1016/j.biortech.2017.11.048] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 11/14/2017] [Accepted: 11/15/2017] [Indexed: 05/23/2023]
Abstract
The production of bioethanol was studied by the cultivation of Clostridium thermocellum ATCC 31924 in MTC medium including crystalline cellulose as the sole substrate. The effects of key operational parameters that affect bioethanol production from microcrystalline cellulose were optimized. Under optimum conditions (pH 8.0, temperature 55 °C, inoculum size 4% (v/v) and 0.5% (w/v) substrate concentration), a maximum ethanol yield of 0.30 g ethanol/g cellulose consumed and 95.32% cellulose conversion was obtained. An inclusion of modest acetate concentration in the medium showed that carbon flux shifted away from lactate accompanied by 20% increase in ethanol production. It suggests that strain ATCC 31924 differed in its cellulose conversion efficacy and optimum pH requirements compared to the other reported strains of Clostridium thermocellum. The purified cellulosome of strain ATCC 31924 found to be rich in both cellulase and xylanase enzymes emphasizing the importance of this strain for the degradation of lignocellulosic biomass.
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Affiliation(s)
- Nisha Singh
- Centre for Chemistry and Biotechnology, Deakin University, Waurn Ponds, Geelong, Victoria 3216, Australia; DBT-IOC Centre for Advance Bioenergy Research, Research & Development Centre, Indian Oil Corporation Limited, Sector-13, Faridabad 121007, India
| | - Anshu S Mathur
- DBT-IOC Centre for Advance Bioenergy Research, Research & Development Centre, Indian Oil Corporation Limited, Sector-13, Faridabad 121007, India
| | - Ravi P Gupta
- DBT-IOC Centre for Advance Bioenergy Research, Research & Development Centre, Indian Oil Corporation Limited, Sector-13, Faridabad 121007, India
| | - Colin J Barrow
- Centre for Chemistry and Biotechnology, Deakin University, Waurn Ponds, Geelong, Victoria 3216, Australia
| | - Deepak Tuli
- DBT-IOC Centre for Advance Bioenergy Research, Research & Development Centre, Indian Oil Corporation Limited, Sector-13, Faridabad 121007, India
| | - Munish Puri
- Centre for Chemistry and Biotechnology, Deakin University, Waurn Ponds, Geelong, Victoria 3216, Australia.
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12
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Jiang Y, Xin F, Lu J, Dong W, Zhang W, Zhang M, Wu H, Ma J, Jiang M. State of the art review of biofuels production from lignocellulose by thermophilic bacteria. BIORESOURCE TECHNOLOGY 2017. [PMID: 28634129 DOI: 10.1016/j.biortech.2017.05.142] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Biofuels, including ethanol and butanol, are mainly produced by mesophilic solventogenic yeasts and Clostridium species. However, these microorganisms cannot directly utilize lignocellulosic materials, which are abundant, renewable and non-compete with human demand. More recently, thermophilic bacteria show great potential for biofuels production, which could efficiently degrade lignocellulose through the cost effective consolidated bioprocessing. Especially, it could avoid contamination in the whole process owing to its relatively high fermentation temperature. However, wild types thermophiles generally produce low levels of biofuels, hindering their large scale production. This review comprehensively summarizes the state of the art development of biofuels production by reported thermophilic microorganisms, and also concludes strategies to improve biofuels production including the metabolic pathways construction, co-culturing systems and biofuels tolerance. In addition, strategies to further improve butanol production are proposed.
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Affiliation(s)
- Yujia Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Fengxue Xin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Jiasheng Lu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Weiliang Dong
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Wenming Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China; Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211800, PR China
| | - Min Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Hao Wu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China; Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211800, PR China
| | - Jiangfeng Ma
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Min Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China; Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211800, PR China.
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Sangavai C, Chellapandi P. Amino acid catabolism-directed biofuel production in Clostridium sticklandii: An insight into model-driven systems engineering. ACTA ACUST UNITED AC 2017; 16:32-43. [PMID: 29167757 PMCID: PMC5686429 DOI: 10.1016/j.btre.2017.11.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 10/17/2017] [Accepted: 11/03/2017] [Indexed: 01/01/2023]
Abstract
Model-driven systems engineering has been more fascinating process for microbial biofuel production. Clostridium sticklandii is a potential strain for the solventogenesis and acidogenesis. The present review provides an insight for the protein catabolism-directed biofuel production.
Model-driven systems engineering has been more fascinating process for the microbial production of biofuel and bio-refineries in chemical and pharmaceutical industries. Genome-scale modeling and simulations have been guided for metabolic engineering of Clostridium species for the production of organic solvents and organic acids. Among them, Clostridium sticklandii is one of the potential organisms to be exploited as a microbial cell factory for biofuel production. It is a hyper-ammonia producing bacterium and is able to catabolize amino acids as important carbon and energy sources via Stickland reactions and the development of the specific pathways. Current genomic and metabolic aspects of this bacterium are comprehensively reviewed herein, which provided information for learning about protein catabolism-directed biofuel production. It has a metabolic potential to drive energy and direct solventogenesis as well as acidogenesis from protein catabolism. It produces by-products such as ethanol, acetate, n-butanol, n-butyrate and hydrogen from amino acid catabolism. Model-driven systems engineering of this organism would improve the performance of the industrial sectors and enhance the industrial economy by using protein-based waste in environment-friendly ways.
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Affiliation(s)
- C Sangavai
- Molecular Systems Engineering Lab, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli, 620 024, Tamil Nadu, India
| | - P Chellapandi
- Molecular Systems Engineering Lab, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli, 620 024, Tamil Nadu, India
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14
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Yoav S, Barak Y, Shamshoum M, Borovok I, Lamed R, Dassa B, Hadar Y, Morag E, Bayer EA. How does cellulosome composition influence deconstruction of lignocellulosic substrates in Clostridium ( Ruminiclostridium) thermocellum DSM 1313? BIOTECHNOLOGY FOR BIOFUELS 2017; 10:222. [PMID: 28932263 PMCID: PMC5604425 DOI: 10.1186/s13068-017-0909-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 09/07/2017] [Indexed: 05/23/2023]
Abstract
BACKGROUND Bioethanol production processes involve enzymatic hydrolysis of pretreated lignocellulosic biomass into fermentable sugars. Due to the relatively high cost of enzyme production, the development of potent and cost-effective cellulolytic cocktails is critical for increasing the cost-effectiveness of bioethanol production. In this context, the multi-protein cellulolytic complex of Clostridium (Ruminiclostridium) thermocellum, the cellulosome, was studied here. C. thermocellum is known to assemble cellulosomes of various subunit (enzyme) compositions, in response to the available carbon source. In the current study, different carbon sources were used, and their influence on both cellulosomal composition and the resultant activity was investigated. RESULTS Glucose, cellobiose, microcrystalline cellulose, alkaline-pretreated switchgrass, alkaline-pretreated corn stover, and dilute acid-pretreated corn stover were used as sole carbon sources in the growth media of C. thermocellum strain DSM 1313. The purified cellulosomes were compared for their activity on selected cellulosic substrates. Interestingly, cellulosomes derived from cells grown on lignocellulosic biomass showed no advantage in hydrolyzing the original carbon source used for their production. Instead, microcrystalline cellulose- and glucose-derived cellulosomes were equal or superior in their capacity to deconstruct lignocellulosic biomass. Mass spectrometry analysis revealed differential composition of catalytic and structural subunits (scaffoldins) in the different cellulosome samples. The most abundant catalytic subunits in all cellulosome types include Cel48S, Cel9K, Cel9Q, Cel9R, and Cel5G. Microcrystalline cellulose- and glucose-derived cellulosome samples showed higher endoglucanase-to-exoglucanase ratios and higher catalytic subunit-per-scaffoldin ratios compared to lignocellulose-derived cellulosome types. CONCLUSION The results reported here highlight the finding that cellulosomes derived from cells grown on glucose and microcrystalline cellulose are more efficient in their action on cellulosic substrates than other cellulosome preparations. These results should be considered in the future development of C. thermocellum-based cellulolytic cocktails, designer cellulosomes, or engineering of improved strains for deconstruction of lignocellulosic biomass.
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Affiliation(s)
- Shahar Yoav
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, The Advanced School for Environmental Studies, The Hebrew University of Jerusalem, 76100 Rehovot, Israel
- Designer Energy Ltd, 2 Bergman Street, Rehovot, Israel
| | - Yoav Barak
- Bio-Nano Unit, Chemical Research Support, The Weizmann Institute of Science, 761000 Rehovot, Israel
| | - Melina Shamshoum
- Department of Biomolecular Sciences, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Ilya Borovok
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, Israel
| | - Raphael Lamed
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, Israel
| | - Bareket Dassa
- Department of Biomolecular Sciences, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Yitzhak Hadar
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, The Advanced School for Environmental Studies, The Hebrew University of Jerusalem, 76100 Rehovot, Israel
| | - Ely Morag
- Department of Biomolecular Sciences, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Edward A. Bayer
- Department of Biomolecular Sciences, The Weizmann Institute of Science, 76100 Rehovot, Israel
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Bozan M, Akyol Ç, Ince O, Aydin S, Ince B. Application of next-generation sequencing methods for microbial monitoring of anaerobic digestion of lignocellulosic biomass. Appl Microbiol Biotechnol 2017; 101:6849-6864. [PMID: 28779289 DOI: 10.1007/s00253-017-8438-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 07/14/2017] [Accepted: 07/17/2017] [Indexed: 10/19/2022]
Abstract
The anaerobic digestion of lignocellulosic wastes is considered an efficient method for managing the world's energy shortages and resolving contemporary environmental problems. However, the recalcitrance of lignocellulosic biomass represents a barrier to maximizing biogas production. The purpose of this review is to examine the extent to which sequencing methods can be employed to monitor such biofuel conversion processes. From a microbial perspective, we present a detailed insight into anaerobic digesters that utilize lignocellulosic biomass and discuss some benefits and disadvantages associated with the microbial sequencing techniques that are typically applied. We further evaluate the extent to which a hybrid approach incorporating a variation of existing methods can be utilized to develop a more in-depth understanding of microbial communities. It is hoped that this deeper knowledge will enhance the reliability and extent of research findings with the end objective of improving the stability of anaerobic digesters that manage lignocellulosic biomass.
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Affiliation(s)
- Mahir Bozan
- Institute of Environmental Sciences, Boğaziçi University, Bebek, 34342, Istanbul, Turkey
| | - Çağrı Akyol
- Institute of Environmental Sciences, Boğaziçi University, Bebek, 34342, Istanbul, Turkey
| | - Orhan Ince
- Department of Environmental Engineering, Istanbul Technical University, Maslak, 34469, Istanbul, Turkey
| | - Sevcan Aydin
- Department of Genetics and Bioengineering, Nişantaşı University, Maslak, 34469, Istanbul, Turkey.
| | - Bahar Ince
- Institute of Environmental Sciences, Boğaziçi University, Bebek, 34342, Istanbul, Turkey
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16
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Qu XS, Hu BB, Zhu MJ. Enhanced saccharification of cellulose and sugarcane bagasse by Clostridium thermocellum cultures with Triton X-100 and β-glucosidase/Cellic®CTec2 supplementation. RSC Adv 2017; 7:21360-21365. [DOI: 10.1039/c7ra02477k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023] Open
Abstract
Increased saccharification and utilization of biomass directly byC. thermocellumcultures with Triton X-100 and β-glucosidase supplementation.
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Affiliation(s)
- Xiao-Su Qu
- School of Bioscience and Bioengineering
- South China University of Technology
- Guangzhou Higher Education Mega Center
- Guangzhou 510006
- People's Republic of China
| | - Bin-Bin Hu
- School of Bioscience and Bioengineering
- South China University of Technology
- Guangzhou Higher Education Mega Center
- Guangzhou 510006
- People's Republic of China
| | - Ming-Jun Zhu
- School of Bioscience and Bioengineering
- South China University of Technology
- Guangzhou Higher Education Mega Center
- Guangzhou 510006
- People's Republic of China
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17
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Genome-Scale Modeling of Thermophilic Microorganisms. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2016. [PMID: 27913830 DOI: 10.1007/10_2016_45] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register]
Abstract
Thermophilic microorganisms are of increasing interest for many industries as their enzymes and metabolisms are highly efficient at elevated temperatures. However, their metabolic processes are often largely different from their mesophilic counterparts. These differences can lead to metabolic engineering strategies that are doomed to fail. Genome-scale metabolic modeling is an effective and highly utilized way to investigate cellular phenotypes and to test metabolic engineering strategies. In this review we chronicle a number of thermophilic organisms that have recently been studied with genome-scale models. The microorganisms spread across archaea and bacteria domains, and their study gives insights that can be applied in a broader context than just the species they describe. We end with a perspective on the future development and applications of genome-scale models of thermophilic organisms.
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Advances in Consolidated Bioprocessing Using Clostridium thermocellumand Thermoanaerobacter saccharolyticum. Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1002/9783527807796.ch10] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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CO2-fixing one-carbon metabolism in a cellulose-degrading bacterium Clostridium thermocellum. Proc Natl Acad Sci U S A 2016; 113:13180-13185. [PMID: 27794122 DOI: 10.1073/pnas.1605482113] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Clostridium thermocellum can ferment cellulosic biomass to formate and other end products, including CO2 This organism lacks formate dehydrogenase (Fdh), which catalyzes the reduction of CO2 to formate. However, feeding the bacterium 13C-bicarbonate and cellobiose followed by NMR analysis showed the production of 13C-formate in C. thermocellum culture, indicating the presence of an uncharacterized pathway capable of converting CO2 to formate. Combining genomic and experimental data, we demonstrated that the conversion of CO2 to formate serves as a CO2 entry point into the reductive one-carbon (C1) metabolism, and internalizes CO2 via two biochemical reactions: the reversed pyruvate:ferredoxin oxidoreductase (rPFOR), which incorporates CO2 using acetyl-CoA as a substrate and generates pyruvate, and pyruvate-formate lyase (PFL) converting pyruvate to formate and acetyl-CoA. We analyzed the labeling patterns of proteinogenic amino acids in individual deletions of all five putative PFOR mutants and in a PFL deletion mutant. We identified two enzymes acting as rPFOR, confirmed the dual activities of rPFOR and PFL crucial for CO2 uptake, and provided physical evidence of a distinct in vivo "rPFOR-PFL shunt" to reduce CO2 to formate while circumventing the lack of Fdh. Such a pathway precedes CO2 fixation via the reductive C1 metabolic pathway in C. thermocellum These findings demonstrated the metabolic versatility of C. thermocellum, which is thought of as primarily a cellulosic heterotroph but is shown here to be endowed with the ability to fix CO2 as well.
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Application of Long Sequence Reads To Improve Genomes for Clostridium thermocellum AD2, Clostridium thermocellum LQRI, and Pelosinus fermentans R7. GENOME ANNOUNCEMENTS 2016; 4:4/5/e01043-16. [PMID: 27688341 PMCID: PMC5043559 DOI: 10.1128/genomea.01043-16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
We and others have shown the utility of long sequence reads to improve genome assembly quality. In this study, we generated PacBio DNA sequence data to improve the assemblies of draft genomes for Clostridium thermocellum AD2, Clostridium thermocellum LQRI, and Pelosinus fermentans R7.
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21
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Thompson RA, Dahal S, Garcia S, Nookaew I, Trinh CT. Exploring complex cellular phenotypes and model-guided strain design with a novel genome-scale metabolic model of Clostridium thermocellum DSM 1313 implementing an adjustable cellulosome. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:194. [PMID: 27602057 PMCID: PMC5012057 DOI: 10.1186/s13068-016-0607-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 08/26/2016] [Indexed: 05/06/2023]
Abstract
BACKGROUND Clostridium thermocellum is a gram-positive thermophile that can directly convert lignocellulosic material into biofuels. The metabolism of C. thermocellum contains many branches and redundancies which limit biofuel production, and typical genetic techniques are time-consuming. Further, the genome sequence of a genetically tractable strain C. thermocellum DSM 1313 has been recently sequenced and annotated. Therefore, developing a comprehensive, predictive, genome-scale metabolic model of DSM 1313 is desired for elucidating its complex phenotypes and facilitating model-guided metabolic engineering. RESULTS We constructed a genome-scale metabolic model iAT601 for DSM 1313 using the KEGG database as a scaffold and an extensive literature review and bioinformatic analysis for model refinement. Next, we used several sets of experimental data to train the model, e.g., estimation of the ATP requirement for growth-associated maintenance (13.5 mmol ATP/g DCW/h) and cellulosome synthesis (57 mmol ATP/g cellulosome/h). Using our tuned model, we investigated the effect of cellodextrin lengths on cell yields, and could predict in silico experimentally observed differences in cell yield based on which cellodextrin species is assimilated. We further employed our tuned model to analyze the experimentally observed differences in fermentation profiles (i.e., the ethanol to acetate ratio) between cellobiose- and cellulose-grown cultures and infer regulatory mechanisms to explain the phenotypic differences. Finally, we used the model to design over 250 genetic modification strategies with the potential to optimize ethanol production, 6155 for hydrogen production, and 28 for isobutanol production. CONCLUSIONS Our developed genome-scale model iAT601 is capable of accurately predicting complex cellular phenotypes under a variety of conditions and serves as a high-quality platform for model-guided strain design and metabolic engineering to produce industrial biofuels and chemicals of interest.
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Affiliation(s)
- R. Adam Thompson
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN 37996 USA
- Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Sanjeev Dahal
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Comparative Genomics Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Sergio Garcia
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Department of Chemical and Biomolecular Engineering, University of Tennessee, 1512 Middle Dr., DO#432, Knoxville, TN 37996 USA
| | - Intawat Nookaew
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Comparative Genomics Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205 USA
| | - Cong T. Trinh
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN 37996 USA
- Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Department of Chemical and Biomolecular Engineering, University of Tennessee, 1512 Middle Dr., DO#432, Knoxville, TN 37996 USA
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22
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Unification of [FeFe]-hydrogenases into three structural and functional groups. Biochim Biophys Acta Gen Subj 2016; 1860:1910-21. [DOI: 10.1016/j.bbagen.2016.05.034] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 05/20/2016] [Accepted: 05/26/2016] [Indexed: 11/22/2022]
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23
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Lal S, Levin DB. Comparative Genomics of Core Metabolism Genes of Cellulolytic and Non-cellulolytic Clostridium Species. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2016; 156:79-112. [PMID: 26907553 DOI: 10.1007/10_2015_5007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Microbial production of fuels such as ethanol, butanol, hydrogen (H2), and methane (CH4) from waste biomass has the potential to provide sustainable energy systems that can displace fossil fuel consumption. Screening for microbial diversity and genome sequencing of a wide-range of microorganisms can identify organisms with natural abilities to synthesize these alternative fuels and/or other biotechnological applications. Clostridium species are the most widely studied strict anaerobes capable of fermentative synthesis of ethanol, butanol, or hydrogen directly from waste biomass. Clostridium termitidis CT1112 is a mesophilic, cellulolytic species capable of direct cellulose fermentation to ethanol and organic acids, with concomitant synthesis of H2 and CO2. On the basis of 16S ribosomal RNA (rRNA) and chaperonin 60 (cpn60) gene sequence data, phylogenetic analyses revealed a close relationship between C. termitidis and C. cellobioparum. Comparative bioinformatic analyses of the C. termitidis genome with 18 cellulolytic and 10 non-cellulolytic Clostridium species confirmed this relationship, and further revealed that the majority of core metabolic pathway genes in C. termitidis and C. cellobioparum share more than 90% amino acid sequence identity. The gene loci and corresponding amino acid sequences of the encoded enzymes for each pathway were correlated by percentage identity, higher score (better alignment), and lowest e-value (most significant "hit"). In addition, the function of each enzyme was proposed by conserved domain analysis. In this chapter we discuss the comparative analysis of metabolic pathways involved in synthesis of various useful products by cellulolytic and non-cellulolytic biofuel and solvent producing Clostridium species. This study has generated valuable information concerning the core metabolism genes and pathways of C. termitidis CT1112, which is helpful in developing metabolic engineering strategies to enhance its natural capacity for better industrial applications.
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Affiliation(s)
- Sadhana Lal
- Department of Biosystems Engineering, University of Manitoba, Winnipeg, MB, Canada, R3T 5V6
| | - David B Levin
- Department of Biosystems Engineering, University of Manitoba, Winnipeg, MB, Canada, R3T 5V6.
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24
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Dash S, Ng CY, Maranas CD. Metabolic modeling of clostridia: current developments and applications. FEMS Microbiol Lett 2016; 363:fnw004. [PMID: 26755502 DOI: 10.1093/femsle/fnw004] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/06/2016] [Indexed: 12/12/2022] Open
Abstract
Anaerobic Clostridium spp. is an important bioproduction microbial genus that can produce solvents and utilize a broad spectrum of substrates including cellulose and syngas. Genome-scale metabolic (GSM) models are increasingly being put forth for various clostridial strains to explore their respective metabolic capabilities and suitability for various bioconversions. In this study, we have selected representative GSM models for six different clostridia (Clostridium acetobutylicum, C. beijerinckii, C. butyricum, C. cellulolyticum, C. ljungdahlii and C. thermocellum) and performed a detailed model comparison contrasting their metabolic repertoire. We also discuss various applications of these GSM models to guide metabolic engineering interventions as well as assessing cellular physiology.
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Affiliation(s)
- Satyakam Dash
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802-1503, USA
| | - Chiam Yu Ng
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802-1503, USA
| | - Costas D Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802-1503, USA
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25
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Chundawat SPS, Paavola CD, Raman B, Nouailler M, Chan SL, Mielenz JR, Receveur-Brechot V, Trent JD, Dale BE. Saccharification of thermochemically pretreated cellulosic biomass using native and engineered cellulosomal enzyme systems. REACT CHEM ENG 2016. [DOI: 10.1039/c6re00172f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Tethering hydrolytic enzymes (e.g., cellulases) to protein scaffolds enhances biomass saccharification to sugars.
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Affiliation(s)
- Shishir P. S. Chundawat
- Department of Chemical & Biochemical Engineering
- The State University of New Jersey
- Piscataway
- USA
- DOE Great Lakes Bioenergy Research Center (GLBRC)
| | | | - Babu Raman
- Biosciences Division and BioEnergy Science Center
- Oak Ridge National Laboratory
- Oak Ridge
- USA
| | - Matthieu Nouailler
- LISM-UMR 7255 Institut De Microbiologie De La Mediterranee
- CNRS and Aix-Marseille University
- 13402 Marseille Cedex 20
- France
| | | | - Jonathan R. Mielenz
- Biosciences Division and BioEnergy Science Center
- Oak Ridge National Laboratory
- Oak Ridge
- USA
| | | | - Jonathan D. Trent
- Bioengineering Branch
- NASA Ames
- Moffett Field
- USA
- Biomolecular Engineering Department
| | - Bruce E. Dale
- DOE Great Lakes Bioenergy Research Center (GLBRC)
- Michigan State University
- East Lansing
- USA
- Chemical Engineering and Materials Science
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26
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Deng K, Takasuka TE, Bianchetti CM, Bergeman LF, Adams PD, Northen TR, Fox BG. Use of Nanostructure-Initiator Mass Spectrometry to Deduce Selectivity of Reaction in Glycoside Hydrolases. Front Bioeng Biotechnol 2015; 3:165. [PMID: 26579511 PMCID: PMC4621489 DOI: 10.3389/fbioe.2015.00165] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 10/02/2015] [Indexed: 12/20/2022] Open
Abstract
Chemically synthesized nanostructure-initiator mass spectrometry (NIMS) probes derivatized with tetrasaccharides were used to study the reactivity of representative Clostridium thermocellum β-glucosidase, endoglucanases, and cellobiohydrolase. Diagnostic patterns for reactions of these different classes of enzymes were observed. Results show sequential removal of glucose by the β-glucosidase and a progressive increase in specificity of reaction from endoglucanases to cellobiohydrolase. Time-dependent reactions of these polysaccharide-selective enzymes were modeled by numerical integration, which provides a quantitative basis to make functional distinctions among a continuum of naturally evolved catalytic properties. Consequently, our method, which combines automated protein translation with high-sensitivity and time-dependent detection of multiple products, provides a new approach to annotate glycoside hydrolase phylogenetic trees with functional measurements.
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Affiliation(s)
- Kai Deng
- US Department of Energy Joint BioEnergy Institute , Emeryville, CA , USA ; Sandia National Laboratories , Livermore, CA , USA
| | - Taichi E Takasuka
- US Department of Energy Great Lakes Bioenergy Research Center , Madison, WI , USA
| | - Christopher M Bianchetti
- US Department of Energy Great Lakes Bioenergy Research Center , Madison, WI , USA ; Department of Chemistry, University of Wisconsin-Oshkosh , Oshkosh, WI , USA
| | - Lai F Bergeman
- US Department of Energy Great Lakes Bioenergy Research Center , Madison, WI , USA
| | - Paul D Adams
- US Department of Energy Joint BioEnergy Institute , Emeryville, CA , USA ; Lawrence Berkeley National Laboratory , Berkeley, CA , USA ; Department of Bioengineering, University of California Berkeley , Berkeley, CA , USA
| | - Trent R Northen
- US Department of Energy Joint BioEnergy Institute , Emeryville, CA , USA ; Lawrence Berkeley National Laboratory , Berkeley, CA , USA
| | - Brian G Fox
- US Department of Energy Great Lakes Bioenergy Research Center , Madison, WI , USA ; Department of Biochemistry, University of Wisconsin-Madison , Madison, WI , USA
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Thompson RA, Layton DS, Guss AM, Olson DG, Lynd LR, Trinh CT. Elucidating central metabolic redox obstacles hindering ethanol production in Clostridium thermocellum. Metab Eng 2015; 32:207-219. [PMID: 26497628 DOI: 10.1016/j.ymben.2015.10.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 10/08/2015] [Accepted: 10/12/2015] [Indexed: 01/24/2023]
Abstract
Clostridium thermocellum is an anaerobic, Gram-positive, thermophilic bacterium that has generated great interest due to its ability to ferment lignocellulosic biomass to ethanol. However, ethanol production is low due to the complex and poorly understood branched metabolism of C. thermocellum, and in some cases overflow metabolism as well. In this work, we developed a predictive stoichiometric metabolic model for C. thermocellum which incorporates the current state of understanding, with particular attention to cofactor specificity in the atypical glycolytic enzymes and the complex energy, redox, and fermentative pathways with the goal of aiding metabolic engineering efforts. We validated the model's capability to encompass experimentally observed phenotypes for the parent strain and derived mutants designed for significant perturbation of redox and energy pathways. Metabolic flux distributions revealed significant alterations in key metabolic branch points (e.g., phosphoenol pyruvate, pyruvate, acetyl-CoA, and cofactor nodes) in engineered strains for channeling electron and carbon fluxes for enhanced ethanol synthesis, with the best performing strain doubling ethanol yield and titer compared to the parent strain. In silico predictions of a redox-imbalanced genotype incapable of growth were confirmed in vivo, and a mutant strain was used as a platform to probe redox bottlenecks in the central metabolism that hinder efficient ethanol production. The results highlight the robustness of the redox metabolism of C. thermocellum and the necessity of streamlined electron flux from reduced ferredoxin to NAD(P)H for high ethanol production. The model was further used to design a metabolic engineering strategy to phenotypically constrain C. thermocellum to achieve high ethanol yields while requiring minimal genetic manipulations. The model can be applied to design C. thermocellum as a platform microbe for consolidated bioprocessing to produce ethanol and other reduced metabolites.
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Affiliation(s)
- R Adam Thompson
- Bredesen Center for Interdisciplinary Research and Graduate Education, The University of Tennessee, Knoxville and Oak Ridge National Laboratory, Oak Ridge, TN, USA; BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Donovan S Layton
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, USA; Department of Chemical and Biomolecular Engineering, The University of Tennessee, Knoxville, TN, USA
| | - Adam M Guss
- Bredesen Center for Interdisciplinary Research and Graduate Education, The University of Tennessee, Knoxville and Oak Ridge National Laboratory, Oak Ridge, TN, USA; BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, USA; Biosciecnes Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Daniel G Olson
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, USA; Thayer School of Engineering, Dartmouth College, Hanover, NH, USA
| | - Lee R Lynd
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, USA; Thayer School of Engineering, Dartmouth College, Hanover, NH, USA
| | - Cong T Trinh
- Bredesen Center for Interdisciplinary Research and Graduate Education, The University of Tennessee, Knoxville and Oak Ridge National Laboratory, Oak Ridge, TN, USA; BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, USA; Department of Chemical and Biomolecular Engineering, The University of Tennessee, Knoxville, TN, USA.
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Development of a regulatable plasmid-based gene expression system for Clostridium thermocellum. Appl Microbiol Biotechnol 2015; 99:7589-99. [DOI: 10.1007/s00253-015-6610-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 04/07/2015] [Accepted: 04/15/2015] [Indexed: 01/31/2023]
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29
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Stolze Y, Zakrzewski M, Maus I, Eikmeyer F, Jaenicke S, Rottmann N, Siebner C, Pühler A, Schlüter A. Comparative metagenomics of biogas-producing microbial communities from production-scale biogas plants operating under wet or dry fermentation conditions. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:14. [PMID: 25688290 PMCID: PMC4329661 DOI: 10.1186/s13068-014-0193-8] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 12/22/2014] [Indexed: 05/23/2023]
Abstract
BACKGROUND Decomposition of biomass for biogas production can be practiced under wet and dry fermentation conditions. In contrast to the dry fermentation technology, wet fermentation is characterized by a high liquid content and a relatively low total solid content. In this study, the composition and functional potential of a biogas-producing microbial community in an agricultural biogas reactor operating under wet fermentation conditions was analyzed by a metagenomic approach applying 454-pyrosequencing. The obtained metagenomic dataset and corresponding 16S rRNA gene amplicon sequences were compared to the previously sequenced comparable metagenome from a dry fermentation process, meeting explicitly identical boundary conditions regarding sample and community DNA preparation, sequencing technology, processing of sequence reads and data analyses by bioinformatics tools. RESULTS High-throughput metagenome sequencing of community DNA from the wet fermentation process applying the pyrosequencing approach resulted in 1,532,780 reads, with an average read length of 397 bp, accounting for approximately 594 million bases of sequence information in total. Taxonomic comparison of the communities from wet and dry fermentation revealed similar microbial profiles with Bacteria being the predominant superkingdom, while the superkingdom Archaea was less abundant. In both biogas plants, the bacterial phyla Firmicutes, Bacteroidetes, Spirochaetes and Proteobacteria were identified with descending frequencies. Within the archaeal superkingdom, the phylum Euryarchaeota was most abundant with the dominant class Methanomicrobia. Functional profiles of the communities revealed that environmental gene tags representing methanogenesis enzymes were present in both biogas plants in comparable frequencies. 16S rRNA gene amplicon high-throughput sequencing disclosed differences in the sub-communities comprising methanogenic Archaea between both processes. Fragment recruitments of metagenomic reads to the reference genome of the archaeon Methanoculleus bourgensis MS2(T) revealed that dominant methanogens within the dry fermentation process were highly related to the reference. CONCLUSIONS Although process parameters, substrates and technology differ between the wet and dry biogas fermentations analyzed in this study, community profiles are very similar at least at higher taxonomic ranks, illustrating that core community taxa perform key functions in biomass decomposition and methane synthesis. Regarding methanogenesis, Archaea highly related to the type strain M. bourgensis MS2(T) dominate the dry fermentation process, suggesting the adaptation of members belonging to this species to specific fermentation process parameters.
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Affiliation(s)
- Yvonne Stolze
- />Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, Universitätsstraße 25, D-33615 Bielefeld, Germany
| | - Martha Zakrzewski
- />QIMR Berghofer Medical Research Institute Herston, 300 Herston Road, Brisbane, QLD 4006 Australia
| | - Irena Maus
- />Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, Universitätsstraße 25, D-33615 Bielefeld, Germany
| | - Felix Eikmeyer
- />Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, Universitätsstraße 25, D-33615 Bielefeld, Germany
| | - Sebastian Jaenicke
- />Bioinformatics Resource Facility, CeBiTec, Bielefeld University, Universitätsstraße 25, D-33615 Bielefeld, Germany
| | - Nils Rottmann
- />NORTH-TEC Maschinenbau GmbH, Oldenhörn 1, 25821 Bredstedt, Germany
| | - Clemens Siebner
- />Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, Universitätsstraße 25, D-33615 Bielefeld, Germany
| | - Alfred Pühler
- />Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, Universitätsstraße 25, D-33615 Bielefeld, Germany
| | - Andreas Schlüter
- />Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, Universitätsstraße 25, D-33615 Bielefeld, Germany
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Lee S, J. Mitchell R. Perspectives on the use of transcriptomics to advance biofuels. AIMS BIOENGINEERING 2015. [DOI: 10.3934/bioeng.2015.4.487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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31
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Biswas R, Zheng T, Olson DG, Lynd LR, Guss AM. Elimination of hydrogenase active site assembly blocks H2 production and increases ethanol yield in Clostridium thermocellum. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:20. [PMID: 25763101 PMCID: PMC4355364 DOI: 10.1186/s13068-015-0204-4] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 01/13/2015] [Indexed: 05/18/2023]
Abstract
BACKGROUND The native ability of Clostridium thermocellum to rapidly consume cellulose and produce ethanol makes it a leading candidate for a consolidated bioprocessing (CBP) biofuel production strategy. C. thermocellum also synthesizes lactate, formate, acetate, H2, and amino acids that compete with ethanol production for carbon and electrons. Elimination of H2 production could redirect carbon flux towards ethanol production by making more electrons available for acetyl coenzyme A reduction to ethanol. RESULTS H2 production in C. thermocellum is encoded by four hydrogenases. Rather than delete each individually, we targeted hydrogenase maturase gene hydG, involved in converting the three [FeFe] hydrogenase apoenzymes into holoenzymes. Further deletion of the [NiFe] hydrogenase (ech) resulted in a mutant that functionally lacks all four hydrogenases. H2 production in ∆hydG∆ech was undetectable, and the ethanol yield nearly doubled to 64% of the maximum theoretical yield. Genomic analysis of ∆hydG revealed a mutation in adhE, resulting in a strain with both NADH- and NADPH-dependent alcohol dehydrogenase activities. While this same adhE mutation was found in ethanol-tolerant C. thermocellum strain E50C, ∆hydG and ∆hydG∆ech are not more ethanol tolerant than the wild type, illustrating the complicated interactions between redox balancing and ethanol tolerance in C. thermocellum. CONCLUSIONS The dramatic increase in ethanol production suggests that targeting protein post-translational modification is a promising new approach for simultaneous inactivation of multiple enzymes.
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Affiliation(s)
- Ranjita Biswas
- />Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
- />BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
- />Current address: Centre for Rural Development and Technology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016 India
| | - Tianyong Zheng
- />BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
- />Thayer School of Engineering at Dartmouth College, Hanover, NH 03755 USA
| | - Daniel G Olson
- />BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
- />Thayer School of Engineering at Dartmouth College, Hanover, NH 03755 USA
| | - Lee R Lynd
- />BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
- />Thayer School of Engineering at Dartmouth College, Hanover, NH 03755 USA
| | - Adam M Guss
- />Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
- />BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
- />One Bethel Valley Road, Oak Ridge, TN 37831-6038 USA
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Akinosho H, Yee K, Close D, Ragauskas A. The emergence of Clostridium thermocellum as a high utility candidate for consolidated bioprocessing applications. Front Chem 2014; 2:66. [PMID: 25207268 PMCID: PMC4143619 DOI: 10.3389/fchem.2014.00066] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 07/28/2014] [Indexed: 01/25/2023] Open
Abstract
First isolated in 1926, Clostridium thermocellum has recently received increased attention as a high utility candidate for use in consolidated bioprocessing (CBP) applications. These applications, which seek to process lignocellulosic biomass directly into useful products such as ethanol, are gaining traction as economically feasible routes toward the production of fuel and other high value chemical compounds as the shortcomings of fossil fuels become evident. This review evaluates C. thermocellum's role in this transitory process by highlighting recent discoveries relating to its genomic, transcriptomic, proteomic, and metabolomic responses to varying biomass sources, with a special emphasis placed on providing an overview of its unique, multivariate enzyme cellulosome complex and the role that this structure performs during biomass degradation. Both naturally evolved and genetically engineered strains are examined in light of their unique attributes and responses to various biomass treatment conditions, and the genetic tools that have been employed for their creation are presented. Several future routes for potential industrial usage are presented, and it is concluded that, although there have been many advances to significantly improve C. thermocellum's amenability to industrial use, several hurdles still remain to be overcome as this unique organism enjoys increased attention within the scientific community.
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Affiliation(s)
- Hannah Akinosho
- School of Chemistry and Biochemistry, Institute of Paper Science and Technology, Georgia Institute of Technology Atlanta, GA, USA ; Oak Ridge National Laboratory, BioEnergy Science Center Oak Ridge, TN, USA
| | - Kelsey Yee
- Oak Ridge National Laboratory, BioEnergy Science Center Oak Ridge, TN, USA ; Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
| | - Dan Close
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
| | - Arthur Ragauskas
- Oak Ridge National Laboratory, BioEnergy Science Center Oak Ridge, TN, USA ; Department of Chemical and Biomolecular Engineering and Department of Forestry, Wildlife, and Fisheries, University of Tennessee Knoxville, TN, USA
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Hydrogen formation and its regulation in Ruminococcus albus: involvement of an electron-bifurcating [FeFe]-hydrogenase, of a non-electron-bifurcating [FeFe]-hydrogenase, and of a putative hydrogen-sensing [FeFe]-hydrogenase. J Bacteriol 2014; 196:3840-52. [PMID: 25157086 DOI: 10.1128/jb.02070-14] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ruminococcus albus 7 has played a key role in the development of the concept of interspecies hydrogen transfer. The rumen bacterium ferments glucose to 1.3 acetate, 0.7 ethanol, 2 CO2, and 2.6 H2 when growing in batch culture and to 2 acetate, 2 CO2, and 4 H2 when growing in continuous culture in syntrophic association with H2-consuming microorganisms that keep the H2 partial pressure low. The organism uses NAD(+) and ferredoxin for glucose oxidation to acetyl coenzyme A (acetyl-CoA) and CO2, NADH for the reduction of acetyl-CoA to ethanol, and NADH and reduced ferredoxin for the reduction of protons to H2. Of all the enzymes involved, only the enzyme catalyzing the formation of H2 from NADH remained unknown. Here, we report that R. albus 7 grown in batch culture on glucose contained, besides a ferredoxin-dependent [FeFe]-hydrogenase (HydA2), a ferredoxin- and NAD-dependent electron-bifurcating [FeFe]-hydrogenase (HydABC) that couples the endergonic formation of H2 from NADH to the exergonic formation of H2 from reduced ferredoxin. Interestingly, hydA2 is adjacent to the hydS gene, which is predicted to encode an [FeFe]-hydrogenase with a C-terminal PAS domain. We showed that hydS and hydA2 are part of a larger transcriptional unit also harboring putative genes for a bifunctional acetaldehyde/ethanol dehydrogenase (Aad), serine/threonine protein kinase, serine/threonine protein phosphatase, and a redox-sensing transcriptional repressor. Since HydA2 and Aad are required only when R. albus grows at high H2 partial pressures, HydS could be a H2-sensing [FeFe]-hydrogenase involved in the regulation of their biosynthesis.
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Zhou C, Ma Q, Li G. Elucidation of operon structures across closely related bacterial genomes. PLoS One 2014; 9:e100999. [PMID: 24959722 PMCID: PMC4069176 DOI: 10.1371/journal.pone.0100999] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 06/01/2014] [Indexed: 11/30/2022] Open
Abstract
About half of the protein-coding genes in prokaryotic genomes are organized into operons to facilitate co-regulation during transcription. With the evolution of genomes, operon structures are undergoing changes which could coordinate diverse gene expression patterns in response to various stimuli during the life cycle of a bacterial cell. Here we developed a graph-based model to elucidate the diversity of operon structures across a set of closely related bacterial genomes. In the constructed graph, each node represents one orthologous gene group (OGG) and a pair of nodes will be connected if any two genes, from the corresponding two OGGs respectively, are located in the same operon as immediate neighbors in any of the considered genomes. Through identifying the connected components in the above graph, we found that genes in a connected component are likely to be functionally related and these identified components tend to form treelike topology, such as paths and stars, corresponding to different biological mechanisms in transcriptional regulation as follows. Specifically, (i) a path-structure component integrates genes encoding a protein complex, such as ribosome; and (ii) a star-structure component not only groups related genes together, but also reflects the key functional roles of the central node of this component, such as the ABC transporter with a transporter permease and substrate-binding proteins surrounding it. Most interestingly, the genes from organisms with highly diverse living environments, i.e., biomass degraders and animal pathogens of clostridia in our study, can be clearly classified into different topological groups on some connected components.
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Affiliation(s)
- Chuan Zhou
- School of Mathematics, Shandong University, Jinan, China
| | - Qin Ma
- Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America
| | - Guojun Li
- School of Mathematics, Shandong University, Jinan, China
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35
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Hong W, Zhang J, Feng Y, Mohr G, Lambowitz AM, Cui GZ, Liu YJ, Cui Q. The contribution of cellulosomal scaffoldins to cellulose hydrolysis by Clostridium thermocellum analyzed by using thermotargetrons. BIOTECHNOLOGY FOR BIOFUELS 2014; 7:80. [PMID: 24955112 PMCID: PMC4045903 DOI: 10.1186/1754-6834-7-80] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2013] [Accepted: 05/13/2014] [Indexed: 05/23/2023]
Abstract
BACKGROUND Clostridium thermocellum is a thermophilic anaerobic bacterium that degrades cellulose by using a highly effective cellulosome, a macromolecular complex consisting of multiple cellulose degrading enzymes organized and attached to the cell surface by non-catalytic scaffoldins. However, due largely to lack of efficient methods for genetic manipulation of C. thermocellum, it is still unclear how the different scaffoldins and their functional modules contribute to cellulose hydrolysis. RESULTS We constructed C. thermocellum mutants with the primary scaffoldin CipA (cellulosome-integrating protein A) truncated at different positions or lacking four different secondary scaffoldins by using a newly developed thermotargetron system, and we analyzed cellulose hydrolysis, cellulosome formation, and cellulose binding of the mutants. A CipA truncation that deletes six type I cohesin modules, which bind cellulolytic enzymes, decreased cellulose hydrolysis rates by 46%, and slightly longer truncations that also delete the carbohydrate binding module decreased rates by 89 to 92%, indicating strong cellulosome-substrate synergy. By contrast, a small CipA truncation that deletes only the C-terminal type II dockerin (XDocII) module detached cellulosomes from the cells, but decreased cellulose hydrolysis rates by only 9%, suggesting a relatively small contribution of cellulosome-cell synergy. Disruptants lacking any of four different secondary scaffoldins (OlpB, 7CohII, Orf2p, or SdbA) showed moderately decreased cellulose hydrolysis rates, suggesting additive contributions. Surprisingly, the CipA-ΔXDocII mutant, which lacks cell-associated polycellulosomes, adheres to cellulose almost as strongly as wild-type cells, revealing an alternate, previously unknown cellulose-binding mechanism. CONCLUSIONS Our results emphasize the important role of cellulosome-substrate synergy in cellulose degradation, demonstrate a contribution of secondary scaffoldins, and suggest a previously unknown, non-cellulosomal system for binding insoluble cellulose. Our findings provide new insights into cellulosome function and impact genetic engineering of microorganisms to enhance bioconversions of cellulose substrates.
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Affiliation(s)
- Wei Hong
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, P R China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100049, P R China
| | - Jie Zhang
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, P R China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100049, P R China
| | - Yingang Feng
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, P R China
| | - Georg Mohr
- Departments of Molecular Biosciences and Chemistry, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Alan M Lambowitz
- Departments of Molecular Biosciences and Chemistry, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Gu-Zhen Cui
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, P R China
| | - Ya-Jun Liu
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, P R China
| | - Qiu Cui
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, P R China
- Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, P R China
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36
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Blumer-Schuette SE, Brown SD, Sander KB, Bayer EA, Kataeva I, Zurawski JV, Conway JM, Adams MWW, Kelly RM. Thermophilic lignocellulose deconstruction. FEMS Microbiol Rev 2014; 38:393-448. [DOI: 10.1111/1574-6976.12044] [Citation(s) in RCA: 128] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Revised: 08/20/2013] [Accepted: 08/28/2013] [Indexed: 11/28/2022] Open
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Draft Genome Sequence of Clostridium straminisolvens Strain JCM 21531T, Isolated from a Cellulose-Degrading Bacterial Community. GENOME ANNOUNCEMENTS 2014; 2:2/1/e00110-14. [PMID: 24558248 PMCID: PMC3931369 DOI: 10.1128/genomea.00110-14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Here, we report the draft genome sequence of a fibrolytic bacterium, Clostridium straminisolvens JCM 21531(T), isolated from a cellulose-degrading bacterial community. The genome information of this strain will be useful for studies on the degradation enzymes and functional interactions with other members in the community.
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38
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Ravachol J, Borne R, Tardif C, de Philip P, Fierobe HP. Characterization of all family-9 glycoside hydrolases synthesized by the cellulosome-producing bacterium Clostridium cellulolyticum. J Biol Chem 2014; 289:7335-48. [PMID: 24451379 DOI: 10.1074/jbc.m113.545046] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The genome of Clostridium cellulolyticum encodes 13 GH9 enzymes that display seven distinct domain organizations. All but one contain a dockerin module and were formerly detected in the cellulosomes, but only three of them were previously studied (Cel9E, Cel9G, and Cel9M). In this study, the 10 uncharacterized GH9 enzymes were overproduced in Escherichia coli and purified, and their activity pattern was investigated in the free state or in cellulosome chimeras with key cellulosomal cellulases. The newly purified GH9 enzymes, including those that share similar organization, all exhibited distinct activity patterns, various binding capacities on cellulosic substrates, and different synergies with pivotal cellulases in mini-cellulosomes. Furthermore, one enzyme (Cel9X) was characterized as the first genuine endoxyloglucanase belonging to this family, with no activity on soluble and insoluble celluloses. Another GH9 enzyme (Cel9V), whose sequence is 78% identical to the cellulosomal cellulase Cel9E, was found inactive in the free and complexed states on all tested substrates. The sole noncellulosomal GH9 (Cel9W) is a cellulase displaying a broad substrate specificity, whose engineered form bearing a dockerin can act synergistically in minicomplexes. Finally, incorporation of all GH9 cellulases in trivalent cellulosome chimera containing Cel48F and Cel9G generated a mixture of heterogeneous mini-cellulosomes that exhibit more activity on crystalline cellulose than the best homogeneous tri-functional complex. Altogether, our data emphasize the importance of GH9 diversity in bacterial cellulosomes, confirm that Cel9G is the most synergistic GH9 with the major endoprocessive cellulase Cel48F, but also identify Cel9U as an important cellulosomal component during cellulose depolymerization.
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Affiliation(s)
- Julie Ravachol
- From the Aix-Marseille Université-CNRS, Laboratoire de Chimie Bactérienne UMR7283, Institut de Microbiologie de la Méditerranée, Marseille Cedex 20, France
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Brown SD, Nagaraju S, Utturkar S, De Tissera S, Segovia S, Mitchell W, Land ML, Dassanayake A, Köpke M. Comparison of single-molecule sequencing and hybrid approaches for finishing the genome of Clostridium autoethanogenum and analysis of CRISPR systems in industrial relevant Clostridia. BIOTECHNOLOGY FOR BIOFUELS 2014; 7:40. [PMID: 24655715 PMCID: PMC4022347 DOI: 10.1186/1754-6834-7-40] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Accepted: 02/19/2014] [Indexed: 05/04/2023]
Abstract
BACKGROUND Clostridium autoethanogenum strain JA1-1 (DSM 10061) is an acetogen capable of fermenting CO, CO2 and H2 (e.g. from syngas or waste gases) into biofuel ethanol and commodity chemicals such as 2,3-butanediol. A draft genome sequence consisting of 100 contigs has been published. RESULTS A closed, high-quality genome sequence for C. autoethanogenum DSM10061 was generated using only the latest single-molecule DNA sequencing technology and without the need for manual finishing. It is assigned to the most complex genome classification based upon genome features such as repeats, prophage, nine copies of the rRNA gene operons. It has a low G + C content of 31.1%. Illumina, 454, Illumina/454 hybrid assemblies were generated and then compared to the draft and PacBio assemblies using summary statistics, CGAL, QUAST and REAPR bioinformatics tools and comparative genomic approaches. Assemblies based upon shorter read DNA technologies were confounded by the large number repeats and their size, which in the case of the rRNA gene operons were ~5 kb. CRISPR (Clustered Regularly Interspaced Short Paloindromic Repeats) systems among biotechnologically relevant Clostridia were classified and related to plasmid content and prophages. Potential associations between plasmid content and CRISPR systems may have implications for historical industrial scale Acetone-Butanol-Ethanol (ABE) fermentation failures and future large scale bacterial fermentations. While C. autoethanogenum contains an active CRISPR system, no such system is present in the closely related Clostridium ljungdahlii DSM 13528. A common prophage inserted into the Arg-tRNA shared between the strains suggests a common ancestor. However, C. ljungdahlii contains several additional putative prophages and it has more than double the amount of prophage DNA compared to C. autoethanogenum. Other differences include important metabolic genes for central metabolism (as an additional hydrogenase and the absence of a phophoenolpyruvate synthase) and substrate utilization pathway (mannose and aromatics utilization) that might explain phenotypic differences between C. autoethanogenum and C. ljungdahlii. CONCLUSIONS Single molecule sequencing will be increasingly used to produce finished microbial genomes. The complete genome will facilitate comparative genomics and functional genomics and support future comparisons between Clostridia and studies that examine the evolution of plasmids, bacteriophage and CRISPR systems.
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Affiliation(s)
- Steven D Brown
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37996, USA
| | | | - Sagar Utturkar
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37996, USA
| | | | | | | | - Miriam L Land
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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Lin L, Xu J. Dissecting and engineering metabolic and regulatory networks of thermophilic bacteria for biofuel production. Biotechnol Adv 2013; 31:827-37. [DOI: 10.1016/j.biotechadv.2013.03.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 03/06/2013] [Accepted: 03/10/2013] [Indexed: 01/08/2023]
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41
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Slutzki M, Jobby MK, Chitayat S, Karpol A, Dassa B, Barak Y, Lamed R, Smith SP, Bayer EA. Intramolecular clasp of the cellulosomal Ruminococcus flavefaciens ScaA dockerin module confers structural stability. FEBS Open Bio 2013; 3:398-405. [PMID: 24251102 PMCID: PMC3821032 DOI: 10.1016/j.fob.2013.09.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Revised: 09/20/2013] [Accepted: 09/20/2013] [Indexed: 12/02/2022] Open
Abstract
The cellulosome is a large extracellular multi-enzyme complex that facilitates the efficient hydrolysis and degradation of crystalline cellulosic substrates. During the course of our studies on the cellulosome of the rumen bacterium Ruminococcus flavefaciens, we focused on the critical ScaA dockerin (ScaADoc), the unique dockerin that incorporates the primary enzyme-integrating ScaA scaffoldin into the cohesin-bearing ScaB adaptor scaffoldin. In the absence of a high-resolution structure of the ScaADoc module, we generated a computational model, and, upon its analysis, we were surprised to discover a putative stacking interaction between an N-terminal Trp and a C-terminal Pro, which we termed intramolecular clasp. In order to verify the existence of such an interaction, these residues were mutated to alanine. Circular dichroism spectroscopy, intrinsic tryptophan and ANS fluorescence, and NMR spectroscopy indicated that mutation of these residues has a destabilizing effect on the functional integrity of the Ca2+-bound form of ScaADoc. Analysis of recently determined dockerin structures from other species revealed the presence of other well-defined intramolecular clasps, which consist of different types of interactions between selected residues at the dockerin termini. We propose that this thematic interaction may represent a major distinctive structural feature of the dockerin module. A structural model for the Ruminococcus flavefaciens ScaA dockerin is proposed. A stacking interaction between N- and C-terminal residues was derived from the model. Mutations of putative interacting residues resulted in reduced stability and binding. Similar intramodular “clasp” interactions were observed in other dockerin structures.
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Key Words
- ANS, 8-anilino-1-naphthalenesulfonate
- CBM, carbohydrate-binding module family 3a from C. thermocellum
- Cc, Clostridium cellulolyticum
- Coh, cohesin
- Cohesin
- Ct, Clostridium thermocellum
- Doc, dockerin
- HBS, hepes-buffered saline
- IPTG, isopropyl-1-thio-β-d-galactoside
- Protein stability
- Scaffoldin
- Stacking interaction
- TMB, 3,3′,5,5′-tetramethylbenzidine
- Xyn, xylanase T6 from Geobacillus stearothemophilus
- cELISA, competitive enzyme-linked interaction assay
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Affiliation(s)
- Michal Slutzki
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
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Wilson CM, Yang S, Rodriguez M, Ma Q, Johnson CM, Dice L, Xu Y, Brown SD. Clostridium thermocellum transcriptomic profiles after exposure to furfural or heat stress. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:131. [PMID: 24028713 PMCID: PMC3848806 DOI: 10.1186/1754-6834-6-131] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Accepted: 09/04/2013] [Indexed: 05/23/2023]
Abstract
BACKGROUND The thermophilic anaerobe Clostridium thermocellum is a candidate consolidated bioprocessing (CBP) biocatalyst for cellulosic ethanol production. It is capable of both cellulose solubilization and its fermentation to produce lignocellulosic ethanol. Intolerance to stresses routinely encountered during industrial fermentations may hinder the commercial development of this organism. A previous C. thermocellum ethanol stress study showed that the largest transcriptomic response was in genes and proteins related to nitrogen uptake and metabolism. RESULTS In this study, C. thermocellum was grown to mid-exponential phase and treated with furfural or heat to a final concentration of 3 g.L-1 or 68°C respectively to investigate general and specific physiological and regulatory stress responses. Samples were taken at 10, 30, 60 and 120 min post-shock, and from untreated control fermentations, for transcriptomic analyses and fermentation product determinations and compared to a published dataset from an ethanol stress study. Urea uptake genes were induced following furfural stress, but not to the same extent as ethanol stress and transcription from these genes was largely unaffected by heat stress. The largest transcriptomic response to furfural stress was genes for sulfate transporter subunits and enzymes in the sulfate assimilatory pathway, although these genes were also affected late in the heat and ethanol stress responses. Lactate production was higher in furfural treated culture, although the lactate dehydrogenase gene was not differentially expressed under this condition. Other redox related genes such as a copy of the rex gene, a bifunctional acetaldehyde-CoA/alcohol dehydrogenase and adjacent genes did show lower expression after furfural stress compared to the control, heat and ethanol fermentation profiles. Heat stress induced expression from chaperone related genes and overlap was observed with the responses to the other stresses. This study suggests the involvement of C. thermocellum genes with functions in oxidative stress protection, electron transfer, detoxification, sulfur and nitrogen acquisition, and DNA repair mechanisms in its stress responses and the use of different regulatory networks to coordinate and control adaptation. CONCLUSIONS This study has identified C. thermocellum gene regulatory motifs and aspects of physiology and gene regulation for further study. The nexus between future systems biology studies and recently developed genetic tools for C. thermocellum offers the potential for more rapid strain development and for broader insights into this organism's physiology and regulation.
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Affiliation(s)
- Charlotte M Wilson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, 37831 TN, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Shihui Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, 37831 TN, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Present address: National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Miguel Rodriguez
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, 37831 TN, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Qin Ma
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, Computational Systems Biology Laboratory, University of Georgia, Athens, GA 30602, USA
| | - Courtney M Johnson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, 37831 TN, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Lezlee Dice
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, 37831 TN, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Ying Xu
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, Computational Systems Biology Laboratory, University of Georgia, Athens, GA 30602, USA
- College of Computer Science and Technology, Jilin University, Changchun, Jilin, China
| | - Steven D Brown
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, 37831 TN, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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Draft genome sequence of the cellulolytic Clostridium thermocellum wild-type strain BC1 playing a role in cellulosic biomass degradation. J Biotechnol 2013; 168:62-3. [PMID: 23968723 DOI: 10.1016/j.jbiotec.2013.08.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 08/09/2013] [Indexed: 01/14/2023]
Abstract
The bacterium Clostridium thermocellum BC1, a thermophilic, anaerobic bacterium of the family Clostridiaceae, was isolated from a compost treatment site in Germany. It is able to grow efficiently on cellulose and cellodextrins. The draft genome sequence of C. thermocellum BC1 has been established and provides the genetic basis for application of this microorganism in thermophilic degradation of cellulosic biomass.
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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] [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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Chung D, Farkas J, Westpheling J. Detection of a novel active transposable element in Caldicellulosiruptor hydrothermalis and a new search for elements in this genus. J Ind Microbiol Biotechnol 2013; 40:517-21. [PMID: 23475285 DOI: 10.1007/s10295-013-1244-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Accepted: 02/12/2013] [Indexed: 01/30/2023]
Abstract
We show that a previously annotated hypothetical protein is the transposase of a new and active IS element, ISCahy1, widespread in Caldicellulosiruptor species. Transposition generated an 11-bp direct repeat at the insertion site in Caldicellulosiruptor hydrothermalis, suggesting a cut-and-paste mechanism. The discovery of an active insertion sequence in Caldicellulosiruptor species led to a survey of potential IS elements in the genome sequences of eight Caldicellulosiruptor species that identified several new elements, including one novel to this genus.
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Affiliation(s)
- Daehwan Chung
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
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Comparative quantitative analysis of gene expression profiles of glycoside hydrolase family 10 xylanases in the sheep rumen during a feeding cycle. Appl Environ Microbiol 2012; 79:1212-20. [PMID: 23220966 DOI: 10.1128/aem.02733-12] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Xylanase is a crucial hydrolytic enzyme that degrades plant polysaccharides in the rumen. To date, there is no information on the genetic composition and expression characteristics of ruminal xylanase during feeding cycles of ruminants. Here, the major xylanase of the glycoside hydrolase family 10 (GH 10) from the rumen of small-tail Han sheep was investigated during a feeding cycle. We identified 44 distinct GH 10 xylanase gene fragments at both the genomic and transcriptional levels. Comparison of their relative abundance showed that results from the evaluation of functional genes at the transcriptional level are more reliable indicators for understanding fluctuations in xylanase levels. The expression patterns of six xylanase genes, detected at all time points of the feeding cycle, were investigated; we observed a complex trend of gene expression over 24 h, revealing the dynamic expression of xylanases in the rumen. Further correlation analysis indicated that the rumen is a dynamic ecosystem where the transcript profiles of xylanase genes are closely related to ruminal conditions, especially rumen pH and bacterial population. Given the huge diversity and changing composition of enzymes over the entire rumen, this research provides valuable information for understanding the role of functional genes in the digestion of plant material.
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Redirecting carbon flux through exogenous pyruvate kinase to achieve high ethanol yields in Clostridium thermocellum. Metab Eng 2012. [PMID: 23202749 DOI: 10.1016/j.ymben.2012.11.006] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In Clostridium thermocellum, a thermophilic anaerobic bacterium able to rapidly ferment cellulose to ethanol, pyruvate kinase (EC 2.7.1.40) is absent based on both the genome sequence and enzymatic assays. Instead, a new pathway converting phosphoenolpyruvate to pyruvate via a three-step pathway involving phosphoenolpyruvate carboxykinase, NADH-linked malate dehydrogenase, and NADP-dependent malic enzyme has been found. We examined the impact of targeted modification of enzymes associated with this pathway, termed the "malate shunt", including expression of the pyruvate kinase gene from Thermoanaerobacterium saccharolyticum, mutation of the phosphoenolpyruvate carboxykinase and deletion of malic enzyme gene. Strain YD01 with exogenous pyruvate kinase, in which phosphoenolpyruvate carboxykinase expression was diminished by modifying the start codon from ATG to GTG, exhibited 3.25-fold higher ethanol yield than the wild-type strain. A second strain, YD02 with exogenous pyruvate kinase, in which the gene for malic enzyme and part of malate dehydrogenase were deleted, had over 3-fold higher ethanol yield than the wild-type strain.
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Draft genome sequences for Clostridium thermocellum wild-type strain YS and derived cellulose adhesion-defective mutant strain AD2. J Bacteriol 2012; 194:3290-1. [PMID: 22628515 DOI: 10.1128/jb.00473-12] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Clostridium thermocellum wild-type strain YS is an anaerobic, thermophilic, cellulolytic bacterium capable of directly converting cellulosic substrates into ethanol. Strain YS and a derived cellulose adhesion-defective mutant strain, AD2, played pivotal roles in describing the original cellulosome concept. We present their draft genome sequences.
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Tracy BP, Jones SW, Fast AG, Indurthi DC, Papoutsakis ET. Clostridia: the importance of their exceptional substrate and metabolite diversity for biofuel and biorefinery applications. Curr Opin Biotechnol 2012; 23:364-81. [DOI: 10.1016/j.copbio.2011.10.008] [Citation(s) in RCA: 313] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2011] [Revised: 10/06/2011] [Accepted: 10/20/2011] [Indexed: 12/19/2022]
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Guss AM, Olson DG, Caiazza NC, Lynd LR. Dcm methylation is detrimental to plasmid transformation in Clostridium thermocellum. BIOTECHNOLOGY FOR BIOFUELS 2012; 5:30. [PMID: 22559230 PMCID: PMC3536630 DOI: 10.1186/1754-6834-5-30] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Accepted: 03/29/2012] [Indexed: 05/18/2023]
Abstract
BACKGROUND Industrial production of biofuels and other products by cellulolytic microorganisms is of interest but hindered by the nascent state of genetic tools. Although a genetic system for Clostridium thermocellum DSM1313 has recently been developed, available methods achieve relatively low efficiency and similar plasmids can transform C. thermocellum at dramatically different efficiencies. RESULTS We report an increase in transformation efficiency of C. thermocellum for a variety of plasmids by using DNA that has been methylated by Escherichia coli Dam but not Dcm methylases. When isolated from a dam+dcm+E. coli strain, pAMG206 transforms C. thermocellum 100-fold better than the similar plasmid pAMG205, which contains an additional Dcm methylation site in the pyrF gene. Upon removal of Dcm methylation, transformation with pAMG206 showed a four- to seven-fold increase in efficiency; however, transformation efficiency of pAMG205 increased 500-fold. Removal of the Dcm methylation site from the pAMG205 pyrF gene via silent mutation resulted in increased transformation efficiencies equivalent to that of pAMG206. Upon proper methylation, transformation efficiency of plasmids bearing the pMK3 and pB6A origins of replication increased ca. three orders of magnitude. CONCLUSIONS E. coli Dcm methylation decreases transformation efficiency in C. thermocellum DSM1313. The use of properly methylated plasmid DNA should facilitate genetic manipulation of this industrially relevant bacterium.
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Affiliation(s)
- Adam M Guss
- Thayer School of Engineering, Dartmouth College, 8000 Cummings Hall, Hanover, NH 03755, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Daniel G Olson
- Thayer School of Engineering, Dartmouth College, 8000 Cummings Hall, Hanover, NH 03755, USA
- Mascoma Corporation, 67 Etna Rd, Suite 300, Lebanon, NH 03755, USA
| | - Nicky C Caiazza
- Mascoma Corporation, 67 Etna Rd, Suite 300, Lebanon, NH 03755, USA
- Current address: Synthetic Genomics Inc, La Jolla, CA 92037, USA
| | - Lee R Lynd
- Thayer School of Engineering, Dartmouth College, 8000 Cummings Hall, Hanover, NH 03755, USA
- Mascoma Corporation, 67 Etna Rd, Suite 300, Lebanon, NH 03755, USA
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