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Dokka N, Tyagi S, Ramkumar MK, Rathinam M, Senthil K, Sreevathsa R. Genome-wide identification and characterization of DIRIGENT gene family (CcDIR) in pigeonpea (Cajanus cajan L.) provide insights on their spatial expression pattern and relevance to stress response. Gene 2024; 914:148417. [PMID: 38555003 DOI: 10.1016/j.gene.2024.148417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 03/20/2024] [Accepted: 03/26/2024] [Indexed: 04/02/2024]
Abstract
This study is a thorough characterization of pigeonpea dirigent gene (CcDIR) family, an important component of the lignin biosynthesis pathway. Genome-wide analysis identified 25 CcDIR genes followed by a range of analytical approaches employed to unravel their structural and functional characteristics. Structural examination revealed a classic single exon and no intron arrangement in CcDIRs contributing to our understanding on evolutionary dynamics. Phylogenetic analysis elucidated evolutionary relationships among CcDIR genes with six DIR sub-families, while motif distribution analysis displayed and highlighted ten conserved protein motifs in CcDIRs. Promoter analyses of all the dirigent genes detected 18 stress responsive cis-acting elements offering insights into transcriptional regulation. While spatial expression analyses across six plant tissues showed preferential expression of CcDIR genes, exposure to salt (CcDIR2 and CcDIR9) and herbivory (CcDIR1, CcDIR2, CcDIR3 and CcDIR11), demonstrated potential roles of specific DIRs in plant defense. Interestingly, increased gene expression during herbivory, also correlated with increased lignin content authenticating the specific response. Furthermore, exogenous application of stress hormones, SA and MeJA on leaves significantly induced the expression of CcDIRs that responded to herbivory. Taken together, these findings contribute to a comprehensive understanding of CcDIR genes impacting development and stress response in the important legume pigeonpea.
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Affiliation(s)
- Narasimham Dokka
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India
| | - Shaily Tyagi
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India
| | - M K Ramkumar
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India
| | - Maniraj Rathinam
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India
| | - Kameshwaran Senthil
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India
| | - Rohini Sreevathsa
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India.
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Ushimaru R. Functions and mechanisms of enzymes assembling lignans and norlignans. Curr Opin Chem Biol 2024; 80:102462. [PMID: 38692182 DOI: 10.1016/j.cbpa.2024.102462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Revised: 04/08/2024] [Accepted: 04/08/2024] [Indexed: 05/03/2024]
Abstract
Lignans and norlignans are distributed throughout the plant kingdom and exhibit diverse chemical structures and biological properties that offer potential for therapeutic use. Originating from the phenylpropanoid biosynthesis pathway, their characteristic carbon architectures are formed through unique enzyme catalysis, featuring regio- and stereoselective C-C bond forming processes. Despite extensive research on these plant natural products, their biosynthetic pathways, and enzyme mechanisms remain enigmatic. This review highlights recent advancements in elucidating the functions and mechanisms of the biosynthetic enzymes responsible for constructing the distinct carbon frameworks of lignans and norlignans.
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Affiliation(s)
- Richiro Ushimaru
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo 113-8657, Japan.
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3
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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] [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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Lin JL, Fang X, Li JX, Chen ZW, Wu WK, Guo XX, Liu NJ, Huang JF, Chen FY, Wang LJ, Xu B, Martin C, Chen XY, Huang JQ. Dirigent gene editing of gossypol enantiomers for toxicity-depleted cotton seeds. NATURE PLANTS 2023; 9:605-615. [PMID: 36928775 DOI: 10.1038/s41477-023-01376-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 02/19/2023] [Indexed: 06/18/2023]
Abstract
Axial chirality of biaryls can generate varied bioactivities. Gossypol is a binaphthyl compound made by cotton plants. Of its two axially chiral isomers, (-)-gossypol is the bioactive form in mammals and has antispermatogenic activity, and its accumulation in cotton seeds poses health concerns. Here we identified two extracellular dirigent proteins (DIRs) from Gossypium hirsutum, GhDIR5 and GhDIR6, which impart the hemigossypol oxidative coupling into (-)- and (+)-gossypol, respectively. To reduce cotton seed toxicity, we disrupted GhDIR5 by genome editing, which eliminated (-)-gossypol but had no effects on other phytoalexins, including (+)-gossypol, that provide pest resistance. Reciprocal mutagenesis identified three residues responsible for enantioselectivity. The (-)-gossypol-forming DIRs emerged later than their enantiocomplementary counterparts, from tandem gene duplications that occurred shortly after the cotton genus diverged. Our study offers insight into how plants control enantiomeric ratios and how to selectively modify the chemical spectra of cotton plants and thereby improve crop quality.
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Affiliation(s)
- Jia-Ling Lin
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Xin Fang
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Jian-Xu Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | | | - Wen-Kai Wu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xiao-Xiang Guo
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Ning-Jing Liu
- School of Life Sciences, East China Normal University, Shanghai, China
| | - Jia-Fa Huang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Fang-Yan Chen
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Ling-Jian Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Baofu Xu
- Shandong Laboratory of Yantai Drug Discovery, Bohai Rim Advanced Research Institute for Drug Discovery, Yantai, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | | | - Xiao-Ya Chen
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, China.
| | - Jin-Quan Huang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
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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] [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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Perez Rojo F, Pillow JJ, Kaur P. Bioprospecting microbes and enzymes for the production of pterocarpans and coumestans. Front Bioeng Biotechnol 2023; 11:1154779. [PMID: 37187887 PMCID: PMC10175578 DOI: 10.3389/fbioe.2023.1154779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 04/18/2023] [Indexed: 05/17/2023] Open
Abstract
The isoflavonoid derivatives, pterocarpans and coumestans, are explored for multiple clinical applications as osteo-regenerative, neuroprotective and anti-cancer agents. The use of plant-based systems to produce isoflavonoid derivatives is limited due to cost, scalability, and sustainability constraints. Microbial cell factories overcome these limitations in which model organisms such as Saccharomyces cerevisiae offer an efficient platform to produce isoflavonoids. Bioprospecting microbes and enzymes can provide an array of tools to enhance the production of these molecules. Other microbes that naturally produce isoflavonoids present a novel alternative as production chassis and as a source of novel enzymes. Enzyme bioprospecting allows the complete identification of the pterocarpans and coumestans biosynthetic pathway, and the selection of the best enzymes based on activity and docking parameters. These enzymes consolidate an improved biosynthetic pathway for microbial-based production systems. In this review, we report the state-of-the-art for the production of key pterocarpans and coumestans, describing the enzymes already identified and the current gaps. We report available databases and tools for microbial bioprospecting to select the best production chassis. We propose the use of a holistic and multidisciplinary bioprospecting approach as the first step to identify the biosynthetic gaps, select the best microbial chassis, and increase productivity. We propose the use of microalgal species as microbial cell factories to produce pterocarpans and coumestans. The application of bioprospecting tools provides an exciting field to produce plant compounds such as isoflavonoid derivatives, efficiently and sustainably.
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Affiliation(s)
- Fernando Perez Rojo
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
- *Correspondence: Fernando Perez Rojo, ; Parwinder Kaur,
| | - J. Jane Pillow
- UWA School of Human Sciences, The University of Western Australia, Perth, WA, Australia
| | - Parwinder Kaur
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
- *Correspondence: Fernando Perez Rojo, ; Parwinder Kaur,
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Bo S, Chang SK, Chen Y, Sheng Z, Jiang Y, Yang B. The structure characteristics, biosynthesis and health benefits of naturally occurring rare flavonoids. Crit Rev Food Sci Nutr 2022; 64:2490-2512. [PMID: 36123801 DOI: 10.1080/10408398.2022.2124396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Rare flavonoids, a special subclass of naturally occurring flavonoids with diverse structures including pterocarpans, aurones, neoflavonoids, homoisoflavones, diphenylpropanes, rotenoids and 2-phenylethyl-chromones. They are mainly found in legumes with numerous health benefits. Rare flavonoids are regarded as minor flavonoids due to their very limited abundance in nature. This review gives an overview of the natural occurrences of rare flavonoids from previous literatures. Recent findings on the biosynthesis of rare flavonoids have been updated by describing their structural characteristics and classifications. Recent findings on the health benefits of rare flavonoids have also been compiled and discussed. Natural rare flavonoids with various characteristics from different subclasses from plant-based food sources are stated. They show a wide range of health benefits, including antibacterial, anticancer, anti-osteoporosis and antiviral activities. Studies reviewed suggest that rare flavonoids possessing different skeletons demonstrate different characteristic bioactivities by discussing their mechanism of actions and structure-activity relationships. Besides, recent advances on the biosynthesis of rare flavonoids, such as pterocarpans, rotenoids and aurones are well-known, while the biosynthesis of other subclasses remain unknown. The perspectives and further applications of rare flavonoids using metabolic engineering strategies also be expected.
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Affiliation(s)
- Shengtao Bo
- Guangdong Provincial Key Laboratory of Applied Botany, Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Sui Kiat Chang
- Department of Allied Health Sciences, Faculty of Science, Universiti Tunku Abdul, Rahman, Kampar, Malaysia
| | - Yipeng Chen
- Guangdong Provincial Key Laboratory of Applied Botany, Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhili Sheng
- Guangdong Provincial Key Laboratory of Applied Botany, Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yueming Jiang
- Guangdong Provincial Key Laboratory of Applied Botany, Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Bao Yang
- Guangdong Provincial Key Laboratory of Applied Botany, Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
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Huwa N, Weiergräber OH, Fejzagić AV, Kirsch C, Schaffrath U, Classen T. The Crystal Structure of the Defense Conferring Rice Protein OsJAC1 Reveals a Carbohydrate Binding Site on the Dirigent-like Domain. Biomolecules 2022; 12:biom12081126. [PMID: 36009020 PMCID: PMC9405769 DOI: 10.3390/biom12081126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 07/31/2022] [Accepted: 08/11/2022] [Indexed: 11/16/2022] Open
Abstract
Pesticides are routinely used to prevent severe losses in agriculture. This practice is under debate because of its potential negative environmental impact and selection of resistances in pathogens. Therefore, the development of disease resistant plants is mandatory. It was shown that the rice (Oryza sativa) protein OsJAC1 enhances resistance against different bacterial and fungal plant pathogens in rice, barley, and wheat. Recently we reported possible carbohydrate interaction partners for both domains of OsJAC1 (a jacalin-related lectin (JRL) and a dirigent (DIR) domain), however, a mechanistic understanding of its function is still lacking. Here, we report crystal structures for both individual domains and the complex of galactobiose with the DIR domain, which revealed a new carbohydrate binding motif for DIR proteins. Docking studies of the two domains led to a model of the full-length protein. Our findings offer insights into structure and binding properties of OsJAC1 and its possible function in pathogen resistance.
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Affiliation(s)
- Nikolai Huwa
- Institute for Bioorganic Chemistry, Heinrich Heine University Düsseldorf, 52425 Jülich, Germany
| | - Oliver H. Weiergräber
- Institute of Biological Information Processing 7: Structural Biochemistry and Jülich Centre for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Alexander V. Fejzagić
- Institute for Bioorganic Chemistry, Heinrich Heine University Düsseldorf, 52425 Jülich, Germany
| | - Christian Kirsch
- Institute for Biology III, Department of Plant Physiology, RWTH Aachen University, 52056 Aachen, Germany
| | - Ulrich Schaffrath
- Institute for Biology III, Department of Plant Physiology, RWTH Aachen University, 52056 Aachen, Germany
| | - Thomas Classen
- Institute for Bio- and Geosciences 1: Bioorganic Chemistry, Forschungszentrum Jülich, 52425 Jülich, Germany
- Correspondence:
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Bardin M, Rousselot-Pailley P, Tron T, Robert V. Investigation of dirigent like domains from bacterial genomes. BMC Bioinformatics 2022; 23:313. [PMID: 35918655 PMCID: PMC9344732 DOI: 10.1186/s12859-022-04832-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 07/04/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND DIRs are mysterious protein that have the ability to scavenge free radicals, which, are highly reactive with molecules in their vicinity. What is even more fascinating is that they carry out from these highly unstable species, a selective reaction (i.e., stereoenantioselective) from a well-defined substrate to give a very precise product. Unfortunately, to date, only three products have been demonstrated following studies on DIRs from the plant world, which until now was the kingdom where these proteins had been demonstrated. Within this kingdom, each DIR protein has its own type of substrate. The products identified to date, have on the other hand, a strong economic impact: in agriculture for example, the biosynthesis of (+)-gossypol could be highlighted (a repellent antifood produced by the cotton plant) by the DIRs of cotton. In forsythia plant species, it is the biosynthesis of (-)-pinoresinol, an intermediate leading to the synthesis of podophyllotoxine (a powerful anicancerous agent) which has been revealed. Recently, a clear path of study, potentially with strong impact, appeared by the hypothesis of the potential existence of protein DIR within the genomes of prokaryotes. The possibility of working with this type of organism is an undeniable advantage: since many sequenced genomes are available and the molecular tools are already developed. Even easier to implement and working on microbes, of less complex composition, offers many opportunities for laboratory studies. On the other hand, the diversity of their environment (e.g., soil, aquatic environments, extreme environmental conditions (pH, temperature, pressure) make them very diverse and varied subjects of study. Identifying new DIR proteins from bacteria means identifying new substrate or product molecules from these organisms. It is the promise of going further in understanding the mechanism of action of these proteins and this will most likely have a strong impact in the fields of agricultural, pharmaceutical and/or food chemistry. RESULTS Our goal is to obtain as much information as possible about these proteins to unlock the secrets of their exceptional functioning. Analyzes of structural and functional genomic data led to the identification of the Pfam PF03018 domain as characteristic of DIR proteins. This domain has been further identified in the sequence of bacterial proteins therefore named as DIR-like (DIRL). We have chosen a multidisciplinary bioinformatic approach centered on bacterial genome identification, gene expression and regulation signals, protein structures, and their molecular information content. The objective of this study was to perform a thorough bioinformatic analysis on these DIRLs to highlight any information leading to the selection of candidate bacteria for further cloning, purification, and characterization of bacterial DIRs. CONCLUSIONS From studies of DIRL genes identification, primary structures, predictions of their secondary and tertiary structures, prediction of DIRL signals sequences, analysis of their gene organization and potential regulation, a list of primary bacterial candidates is proposed.
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Affiliation(s)
- Merlin Bardin
- CNRS, Centrale Marseille, iSm2, Aix Marseille Univ, Marseille, France
| | | | - Thierry Tron
- CNRS, Centrale Marseille, iSm2, Aix Marseille Univ, Marseille, France
| | - Viviane Robert
- CNRS, Centrale Marseille, iSm2, Aix Marseille Univ, Marseille, France.
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Shen S, Tong Y, Luo Y, Huang L, Gao W. Biosynthesis, total synthesis, and pharmacological activities of aryltetralin-type lignan podophyllotoxin and its derivatives. Nat Prod Rep 2022; 39:1856-1875. [PMID: 35913409 DOI: 10.1039/d2np00028h] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Covering: up to 2022Podophyllotoxin (PTOX, 1), a kind of aryltetralin-type lignan, was first discovered in the plant Podophyllum peltatum and its structure was clarified by W. Borsche and J. Niemann in 1932. Due to its potent anti-cancer and anti-viral activities, it is considered one of the molecules most likely to be developed into modern drugs. With the increasing market demand and insufficient storage of natural resources, it is crucial to expand the sources of PTOXs. The original extraction method from plants has gradually failed to meet the requirements, and the biosynthesis and total synthesis have become the forward-looking alternatives. As key enzymes in the biosynthetic pathway of PTOXs and their catalytic mechanisms being constantly revealed, it is possible to realize the heterogeneous biosynthesis of PTOXs in the future. Chemical and chemoenzymatic synthesis also provide schemes for strictly controlling the asymmetric configuration of the tetracyclic core. Currently, the pharmacological activities of some PTOX derivatives have been extensively studied, laying the foundation for clinical candidate drugs. This review focuses primarily on the latest research progress in the biosynthesis, total synthesis, and pharmacological activities of PTOX and its derivatives, providing a more comprehensive understanding of these widely used compounds and supporting the future search for clinical applications.
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Affiliation(s)
- Siyu Shen
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, 100069, China. .,Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, China
| | - Yuru Tong
- School of Pharmaceutical Sciences, Capital Medical University, Beijing, 100069, China
| | - Yunfeng Luo
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, 100069, China.
| | - Luqi Huang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Wei Gao
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, 100069, China. .,Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, China
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11
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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] [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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12
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Xu W, Liu T, Zhang H, Zhu H. Mungbean DIRIGENT Gene Subfamilies and Their Expression Profiles Under Salt and Drought Stresses. Front Genet 2021; 12:658148. [PMID: 34630501 PMCID: PMC8493098 DOI: 10.3389/fgene.2021.658148] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 09/10/2021] [Indexed: 11/13/2022] Open
Abstract
DIRIGENT (DIR) genes are key players in environmental stress responses that have been identified in many vascular plant species. However, few studies have examined the VrDIR genes in mungbean. In this study, we characterized 37 VrDIR genes in mungbean using a genome-wide identification method. VrDIRs were distributed on seven of the 11 mungbean chromosomes, and chromosome three contained the most VrDIR genes, with seven members. Thirty-two of the 37 VrDIRs contained a typical DIR gene structure, with one exon; the conserved DIR domain (i.e., Pfam domain) occupied most of the protein in 33 of the 37 VrDIRs. The gene structures of VrDIR genes were analyzed, and a total of 19 distinct motifs were detected. VrDIR genes were classified into five groups based on their phylogenetic relationships, and 13 duplicated gene pairs were identified. In addition, a total of 92 cis-acting elements were detected in all 37 VrDIR promoter regions, and VrDIR genes contained different numbers and types of cis-acting elements. As a result, VrDIR genes showed distinct expression patterns in different tissues and in response to salt and drought stress.
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Affiliation(s)
- Wenying Xu
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Tong Liu
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Huiying Zhang
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Hong Zhu
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
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13
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Biochemical and Initial Structural Characterization of the Monocot Chimeric Jacalin OsJAC1. Int J Mol Sci 2021; 22:ijms22115639. [PMID: 34073266 PMCID: PMC8197871 DOI: 10.3390/ijms22115639] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/17/2021] [Accepted: 05/21/2021] [Indexed: 01/17/2023] Open
Abstract
The monocot chimeric jacalin OsJAC1 from Oryza sativa consists of a dirigent and a jacalin-related lectin domain. The corresponding gene is expressed in response to different abiotic and biotic stimuli. However, there is a lack of knowledge about the basic function of the individual domains and their contribution to the physiological role of the entire protein. In this study, we have established a heterologous expression in Escherichia coli with high yields for the full-length protein OsJAC1 as well as its individual domains. Our findings showed that the secondary structure of both domains is dominated by β-strand elements. Under reducing conditions, the native protein displayed clearly visible transition points of thermal unfolding at 59 and 85 °C, which could be attributed to the lectin and the dirigent domain, respectively. Our study identified a single carbohydrate-binding site for each domain with different specificities towards mannose and glucose (jacalin domain), and galactose moieties (dirigent domain), respectively. The recognition of different carbohydrates might explain the ability of OsJAC1 to respond to different abiotic and biotic factors. This is the first report of specific carbohydrate-binding activity of a DIR domain, shedding new light on its function in the context of this monocot chimeric jacalin.
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14
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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. JOURNAL OF NATURAL PRODUCTS 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] [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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15
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Yonekura-Sakakibara K, Yamamura M, Matsuda F, Ono E, Nakabayashi R, Sugawara S, Mori T, Tobimatsu Y, Umezawa T, Saito K. Seed-coat protective neolignans are produced by the dirigent protein AtDP1 and the laccase AtLAC5 in Arabidopsis. THE PLANT CELL 2021; 33:129-152. [PMID: 33751095 PMCID: PMC8136895 DOI: 10.1093/plcell/koaa014] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 10/20/2020] [Indexed: 05/03/2023]
Abstract
Lignans/neolignans are generally synthesized from coniferyl alcohol (CA) in the cinnamate/monolignol pathway by oxidation to generate the corresponding radicals with subsequent stereoselective dimerization aided by dirigent proteins (DIRs). Genes encoding oxidases and DIRs for neolignan biosynthesis have not been identified previously. In Arabidopsis thaliana, the DIR AtDP1/AtDIR12 plays an essential role in the 8-O-4' coupling in neolignan biosynthesis by unequivocal structural determination of the compound missing in the atdp1 mutant as a sinapoylcholine (SC)-conjugated neolignan, erythro-3-{4-[2-hydroxy-2-(4-hydroxy-3-methoxyphenyl)-1-hydroxymethylethoxy]-3,5-dimethoxyphenyl}acryloylcholine. Phylogenetic analyses showed that AtDP1/AtDIR12 belongs to the DIR-a subfamily composed of DIRs for 8-8' coupling of monolignol radicals. AtDP1/AtDIR12 is specifically expressed in outer integument 1 cells in developing seeds. As a putative oxidase for neolignan biosynthesis, we focused on AtLAC5, a laccase gene coexpressed with AtDP1/AtDIR12. In lac5 mutants, the abundance of feruloylcholine (FC)-conjugated neolignans decreased to a level comparable to those in the atdp1 mutant. In addition, SC/FC-conjugated neolignans were missing in the seeds of mutants defective in SCT/SCPL19, an enzyme that synthesizes SC. These results strongly suggest that AtDP1/AtDIR12 and AtLAC5 are involved in neolignan biosynthesis via SC/FC. A tetrazolium penetration assay showed that seed coat permeability increased in atdp1 mutants, suggesting a protective role of neolignans in A. thaliana seeds.
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Affiliation(s)
- Keiko Yonekura-Sakakibara
- RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Masaomi Yamamura
- Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Fumio Matsuda
- RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Eiichiro Ono
- Research Institute, Suntory Global Innovation Center Ltd., 8-1-1 Seikadai, Seika, Soraku-gun, Kyoto 619-0284, Japan
| | - Ryo Nakabayashi
- RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Satoko Sugawara
- RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Tetsuya Mori
- RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Yuki Tobimatsu
- Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Toshiaki Umezawa
- Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
- Research Unit for Development of Global Sustainability, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Kazuki Saito
- RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
- Plant Molecular Science Center, Chiba University, 1-8-1, Inohana, Chuo-ku, Chiba 260-8675, Japan
- Author for correspondence: ,
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16
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Modolo C, Ren L, Besson E, Robert V, Gastaldi S, Rousselot-Pailley P, Tron T. Coniferyl Alcohol Radical Detection by the Dirigent Protein AtDIR6 Monitored by EPR. Chembiochem 2020; 22:992-995. [PMID: 33112043 DOI: 10.1002/cbic.202000650] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/13/2020] [Indexed: 11/10/2022]
Abstract
Plant dirigent proteins (DIRs) control the stereoselectivity of the monolignol coniferyl alcohol radical coupling. The main mechanistic hypothesis on this chemo- and stereoselective reaction invokes a binding of coniferyl alcohol radical substrates in the dirigent protein active site so that only one enantiomeric form can be produced. We have studied the influence of the Arabidopsis thaliana AtDIR6 protein on the transient coniferyl alcohol radical by EPR. Herein, we show that AtDIR6 stabilizes coniferyl alcohol radicals prior to directing their coupling towards the formation of (-)-pinoresinol.
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Affiliation(s)
| | - Lu Ren
- Aix Marseille Univ, Centrale Marseille, CNRS, iSm2
| | - Eric Besson
- Aix Marseille Univ, CNRS, ICR, 13013, Marseille, France
| | | | | | | | - Thierry Tron
- Aix Marseille Univ, Centrale Marseille, CNRS, iSm2
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