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Meng Q, Moinuddin SGA, Celoy RM, Smith CA, Young RP, Costa MA, Freeman RA, Fukaya M, Kim DN, Cort JR, Hawes MC, van Etten HD, Pandey P, Chittiboyina AG, Ferreira D, Davin LB, Lewis NG. Dirigent isoflavene-forming PsPTS2: 3D structure, stereochemical, and kinetic characterization comparison with pterocarpan-forming PsPTS1 homolog in pea. J Biol Chem 2024; 300:105647. [PMID: 38219818 PMCID: PMC10882141 DOI: 10.1016/j.jbc.2024.105647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 12/21/2023] [Accepted: 01/05/2024] [Indexed: 01/16/2024] Open
Abstract
Pea phytoalexins (-)-maackiain and (+)-pisatin have opposite C6a/C11a configurations, but biosynthetically how this occurs is unknown. Pea dirigent-protein (DP) PsPTS2 generates 7,2'-dihydroxy-4',5'-methylenedioxyisoflav-3-ene (DMDIF), and stereoselectivity toward four possible 7,2'-dihydroxy-4',5'-methylenedioxyisoflavan-4-ol (DMDI) stereoisomers was investigated. Stereoisomer configurations were determined using NMR spectroscopy, electronic circular dichroism, and molecular orbital analyses. PsPTS2 efficiently converted cis-(3R,4R)-DMDI into DMDIF 20-fold faster than the trans-(3R,4S)-isomer. The 4R-configured substrate's near β-axial OH orientation significantly enhanced its leaving group abilities in generating A-ring mono-quinone methide (QM), whereas 4S-isomer's α-equatorial-OH was a poorer leaving group. Docking simulations indicated that the 4R-configured β-axial OH was closest to Asp51, whereas 4S-isomer's α-equatorial OH was further away. Neither cis-(3S,4S)- nor trans-(3S,4R)-DMDIs were substrates, even with the former having C3/C4 stereochemistry as in (+)-pisatin. PsPTS2 used cis-(3R,4R)-7,2'-dihydroxy-4'-methoxyisoflavan-4-ol [cis-(3R,4R)-DMI] and C3/C4 stereoisomers to give 2',7-dihydroxy-4'-methoxyisoflav-3-ene (DMIF). DP homologs may exist in licorice (Glycyrrhiza pallidiflora) and tree legume Bolusanthus speciosus, as DMIF occurs in both species. PsPTS1 utilized cis-(3R,4R)-DMDI to give (-)-maackiain 2200-fold more efficiently than with cis-(3R,4R)-DMI to give (-)-medicarpin. PsPTS1 also slowly converted trans-(3S,4R)-DMDI into (+)-maackiain, reflecting the better 4R configured OH leaving group. PsPTS2 and PsPTS1 provisionally provide the means to enable differing C6a and C11a configurations in (+)-pisatin and (-)-maackiain, via identical DP-engendered mono-QM bound intermediate generation, which PsPTS2 either re-aromatizes to give DMDIF or PsPTS1 intramolecularly cyclizes to afford (-)-maackiain. Substrate docking simulations using PsPTS2 and PsPTS1 indicate cis-(3R,4R)-DMDI binds in the anti-configuration in PsPTS2 to afford DMDIF, and the syn-configuration in PsPTS1 to give maackiain.
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Affiliation(s)
- Qingyan Meng
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, USA
| | - Syed G A Moinuddin
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, USA
| | - Rhodesia M Celoy
- School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Clyde A Smith
- Stanford Synchrotron Radiation Lightsource, Stanford University, Menlo Park, California, USA
| | - Robert P Young
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Michael A Costa
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, USA
| | - Rachel A Freeman
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, USA
| | - Masashi Fukaya
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, USA
| | - Doo Nam Kim
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - John R Cort
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, USA; Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Martha C Hawes
- School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Hans D van Etten
- School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Pankaj Pandey
- National Center for Natural Products Research, School of Pharmacy, University of Mississippi, University, Mississippi, USA
| | - Amar G Chittiboyina
- National Center for Natural Products Research, School of Pharmacy, University of Mississippi, University, Mississippi, USA
| | - Daneel Ferreira
- National Center for Natural Products Research, School of Pharmacy, University of Mississippi, University, Mississippi, USA; Division of Pharmacognosy, Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, University, Mississippi, USA
| | - Laurence B Davin
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, USA
| | - Norman G Lewis
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, USA.
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2
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Hixson KK, Fajardo DA, Devitt NP, Sena JA, Costa MA, Meng Q, Boschiero C, Zhao PX, Baack E, Paurus VL, Davin LB, Lewis NG, Bell CJ. Annotated genome sequence of a fast-growing diploid clone of red alder (Alnus rubra Bong.). G3 (Bethesda) 2023:7086176. [PMID: 36966434 DOI: 10.1093/g3journal/jkad060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 12/21/2022] [Accepted: 03/10/2023] [Indexed: 03/27/2023]
Abstract
Red alder (Alnus rubra Bong.) is an ecologically significant and important, fast-growing commercial tree species native to western coastal and riparian regions of North America, having highly desirable wood, pigment and medicinal properties. We have sequenced the genome of a rapidly growing clone. The assembly is nearly complete, containing the full complement of expected genes. This supports our objectives of identifying and studying genes and pathways involved in nitrogen fixing symbiosis, and those related to secondary metabolites that underlie red alder's many interesting defense, pigmentation and wood quality traits. We established that this clone is most likely diploid, and identified a set of SNPs that will have utility in future breeding and selection endeavors, as well as in ongoing population studies. We have added a well-characterized genome to others from the order Fagales. In particular, it improves significantly upon the only other published alder genome sequence, that of Alnus glutinosa. Our work initiated a detailed comparative analysis of members of the order Fagales, and established some similarities with previous reports in this clade suggesting biased retention of certain gene functions in the vestiges of an ancient genome duplication as compared to more recent tandem duplications.
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Affiliation(s)
- Kim K Hixson
- Institute of Biological Chemistry, Washington State University (WSU), Pullman, WA 99164 USA
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory (PNNL), Richland, WA 99352, USA
| | - Diego A Fajardo
- National Center for Genome Resources (NCGR), Santa Fe, NM 87505, USA
| | - Nicholas P Devitt
- National Center for Genome Resources (NCGR), Santa Fe, NM 87505, USA
| | - Johnny A Sena
- National Center for Genome Resources (NCGR), Santa Fe, NM 87505, USA
| | - Michael A Costa
- Institute of Biological Chemistry, Washington State University (WSU), Pullman, WA 99164 USA
| | - Qingyan Meng
- Institute of Biological Chemistry, Washington State University (WSU), Pullman, WA 99164 USA
| | | | | | - Eric Baack
- Biology Department, Luther College, Decorah, IA 52101, USA
| | - Vanessa L Paurus
- Biological Science Division, Pacific Northwest National Laboratory (PNNL), Richland, WA 99352, USA
| | - Laurence B Davin
- Institute of Biological Chemistry, Washington State University (WSU), Pullman, WA 99164 USA
| | - Norman G Lewis
- Institute of Biological Chemistry, Washington State University (WSU), Pullman, WA 99164 USA
| | - Callum J Bell
- National Center for Genome Resources (NCGR), Santa Fe, NM 87505, USA
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3
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Barker R, Kruse CPS, Johnson C, Saravia-Butler A, Fogle H, Chang HS, Trane RM, Kinscherf N, Villacampa A, Manzano A, Herranz R, Davin LB, Lewis NG, Perera I, Wolverton C, Gupta P, Jaiswal P, Reinsch SS, Wyatt S, Gilroy S. Meta-analysis of the space flight and microgravity response of the Arabidopsis plant transcriptome. NPJ Microgravity 2023; 9:21. [PMID: 36941263 PMCID: PMC10027818 DOI: 10.1038/s41526-023-00247-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 01/10/2023] [Indexed: 03/23/2023] Open
Abstract
Spaceflight presents a multifaceted environment for plants, combining the effects on growth of many stressors and factors including altered gravity, the influence of experiment hardware, and increased radiation exposure. To help understand the plant response to this complex suite of factors this study compared transcriptomic analysis of 15 Arabidopsis thaliana spaceflight experiments deposited in the National Aeronautics and Space Administration's GeneLab data repository. These data were reanalyzed for genes showing significant differential expression in spaceflight versus ground controls using a single common computational pipeline for either the microarray or the RNA-seq datasets. Such a standardized approach to analysis should greatly increase the robustness of comparisons made between datasets. This analysis was coupled with extensive cross-referencing to a curated matrix of metadata associated with these experiments. Our study reveals that factors such as analysis type (i.e., microarray versus RNA-seq) or environmental and hardware conditions have important confounding effects on comparisons seeking to define plant reactions to spaceflight. The metadata matrix allows selection of studies with high similarity scores, i.e., that share multiple elements of experimental design, such as plant age or flight hardware. Comparisons between these studies then helps reduce the complexity in drawing conclusions arising from comparisons made between experiments with very different designs.
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Affiliation(s)
- Richard Barker
- Department of Botany, University of Wisconsin, Madison, WI, 53706, USA
| | - Colin P S Kruse
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, NM, 87545, USA
| | | | - Amanda Saravia-Butler
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, 94035, USA
- Logyx, LLC, Mountain View, CA, 94043, USA
| | - Homer Fogle
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, 94035, USA
- Bionetics, Yorktown, VA, 23693, USA
| | - Hyun-Seok Chang
- Department of Botany, University of Wisconsin, Madison, WI, 53706, USA
| | - Ralph Møller Trane
- Department of Statistics, University of Wisconsin, Madison, WI, 53706, USA
| | - Noah Kinscherf
- Department of Botany, University of Wisconsin, Madison, WI, 53706, USA
| | - Alicia Villacampa
- Centro de Investigaciones Biológicas Margarita Salas (CSIC), 28040, Madrid, Spain
| | - Aránzazu Manzano
- Centro de Investigaciones Biológicas Margarita Salas (CSIC), 28040, Madrid, Spain
| | - Raúl Herranz
- Centro de Investigaciones Biológicas Margarita Salas (CSIC), 28040, Madrid, Spain
| | - Laurence B Davin
- Institute of Biological Chemistry, Washington State University, Pullman, WA, 99164-741, USA
| | - Norman G Lewis
- Institute of Biological Chemistry, Washington State University, Pullman, WA, 99164-741, USA
| | - Imara Perera
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Chris Wolverton
- Department of Botany and Microbiology, Ohio Wesleyan University, Delaware, OH, 43015, USA
| | - Parul Gupta
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - Sigrid S Reinsch
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, 94035, USA
| | - Sarah Wyatt
- Department of Environmental and Plant Biology, Ohio University, Athens, OH, 45701, USA
| | - Simon Gilroy
- Department of Botany, University of Wisconsin, Madison, WI, 53706, USA.
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4
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Meng Q, Kim SJ, Costa MA, Moinuddin SGA, Celoy RM, Smith CA, Cort JR, Davin LB, Lewis NG. Dirigent protein subfamily function and structure in terrestrial plant phenol metabolism. Methods Enzymol 2023; 683:101-150. [PMID: 37087184 DOI: 10.1016/bs.mie.2023.02.025] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/24/2023]
Abstract
Aquatic plant transition to land, and subsequent terrestrial plant species diversification, was accompanied by the emergence and massive elaboration of plant phenol chemo-diversity. Concomitantly, dirigent protein (DP) and dirigent-like protein subfamilies, derived from large multigene families, emerged and became extensively diversified. DP biochemical functions as gateway entry points into new and diverse plant phenol skeletal types then markedly expanded. DPs have at least eight non-uniformly distributed subfamilies, with different DP subfamily members of known biochemical/physiological function now implicated as gateway entries to lignan, lignin, aromatic diterpenoid, pterocarpan and isoflavene pathways. While some other DP subfamily members have jacalin domains, both these and indeed the majority of DPs throughout the plant kingdom await discovery of their biochemical roles. Methods and approaches were developed to discover DP biochemical function as gateway entry points to distinct plant phenol skeletal types in land plants. Various DP 3D X-ray structural determinations enabled structure-based comparative sequence analysis and modeling to understand similarities and differences among the different DP subfamilies. We consider that the core DP β-barrel fold and associated characteristics are likely common to all DPs, with several residues conserved and nearly invariant. There is also considerable variation in residue composition and topography of the putative substrate binding pockets, as well as substantial differences in several loops, such as the β1-β2 loop. All DPs likely bind and stabilize quinone methide intermediates, while guiding distinctive regio- and/or stereo-chemical entry into Nature's chemo-diverse land plant phenol metabolic classes.
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Affiliation(s)
- Qingyan Meng
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
| | - Sung-Jin Kim
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
| | - Michael A Costa
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
| | - Syed G A Moinuddin
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
| | - Rhodesia M Celoy
- School of Plant Sciences, University of Arizona, Tucson, AZ, United States
| | - Clyde A Smith
- Stanford Synchrotron Radiation Lightsource, Menlo Park, CA, United States
| | - John R Cort
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States; Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Laurence B Davin
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
| | - Norman G Lewis
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States.
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5
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Zhou M, Laureanti JA, Bell CJ, Kwon M, Meng Q, Novikova IV, Thomas DG, Nicora CD, Sontag RL, Bedgar DL, O'Bryon I, Merkley ED, Ginovska B, Cort JR, Davin LB, Lewis NG. De novo sequencing and native mass spectrometry revealed hetero-association of dirigent protein homologs and potential interacting proteins in Forsythia × intermedia. Analyst 2021; 146:7670-7681. [PMID: 34806721 DOI: 10.1039/d1an01476e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The discovery of dirigent proteins (DPs) and their functions in plant phenol biochemistry was made over two decades ago with Forsythia × intermedia. Stereo-selective, DP-guided, monolignol-derived radical coupling in vitro was then reported to afford the optically active lignan, (+)-pinoresinol from coniferyl alcohol, provided one-electron oxidase/oxidant capacity was present. It later became evident that DPs have several distinct sub-families, presumably with different functions. Some known DPs require other essential enzymes/proteins (e.g. oxidases) for their functions. However, the lack of a fully sequenced genome for Forsythia × intermedia made it difficult to profile other components co-purified with the (+)-pinoresinol forming DP. Herein, we used an integrated bottom-up, top-down, and native mass spectrometry (MS) approach to de novo sequence the extracted proteins via adaptation of our initial report of DP solubilization and purification. Using publicly available transcriptome and genomic data from closely related species, we identified 14 proteins that were putatively associated with either DP function or the cell wall. Although their co-occurrence after extraction and chromatographic separation is suggestive for potential protein-protein interactions, none were found to form stable protein complexes with DPs in native MS under the specific experimental conditions we have explored. Interestingly, two new DP homologs were found and they formed hetero-trimers. Molecular dynamics simulations suggested that similar hetero-trimers were possible between Arabidopsis DP homologs with comparable sequence similarities. Nevertheless, our integrated mass spectrometry method development helped prepare for future investigations directed to the discovery of novel proteins and protein-protein interactions. These advantages can be highly beneficial for plant and microbial research where fully sequenced genomes may not be readily available.
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Affiliation(s)
- Mowei Zhou
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA.
| | - Joseph A Laureanti
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Callum J Bell
- National Center for Genome Resources, Santa Fe, NM, USA
| | - Mi Kwon
- Institute of Biological Chemistry, Washington State University, Pullman, WA, USA
| | - Qingyan Meng
- Institute of Biological Chemistry, Washington State University, Pullman, WA, USA
| | - Irina V Novikova
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA.
| | - Dennis G Thomas
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Carrie D Nicora
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Ryan L Sontag
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Diana L Bedgar
- Institute of Biological Chemistry, Washington State University, Pullman, WA, USA
| | - Isabelle O'Bryon
- Chemical and Biological Signatures Group, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Eric D Merkley
- Chemical and Biological Signatures Group, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Bojana Ginovska
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - John R Cort
- Institute of Biological Chemistry, Washington State University, Pullman, WA, USA.,Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Laurence B Davin
- Institute of Biological Chemistry, Washington State University, Pullman, WA, USA
| | - Norman G Lewis
- Institute of Biological Chemistry, Washington State University, Pullman, WA, USA
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6
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Hixson KK, Marques JV, Wendler JP, McDermott JE, Weitz KK, Clauss TR, Monroe ME, Moore RJ, Brown J, Lipton MS, Bell CJ, Paša-Tolić L, Davin LB, Lewis NG. New Insights Into Lignification via Network and Multi-Omics Analyses of Arogenate Dehydratase Knock-Out Mutants in Arabidopsis thaliana. Front Plant Sci 2021; 12:664250. [PMID: 34113365 PMCID: PMC8185232 DOI: 10.3389/fpls.2021.664250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 03/15/2021] [Indexed: 06/12/2023]
Abstract
Multiple Arabidopsis arogenate dehydratase (ADT) knock-out (KO) mutants, with phenotypes having variable lignin levels (up to circa 70% reduction), were studied to investigate how differential reductions in ADTs perturb its overall plant systems biology. Integrated "omics" analyses (metabolome, transcriptome, and proteome) of wild type (WT), single and multiple ADT KO lines were conducted. Transcriptome and proteome data were collapsed into gene ortholog (GO) data, with this allowing for enzymatic reaction and metabolome cross-comparisons to uncover dominant or likely metabolic biosynthesis reactions affected. Network analysis of enzymes-highly correlated to stem lignin levels-deduced the involvement of novel putative lignin related proteins or processes. These included those associated with ribosomes, the spliceosome, mRNA transport, aminoacyl tRNA biosynthesis, and phosphorylation. While prior work helped explain lignin biosynthesis regulation at the transcriptional level, our data here provide support for a new hypothesis that there are additional post-transcriptional and translational level processes that need to be considered. These findings are anticipated to lead to development of more accurate depictions of lignin/phenylpropanoid biosynthesis models in situ, with new protein targets identified for further biochemical analysis and/or plant bioengineering. Additionally, using KEGG defined functional categorization of proteomics and transcriptomics analyses, we detected significant changes to glucosinolate, α-linolenic acid, nitrogen, carotenoid, aromatic amino acid, phenylpropanoid, and photosynthesis-related metabolic pathways in ADT KO mutants. Metabolomics results also revealed that putative carotenoid and galactolipid levels were generally increased in amount, whereas many glucosinolates and phenylpropanoids (including flavonoids and lignans) were decreased in the KO mutants.
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Affiliation(s)
- Kim K. Hixson
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Joaquim V. Marques
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
| | - Jason P. Wendler
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Jason E. McDermott
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Karl K. Weitz
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Therese R. Clauss
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Matthew E. Monroe
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Ronald J. Moore
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Joseph Brown
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Mary S. Lipton
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Callum J. Bell
- National Center for Genome Resources, Santa Fe, NM, United States
| | - Ljiljana Paša-Tolić
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Laurence B. Davin
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
| | - Norman G. Lewis
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
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7
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Cardenas CL, Costa MA, Laskar DD, Moinuddin SGA, Lee C, Davin LB, Lewis NG. RNA i Modulation of Chlorogenic Acid and Lignin Deposition in Nicotiana tabacum and Insufficient Compensatory Metabolic Cross-Talk. J Nat Prod 2021; 84:694-706. [PMID: 33687206 DOI: 10.1021/acs.jnatprod.1c00054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Chlorogenic acid (CGA) and guaiacyl/syringyl (G/S) lignin formation involves hydroxycinnamoyl ester intermediacy, the latter formed via hydroxycinnamoyl CoA:shikimate hydroxycinnamoyl transferase (HCT) and hydroxycinnamoyl CoA:quinate hydroxycinnamoyl transferase (HQT) activities. HQT and HCT RNAi silencing of a commercial tobacco (Nicotiana tabacum) K326 line was examined herein. NtHQT gene silencing gave relatively normal plant phenotypes, with CGA levels reduced (down to 1% of wild type) with no effects on lignin. RNAi NtHCT silencing had markedly adverse phenotypes (e.g., stunted, multiple stems, delayed flowering, with senescence delayed by several months). Lignin contents were partially lowered, with a small increase in cleavable p-hydroxyphenyl (H) monomers; those plants had no detectable CGA level differences relative to wild type. In vitro NtHCT kinetic parameters revealed preferential p-coumaroyl CoA and shikimate esterification, as compared to other structurally related potential acyl group donors and acceptors. In the presence of coenzyme A, NtHCT catalyzed the reverse reaction. Site-directed mutagenesis of NtHCT (His153Ala) abolished enzymatic activity. NtHQT, by comparison, catalyzed preferential conversion of p-coumaroyl CoA and quinic acid to form p-coumaroyl quinate, the presumed CGA precursor. In sum, metabolic pathways to CGA and lignins appear to be fully independent, and previous conflicting reports of substrate versatilities and metabolic cross-talk are resolved.
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Affiliation(s)
- Claudia L Cardenas
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164-6340, United States
| | - Michael A Costa
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164-6340, United States
| | - Dhrubojyoti D Laskar
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164-6340, United States
| | - Syed G A Moinuddin
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164-6340, United States
| | - Choonseok Lee
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164-6340, United States
| | - Laurence B Davin
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164-6340, United States
| | - Norman G Lewis
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164-6340, United States
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8
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Overbey EG, Saravia-Butler AM, Zhang Z, Rathi KS, Fogle H, da Silveira WA, Barker RJ, Bass JJ, Beheshti A, Berrios DC, Blaber EA, Cekanaviciute E, Costa HA, Davin LB, Fisch KM, Gebre SG, Geniza M, Gilbert R, Gilroy S, Hardiman G, Herranz R, Kidane YH, Kruse CPS, Lee MD, Liefeld T, Lewis NG, McDonald JT, Meller R, Mishra T, Perera IY, Ray S, Reinsch SS, Rosenthal SB, Strong M, Szewczyk NJ, Tahimic CGT, Taylor DM, Vandenbrink JP, Villacampa A, Weging S, Wolverton C, Wyatt SE, Zea L, Costes SV, Galazka JM. NASA GeneLab RNA-seq consensus pipeline: standardized processing of short-read RNA-seq data. iScience 2021; 24:102361. [PMID: 33870146 PMCID: PMC8044432 DOI: 10.1016/j.isci.2021.102361] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 10/30/2020] [Accepted: 03/23/2021] [Indexed: 12/15/2022] Open
Abstract
With the development of transcriptomic technologies, we are able to quantify precise changes in gene expression profiles from astronauts and other organisms exposed to spaceflight. Members of NASA GeneLab and GeneLab-associated analysis working groups (AWGs) have developed a consensus pipeline for analyzing short-read RNA-sequencing data from spaceflight-associated experiments. The pipeline includes quality control, read trimming, mapping, and gene quantification steps, culminating in the detection of differentially expressed genes. This data analysis pipeline and the results of its execution using data submitted to GeneLab are now all publicly available through the GeneLab database. We present here the full details and rationale for the construction of this pipeline in order to promote transparency, reproducibility, and reusability of pipeline data; to provide a template for data processing of future spaceflight-relevant datasets; and to encourage cross-analysis of data from other databases with the data available in GeneLab. Analysis of omics data from different spaceflight studies presents unique challenges A standardized pipeline for RNA-seq analysis eliminates data processing variation The GeneLab RNA-seq pipeline includes QC, trimming, mapping, quantification, and DGE Space-relevant data processed with this pipeline are available at genelab.nasa.gov
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Affiliation(s)
- Eliah G Overbey
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Amanda M Saravia-Butler
- Logyx, LLC, Mountain View, CA 94043, USA.,Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Zhe Zhang
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Komal S Rathi
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Homer Fogle
- The Bionetics Corporation, NASA Ames Research Center, Moffett Field, CA 94035, USA.,Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Willian A da Silveira
- Institute for Global Food Security (IGFS) & School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | - Richard J Barker
- Department of Botany, University of Wisconsin, Madison, WI 53706, USA
| | - Joseph J Bass
- MRC Versus Arthritis Centre for Musculoskeletal Ageing Research, Royal Derby Hospital, University of Nottingham & National Institute for Health Research Nottingham Biomedical Research Centre, Derby DE22 3DT, UK
| | - Afshin Beheshti
- KBR, NASA Ames Research Center, Moffett Field, CA 94035, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Daniel C Berrios
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Elizabeth A Blaber
- Center for Biotechnology and Interdisciplinary Studies, Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Egle Cekanaviciute
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Helio A Costa
- Departments of Pathology, and of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Laurence B Davin
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164, USA
| | - Kathleen M Fisch
- Center for Computational Biology & Bioinformatics, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Samrawit G Gebre
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA.,KBR, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | | | - Rachel Gilbert
- NASA Postdoctoral Program, Universities Space Research Association, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Simon Gilroy
- Department of Botany, University of Wisconsin, Madison, WI 53706, USA
| | - Gary Hardiman
- Institute for Global Food Security (IGFS) & School of Biological Sciences, Queen's University Belfast, Belfast, UK.,Medical University of South Carolina, Charleston, SC, USA
| | - Raúl Herranz
- Centro de Investigaciones Biológicas Margarita Salas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Yared H Kidane
- Center for Pediatric Bone Biology and Translational Research, Texas Scottish Rite Hospital for Children, 2222 Welborn St., Dallas, TX 75219, USA
| | - Colin P S Kruse
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, NM 87545, USA
| | - Michael D Lee
- Exobiology Branch, NASA Ames Research Center, Mountain View, CA 94035, USA.,Blue Marble Space Institute of Science, Seattle, WA 98154, USA
| | - Ted Liefeld
- Department of Medicine, University of California San Diego, San Diego, CA 92093, USA
| | - Norman G Lewis
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164, USA
| | - J Tyson McDonald
- Department of Radiation Medicine, Georgetown University Medical Center, Washington, DC 20007, USA
| | - Robert Meller
- Department of Neurobiology and Pharmacology, Morehouse School of Medicine, Atlanta, GA 30310, USA
| | - Tejaswini Mishra
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Imara Y Perera
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Shayoni Ray
- NGM Biopharmaceuticals, South San Francisco, CA 94080, USA
| | - Sigrid S Reinsch
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Sara Brin Rosenthal
- Center for Computational Biology & Bioinformatics, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Michael Strong
- National Jewish Health, Center for Genes, Environment, and Health, 1400 Jackson Street, Denver, CO 80206, USA
| | - Nathaniel J Szewczyk
- Ohio Musculoskeletal and Neurological Institute and Department of Biomedical Sciences, Ohio University, Athens, OH 43147, USA
| | - Candice G T Tahimic
- Department of Biology, University of North Florida, Jacksonville, FL 32224, USA
| | - Deanne M Taylor
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia and the Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Alicia Villacampa
- Centro de Investigaciones Biológicas Margarita Salas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Silvio Weging
- Institute of Computer Science, Martin-Luther University Halle-Wittenberg, Von-Seckendorff-Platz 1, Halle 06120, Germany
| | - Chris Wolverton
- Department of Botany and Microbiology, Ohio Wesleyan University, Delaware, OH, USA
| | - Sarah E Wyatt
- Department of Environmental and Plant Biology, Ohio University, Athens, OH 45701, USA.,Interdisciplinary Program in Molecular and Cellular Biology, Ohio University, Athens, OH 45701, USA
| | - Luis Zea
- BioServe Space Technologies, Aerospace Engineering Sciences Department, University of Colorado Boulder, Boulder 80303 USA
| | - Sylvain V Costes
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Jonathan M Galazka
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
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9
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Meng Q, Moinuddin SGA, Kim SJ, Bedgar DL, Costa MA, Thomas DG, Young RP, Smith CA, Cort JR, Davin LB, Lewis NG. Pterocarpan synthase (PTS) structures suggest a common quinone methide-stabilizing function in dirigent proteins and proteins with dirigent-like domains. J Biol Chem 2020; 295:11584-11601. [PMID: 32565424 PMCID: PMC7450108 DOI: 10.1074/jbc.ra120.012444] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 06/17/2020] [Indexed: 11/28/2022] Open
Abstract
The biochemical activities of dirigent proteins (DPs) give rise to distinct complex classes of plant phenolics. DPs apparently began to emerge during the aquatic-to-land transition, with phylogenetic analyses revealing the presence of numerous DP subfamilies in the plant kingdom. The vast majority (>95%) of DPs in these large multigene families still await discovery of their biochemical functions. Here, we elucidated the 3D structures of two pterocarpan-forming proteins with dirigent-like domains. Both proteins stereospecifically convert distinct diastereomeric chiral isoflavonoid precursors to the chiral pterocarpans, (-)- and (+)-medicarpin, respectively. Their 3D structures enabled comparisons with stereoselective lignan- and aromatic terpenoid-forming DP orthologs. Each protein provides entry into diverse plant natural products classes, and our experiments suggest a common biochemical mechanism in binding and stabilizing distinct plant phenol-derived mono- and bis-quinone methide intermediates during different C-C and C-O bond-forming processes. These observations provide key insights into both their appearance and functional diversification of DPs during land plant evolution/adaptation. The proposed biochemical mechanisms based on our findings provide important clues to how additional physiological roles for DPs and proteins harboring dirigent-like domains can now be rationally and systematically identified.
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Affiliation(s)
- Qingyan Meng
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, USA
| | - Syed G A Moinuddin
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, USA
| | - Sung-Jin Kim
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, USA
| | - Diana L Bedgar
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, USA
| | - Michael A Costa
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, USA
| | - Dennis G Thomas
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Robert P Young
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Clyde A Smith
- Stanford Synchrotron Radiation Lightsource, Stanford University, Menlo Park, California, USA
| | - John R Cort
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, USA
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Laurence B Davin
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, USA
| | - Norman G Lewis
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, USA
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10
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Hwang JK, Moinuddin SG, Davin LB, Lewis NG. Pinoresinol‐lariciresinol reductase: Substrate versatility, enantiospecificity, and kinetic properties. Chirality 2020; 32:770-789. [DOI: 10.1002/chir.23218] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 02/24/2020] [Indexed: 11/11/2022]
Affiliation(s)
- Julianne K. Hwang
- Institute of Biological ChemistryWashington State University Pullman Washington
| | - Syed G.A. Moinuddin
- Institute of Biological ChemistryWashington State University Pullman Washington
| | - Laurence B. Davin
- Institute of Biological ChemistryWashington State University Pullman Washington
| | - Norman G. Lewis
- Institute of Biological ChemistryWashington State University Pullman Washington
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11
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Hano CF, Dinkova-Kostova AT, Davin LB, Cort JR, Lewis NG. Editorial: Lignans: Insights Into Their Biosynthesis, Metabolic Engineering, Analytical Methods and Health Benefits. Front Plant Sci 2020; 11:630327. [PMID: 33510765 PMCID: PMC7835672 DOI: 10.3389/fpls.2020.630327] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 12/08/2020] [Indexed: 05/03/2023]
Affiliation(s)
- Christophe F. Hano
- Laboratoire de Biologie des Ligneux et des Grandes Cultures, INRAE USC1328, Université d'Orléans, Chartres, France
- COSM'ACTIFS, CNRS GDR3711, Chartres, France
- *Correspondence: Christophe F. Hano
| | - Albena T. Dinkova-Kostova
- Division of Cellular Medicine, Jacqui Wood Cancer Centre, Ninewells Hospital and Medical School, University of Dundee, Dundee, United Kingdom
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Albena T. Dinkova-Kostova
| | - Laurence B. Davin
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
- Laurence B. Davin
| | - John R. Cort
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
- John R. Cort
| | - Norman G. Lewis
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
- Norman G. Lewis
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12
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Garcellano RC, Moinuddin SGA, Young RP, Zhou M, Bowden ME, Renslow RS, Yesiltepe Y, Thomas DG, Colby SM, Chouinard CD, Nagy G, Attah IK, Ibrahim YM, Ma R, Franzblau SG, Lewis NG, Aguinaldo AM, Cort JR. Isolation of Tryptanthrin and Reassessment of Evidence for Its Isobaric Isostere Wrightiadione in Plants of the Wrightia Genus. J Nat Prod 2019; 82:440-448. [PMID: 30295480 DOI: 10.1021/acs.jnatprod.8b00567] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
A series of Wrightia hanleyi extracts was screened for activity against Mycobacterium tuberculosis H37Rv. One active fraction contained a compound that initially appeared to be either the isoflavonoid wrightiadione or the alkaloid tryptanthrin, both of which have been previously reported in other Wrightia species. Characterization by NMR and MS, as well as evaluation of the literature describing these compounds, led to the conclusion that wrightiadione (1) was misidentified in the first report of its isolation from W. tomentosa in 1992 and again in 2015 when reported in W. pubescens and W. religiosa. Instead, the molecule described in these reports and in the present work is almost certainly the isobaric (same nominal mass) and isosteric (same number of atoms, valency, and shape) tryptanthrin (2), a well-known quinazolinone alkaloid found in a variety of plants including Wrightia species. Tryptanthrin (2) is also accessible synthetically via several routes and has been thoroughly characterized. Wrightiadione (1) has been synthesized and characterized and may have useful biological activity; however, this compound can no longer be said to be known to exist in Nature. To our knowledge, this misidentification of wrightiadione (1) has heretofore been unrecognized.
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Affiliation(s)
- Rhea C Garcellano
- Graduate School , University of Santo Tomas , Manila 1015 , Philippines
- Palawan State University , Tiniguiban Heights, Puerto Princesa City 5300 , Palawan , Philippines
- Institute of Biological Chemistry , Washington State University , Pullman , Washington 99164-6340 , United States
| | - Syed G A Moinuddin
- Institute of Biological Chemistry , Washington State University , Pullman , Washington 99164-6340 , United States
| | - Robert P Young
- Earth and Biological Sciences Directorate , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Mowei Zhou
- Earth and Biological Sciences Directorate , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Mark E Bowden
- Earth and Biological Sciences Directorate , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Ryan S Renslow
- Earth and Biological Sciences Directorate , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Yasemin Yesiltepe
- Earth and Biological Sciences Directorate , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Dennis G Thomas
- Earth and Biological Sciences Directorate , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Sean M Colby
- Earth and Biological Sciences Directorate , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Christopher D Chouinard
- Earth and Biological Sciences Directorate , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Gabe Nagy
- Earth and Biological Sciences Directorate , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Isaac K Attah
- Earth and Biological Sciences Directorate , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Yehia M Ibrahim
- Earth and Biological Sciences Directorate , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Rui Ma
- Institute for Tuberculosis Research, College of Pharmacy , University of Illinois at Chicago , Chicago , Illinois 60612 , United States
| | - Scott G Franzblau
- Institute for Tuberculosis Research, College of Pharmacy , University of Illinois at Chicago , Chicago , Illinois 60612 , United States
| | - Norman G Lewis
- Institute of Biological Chemistry , Washington State University , Pullman , Washington 99164-6340 , United States
| | - Alicia M Aguinaldo
- Graduate School , University of Santo Tomas , Manila 1015 , Philippines
- Phytochemistry Laboratory, Research Center for the Natural and Applied Sciences , University of Santo Tomas , Manila 1015 , Philippines
| | - John R Cort
- Institute of Biological Chemistry , Washington State University , Pullman , Washington 99164-6340 , United States
- Earth and Biological Sciences Directorate , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
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13
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Höhner R, Marques JV, Ito T, Amakura Y, Budgeon AD, Weitz K, Hixson KK, Davin LB, Kirchhoff H, Lewis NG. Reduced Arogenate Dehydratase Expression: Ramifications for Photosynthesis and Metabolism. Plant Physiol 2018; 177:115-131. [PMID: 29523714 PMCID: PMC5933128 DOI: 10.1104/pp.17.01766] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 02/28/2018] [Indexed: 05/25/2023]
Abstract
Arogenate dehydratase (ADT) catalyzes the final step of phenylalanine (Phe) biosynthesis. Previous work showed that ADT-deficient Arabidopsis (Arabidopsis thaliana) mutants had significantly reduced lignin contents, with stronger reductions in lines that had deficiencies in more ADT isoforms. Here, by analyzing Arabidopsis ADT mutants using our phenomics facility and ultra-performance liquid chromatography-mass spectrometry-based metabolomics, we describe the effects of the modulation of ADT on photosynthetic parameters and secondary metabolism. Our data indicate that a reduced carbon flux into Phe biosynthesis in ADT mutants impairs the consumption of photosynthetically produced ATP, leading to an increased ATP/ADP ratio, the overaccumulation of transitory starch, and lower electron transport rates. The effect on electron transport rates is caused by an increase in proton motive force across the thylakoid membrane that down-regulates photosystem II activity by the high-energy quenching mechanism. Furthermore, quantitation of secondary metabolites in ADT mutants revealed reduced flavonoid, phenylpropanoid, lignan, and glucosinolate contents, including glucosinolates that are not derived from aromatic amino acids, and significantly increased contents of putative galactolipids and apocarotenoids. Additionally, we used real-time atmospheric monitoring mass spectrometry to compare respiration and carbon fixation rates between the wild type and adt3/4/5/6, our most extreme ADT knockout mutant, which revealed no significant difference in both night- and day-adapted plants. Overall, these data reveal the profound effects of altered ADT activity and Phe metabolism on secondary metabolites and photosynthesis with implications for plant improvement.
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Affiliation(s)
- Ricarda Höhner
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164
| | - Joaquim V Marques
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164
| | - Tetsuro Ito
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164
| | - Yoshiaki Amakura
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164
| | - Alan D Budgeon
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164
| | - Karl Weitz
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352
| | - Kim K Hixson
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352
| | - Laurence B Davin
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164
| | - Helmut Kirchhoff
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164
| | - Norman G Lewis
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164
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14
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Corbin C, Drouet S, Markulin L, Auguin D, Lainé É, Davin LB, Cort JR, Lewis NG, Hano C. A genome-wide analysis of the flax (Linum usitatissimum L.) dirigent protein family: from gene identification and evolution to differential regulation. Plant Mol Biol 2018; 97:73-101. [PMID: 29713868 DOI: 10.1007/s11103-018-0725-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Accepted: 04/02/2018] [Indexed: 05/21/2023]
Abstract
Identification of DIR encoding genes in flax genome. Analysis of phylogeny, gene/protein structures and evolution. Identification of new conserved motifs linked to biochemical functions. Investigation of spatio-temporal gene expression and response to stress. Dirigent proteins (DIRs) were discovered during 8-8' lignan biosynthesis studies, through identification of stereoselective coupling to afford either (+)- or (-)-pinoresinols from E-coniferyl alcohol. DIRs are also involved or potentially involved in terpenoid, allyl/propenyl phenol lignan, pterocarpan and lignin biosynthesis. DIRs have very large multigene families in different vascular plants including flax, with most still of unknown function. DIR studies typically focus on a small subset of genes and identification of biochemical/physiological functions. Herein, a genome-wide analysis and characterization of the predicted flax DIR 44-membered multigene family was performed, this species being a rich natural grain source of 8-8' linked secoisolariciresinol-derived lignan oligomers. All predicted DIR sequences, including their promoters, were analyzed together with their public gene expression datasets. Expression patterns of selected DIRs were examined using qPCR, as well as through clustering analysis of DIR gene expression. These analyses further implicated roles for specific DIRs in (-)-pinoresinol formation in seed-coats, as well as (+)-pinoresinol in vegetative organs and/or specific responses to stress. Phylogeny and gene expression analysis segregated flax DIRs into six distinct clusters with new cluster-specific motifs identified. We propose that these findings can serve as a foundation to further systematically determine functions of DIRs, i.e. other than those already known in lignan biosynthesis in flax and other species. Given the differential expression profiles and inducibility of the flax DIR family, we provisionally propose that some DIR genes of unknown function could be involved in different aspects of secondary cell wall biosynthesis and plant defense.
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Affiliation(s)
- Cyrielle Corbin
- Laboratoire de Biologie des Ligneux et des Grandes Cultures, INRA USC1328, Université d'Orléans, 28000, Chartres, France
- COSM'ACTIFS, CNRS GDR3711, 28000, Chartres, France
| | - Samantha Drouet
- Laboratoire de Biologie des Ligneux et des Grandes Cultures, INRA USC1328, Université d'Orléans, 28000, Chartres, France
- COSM'ACTIFS, CNRS GDR3711, 28000, Chartres, France
| | - Lucija Markulin
- Laboratoire de Biologie des Ligneux et des Grandes Cultures, INRA USC1328, Université d'Orléans, 28000, Chartres, France
- COSM'ACTIFS, CNRS GDR3711, 28000, Chartres, France
| | - Daniel Auguin
- Laboratoire de Biologie des Ligneux et des Grandes Cultures, INRA USC1328, Université d'Orléans, 28000, Chartres, France
- COSM'ACTIFS, CNRS GDR3711, 28000, Chartres, France
| | - Éric Lainé
- Laboratoire de Biologie des Ligneux et des Grandes Cultures, INRA USC1328, Université d'Orléans, 28000, Chartres, France
- COSM'ACTIFS, CNRS GDR3711, 28000, Chartres, France
| | - Laurence B Davin
- Institute of Biological Chemistry, Washington State University, Pullman, WA, 99164-6340, USA
| | - John R Cort
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Norman G Lewis
- Institute of Biological Chemistry, Washington State University, Pullman, WA, 99164-6340, USA.
| | - Christophe Hano
- Laboratoire de Biologie des Ligneux et des Grandes Cultures, INRA USC1328, Université d'Orléans, 28000, Chartres, France.
- COSM'ACTIFS, CNRS GDR3711, 28000, Chartres, France.
- Pôle Universitaire d'Eure et Loir, 21 Rue de Loigny la Bataille, 28000, Chartres, France.
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15
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Lu D, Yuan X, Kim S, Marques JV, Chakravarthy PP, Moinuddin SGA, Luchterhand R, Herman B, Davin LB, Lewis NG. Eugenol specialty chemical production in transgenic poplar (Populus tremula × P. alba) field trials. Plant Biotechnol J 2017; 15:970-981. [PMID: 28064439 PMCID: PMC5506655 DOI: 10.1111/pbi.12692] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 12/20/2016] [Accepted: 01/05/2017] [Indexed: 05/09/2023]
Abstract
A foundational study assessed effects of biochemical pathway introduction into poplar to produce eugenol, chavicol, p-anol, isoeugenol and their sequestered storage products, from potentially available substrates, coniferyl and p-coumaryl alcohols. At the onset, it was unknown whether significant carbon flux to monolignols vs. other phenylpropanoid (acetate) pathway metabolites would be kinetically favoured. Various transgenic poplar lines generated eugenol and chavicol glucosides in ca. 0.45% (~0.35 and ~0.1%, respectively) of dry weight foliage tissue in field trials, as well as their corresponding aglycones in trace amounts. There were only traces of any of these metabolites in branch tissues, even after ~4-year field trials. Levels of bioproduct accumulation in foliage plateaued, even at the lowest introduced gene expression levels, suggesting limited monolignol substrate availability. Nevertheless, this level still allows foliage collection for platform chemical production, with the remaining (stem) biomass available for wood, pulp/paper and bioenergy product purposes. Several transformed lines displayed unexpected precocious flowering after 4-year field trial growth. This necessitated terminating (felling) these particular plants, as USDA APHIS prohibits the possibility of their interacting (cross-pollination, etc.) with wild-type (native plant) lines. In future, additional biotechnological approaches can be employed (e.g. gene editing) to produce sterile plant lines, to avoid such complications. While increased gene expression did not increase target bioproduct accumulation, the exciting possibility now exists of significantly increasing their amounts (e.g. 10- to 40-fold plus) in foliage and stems via systematic deployment of numerous 'omics', systems biology, synthetic biology and metabolic flux modelling approaches.
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Affiliation(s)
- Da Lu
- Institute of Biological ChemistryWashington State UniversityPullmanWAUSA
| | - Xianghe Yuan
- Institute of Biological ChemistryWashington State UniversityPullmanWAUSA
| | - Sung‐Jin Kim
- Institute of Biological ChemistryWashington State UniversityPullmanWAUSA
| | - Joaquim V. Marques
- Institute of Biological ChemistryWashington State UniversityPullmanWAUSA
| | | | | | - Randi Luchterhand
- Puyallup Research and Extension CenterWashington State UniversityPuyallupWAUSA
| | - Barri Herman
- Institute of Biological ChemistryWashington State UniversityPullmanWAUSA
- Puyallup Research and Extension CenterWashington State UniversityPuyallupWAUSA
| | - Laurence B. Davin
- Institute of Biological ChemistryWashington State UniversityPullmanWAUSA
| | - Norman G. Lewis
- Institute of Biological ChemistryWashington State UniversityPullmanWAUSA
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16
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Komvongsa J, Luang S, Marques JV, Phasai K, Davin LB, Lewis NG, Ketudat Cairns JR. Active site cleft mutants of Os9BGlu31 transglucosidase modify acceptor substrate specificity and allow production of multiple kaempferol glycosides. Biochim Biophys Acta Gen Subj 2015; 1850:1405-14. [DOI: 10.1016/j.bbagen.2015.03.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2014] [Revised: 03/23/2015] [Accepted: 03/25/2015] [Indexed: 12/01/2022]
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17
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Dalisay DS, Kim KW, Lee C, Yang H, Rübel O, Bowen BP, Davin LB, Lewis NG. Dirigent Protein-Mediated Lignan and Cyanogenic Glucoside Formation in Flax Seed: Integrated Omics and MALDI Mass Spectrometry Imaging. J Nat Prod 2015; 78:1231-42. [PMID: 25981198 DOI: 10.1021/acs.jnatprod.5b00023] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
An integrated omics approach using genomics, transcriptomics, metabolomics (MALDI mass spectrometry imaging, MSI), and bioinformatics was employed to study spatiotemporal formation and deposition of health-protecting polymeric lignans and plant defense cyanogenic glucosides. Intact flax (Linum usitatissimum) capsules and seed tissues at different development stages were analyzed. Transcriptome analyses indicated distinct expression patterns of dirigent protein (DP) gene family members encoding (-)- and (+)-pinoresinol-forming DPs and their associated downstream metabolic processes, respectively, with the former expressed at early seed coat development stages. Genes encoding (+)-pinoresinol-forming DPs were, in contrast, expressed at later development stages. Recombinant DP expression and DP assays also unequivocally established their distinct stereoselective biochemical functions. Using MALDI MSI and ion mobility separation analyses, the pinoresinol downstream derivatives, secoisolariciresinol diglucoside (SDG) and SDG hydroxymethylglutaryl ester, were localized and detectable only in early seed coat development stages. SDG derivatives were then converted into higher molecular weight phenolics during seed coat maturation. By contrast, the plant defense cyanogenic glucosides, the monoglucosides linamarin/lotaustralin, were detected throughout the flax capsule, whereas diglucosides linustatin/neolinustatin only accumulated in endosperm and embryo tissues. A putative biosynthetic pathway to the cyanogens is proposed on the basis of transcriptome coexpression data. Localization of all metabolites was at ca. 20 μm resolution, with the web based tool OpenMSI enabling not only resolution enhancement but also an interactive system for real-time searching for any ion in the tissue under analysis.
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Affiliation(s)
- Doralyn S Dalisay
- †Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164-6340, United States
| | - Kye Won Kim
- †Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164-6340, United States
| | - Choonseok Lee
- †Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164-6340, United States
| | - Hong Yang
- †Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164-6340, United States
| | - Oliver Rübel
- ‡Computational Research Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, California 94720, United States
| | - Benjamin P Bowen
- §Life Sciences Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, California 94720, United States
| | - Laurence B Davin
- †Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164-6340, United States
| | - Norman G Lewis
- †Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164-6340, United States
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Facchini P, Bohlmann J, Ibrahim R, Lewis NG. Professor Vincenzo de Luca. Phytochemistry 2015; 113:7-8. [PMID: 24950670 DOI: 10.1016/j.phytochem.2014.05.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
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Seneviratne HK, Dalisay DS, Kim KW, Moinuddin SGA, Yang H, Hartshorn CM, Davin LB, Lewis NG. Non-host disease resistance response in pea (Pisum sativum) pods: Biochemical function of DRR206 and phytoalexin pathway localization. Phytochemistry 2015; 113:140-8. [PMID: 25457488 DOI: 10.1016/j.phytochem.2014.10.013] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 10/11/2014] [Accepted: 10/15/2014] [Indexed: 05/20/2023]
Abstract
Continually exposed to potential pathogens, vascular plants have evolved intricate defense mechanisms to recognize encroaching threats and defend themselves. They do so by inducing a set of defense responses that can help defeat and/or limit effects of invading pathogens, of which the non-host disease resistance response is the most common. In this regard, pea (Pisum sativum) pod tissue, when exposed to Fusarium solani f. sp. phaseoli spores, undergoes an inducible transcriptional activation of pathogenesis-related genes, and also produces (+)-pisatin, its major phytoalexin. One of the inducible pathogenesis-related genes is Disease Resistance Response-206 (DRR206), whose role in vivo was unknown. DRR206 is, however, related to the dirigent protein (DP) family. In this study, its biochemical function was investigated in planta, with the metabolite associated with its gene induction being pinoresinol monoglucoside. Interestingly, both pinoresinol monoglucoside and (+)-pisatin were co-localized in pea pod endocarp epidermal cells, as demonstrated using matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging. In addition, endocarp epidermal cells are also the site for both chalcone synthase and DRR206 gene expression. Taken together, these data indicate that both (+)-pisatin and pinoresinol monoglucoside function in the overall phytoalexin responses.
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Affiliation(s)
| | - Doralyn S Dalisay
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, USA
| | - Kye-Won Kim
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, USA
| | - Syed G A Moinuddin
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, USA
| | - Hong Yang
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, USA
| | | | - Laurence B Davin
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, USA
| | - Norman G Lewis
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, USA.
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Lewis NG, Robins RJ. Appreciation--Professor Godfrey Paul Bolwell MA DSc: 13 December 1946-13 April 2012. Phytochemistry 2015; 112:8-12. [PMID: 25711947 DOI: 10.1016/j.phytochem.2015.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
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21
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Kim KW, Smith CA, Daily MD, Cort JR, Davin LB, Lewis NG. Trimeric structure of (+)-pinoresinol-forming dirigent protein at 1.95 Å resolution with three isolated active sites. J Biol Chem 2015; 290:1308-18. [PMID: 25411250 PMCID: PMC4340379 DOI: 10.1074/jbc.m114.611780] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 11/11/2014] [Indexed: 11/28/2022] Open
Abstract
Control over phenoxy radical-radical coupling reactions in vivo in vascular plants was enigmatic until our discovery of dirigent proteins (DPs, from the Latin dirigere, to guide or align). The first three-dimensional structure of a DP ((+)-pinoresinol-forming DP, 1.95 Å resolution, rhombohedral space group H32)) is reported herein. It has a tightly packed trimeric structure with an eight-stranded β-barrel topology for each DP monomer. Each putative substrate binding and orientation coupling site is located on the trimer surface but too far apart for intermolecular coupling between sites. It is proposed that each site enables stereoselective coupling (using either two coniferyl alcohol radicals or a radical and a monolignol). Interestingly, there are six differentially conserved residues in DPs affording either the (+)- or (-)-antipodes in the vicinity of the putative binding site and region known to control stereoselectivity. DPs are involved in lignan biosynthesis, whereas dirigent domains/sites have been implicated in lignin deposition.
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Affiliation(s)
- Kye-Won Kim
- From the Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164-6340
| | - Clyde A Smith
- the Stanford Synchrotron Radiation Lightsource, Menlo Park, California 94025, and
| | - Michael D Daily
- the Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354
| | - John R Cort
- the Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354
| | - Laurence B Davin
- From the Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164-6340
| | - Norman G Lewis
- From the Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164-6340,
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Marques JV, Dalisay DS, Yang H, Lee C, Davin LB, Lewis NG. A multi-omics strategy resolves the elusive nature of alkaloids in Podophyllum species. ACTA ACUST UNITED AC 2014; 10:2838-49. [DOI: 10.1039/c4mb00403e] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Advanced metabolomics/metabolite imaging in situ, transcriptome sequencing, and bioinformatics enabled discovery and localization of a previously undetectable biochemical pathway to aporphine alkaloids in Podophyllum hexandrum/peltatum. This discovery settles a century old enigma.
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Affiliation(s)
- Joaquim V. Marques
- Institute of Biological Chemistry
- Washington State University
- Pullman, USA
| | - Doralyn S. Dalisay
- Institute of Biological Chemistry
- Washington State University
- Pullman, USA
| | - Hong Yang
- Institute of Biological Chemistry
- Washington State University
- Pullman, USA
| | - Choonseok Lee
- Institute of Biological Chemistry
- Washington State University
- Pullman, USA
| | - Laurence B. Davin
- Institute of Biological Chemistry
- Washington State University
- Pullman, USA
| | - Norman G. Lewis
- Institute of Biological Chemistry
- Washington State University
- Pullman, USA
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Costa MA, Marques JV, Dalisay DS, Herman B, Bedgar DL, Davin LB, Lewis NG. Transgenic hybrid poplar for sustainable and scalable production of the commodity/specialty chemical, 2-phenylethanol. PLoS One 2013; 8:e83169. [PMID: 24386157 PMCID: PMC3873308 DOI: 10.1371/journal.pone.0083169] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2013] [Accepted: 10/30/2013] [Indexed: 11/18/2022] Open
Abstract
Fast growing hybrid poplar offers the means for sustainable production of specialty and commodity chemicals, in addition to rapid biomass production for lignocellulosic deconstruction. Herein we describe transformation of fast-growing transgenic hybrid poplar lines to produce 2-phenylethanol, this being an important fragrance, flavor, aroma, and commodity chemical. It is also readily converted into styrene or ethyl benzene, the latter being an important commodity aviation fuel component. Introducing this biochemical pathway into hybrid poplars marks the beginnings of developing a platform for a sustainable chemical delivery system to afford this and other valuable specialty/commodity chemicals at the scale and cost needed. These modified plant lines mainly sequester 2-phenylethanol via carbohydrate and other covalently linked derivatives, thereby providing an additional advantage of effective storage until needed. The future potential of this technology is discussed. MALDI metabolite tissue imaging also established localization of these metabolites in the leaf vasculature.
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Affiliation(s)
- Michael A. Costa
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, United States of America
| | - Joaquim V. Marques
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, United States of America
| | - Doralyn S. Dalisay
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, United States of America
| | - Barrington Herman
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, United States of America
| | - Diana L. Bedgar
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, United States of America
| | - Laurence B. Davin
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, United States of America
| | - Norman G. Lewis
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, United States of America
- Ealasid, Inc., Pullman, Washington, United States of America
- * E-mail:
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Lee C, Bedgar DL, Davin LB, Lewis NG. Assessment of a putative proton relay in Arabidopsis cinnamyl alcohol dehydrogenase catalysis. Org Biomol Chem 2013; 11:1127-34. [PMID: 23296200 DOI: 10.1039/c2ob27189c] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Extended proton relay systems have been proposed for various alcohol dehydrogenases, including the Arabidopsis thaliana cinnamyl alcohol dehydrogenases (AtCADs). Following a previous structural biology investigation of AtCAD5, the potential roles of three amino acid residues in a putative proton relay system, namely Thr49, His52 and Asp57, in AtCAD5, were investigated herein. Using site-directed mutagenesis, kinetic and isothermal titration calorimetry (ITC) analyses, it was established that the Thr49 residue was essential for overall catalytic conversion, whereas His52 and Asp57 residues were not. Mutation of the Thr49 residue to Ala resulted in near abolition of catalysis, with thermodynamic data indicating a negative enthalpic change (ΔH), as well as a significant decrease in binding affinity with NADPH, in contrast to wild type AtCAD5. Mutation of His52 and Asp57 residues by Ala did not significantly change either catalytic efficiency or thermodynamic parameters. Therefore, only the Thr49 residue is demonstrably essential for catalytic function. ITC analyses also suggested that for AtCAD5 catalysis, NADPH was bound first followed by p-coumaryl aldehyde.
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Affiliation(s)
- Choonseok Lee
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, USA
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Kim SJ, Vassão DG, Moinuddin SGA, Bedgar DL, Davin LB, Lewis NG. Allyl/propenyl phenol synthases from the creosote bush and engineering production of specialty/commodity chemicals, eugenol/isoeugenol, in Escherichia coli. Arch Biochem Biophys 2013; 541:37-46. [PMID: 24189289 DOI: 10.1016/j.abb.2013.10.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 10/24/2013] [Accepted: 10/25/2013] [Indexed: 10/26/2022]
Abstract
The creosote bush (Larrea tridentata) harbors members of the monolignol acyltransferase, allylphenol synthase, and propenylphenol synthase gene families, whose products together are able to catalyze distinct regiospecific conversions of various monolignols into their corresponding allyl- and propenyl-phenols, respectively. In this study, co-expression of a monolignol acyltransferase with either substrate versatile allylphenol or propenylphenol synthases in Escherichia coli established that various monolignol substrates were efficiently converted into their corresponding allyl/propenyl phenols, as well as providing proof of concept for efficacious conversion in a bacterial platform. This capability thus potentially provides an alternate source to these important plant phytochemicals, whether for flavor/fragrance and fine chemicals, or ultimately as commodities, e.g., for renewable energy or other intermediate chemical purposes. Previous reports had indicated that specific and highly conserved amino acid residues 84 (Phe or Val) and 87 (Ile or Tyr) of two highly homologous allyl/propenyl phenol synthases (circa 96% identity) from a Clarkia species mainly dictate their distinct regiospecific catalyzed conversions to afford either allyl- or propenyl-phenols, respectively. However, several other allyl/propenyl phenol synthase homologs isolated by us have established that the two corresponding amino acid 84 and 87 residues are not, in fact, conserved.
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Affiliation(s)
- Sung-Jin Kim
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, United States
| | - Daniel G Vassão
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, United States
| | - Syed G A Moinuddin
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, United States
| | - Diana L Bedgar
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, United States
| | - Laurence B Davin
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, United States
| | - Norman G Lewis
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, United States.
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26
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Lewis NG. Professor Meinhart H. Zenk: keeping the legacy alive. Phytochemistry 2013; 91:8. [PMID: 23648002 DOI: 10.1016/j.phytochem.2013.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
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27
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Cuthbertson DJ, Johnson SR, Piljac-Žegarac J, Kappel J, Schäfer S, Wüst M, Ketchum REB, Croteau RB, Marques JV, Davin LB, Lewis NG, Rolf M, Kutchan TM, Soejarto DD, Lange BM. Accurate mass-time tag library for LC/MS-based metabolite profiling of medicinal plants. Phytochemistry 2013; 91:187-97. [PMID: 23597491 PMCID: PMC3697863 DOI: 10.1016/j.phytochem.2013.02.018] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Revised: 02/21/2013] [Accepted: 02/25/2013] [Indexed: 05/20/2023]
Abstract
We report the development and testing of an accurate mass-time (AMT) tag approach for the LC/MS-based identification of plant natural products (PNPs) in complex extracts. An AMT tag library was developed for approximately 500 PNPs with diverse chemical structures, detected in electrospray and atmospheric pressure chemical ionization modes (both positive and negative polarities). In addition, to enable peak annotations with high confidence, MS/MS spectra were acquired with three different fragmentation energies. The LC/MS and MS/MS data sets were integrated into online spectral search tools and repositories (Spektraris and MassBank), thus allowing users to interrogate their own data sets for the potential presence of PNPs. The utility of the AMT tag library approach is demonstrated by the detection and annotation of active principles in 27 different medicinal plant species with diverse chemical constituents.
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Affiliation(s)
- Daniel J. Cuthbertson
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA 99164-6340, USA
| | - Sean R. Johnson
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA 99164-6340, USA
| | - Jasenka Piljac-Žegarac
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA 99164-6340, USA
- Ruđer Bošković Institute, Bijenićka cesta 54, HR-10000 Zagreb, Croatia
| | - Julia Kappel
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA 99164-6340, USA
- Institute of Nutrition and Food Sciences, University of Bonn, Endenicher Allee 11-13, 53115 Bonn, Germany
| | - Sarah Schäfer
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA 99164-6340, USA
- Institute of Nutrition and Food Sciences, University of Bonn, Endenicher Allee 11-13, 53115 Bonn, Germany
| | - Matthias Wüst
- Institute of Nutrition and Food Sciences, University of Bonn, Endenicher Allee 11-13, 53115 Bonn, Germany
| | - Raymond E. B. Ketchum
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA 99164-6340, USA
| | - Rodney B. Croteau
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA 99164-6340, USA
| | - Joaquim V. Marques
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA 99164-6340, USA
| | - Laurence B. Davin
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA 99164-6340, USA
| | - Norman G. Lewis
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA 99164-6340, USA
| | - Megan Rolf
- Donald Danforth Plant Science Center, 975 N. Warson Road, St. Louis, MO 63132, USA
| | - Toni M. Kutchan
- Donald Danforth Plant Science Center, 975 N. Warson Road, St. Louis, MO 63132, USA
| | - D. Doel Soejarto
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St. (M/C 781), Chicago, IL 60612, USA
- Botany Department, Field Museum, 1400 S. Lake Shore Drive, Chicago, IL 60605-2496, USA
| | - B. Markus Lange
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA 99164-6340, USA
- Corresponding author: Tel.: 509-335-3794; fax: 509-335-7643. (B.M. Lange)
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Marques JV, Kim KW, Lee C, Costa MA, May GD, Crow JA, Davin LB, Lewis NG. Next generation sequencing in predicting gene function in podophyllotoxin biosynthesis. J Biol Chem 2012; 288:466-79. [PMID: 23161544 DOI: 10.1074/jbc.m112.400689] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Podophyllum species are sources of (-)-podophyllotoxin, an aryltetralin lignan used for semi-synthesis of various powerful and extensively employed cancer-treating drugs. Its biosynthetic pathway, however, remains largely unknown, with the last unequivocally demonstrated intermediate being (-)-matairesinol. Herein, massively parallel sequencing of Podophyllum hexandrum and Podophyllum peltatum transcriptomes and subsequent bioinformatics analyses of the corresponding assemblies were carried out. Validation of the assembly process was first achieved through confirmation of assembled sequences with those of various genes previously established as involved in podophyllotoxin biosynthesis as well as other candidate biosynthetic pathway genes. This contribution describes characterization of two of the latter, namely the cytochrome P450s, CYP719A23 from P. hexandrum and CYP719A24 from P. peltatum. Both enzymes were capable of converting (-)-matairesinol into (-)-pluviatolide by catalyzing methylenedioxy bridge formation and did not act on other possible substrates tested. Interestingly, the enzymes described herein were highly similar to methylenedioxy bridge-forming enzymes from alkaloid biosynthesis, whereas candidates more similar to lignan biosynthetic enzymes were catalytically inactive with the substrates employed. This overall strategy has thus enabled facile further identification of enzymes putatively involved in (-)-podophyllotoxin biosynthesis and underscores the deductive power of next generation sequencing and bioinformatics to probe and deduce medicinal plant biosynthetic pathways.
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Affiliation(s)
- Joaquim V Marques
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164-6340, USA
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29
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Corea ORA, Bedgar DL, Davin LB, Lewis NG. The arogenate dehydratase gene family: towards understanding differential regulation of carbon flux through phenylalanine into primary versus secondary metabolic pathways. Phytochemistry 2012; 82:22-37. [PMID: 22818526 DOI: 10.1016/j.phytochem.2012.05.026] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Revised: 05/18/2012] [Accepted: 05/23/2012] [Indexed: 05/08/2023]
Abstract
Phe is formed from arogenate in planta through the action of arogenate dehydratase (ADT), and there are six ADT isoenzymes in the "model" vascular plant species Arabidopsis thaliana. This raised the possibility that specific ADTs may be differentially regulated so as to control Phe biosynthesis for protein synthesis vs its much more massive deployment for phenylpropanoid metabolism. In our previous reverse genetics study using 25 single/multiple ADT knockout (KO) lines, a subset of these knockouts was differentially reduced in their lignin contents. In the current investigation, it was hypothesized that Phe pool sizes might correlate well with reduction in lignin contents in the affected KO lines. The free amino acid contents of these KO lines were thus comprehensively analyzed in stem, leaf and root tissues, over a growth/developmental time course from 3 to 8 weeks until senescence. The data obtained were then compared to, and contrasted with, the differential extent of lignin deposition occurring in the various lines. Relative changes in pool sizes were also analyzed by performing a pairwise confirmatory factor analysis for Phe:Tyr, Phe:Trp and Tyr:Trp, following determination of the deviation from the mean for Phe, Tyr and Trp in each plant line. It was found that the Phe pool sizes measured were differentially reduced only in lignin-deficient lines, and in tissues and at time points where lignin biosynthesis was constitutively highly active (in wild type lines) under the growth conditions employed. In contrast, this trend was not evident across all ADT KO lines, possibly due to maintenance of Phe pools by non-targeted isoenzymes, or by feedback mechanisms known to be in place.
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Affiliation(s)
- Oliver R A Corea
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, USA
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Kim KW, Moinuddin SGA, Atwell KM, Costa MA, Davin LB, Lewis NG. Opposite stereoselectivities of dirigent proteins in Arabidopsis and schizandra species. J Biol Chem 2012; 287:33957-72. [PMID: 22854967 DOI: 10.1074/jbc.m112.387423] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
How stereoselective monolignol-derived phenoxy radical-radical coupling reactions are differentially biochemically orchestrated in planta, whereby for example they afford (+)- and (-)-pinoresinols, respectively, is both a fascinating mechanistic and evolutionary question. In earlier work, biochemical control of (+)-pinoresinol formation had been established to be engendered by a (+)-pinoresinol-forming dirigent protein in Forsythia intermedia, whereas the presence of a (-)-pinoresinol-forming dirigent protein was indirectly deduced based on the enantiospecificity of downstream pinoresinol reductases (AtPrRs) in Arabidopsis thaliana root tissue. In this study of 16 putative dirigent protein homologs in Arabidopsis, AtDIR6, AtDIR10, and AtDIR13 were established to be root-specific using a β-glucuronidase reporter gene strategy. Of these three, in vitro analyses established that only recombinant AtDIR6 was a (-)-pinoresinol-forming dirigent protein, whose physiological role was further confirmed using overexpression and RNAi strategies in vivo. Interestingly, its closest homolog, AtDIR5, was also established to be a (-)-pinoresinol-forming dirigent protein based on in vitro biochemical analyses. Both of these were compared in terms of properties with a (+)-pinoresinol-forming dirigent protein from Schizandra chinensis. In this context, sequence analyses, site-directed mutagenesis, and region swapping resulted in identification of putative substrate binding sites/regions and candidate residues controlling distinct stereoselectivities of coupling modes.
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Affiliation(s)
- Kye-Won Kim
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164-6340, USA
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Corea ORA, Ki C, Cardenas CL, Kim SJ, Brewer SE, Patten AM, Davin LB, Lewis NG. Arogenate dehydratase isoenzymes profoundly and differentially modulate carbon flux into lignins. J Biol Chem 2012; 287:11446-59. [PMID: 22311980 DOI: 10.1074/jbc.m111.322164] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
How carbon flux differentially occurs in vascular plants following photosynthesis for protein formation, phenylpropanoid metabolism (i.e. lignins), and other metabolic processes is not well understood. Our previous discovery/deduction that a six-membered arogenate dehydratase (ADT1-6) gene family encodes the final step in Phe biosynthesis in Arabidopsis thaliana raised the fascinating question whether individual ADT isoenzymes (or combinations thereof) differentially modulated carbon flux to lignins, proteins, etc. If so, unlike all other lignin pathway manipulations that target cell wall/cytosolic processes, this would be the first example of a plastid (chloroplast)-associated metabolic process influencing cell wall formation. Homozygous T-DNA insertion lines were thus obtained for five of the six ADTs and used to generate double, triple, and quadruple knockouts (KOs) in different combinations. The various mutants so obtained gave phenotypes with profound but distinct reductions in lignin amounts, encompassing a range spanning from near wild type levels to reductions of up to ∼68%. In the various KOs, there were also marked changes in guaiacyl:syringyl ratios ranging from ∼3:1 to 1:1, respectively; these changes were attributed to differential carbon flux into vascular bundles versus that into fiber cells. Laser microscope dissection/pyrolysis GC/MS, histochemical staining/lignin analyses, and pADT::GUS localization indicated that ADT5 preferentially affects carbon flux into the vascular bundles, whereas the adt3456 knock-out additionally greatly reduced carbon flux into fiber cells. This plastid-localized metabolic step can thus profoundly differentially affect carbon flux into lignins in distinct anatomical regions and provides incisive new insight into different factors affecting guaiacyl:syringyl ratios and lignin primary structure.
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Affiliation(s)
- Oliver R A Corea
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164-6340, USA
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Turlapati PV, Kim KW, Davin LB, Lewis NG. The laccase multigene family in Arabidopsis thaliana: towards addressing the mystery of their gene function(s). Planta 2011; 233:439-70. [PMID: 21063888 DOI: 10.1007/s00425-010-1298-3] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2010] [Accepted: 10/08/2010] [Indexed: 05/07/2023]
Abstract
While laccases, multi-copper glycoprotein oxidases, are often able to catalyze oxidation of a broad range of substrates, such as phenols and amines in vitro, their precise physiological/biochemical roles in higher plants remain largely unclear, e.g., Arabidopsis thaliana contains 17 laccases with only 1 having a known physiological function. To begin to explore their roles in planta, spatial and temporal expression patterns of Arabidopsis laccases were compared and contrasted in different tissues at various development stages using RT-PCR and promoter-GUS fusions. Various cell-specific expressions were noted where specific laccases were uniquely expressed, such as LAC4 in interfascicular fibers and seed coat columella, LAC7 in hydathodes and root hairs, LAC8 in pollen grains and phloem, and LAC15 in seed coat cell walls. Such specific cell-type expression patterns provide new leads and/or strategies into determining their precise physiological/biochemical roles. In addition, there was an apparent redundancy of gene expression patterns for several laccases across a wide variety of tissues, lignified and non-lignified, perhaps indicative of overlapping function(s). Preliminary evidence, based on bioinformatics analyses, suggests that most laccases may also be tightly regulated at both transcriptional (antisense transcripts, histone and DNA methylation) and posttranscriptional (microRNAs) levels of gene expression.
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Affiliation(s)
- Phanikanth V Turlapati
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, USA
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Voelker SL, Lachenbruch B, Meinzer FC, Jourdes M, Ki C, Patten AM, Davin LB, Lewis NG, Tuskan GA, Gunter L, Decker SR, Selig MJ, Sykes R, Himmel ME, Kitin P, Shevchenko O, Strauss SH. Antisense down-regulation of 4CL expression alters lignification, tree growth, and saccharification potential of field-grown poplar. Plant Physiol 2010; 154:874-86. [PMID: 20729393 PMCID: PMC2949011 DOI: 10.1104/pp.110.159269] [Citation(s) in RCA: 121] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2010] [Accepted: 08/18/2010] [Indexed: 05/18/2023]
Abstract
Transgenic down-regulation of the Pt4CL1 gene family encoding 4-coumarate:coenzyme A ligase (4CL) has been reported as a means for reducing lignin content in cell walls and increasing overall growth rates, thereby improving feedstock quality for paper and bioethanol production. Using hybrid poplar (Populus tremula × Populus alba), we applied this strategy and examined field-grown transformants for both effects on wood biochemistry and tree productivity. The reductions in lignin contents obtained correlated well with 4CL RNA expression, with a sharp decrease in lignin amount being observed for RNA expression below approximately 50% of the nontransgenic control. Relatively small lignin reductions of approximately 10% were associated with reduced productivity, decreased wood syringyl/guaiacyl lignin monomer ratios, and a small increase in the level of incorporation of H-monomers (p-hydroxyphenyl) into cell walls. Transgenic events with less than approximately 50% 4CL RNA expression were characterized by patches of reddish-brown discolored wood that had approximately twice the extractive content of controls (largely complex polyphenolics). There was no evidence that substantially reduced lignin contents increased growth rates or saccharification potential. Our results suggest that the capacity for lignin reduction is limited; below a threshold, large changes in wood chemistry and plant metabolism were observed that adversely affected productivity and potential ethanol yield. They also underline the importance of field studies to obtain physiologically meaningful results and to support technology development with transgenic trees.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Steven H. Strauss
- Department of Wood Science and Engineering (S.L.V., B.L.) and Department of Forest Ecosystems and Society (O.S., S.H.S.), Oregon State University, Corvallis, Oregon 97331; United States Department of Agriculture Forest Service, Pacific Northwest Research Station, Corvallis, Oregon 97331 (F.C.M.); Washington State University, Institute of Biological Chemistry, Pullman, Washington 99164–6340 (M.J., C.K., A.M.P., L.B.D., N.G.L.); BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831–6422 (G.A.T., L.G., S.R.D., M.J.S., R.S., M.E.H.); National Renewable Energy Laboratory, Golden, Colorado 80401 (S.R.D.,M.J.S., R.S., M.E.H.); Laboratory for Wood Biology and Xylarium, Royal Museum for Central Africa, B–3080 Tervuren, Belgium (P.K.)
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Moinuddin SGA, Jourdes M, Laskar DD, Ki C, Cardenas CL, Kim KW, Zhang D, Davin LB, Lewis NG. Insights into lignin primary structure and deconstruction from Arabidopsis thaliana COMT (caffeic acid O-methyl transferase) mutant Atomt1. Org Biomol Chem 2010; 8:3928-46. [PMID: 20652169 DOI: 10.1039/c004817h] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The Arabidopsis mutant Atomt1 lignin differs from native lignin in wild type plants, in terms of sinapyl (S) alcohol-derived substructures in fiber cell walls being substituted by 5-hydroxyconiferyl alcohol (5OHG)-derived moieties. During programmed lignin assembly, these engender formation of benzodioxane substructures due to intramolecular cyclization of their quinone methides that are transiently formed following 8-O-4' radical-radical coupling. Thioacidolytic cleavage of the 8-O-4' inter-unit linkages in the Atomt1 mutant, relative to the wild type, indicated that cleavable sinapyl (S) and coniferyl (G) alcohol-derived monomeric moieties were stoichiometrically reduced by a circa 2 : 1 ratio. Additionally, lignin degradative analysis resulted in release of a 5OHG-5OHG-G trimer from the Atomt1 mutant, which then underwent further cleavage. Significantly, the trimeric moiety released provides new insight into lignin primary structure: during polymer assembly, the first 5OHG moiety is linked via a C8-O-X inter-unit linkage, whereas subsequent addition of monomers apparently involves sequential addition of 5OHG and G moieties to the growing chain in a 2 : 1 overall stoichiometry. This quantification data thus provides further insight into how inter-unit linkage frequencies in native lignins are apparently conserved (or near conserved) during assembly in both instances, as well as providing additional impetus to resolve how the overall question of lignin macromolecular assembly is controlled in terms of both type of monomer addition and primary sequence.
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Affiliation(s)
- Syed G A Moinuddin
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, USA
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Abstract
The effect of horseradish peroxidase/H(2)O(2) in organic medium (dioxane/aqueous buffer, pH 5, 95:5) on the depolymerization of synthetic (dehydrogenatively polymerized) lignin was reinvestigated. In contrast to previous claims [Dordick, J. S., Marletta, M. A. & Klibanov, A. M. (1986) Proc. Natl. Acad. Sci. USA 83, 6255-6257], our results demonstrated that vigorous depolymerization of this substrate did not occur. Further, during this treatment ferulic acid was not a significant biodegradation product.
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Affiliation(s)
- N G Lewis
- Wood Chemistry and Biochemistry, Department of Forest Products, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061
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Patten AM, Jourdes M, Cardenas CL, Laskar DD, Nakazawa Y, Chung BY, Franceschi VR, Davin LB, Lewis NG. Probing native lignin macromolecular configuration in Arabidopsis thaliana in specific cell wall types: further insights into limited substrate degeneracy and assembly of the lignins of ref8, fah 1-2 and C4H::F5H lines. Mol Biosyst 2009; 6:499-515. [PMID: 20174679 DOI: 10.1039/b819206e] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The interest in renewable, plant-derived, bioenergy/biofuels has resulted in a renaissance of plant cell-wall/lignin research. Herein, effects of modulating lignin monomeric compositions in a single plant species, Arabidopsis, are described. The earliest stage of putative "AcBr/Klason lignin" deposition was apparently unaffected by modulating p-coumarate 3-hydroxylase or ferulate 5-hydroxylase activities. This finding helps account for the inability of many other studies to fully suppress the reported putative levels of lignin deposition through monolignol biosynthesis manipulation, and also underscores limitations in frequently used lignin analytical protocols. The overall putative lignin content was greatly reduced (circa 62%) in a plant line harboring an H-(p-hydroxyphenyl) enriched lignin phenotype. This slightly increased H-monomer deposition level apparently occurred in cell-wall domains normally harboring guaiacyl (G) and/or syringyl (S) lignin moieties. For G- and S-enriched lignin phenotypes, the overall lignification process appeared analogous to wild type, with only xylem fiber and interfascicular fiber cells forming the S-enriched lignins. Laser microscope dissection of vascular bundles and interfascicular fibers, followed by pyrolysis GC/MS, supported these findings. Some cell types, presumably metaxylem and possibly protoxylem, also afforded small amounts of benzodioxane (sub)structures due to limited substrate degeneracy (i.e. utilizing 5-hydroxyconiferyl alcohol rather than sinapyl alcohol). For all plant lines studied, the 8-O-4' inter-unit frequency of cleavable H, G and/or S monomers was essentially invariant of monomeric composition for a given (putative) lignin content. These data again underscore the need for determination of lignin primary structures and identification of all proteins/enzymes involved in control of lignin polymer assembly/macromolecular configuration.
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Affiliation(s)
- Ann M Patten
- The Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, USA
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Patten AM, Davin LB, Lewis NG. Relationship of dirigent protein and 18s RNA transcript localization to heartwood formation in western red cedar. Phytochemistry 2008; 69:3032-3037. [PMID: 18789459 DOI: 10.1016/j.phytochem.2008.06.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2008] [Accepted: 06/18/2008] [Indexed: 05/26/2023]
Abstract
Western red cedar (Thuja plicata) heartwood contains abundant amounts of structurally complex plicatic acid-derived lignans that help confer protective properties and longevity to this tissue type. Although the lignan biochemical entry point is dirigent protein-mediated, the formation of heartwood and its associated lignans in some species remains poorly understood due to technical difficulties of working with the former. To begin to address such questions, this study therefore focused on the anatomical localization of dirigent protein and 18s rRNA (control) gene transcripts within recalcitrant woody tissues, including heartwood. This in situ mRNA hybridization approach enabled detection of dirigent protein transcripts in cork cambia, vascular cambia and ray parenchyma cells of the sapwood, but not the heartwood under the conditions employed. By contrast, the hybridization of the 18s rRNA (control) transcript resulted in its detection in all tissue types, including radial parenchyma cells of apparently preformed heartwood. Application of in situ hybridization to such recalcitrant tissues thus demonstrates the utility of this technique in identifying specific cell types involved in heartwood formation, as well as the relationship of dirigent protein localization to that of heartwood metabolite generation.
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Affiliation(s)
- Ann M Patten
- The Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, USA
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Vassão DG, Davin LB, Lewis NG. Metabolic Engineering of Plant Allyl/Propenyl Phenol and Lignin Pathways: Future Potential for Biofuels/Bioenergy, Polymer Intermediates, and Specialty Chemicals? Bioengineering and Molecular Biology of Plant Pathways 2008. [DOI: 10.1016/s1755-0408(07)01013-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Davin LB, Jourdes M, Patten AM, Kim KW, Vassão DG, Lewis NG. Dissection of lignin macromolecular configuration and assembly: Comparison to related biochemical processes in allyl/propenyl phenol and lignan biosynthesis. Nat Prod Rep 2008; 25:1015-90. [DOI: 10.1039/b510386j] [Citation(s) in RCA: 154] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Vassão DG, Kim SJ, Milhollan JK, Eichinger D, Davin LB, Lewis NG. A pinoresinol–lariciresinol reductase homologue from the creosote bush (Larrea tridentata) catalyzes the efficient in vitro conversion of p-coumaryl/coniferyl alcohol esters into the allylphenols chavicol/eugenol, but not the propenylphenols p-anol/isoeugenol. Arch Biochem Biophys 2007; 465:209-18. [PMID: 17624297 DOI: 10.1016/j.abb.2007.06.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2007] [Revised: 05/24/2007] [Accepted: 06/03/2007] [Indexed: 10/23/2022]
Abstract
The creosote bush (Larrea tridentata) accumulates a complex mixture of 8-8' regiospecifically linked lignans, of which the potent antioxidant nordihydroguaiaretic acid (NDGA) is the most abundant. Its tetra-O-methyl derivative (M4N) is showing considerable promise in the treatment of refractory (hard-to-treat) brain and central nervous system tumors. NDGA and related 9,9'-deoxygenated lignans are thought to be formed by dimerization of allyl/propenyl phenols, phenylpropanoid compounds that lack C-9 oxygenation, thus differentiating them from the more common monolignol-derived lignans. In our ongoing studies dedicated towards elucidating the biochemical pathway to NDGA and its congeners, a pinoresinol-lariciresinol reductase homologue was isolated from L. tridentata, with the protein obtained in functional recombinant form. This protein efficiently catalyzes the conversion of p-coumaryl and coniferyl alcohol esters into the corresponding allylphenols, chavicol and eugenol; neither of their propenylphenol regioisomers, p-anol and isoeugenol, are formed during this enzyme reaction.
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Affiliation(s)
- Daniel G Vassão
- Institute of Biological Chemistry, Washington State University, 467 Clark Hall, Pullman, WA 99164-6340, USA
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Cho MH, Corea ORA, Yang H, Bedgar DL, Laskar DD, Anterola AM, Moog-Anterola FA, Hood RL, Kohalmi SE, Bernards MA, Kang C, Davin LB, Lewis NG. Phenylalanine biosynthesis in Arabidopsis thaliana. Identification and characterization of arogenate dehydratases. J Biol Chem 2007; 282:30827-35. [PMID: 17726025 DOI: 10.1074/jbc.m702662200] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
There is much uncertainty as to whether plants use arogenate, phenylpyruvate, or both as obligatory intermediates in Phe biosynthesis, an essential dietary amino acid for humans. This is because both prephenate and arogenate have been reported to undergo decarboxylative dehydration in plants via the action of either arogenate (ADT) or prephenate (PDT) dehydratases; however, neither enzyme(s) nor encoding gene(s) have been isolated and/or functionally characterized. An in silico data mining approach was thus undertaken to attempt to identify the dehydratase(s) involved in Phe formation in Arabidopsis, based on sequence similarity of PDT-like and ACT-like domains in bacteria. This data mining approach suggested that there are six PDT-like homologues in Arabidopsis, whose phylogenetic analyses separated them into three distinct subgroups. All six genes were cloned and subsequently established to be expressed in all tissues examined. Each was then expressed as a Nus fusion recombinant protein in Escherichia coli, with their substrate specificities measured in vitro. Three of the resulting recombinant proteins, encoded by ADT1 (At1g11790), ADT2 (At3g07630), and ADT6 (At1g08250), more efficiently utilized arogenate than prephenate, whereas the remaining three, ADT3 (At2g27820), ADT4 (At3g44720), and ADT5 (At5g22630) essentially only employed arogenate. ADT1, ADT2, and ADT6 had k(cat)/Km values of 1050, 7650, and 1560 M(-1) S(-1) for arogenate versus 38, 240, and 16 M(-1) S(-1) for prephenate, respectively. By contrast, the remaining three, ADT3, ADT4, and ADT5, had k(cat)/Km values of 1140, 490, and 620 M(-1) S(-1), with prephenate not serving as a substrate unless excess recombinant protein (>150 microg/assay) was used. All six genes, and their corresponding proteins, are thus provisionally classified as arogenate dehydratases and designated ADT1-ADT6.
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Affiliation(s)
- Man-Ho Cho
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164-6340, USA
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Jourdes M, Cardenas CL, Laskar DD, Moinuddin SGA, Davin LB, Lewis NG. Plant cell walls are enfeebled when attempting to preserve native lignin configuration with poly-p-hydroxycinnamaldehydes: evolutionary implications. Phytochemistry 2007; 68:1932-56. [PMID: 17559892 DOI: 10.1016/j.phytochem.2007.03.044] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2007] [Accepted: 03/19/2007] [Indexed: 05/15/2023]
Abstract
The lignin deficient double mutant of cinnamyl alcohol dehydrogenase (CAD, cad-4, cad-5 or cad-c, cad-d) in Arabidopsis thaliana [Sibout, R., Eudes, A., Mouille, G., Pollet, B., Lapierre, C., Jouanin, L., Séguin, A., 2005. Cinnamyl alcohol dehydrogenase-C and -D are the primary genes involved in lignin biosynthesis in the floral stem of Arabidopsis. Plant Cell 17, 2059-2076], was comprehensively examined for effects on disruption of native lignin macromolecular configuration; the two genes encode the catalytically most active CAD's for monolignol/lignin formation [Kim, S.-J., Kim, M.-R., Bedgar, D.L., Moinuddin, S.G.A., Cardenas, C.L., Davin, L.B., Kang, C., Lewis, N.G., 2004. Functional reclassification of the putative cinnamyl alcohol dehydrogenase multigene family in Arabidopsis. Proc. Natl. Acad. Sci., USA 101, 1455-1460]. The inflorescence stems of the double mutant presented a prostrate phenotype with dynamic modulus properties greatly reduced relative to that of the wild type (WT) line due to severe reductions in macromolecular lignin content. Interestingly, initially the overall pattern of phenolic deposition in the mutant was apparently very similar to WT, indicative of comparable assembly processes attempting to be duplicated. However, shortly into the stage involving (monomer cleavable) 8-O-4' linkage formation, deposition was aborted. At this final stage, the double mutant had retained a very limited ability to biosynthesize monolignols as evidenced by cleavage and release of ca. 4% of the monolignol-derived moieties relative to the lignin of the WT line. In addition, while small amounts of cleavable p-hydroxycinnamaldehyde-derived moieties were released, the overall frequency of (monomer cleavable) 8-O-4' inter-unit linkages closely approximated that of WT for the equivalent level of lignin deposition, in spite of the differences in monomer composition. Additionally, 8-5' linked inter-unit structures were clearly evident, albeit as fully aromatized phenylcoumaran-like substructures. The data are interpreted as a small amount of p-hydroxycinnamaldehydes being utilized in highly restricted attempts to preserve native lignin configuration, i.e. through very limited monomer degeneracy during template polymerization which would otherwise afford lignins proper in the cell wall from their precursor monolignols. The defects introduced (e.g. in the vascular integrity) provide important insight as to why p-hydroxycinnamaldehydes never evolved as lignin precursors in the 350,000 or so extant vascular plant species. It is yet unknown at present, however, as to what levels of lignin reduction can be attained in order to maintain the requisite properties for successful agronomic/forestry cultivation. Nor is it known to what extent, if any, such deleterious modulations potentially compromise plant defenses. Finally, prior to investigating lignin primary structure proper, it is essential to initially define the fundamental characteristics of the biopolymer(s) being formed, such as inter-unit frequency and lignin content, in order to design approaches to determine overall sequences of linkages.
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Affiliation(s)
- Michaël Jourdes
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, United States
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Lewis NG. G.H. Neil Towers (1923-2004) phytochemistry pioneer--in memoriam. Phytochemistry 2007; 68:1834-7. [PMID: 17763539 DOI: 10.1016/j.phytochem.2007.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
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Kim SJ, Kim KW, Cho MH, Franceschi VR, Davin LB, Lewis NG. Expression of cinnamyl alcohol dehydrogenases and their putative homologues during Arabidopsis thaliana growth and development: lessons for database annotations? Phytochemistry 2007; 68:1957-74. [PMID: 17467016 DOI: 10.1016/j.phytochem.2007.02.032] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2006] [Revised: 01/29/2007] [Accepted: 02/16/2007] [Indexed: 05/15/2023]
Abstract
A major goal currently in Arabidopsis research is determination of the (biochemical) function of each of its approximately 27,000 genes. To date, however, 12% of its genes actually have known biochemical roles. In this study, we considered it instructive to identify the gene expression patterns of nine (so-called AtCAD1-9) of 17 genes originally annotated by The Arabidopsis Information Resource (TAIR) as cinnamyl alcohol dehydrogenase (CAD, EC 1.1.1.195) homologues [see Costa, M.A., Collins, R.E., Anterola, A.M., Cochrane, F.C., Davin, L.B., Lewis N.G., 2003. An in silico assessment of gene function and organization of the phenylpropanoid pathway metabolic networks in Arabidopsis thaliana and limitations thereof. Phytochemistry 64, 1097-1112.]. In agreement with our biochemical studies in vitro [Kim, S.-J., Kim, M.-R., Bedgar, D.L., Moinuddin, S.G.A., Cardenas, C.L., Davin, L.B., Kang, C.-H., Lewis, N.G., 2004. Functional reclassification of the putative cinnamyl alcohol dehydrogenase multigene family in Arabidopsis. Proc. Natl. Acad. Sci. USA 101, 1455-1460.], and analysis of a double mutant [Sibout, R., Eudes, A., Mouille, G., Pollet, B., Lapierre, C., Jouanin, L., Séguin A., 2005. Cinnamyl Alcohol Dehydrogenase-C and -D are the primary genes involved in lignin biosynthesis in the floral stem of Arabidopsis. Plant Cell 17, 2059-2076.], both AtCAD5 (At4g34230) and AtCAD4 (At3g19450) were found to have expression patterns consistent with development/formation of different forms of the lignified vascular apparatus, e.g. lignifying stem tissues, bases of trichomes, hydathodes, abscission zones of siliques, etc. Expression was also observed in various non-lignifying zones (e.g. root caps) indicative of, perhaps, a role in plant defense. In addition, expression patterns of the four CAD-like homologues were investigated, i.e. AtCAD2 (At2g21730), AtCAD3 (At2g21890), AtCAD7 (At4g37980) and AtCAD8 (At4g37990), each of which previously had been demonstrated to have low CAD enzymatic activity in vitro (relative to AtCAD4/5) [Kim, S.-J., Kim, M.-R., Bedgar, D.L., Moinuddin, S.G.A., Cardenas, C.L., Davin, L.B., Kang, C.-H., Lewis, N.G., 2004. Functional reclassification of the putative cinnamyl alcohol dehydrogenase multigene family in Arabidopsis. Proc. Natl. Acad. Sci. USA 101, 1455-1460.]. Neither AtCAD2 nor AtCAD3, however, were expressed in lignifying tissues, with the latter being found mainly in the meristematic region and non-lignifying root tips, i.e. indicative of involvement in biochemical processes unrelated to lignin formation. By contrast, AtCAD7 and AtCAD8 [surprisingly now currently TAIR-annotated as probable mannitol dehydrogenases, but for which there is still no biochemical or other evidence for same] displayed gene expression patterns largely resembling those of AtCAD4/5, i.e. indicative perhaps of a quite minor role in monolignol/lignin formation. Lastly, AtCAD1 (At1g72680), AtCAD6 (At4g37970) and AtCAD9 (At4g39330), which lacked detectable CAD catalytic activities in vitro, were also expressed predominantly in vascular (lignin-forming) tissues. While their actual biochemical roles remain unknown, definition of their expression patterns, nevertheless, now begins to provide useful insights into potential biochemical/physiological functions, as well as the cell types in which they are expressed. These data thus indicate that the CAD metabolic network is composed primarily of AtCAD4/5 and may provisionally, to a lesser extent, involve AtCAD7/8 based on in vitro catalytic properties and (promoter regions selected to obtain) representative gene expression patterns. This analysis has, therefore, enabled us to systematically map out bona fide CAD gene involvement in both the assembly and differential emergence of the various component parts of the lignified vascular apparatus in Arabidopsis, as well as those having other (e.g. putative plant defense) functions. The data obtained also further underscore the ongoing difficulties and challenges as regards current limitations in gene annotations versus actual determination of gene function. This is exemplified by the annotation of AtCAD2, 3 and 6-9 as purported mannitol dehydrogenases, when, for example, no in vitro studies have been carried out to establish such a function biochemically. Such annotations should thus be discontinued in the absence of reliable biochemical and/or other physiological confirmation. In particular, AtCAD2, 3, 6 and 9 should be designated as dehydrogenases of unknown function. Just as importantly, the different patterns of gene expression noted during distinct phases of growth and development in specific cells/tissues gives insight into the study of the roles that these promoters have.
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Affiliation(s)
- Sung-Jin Kim
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, USA
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Patten AM, Jourdes M, Brown EE, Laborie MP, Davin LB, Lewis NG. Reaction tissue formation and stem tensile modulus properties in wild-type and p-coumarate-3-hydroxylase downregulated lines of alfalfa, Medicago sativa (Fabaceae). Am J Bot 2007; 94:912-25. [PMID: 21636460 DOI: 10.3732/ajb.94.6.912] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
To our knowledge, xylary reaction tissue has never been reported in a forage crop species. Here we report the discovery of reaction tissue in a transgenic line of Medicago sativa (pC3H, for the gene for p-coumarate-3-hydroxylase) with reduced lignin content and in the wild-type (WT) line. Based on microscopy and biomechanical testing of internodal alfalfa branch sections, the transgenic (pC3H-I) line, relative to the WT (1) apparently formed more reaction tissue containing gelatinous fibers with adjacent thick-walled fibers (presumed to be "intermediate" tissue) more rapidly, (2) had more xylem tissue, and (3) had comparable tensile dynamic modulus properties. These findings thus establish the (limited) ability of this perennial angiosperm to form (inducible) reaction tissue in a manner somewhat analogous to that of woody arborescent angiosperms. The potential of effectuating reductions in lignin amounts in (woody) angiosperms with increased formation of reaction (tension wood) tissue is discussed because reaction tissues are often viewed as a deleterious trait in processing for many agronomic/industrial applications, especially with the current interest in biofuels.
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Affiliation(s)
- Ann M Patten
- The Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164-6340 USA
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Davin LB, Lewis NG. Dirigent phenoxy radical coupling: advances and challenges. Curr Opin Biotechnol 2007; 16:398-406. [PMID: 16023845 DOI: 10.1016/j.copbio.2005.06.010] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2005] [Revised: 06/01/2005] [Accepted: 06/29/2005] [Indexed: 10/25/2022]
Abstract
The past seven years have witnessed significant progress in the biochemical characterization of dirigent (monolignol radical binding) proteins in vitro, as well as in the delineation of their associated metabolic networks in planta. Interestingly, both the stereoselective and regiospecific control over phenoxy radical-radical coupling appears to have evolved during the transition of plants to a land base for lignan, norlignan and ellagitannin biosynthesis.
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Affiliation(s)
- Laurence B Davin
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, 99164-6340, USA
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Laskar DD, Jourdes M, Patten AM, Helms GL, Davin LB, Lewis NG. The Arabidopsis cinnamoyl CoA reductase irx4 mutant has a delayed but coherent (normal) program of lignification. Plant J 2006; 48:674-86. [PMID: 17092316 DOI: 10.1111/j.1365-313x.2006.02918.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Previous studies have indicated that the Arabidopsis thalianairregular xylem 4 (irx4) mutant is severely lignin-deficient, forming abnormal lignin from aberrant monomers. Studies of lignin structure in dwarfed cinnamoyl CoA reductase (CCR)-downregulated tobacco were also previously reported to incorporate feruloyl tyramine derivatives. The lignin in the Arabidopsis irx4 mutant was re-investigated at 6 weeks and at maturation (9 weeks). Application of (1)H, (13)C, 2D Heteronuclear Multiple Quantum Coherence and 2D Heteronuclear Multiple Bond Coherence spectroscopic analyses to the lignin-enriched isolates from both Arabidopsis wild-type (Ler) and the CCR-irx4 mutant at both developmental stages revealed that only typical guaiacyl/syringyl lignins were formed. For the irx4 mutant, the syringyl content at 6 weeks growth was lower, in accordance with a delayed but coherent program of lignification. At maturation, however, the syringyl/guaiacyl ratio of the irx4 mutant approached that of wild-type. There was no evidence for feruloyl tyramines, or homologues thereof, accumulating as a chemical signature in lignins resulting from CCR mutation. Nor were there any noticeable increases in other phenolic components, such as hydroxycinnamic acids. These findings were further confirmed by application of thioacidolysis, alkaline nitrobenzene oxidation and acetyl bromide analyses. Moreover, in the case of CCR downregulation in tobacco, there were no NMR spectroscopic correlations that demonstrated feruloyl tyramines being incorporated into the lignin biopolymers. This study thus found no evidence that abnormal lignin formation occurs when CCR activity is modulated.
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Affiliation(s)
- Dhrubojyoti D Laskar
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, USA
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Youn B, Kim SJ, Moinuddin SGA, Lee C, Bedgar DL, Harper AR, Davin LB, Lewis NG, Kang C. Mechanistic and structural studies of apoform, binary, and ternary complexes of the Arabidopsis alkenal double bond reductase At5g16970. J Biol Chem 2006; 281:40076-88. [PMID: 17028190 DOI: 10.1074/jbc.m605900200] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In this study, we determined the crystal structures of the apoform, binary, and ternary complexes of the Arabidopsis alkenal double bond reductase encoded by At5g16970. This protein, one of 11 homologues in Arabidopsis thaliana, is most closely related to the Pinus taeda phenylpropenal double bond reductase, involved in, for example, heartwood formation. Both enzymes also have essential roles in plant defense, and can function by catalyzing the reduction of the 7-8-double bond of phenylpropanal substrates, such as p-coumaryl and coniferyl aldehydes in vitro. At5g16970 is also capable of reducing toxic substrates with the same alkenal functionality, such as 4-hydroxy-(2E)-nonenal. The overall fold of At5g16970 is similar to that of the zinc-independent medium chain dehydrogenase/reductase superfamily, the members of which have two domains and are dimeric in nature, i.e. in contrast to their original classification as being zinc-containing oxidoreductases. As provisionally anticipated from the kinetic data, the shape of the binding pocket can readily accommodate p-coumaryl aldehyde, coniferyl aldehyde, 4-hydroxy-(2E)-nonenal, and 2-alkenals. However, the enzyme kinetic data among these potential substrates differ, favoring p-coumaryl aldehyde. Tyr-260 is provisionally proposed to function as a general acid/base for hydride transfer. A catalytic mechanism for this reduction, and its applicability to related important detoxification mammalian proteins, is also proposed.
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Affiliation(s)
- Buhyun Youn
- School of Molecular Biosciences, Washington State University, Pullman, Washington 99164-4660, USA
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Lewis NG. Rodney B. Croteau. Phytochemistry 2006; 67:1560-1. [PMID: 16904714 DOI: 10.1016/j.phytochem.2006.07.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
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Kasahara H, Jiao Y, Bedgar DL, Kim SJ, Patten AM, Xia ZQ, Davin LB, Lewis NG. Pinus taeda phenylpropenal double-bond reductase: purification, cDNA cloning, heterologous expression in Escherichia coli, and subcellular localization in P. taeda. Phytochemistry 2006; 67:1765-80. [PMID: 16905164 DOI: 10.1016/j.phytochem.2006.07.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2006] [Revised: 07/03/2006] [Accepted: 07/04/2006] [Indexed: 05/11/2023]
Abstract
A phenylpropenal double-bond reductase (PPDBR) was obtained from cell suspension cultures of loblolly pine (Pinus taeda L.). Following trypsin digestion and amino acid sequencing, the cDNA encoding this protein was subsequently cloned, with the functional recombinant protein expressed in Escherichia coli and characterized. PPDBR readily converted both dehydrodiconiferyl and coniferyl aldehydes into dihydrodehydrodiconiferyl and dihydroconiferyl aldehydes, when NADPH was added as cofactor. However, it was unable to reduce directly either the double bond of dehydrodiconiferyl or coniferyl alcohols in the presence of NADPH. During this reductive step, the corresponding 4-proR hydrogen was abstracted from [4R-3H]-NADPH during hydride transfer. This is thus the first report of a double-bond reductase involved in phenylpropanoid metabolism, and which is presumed to be involved in plant defense. In situ mRNA hybridization indicated that the PPDBR transcripts in P. taeda stem sections were localized to the vascular cambium, as well as to radial and axial parenchyma cell types. Additionally, using P. taeda cell suspension culture crude protein extracts, dehydrodiconiferyl and coniferyl alcohols could be dehydrogenated to afford dehydrodiconiferyl and coniferyl aldehydes. Furthermore, these same extracts were able to convert dihydrodehydrodiconiferyl and dihydroconiferyl aldehydes into the corresponding alcohols. Taken together, these results indicate that in the crude extracts dehydrodiconiferyl and coniferyl alcohols can be converted to dihydrodehydrodiconiferyl and dihydroconiferyl alcohols through a three-step process, i.e. by initial phenylpropenol oxidation, then sequential PPDBR and phenylpropanal reductions, respectively.
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Affiliation(s)
- Hiroyuki Kasahara
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, USA
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