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Feng J, Ye H, Lu C, Pan L, Chen H, Zhu L, Chen X. Application of protein engineering to ene-reductase for the synthesis of chiral compounds through asymmetric reaction. Crit Rev Biotechnol 2025; 45:665-682. [PMID: 39134447 DOI: 10.1080/07388551.2024.2382957] [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: 11/20/2023] [Revised: 07/01/2024] [Accepted: 07/09/2024] [Indexed: 04/17/2025]
Abstract
Ene-reductase (ER) has been widely applied for asymmetrical synthesis of chiral intermediates due to its substrate promiscuity, photoexcited reactivity, and excellent property with producing two chiral centers at a time. Natural ERs often exhibit the same stereoselectivity, and they need to be engineered for opposite configuration of chiral compounds. The hydrogenation process toward activated alkenes by ERs is composed of reductive half reaction and oxidative half reaction, which are dependent upon two cofactors NAD(P)H and flavin mononucleotide. The catalytic activity of ERs will be affected by the size of the substrate, the activating strength of the electron-withdrawing groups, redox potential of cofactors, and the loop flexibility around catalytic cavity. Currently, protein engineering to ERs has been successfully employed to enhance various catalytic properties, including photoexcited asymmetric synthesis. This review summarizes the approaches to reverse the stereoselectivity and enhance catalytic activity of ERs and new applications of the engineered ERs in photobiocatalytic asymmetric synthesis, besides the discussion with the existing molecular mechanisms of mutants regarding the improved catalytic performance.
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Affiliation(s)
- Jiacheng Feng
- Institute of Fermentation Engineering, Zhejiang University of Technology, Hangzhou, China
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Huiru Ye
- Institute of Fermentation Engineering, Zhejiang University of Technology, Hangzhou, China
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Changxin Lu
- Institute of Fermentation Engineering, Zhejiang University of Technology, Hangzhou, China
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Linyan Pan
- Institute of Fermentation Engineering, Zhejiang University of Technology, Hangzhou, China
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Hanchi Chen
- Institute of Fermentation Engineering, Zhejiang University of Technology, Hangzhou, China
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Linjiang Zhu
- Institute of Fermentation Engineering, Zhejiang University of Technology, Hangzhou, China
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Xiaolong Chen
- Institute of Fermentation Engineering, Zhejiang University of Technology, Hangzhou, China
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
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2
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Damada PH, Rozeboom HJ, Fraaije MW. Recombinant Production and Characterization of Six Ene-reductases from Penicillium steckii. Chembiochem 2025; 26:e202401007. [PMID: 40072226 PMCID: PMC12002099 DOI: 10.1002/cbic.202401007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2024] [Revised: 03/08/2025] [Accepted: 03/10/2025] [Indexed: 03/26/2025]
Abstract
Fungi, known for their adaptability, are valuable sources of enzymes, making them promising for biocatalyst discovery. This study explored Penicillium steckii, primarily recognized for secondary metabolite production, as a source of ene-reductases (ERs), which reduce α,β-unsaturated compounds. Eleven ER-encoding genes were identified, and plasmids for Escherichia coli expression were generated. Six ERs (PsOYE1-6) were successfully produced and purified as soluble FMN-containing proteins. Sequence analysis classified them into Class II (PsOYE1, PsOYE4, PsOYE6), Class III (PsOYE2, PsOYE3), and Class V (PsOYE5) OYEs. All were active on p-benzoquinone and maleimide, with varying activity on other substrates. Their pH optima ranged from 6 to 7, and they exhibited moderate thermostability (35-50 °C). PsOYE2 was crystallized, and its 2.3 Å structure revealed a stable dimer with a unique active site. PsOYE3, PsOYE4, and PsOYE5 were tested for R-carvone conversion and stereoselectivity, all favouring one diastereomer. These fungal ERs expand the enzymatic toolbox for biocatalysis, emphasizing the need for tailored strategies based on specific applications.
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Affiliation(s)
- Pedro H. Damada
- Molecular Enzymology GroupInstitute of Biomolecular Sciences & BiotechnologyUniversity of GroningenNijenborgh 39747 AGGroningen, theNetherlands
- Laboratório de Química Orgânica e BiocatáliseInstituto de Química de São CarlosUniversidade de São PauloAv. João Dagnone, 1100, “Ed. Prof. Wagner Douglas Franco”, Santa Angelina13563-120São CarlosSPBrazil
| | - Henriette J. Rozeboom
- Molecular Enzymology GroupInstitute of Biomolecular Sciences & BiotechnologyUniversity of GroningenNijenborgh 39747 AGGroningen, theNetherlands
| | - Marco W. Fraaije
- Molecular Enzymology GroupInstitute of Biomolecular Sciences & BiotechnologyUniversity of GroningenNijenborgh 39747 AGGroningen, theNetherlands
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3
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Smith CO, Moran GR. Elucidation of the Catalytic Sequence of Dihydroorotate Dehydrogenase B from Lactoccocus lactis: Evidence for Accumulation of a Flavin Bisemiquinone State in Catalysis. Biochemistry 2024; 63:1347-1358. [PMID: 38691339 DOI: 10.1021/acs.biochem.4c00025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2024]
Abstract
The physiological role of dihydroorotate dehydrogenase (DHOD) enzymes is to catalyze the oxidation of dihydroorotate to orotate in pyrimidine biosynthesis. DHOD enzymes are structurally diverse existing as both soluble and membrane-associated forms. The Family 1 enzymes are soluble and act either as conventional single subunit flavin-dependent dehydrogenases known as Class 1A (DHODA) or as unusual heterodimeric enzymes known as Class 1B (DHODB). DHODBs possess two active sites separated by ∼20 Å, each with a noncovalently bound flavin cofactor. NAD is thought to interact at the FAD containing site, and the pyrimidine substrate is known to bind at the FMN containing site. At the approximate center of the protein is a single Fe2S2 center that is assumed to act as a conduit, facilitating one-electron transfers between the flavins. We present anaerobic transient state analysis of a DHODB enzyme from Lactoccocus lactis. The data presented primarily report the exothermic reaction that reduces orotate to dihydroorotate. The reductive half reaction reveals rapid two-electron reduction that is followed by the accumulation of a four-electron reduced state when NADH is added in excess, suggesting that the initial two electrons acquired reside on the FMN cofactor. Concomitant with the first reduction is the accumulation of a long-wavelength absorption feature consistent with the blue form of a flavin semiquinone. Spectral deconvolution and fitting to a model that includes reversibility for the second electron transfer reveals equilibrium accumulation of a flavin bisemiquinone state that has features of both red and blue semiquinones. Single turnover reactions with limiting NADH and excess orotate reveal that the flavin bisemiquinone accumulates with reduction of the enzyme by NADH and decays with reduction of the pyrimidine substrate, establishing the bisemiquinone as a fractional state of the two-electron reduced intermediate observed.
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Affiliation(s)
- Corine O Smith
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 W Sheridan Rd Chicago Illinois 60660, United States
| | - Graham R Moran
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 W Sheridan Rd Chicago Illinois 60660, United States
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4
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Emmanuel MA, Bender SG, Bilodeau C, Carceller JM, DeHovitz JS, Fu H, Liu Y, Nicholls BT, Ouyang Y, Page CG, Qiao T, Raps FC, Sorigué DR, Sun SZ, Turek-Herman J, Ye Y, Rivas-Souchet A, Cao J, Hyster TK. Photobiocatalytic Strategies for Organic Synthesis. Chem Rev 2023; 123:5459-5520. [PMID: 37115521 PMCID: PMC10905417 DOI: 10.1021/acs.chemrev.2c00767] [Citation(s) in RCA: 82] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Biocatalysis has revolutionized chemical synthesis, providing sustainable methods for preparing various organic molecules. In enzyme-mediated organic synthesis, most reactions involve molecules operating from their ground states. Over the past 25 years, there has been an increased interest in enzymatic processes that utilize electronically excited states accessed through photoexcitation. These photobiocatalytic processes involve a diverse array of reaction mechanisms that are complementary to one another. This comprehensive review will describe the state-of-the-art strategies in photobiocatalysis for organic synthesis until December 2022. Apart from reviewing the relevant literature, a central goal of this review is to delineate the mechanistic differences between the general strategies employed in the field. We will organize this review based on the relationship between the photochemical step and the enzymatic transformations. The review will include mechanistic studies, substrate scopes, and protein optimization strategies. By clearly defining mechanistically-distinct strategies in photobiocatalytic chemistry, we hope to illuminate future synthetic opportunities in the area.
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Affiliation(s)
- Megan A Emmanuel
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Sophie G Bender
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Catherine Bilodeau
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Jose M Carceller
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
- Institute of Chemical Technology (ITQ), Universitat Politècnica de València, València 46022,Spain
| | - Jacob S DeHovitz
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Haigen Fu
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Yi Liu
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Bryce T Nicholls
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Yao Ouyang
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Claire G Page
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Tianzhang Qiao
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Felix C Raps
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Damien R Sorigué
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
- Aix-Marseille University, CEA, CNRS, Institute of Biosciences and Biotechnologies, BIAM Cadarache, 13108 Saint-Paul-lez-Durance, France
| | - Shang-Zheng Sun
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Joshua Turek-Herman
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Yuxuan Ye
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Ariadna Rivas-Souchet
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Jingzhe Cao
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Todd K Hyster
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
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5
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Yamasaki K. Old yellow enzyme of a novel fungi‐specific class. FEBS J 2022; 289:5527-5530. [DOI: 10.1111/febs.16526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 05/09/2022] [Indexed: 11/28/2022]
Affiliation(s)
- Kazuhiko Yamasaki
- Biomedical Research Institute National Institute of Advanced Industrial Science and Technology (AIST) Tsukuba Japan
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6
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Singh Y, Sharma R, Mishra M, Verma PK, Saxena AK. Crystal structure of ArOYE6 reveals a novel C‐terminal helical extension and mechanistic insights into the distinct class III OYEs from pathogenic fungi. FEBS J 2022; 289:5531-5550. [DOI: 10.1111/febs.16445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 03/02/2022] [Accepted: 03/18/2022] [Indexed: 11/28/2022]
Affiliation(s)
- Yeshveer Singh
- Plant Immunity Laboratory National Institute of Plant Genome Research New Delhi India
| | - Ruby Sharma
- Rm‐403/440 Structural Biology Laboratory School of Life Science Jawaharlal Nehru University New Delhi India
| | - Manasi Mishra
- Plant Immunity Laboratory National Institute of Plant Genome Research New Delhi India
| | - Praveen Kumar Verma
- Plant Immunity Laboratory National Institute of Plant Genome Research New Delhi India
- Plant Immunity Laboratory School of Life Science Jawaharlal Nehru University New Delhi India
| | - Ajay Kumar Saxena
- Rm‐403/440 Structural Biology Laboratory School of Life Science Jawaharlal Nehru University New Delhi India
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7
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Robescu MS, Cendron L, Bacchin A, Wagner K, Reiter T, Janicki I, Merusic K, Illek M, Aleotti M, Bergantino E, Hall M. Asymmetric Proton Transfer Catalysis by Stereocomplementary Old Yellow Enzymes for C═C Bond Isomerization Reaction. ACS Catal 2022. [DOI: 10.1021/acscatal.2c01110] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Marina S. Robescu
- Department of Biology, University of Padova, Padova, Province of Padova 35131, Italy
| | - Laura Cendron
- Department of Biology, University of Padova, Padova, Province of Padova 35131, Italy
| | - Arianna Bacchin
- Institute of Chemistry, University of Graz, Graz, Styria 8010, Austria
| | - Karla Wagner
- Institute of Chemistry, University of Graz, Graz, Styria 8010, Austria
| | - Tamara Reiter
- Institute of Chemistry, University of Graz, Graz, Styria 8010, Austria
| | - Ignacy Janicki
- Department of Heteroorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Lodz, Lodz Province 90-001, Poland
| | - Kemal Merusic
- Institute of Chemistry, University of Graz, Graz, Styria 8010, Austria
| | - Maximilian Illek
- Institute of Chemistry, University of Graz, Graz, Styria 8010, Austria
| | - Matteo Aleotti
- Institute of Chemistry, University of Graz, Graz, Styria 8010, Austria
| | - Elisabetta Bergantino
- Department of Biology, University of Padova, Padova, Province of Padova 35131, Italy
| | - Mélanie Hall
- Institute of Chemistry, University of Graz, Graz, Styria 8010, Austria
- Field of Excellence BioHealth, University of Graz, Graz, Styria 8010, Austria
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8
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Robescu MS, Loprete G, Gasparotto M, Vascon F, Filippini F, Cendron L, Bergantino E. The Family Keeps on Growing: Four Novel Fungal OYEs Characterized. Int J Mol Sci 2022; 23:3050. [PMID: 35328465 PMCID: PMC8954901 DOI: 10.3390/ijms23063050] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/07/2022] [Accepted: 03/09/2022] [Indexed: 11/16/2022] Open
Abstract
Aiming at expanding the portfolio of Old Yellow Enzymes (OYEs), which have been systematically studied to be employed in the chemical and pharmaceutical industries as useful biocatalysts, we decided to explore the immense reservoir of filamentous fungi. We drew from the genome of the two Ascomycetes Aspergillus niger and Botryotinia fuckeliana four new members of the OYE superfamily belonging to the classical and thermophilic-like subfamilies. The two BfOYEs show wider substrate spectra than the AnOYE homologues, which appear as more specialized biocatalysts. According to their mesophilic origins, the new enzymes neither show high thermostability nor extreme pH optimums. The crystal structures of BfOYE4 and AnOYE8 have been determined, revealing the conserved features of the thermophilic-like subclass as well as unique properties, such as a peculiar N-terminal loop involved in dimer surface interactions. For the classical representatives BfOYE1 and AnOYE2, model structures were built and analyzed, showing surprisingly wide open access to the active site cavities due to a shorter β6-loop and a disordered capping subdomain.
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Affiliation(s)
| | | | | | | | | | | | - Elisabetta Bergantino
- Synthetic Biology and Biotechnology Unit, Department of Biology, University of Padova, Viale G. Colombo 3, 35131 Padova, Italy; (M.S.R.); (G.L.); (M.G.); (F.V.); (F.F.); (L.C.)
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9
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Shift from morphological to recent advanced molecular approaches for the identification of nematodes. Genomics 2022; 114:110295. [DOI: 10.1016/j.ygeno.2022.110295] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 01/08/2022] [Accepted: 02/01/2022] [Indexed: 11/17/2022]
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10
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Forouzesh DC, Beaupre BA, Butrin A, Wawrzak Z, Liu D, Moran GR. The Interaction of Porcine Dihydropyrimidine Dehydrogenase with the Chemotherapy Sensitizer: 5-Ethynyluracil. Biochemistry 2021; 60:1120-1132. [PMID: 33755421 DOI: 10.1021/acs.biochem.1c00096] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Dihydropyrimidine dehydrogenase (DPD) is a complex enzyme that reduces the 5,6-vinylic bond of pyrimidines, uracil, and thymine. 5-Fluorouracil (5FU) is also a substrate for DPD and a common chemotherapeutic agent used to treat numerous cancers. The reduction of 5FU to 5-fluoro-5,6-dihydrouracil negates its toxicity and efficacy. Patients with high DPD activity levels typically have poor outcomes when treated with 5FU. DPD is thus a central mitigating factor in the treatment of a variety of cancers. 5-Ethynyluracil (5EU) covalently inactivates DPD by cross-linking with the active-site general acid cysteine in the pyrimidine binding site. This reaction is dependent on the simultaneous binding of 5EU and nicotinamide adenine dinucleotide phosphate (NADPH). This ternary complex induces DPD to become activated by taking up two electrons from the NADPH. The covalent inactivation of DPD by 5EU occurs concomitantly with this reductive activation with a rate constant of ∼0.2 s-1. This kinact value is correlated with the rate of reduction of one of the two flavin cofactors and the localization of a mobile loop in the pyrimidine active site that places the cysteine that serves as the general acid in catalysis proximal to the 5EU ethynyl group. Efficient cross-linking is reliant on enzyme activation, but this process appears to also have a conformational aspect in that nonreductive NADPH analogues can also induce a partial inactivation. Cross-linking then renders DPD inactive by severing the proton-coupled electron transfer mechanism that transmits electrons 56 Å across the protein.
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Affiliation(s)
- Dariush C Forouzesh
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 W Sheridan RoadChicago, Illinois 60660, United States
| | - Brett A Beaupre
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 W Sheridan RoadChicago, Illinois 60660, United States
| | - Arseniy Butrin
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 W Sheridan RoadChicago, Illinois 60660, United States
| | - Zdzislaw Wawrzak
- Synchrotron Research Center, Life Sciences Collaborative Access Team, Northwestern University, Argonne, Illinois 60439, United States
| | - Dali Liu
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 W Sheridan RoadChicago, Illinois 60660, United States
| | - Graham R Moran
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 W Sheridan RoadChicago, Illinois 60660, United States
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11
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Böhmer S, Marx C, Gómez-Baraibar Á, Nowaczyk MM, Tischler D, Hemschemeier A, Happe T. Evolutionary diverse Chlamydomonas reinhardtii Old Yellow Enzymes reveal distinctive catalytic properties and potential for whole-cell biotransformations. ALGAL RES 2020. [DOI: 10.1016/j.algal.2020.101970] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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12
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Abstract
Ene reductases enable the asymmetric hydrogenation of activated alkenes allowing the manufacture of valuable chiral products. The enzymes complement existing metal- and organocatalytic approaches for the stereoselective reduction of activated C=C double bonds, and efforts to expand the biocatalytic toolbox with additional ene reductases are of high academic and industrial interest. Here, we present the characterization of a novel ene reductase from Paenibacillus polymyxa, named Ppo-Er1, belonging to the recently identified subgroup III of the old yellow enzyme family. The determination of substrate scope, solvent stability, temperature, and pH range of Ppo-Er1 is one of the first examples of a detailed biophysical characterization of a subgroup III enzyme. Notably, Ppo-Er1 possesses a wide temperature optimum (Topt: 20–45 °C) and retains high conversion rates of at least 70% even at 10 °C reaction temperature making it an interesting biocatalyst for the conversion of temperature-labile substrates. When assaying a set of different organic solvents to determine Ppo-Er1′s solvent tolerance, the ene reductase exhibited good performance in up to 40% cyclohexane as well as 20 vol% DMSO and ethanol. In summary, Ppo-Er1 exhibited activity for thirteen out of the nineteen investigated compounds, for ten of which Michaelis–Menten kinetics could be determined. The enzyme exhibited the highest specificity constant for maleimide with a kcat/KM value of 287 mM−1 s−1. In addition, Ppo-Er1 proved to be highly enantioselective for selected substrates with measured enantiomeric excess values of 92% or higher for 2-methyl-2-cyclohexenone, citral, and carvone.
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13
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Roman JV, Melkonian TR, Silvaggi NR, Moran GR. Transient-State Analysis of Human Isocitrate Dehydrogenase I: Accounting for the Interconversion of Active and Non-Active Conformational States. Biochemistry 2019; 58:5366-5380. [PMID: 31478653 DOI: 10.1021/acs.biochem.9b00518] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Human isocitrate dehydrogenase 1 (HsICDH1) is a cytoplasmic homodimeric Mg(II)-dependent enzyme that converts d-isocitrate (D-ICT) and NADP+ to α-ketoglutarate (AKG), CO2, and NADPH. The active sites are formed at the subunit interface and incorporate residues from both protomers. The turnover number titrates hyperbolically from 17.5 s-1 to a minimum of 7 s-1 with an increasing enzyme concentration. As isolated, the enzyme adopts an inactive open conformation and binds NADPH tightly. The open conformation displaces three of the eight residues that bind D-ICT and Mg(II). Enzyme activation occurs with the addition of Mg(II) or D-ICT with a rate constant of 0.12 s-1. The addition of both Mg(II) and D-ICT activates the enzyme with a rate constant of 0.6 s-1 and displaces half of the bound NADPH. This indicates that HsICDH1 may have a half-site mechanism in which the active sites alternate in catalysis. The X-ray crystal structure of the half-site activated complex reveals asymmetry in the homodimer with a single NADPH bound. The structure also indicates a pseudotetramer interface that impedes the egress of NADPH consistent with the suppression of the turnover number at high enzyme concentrations. When the half-site activated form of the enzyme is reacted with NADP+, NADPH forms with a rate constant of 204 s-1 followed by a shift in the NADPH absorption spectrum with a rate constant of 28 s-1. These data indicate the accumulation of two intermediate states. Once D-ICT is exhausted, HsICDH1 relaxes to the inactive open state with a rate constant of ∼3 s-1.
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Affiliation(s)
- Joseph V Roman
- Department of Chemistry and Biochemistry , Loyola University Chicago , Flanner Hall, 1068 West Sheridan Road , Chicago , Illinois 60660 , United States
| | - Trevor R Melkonian
- Department of Chemistry and Biochemistry , University of Wisconsin-Milwaukee , 3210 North Cramer Street , Milwaukee , Wisconsin 53211-3209 , United States
| | - Nicholas R Silvaggi
- Department of Chemistry and Biochemistry , University of Wisconsin-Milwaukee , 3210 North Cramer Street , Milwaukee , Wisconsin 53211-3209 , United States
| | - Graham R Moran
- Department of Chemistry and Biochemistry , Loyola University Chicago , Flanner Hall, 1068 West Sheridan Road , Chicago , Illinois 60660 , United States
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14
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Peters C, Frasson D, Sievers M, Buller R. Novel Old Yellow Enzyme Subclasses. Chembiochem 2019; 20:1569-1577. [DOI: 10.1002/cbic.201800770] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 02/12/2019] [Indexed: 11/07/2022]
Affiliation(s)
- Christin Peters
- Competence Center for BiocatalysisInstitute of Chemistry and BiotechnologySchool of Life Sciences and Facility ManagementZurich University of Applied Sciences Einsiedlerstrasse 31 8820 Wädenswil Switzerland
| | - David Frasson
- Molecular BiologyInstitute of Chemistry and BiotechnologySchool of Life Sciences and Facility ManagementZurich University of Applied Sciences Einsiedlerstrasse 31 8820 Wädenswil Switzerland
| | - Martin Sievers
- Molecular BiologyInstitute of Chemistry and BiotechnologySchool of Life Sciences and Facility ManagementZurich University of Applied Sciences Einsiedlerstrasse 31 8820 Wädenswil Switzerland
| | - Rebecca Buller
- Competence Center for BiocatalysisInstitute of Chemistry and BiotechnologySchool of Life Sciences and Facility ManagementZurich University of Applied Sciences Einsiedlerstrasse 31 8820 Wädenswil Switzerland
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15
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Veloso-Silva LLW, Dores-Silva PR, Bertolino-Reis DE, Moreno-Oliveira LF, Libardi SH, Borges JC. Structural studies of Old Yellow Enzyme of Leishmania braziliensis in solution. Arch Biochem Biophys 2019; 661:87-96. [DOI: 10.1016/j.abb.2018.11.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Revised: 11/10/2018] [Accepted: 11/11/2018] [Indexed: 01/18/2023]
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16
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The crystal structure of XdpB, the bacterial old yellow enzyme, in an FMN-free form. PLoS One 2018; 13:e0195299. [PMID: 29630677 PMCID: PMC5891007 DOI: 10.1371/journal.pone.0195299] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 03/20/2018] [Indexed: 11/19/2022] Open
Abstract
Old Yellow Enzymes (OYEs) are NAD(P)H dehydrogenases of not fully resolved physiological roles that are widespread among bacteria, plants, and fungi and have a great potential for biotechnological applications. We determined the apo form crystal structure of a member of the OYE class, glycerol trinitrate reductase XdpB, from Agrobacterium bohemicum R89-1 at 2.1 Å resolution. In agreement with the structures of the related bacterial OYEs, the structure revealed the TIM barrel fold with an N-terminal β-hairpin lid, but surprisingly, the structure did not contain its cofactor FMN. Its putative binding site was occupied by a pentapeptide TTSDN from the C-terminus of a symmetry related molecule. Biochemical experiments confirmed a specific concentration-dependent oligomerization and a low FMN content. The blocking of the FMN binding site can exist in vivo and regulates enzyme activity. Our bioinformatic analysis indicated that a similar self-inhibition could be expected in more OYEs which we designated as subgroup OYE C1. This subgroup is widespread among G-bacteria and can be recognized by the conserved sequence GxxDYP in proximity of the C termini. In proteobacteria, the C1 subgroup OYEs are typically coded in one operon with short-chain dehydrogenase. This operon is controlled by the tetR-like transcriptional regulator. OYEs coded in these operons are unlikely to be involved in the oxidative stress response as the other known members of the OYE family because no upregulation of XdpB was observed after exposing A. bohemicum R89-1 to oxidative stress.
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Khilyas IV, Lochnit G, Ilinskaya ON. Proteomic Analysis of 2,4,6-Trinitrotoluene Degrading Yeast Yarrowia lipolytica. Front Microbiol 2017; 8:2600. [PMID: 29312267 PMCID: PMC5744042 DOI: 10.3389/fmicb.2017.02600] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 12/13/2017] [Indexed: 11/28/2022] Open
Abstract
2,4,6-trinitrotoluene (TNT) is a common component of many explosives. The overproduction and extensive usage of TNT significantly contaminates the environment. TNT accumulates in soils and aquatic ecosystems and can primarily be destroyed by microorganisms. Current work is devoted to investigation of Yarrowia lipolytica proteins responsible for TNT transformation through the pathway leading to protonated Meisenheimer complexes and nitrite release. Here, we identified a unique set of upregulated membrane and cytosolic proteins of Y. lipolytica, which biosynthesis increased during TNT transformation through TNT-monohydride-Meisenheimer complexes in the first step of TNT degradation, through TNT-dihydride-Meisenheimer complexes in the second step, and the aromatic ring denitration and degradation in the last step. We established that the production of oxidoreductases, namely, NADH flavin oxidoreductases and NAD(P)+-dependent aldehyde dehydrogenases, as well as transferases was enhanced at all stages of the TNT transformation by Y. lipolytica. The up-regulation of several stress response proteins (superoxide dismutase, catalase, glutathione peroxidase, and glutathione S-transferase) was also detected. The involvement of intracellular nitric oxide dioxygenase in NO formation during nitrite oxidation was shown. Our results present at the first time the full proteome analysis of Y. lipolytica yeast, destructor of TNT.
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Affiliation(s)
- Irina V Khilyas
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russia
| | - Guenter Lochnit
- Protein Analytics, Institute of Biochemistry, Faculty of Medicine, Justus Liebig University Giessen, Giessen, Germany
| | - Olga N Ilinskaya
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russia
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Romagnolo A, Spina F, Poli A, Risso S, Serito B, Crotti M, Monti D, Brenna E, Lanfranco L, Varese GC. Old Yellow Enzyme homologues in Mucor circinelloides: expression profile and biotransformation. Sci Rep 2017; 7:12093. [PMID: 28935878 PMCID: PMC5608841 DOI: 10.1038/s41598-017-12545-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 09/06/2017] [Indexed: 12/05/2022] Open
Abstract
The reduction of C=C double bond, a key reaction in organic synthesis, is mostly achieved by traditional chemical methods. Therefore, the search for enzymes capable of performing this reaction is rapidly increasing. Old Yellow Enzymes (OYEs) are flavin-dependent oxidoreductases, initially isolated from Saccharomyces pastorianus. In this study, the presence and activation of putative OYE enzymes was investigated in the filamentous fungus Mucor circinelloides, which was previously found to mediate C=C reduction. Following an in silico approach, using S. pastorianus OYE1 amminoacidic sequence as template, ten putative genes were identified in the genome of M. circinelloides. A phylogenetic analysis revealed a high homology of McOYE1-9 with OYE1-like proteins while McOYE10 showed similarity with thermophilic-like OYEs. The activation of mcoyes was evaluated during the transformation of three different model substrates. Cyclohexenone, α-methylcinnamaldehyde and methyl cinnamate were completely reduced in few hours and the induction of gene expression, assessed by qRT-PCR, was generally fast, suggesting a substrate-dependent activation. Eight genes were activated in the tested conditions suggesting that they may encode for active OYEs. Their expression over time correlated with C=C double bond reduction.
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Affiliation(s)
- Alice Romagnolo
- Department of Life Sciences and Systems Biology, University of Turin, viale P. A. Mattioli 25, 10125, Turin, Italy
| | - Federica Spina
- Department of Life Sciences and Systems Biology, University of Turin, viale P. A. Mattioli 25, 10125, Turin, Italy
| | - Anna Poli
- Department of Life Sciences and Systems Biology, University of Turin, viale P. A. Mattioli 25, 10125, Turin, Italy
| | - Sara Risso
- Department of Life Sciences and Systems Biology, University of Turin, viale P. A. Mattioli 25, 10125, Turin, Italy
| | - Bianca Serito
- Department of Life Sciences and Systems Biology, University of Turin, viale P. A. Mattioli 25, 10125, Turin, Italy
| | - Michele Crotti
- Department of Chemistry, Materials and Chemical Engineering "G. Natta", Politecnico di Milano, via L. Mancinelli 7, 20131, Milan, Italy
| | - Daniela Monti
- Istituto di Chimica del Riconoscimento Molecolare, CNR, Via M. Bianco 9, 20131, Milan, Italy
| | - Elisabetta Brenna
- Department of Chemistry, Materials and Chemical Engineering "G. Natta", Politecnico di Milano, via L. Mancinelli 7, 20131, Milan, Italy
| | - Luisa Lanfranco
- Department of Life Sciences and Systems Biology, University of Turin, viale P. A. Mattioli 25, 10125, Turin, Italy
| | - Giovanna Cristina Varese
- Department of Life Sciences and Systems Biology, University of Turin, viale P. A. Mattioli 25, 10125, Turin, Italy.
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Verma S, Gazara RK, Verma PK. Transcription Factor Repertoire of Necrotrophic Fungal Phytopathogen Ascochyta rabiei: Predominance of MYB Transcription Factors As Potential Regulators of Secretome. FRONTIERS IN PLANT SCIENCE 2017; 8:1037. [PMID: 28659964 PMCID: PMC5470089 DOI: 10.3389/fpls.2017.01037] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 05/30/2017] [Indexed: 06/02/2023]
Abstract
Transcription factors (TFs) are the key players in gene expression and their study is highly significant for shedding light on the molecular mechanisms and evolutionary history of organisms. During host-pathogen interaction, extensive reprogramming of gene expression facilitated by TFs is likely to occur in both host and pathogen. To date, the knowledge about TF repertoire in filamentous fungi is in infancy. The necrotrophic fungus Ascochyta rabiei, that causes destructive Ascochyta blight (AB) disease of chickpea (Cicer arietinum), demands more comprehensive study for better understanding of Ascochyta-legume pathosystem. In the present study, we performed the genome-wide identification and analysis of TFs in A. rabiei. Taking advantage of A. rabiei genome sequence, we used a bioinformatic approach to predict the TF repertoire of A. rabiei. For identification and classification of A. rabiei TFs, we designed a comprehensive pipeline using a combination of BLAST and InterProScan software. A total of 381 A. rabiei TFs were predicted and divided into 32 fungal specific families of TFs. The gene structure, domain organization and phylogenetic analysis of abundant families of A. rabiei TFs were also carried out. Comparative study of A. rabiei TFs with that of other necrotrophic, biotrophic, hemibiotrophic, symbiotic, and saprotrophic fungi was performed. It suggested presence of both conserved as well as unique features among them. Moreover, cis-acting elements on promoter sequences of earlier predicted A. rabiei secretome were also identified. With the help of published A. rabiei transcriptome data, the differential expression of TF and secretory protein coding genes was analyzed. Furthermore, comprehensive expression analysis of few selected A. rabiei TFs using quantitative real-time polymerase chain reaction revealed variety of expression patterns during host colonization. These genes were expressed in at least one of the time points tested post infection. Overall, this study illustrates the first genome-wide identification and analysis of TF repertoire of A. rabiei. This work would provide the basis for further studies to dissect role of TFs in the molecular mechanisms during A. rabiei-chickpea interactions.
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Affiliation(s)
| | | | - Praveen K. Verma
- Plant Immunity Laboratory, National Institute of Plant Genome ResearchNew Delhi, India
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Old Yellow Enzyme-Catalysed Asymmetric Hydrogenation: Linking Family Roots with Improved Catalysis. Catalysts 2017. [DOI: 10.3390/catal7050130] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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21
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Catucci G, Romagnolo A, Spina F, Varese GC, Gilardi G, Di Nardo G. Enzyme-substrate matching in biocatalysis: in silico studies to predict substrate preference of ten putative ene-reductases from Mucor circinelloides MUT44. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2016.06.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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22
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Verma S, Gazara RK, Nizam S, Parween S, Chattopadhyay D, Verma PK. Draft genome sequencing and secretome analysis of fungal phytopathogen Ascochyta rabiei provides insight into the necrotrophic effector repertoire. Sci Rep 2016; 6:24638. [PMID: 27091329 PMCID: PMC4835772 DOI: 10.1038/srep24638] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 04/04/2016] [Indexed: 01/28/2023] Open
Abstract
Constant evolutionary pressure acting on pathogens refines their molecular strategies to attain successful pathogenesis. Recent studies have shown that pathogenicity mechanisms of necrotrophic fungi are far more intricate than earlier evaluated. However, only a few studies have explored necrotrophic fungal pathogens. Ascochyta rabiei is a necrotrophic fungus that causes devastating blight disease of chickpea (Cicer arietinum). Here, we report a 34.6 megabase draft genome assembly of A. rabiei. The genome assembly covered more than 99% of the gene space and 4,259 simple sequence repeats were identified in the assembly. A total of 10,596 high confidence protein-coding genes were predicted which includes a large and diverse inventory of secretory proteins, transporters and primary and secondary metabolism enzymes reflecting the necrotrophic lifestyle of A. rabiei. A wide range of genes encoding carbohydrate-active enzymes capable for degradation of complex polysaccharides were also identified. Comprehensive analysis predicted a set of 758 secretory proteins including both classical and non-classical secreted proteins. Several of these predicted secretory proteins showed high cysteine content and numerous tandem repeats. Together, our analyses would broadly expand our knowledge and offer insights into the pathogenesis and necrotrophic lifestyle of fungal phytopathogens.
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Affiliation(s)
- Sandhya Verma
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Rajesh Kumar Gazara
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Shadab Nizam
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Sabiha Parween
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Debasis Chattopadhyay
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Praveen Kumar Verma
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
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Srivastava V, Verma PK. Genome Wide Identification of LIM Genes in Cicer arietinum and Response of Ca-2LIMs in Development, Hormone and Pathogenic Stress. PLoS One 2015; 10:e0138719. [PMID: 26418014 PMCID: PMC4587737 DOI: 10.1371/journal.pone.0138719] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2015] [Accepted: 09/02/2015] [Indexed: 11/20/2022] Open
Abstract
The eukaryotic lineage-specific LIM protein (LIN11, ISL1, and MEC3) family play pivotal role in modulation of actin dynamics and transcriptional regulation. The systematic investigation of this family has not been carried in detail and rare in legumes. Current study involves the mining of Cicer arietinum genome for the genes coding for LIM domain proteins and displayed significant homology with LIM genes of other species. The analysis led to the identification of 15 members, which were positioned on chickpea chromosomes. The phylogenetic and motif analysis suggested their categorization into two sub-families i.e., Ca-2LIMs and Ca-DA1/DAR, which comprised of nine and six candidates, respectively. Further sub-categories of Ca-2LIMs were recognised as αLIM, βLIM, δLIM and γLIM. The LIM genes within their sub-families displayed conserved genomic and motif organization. The expression pattern of Ca-2LIMs across developmental and reproductive tissues demonstrated strong correlation with established consensus. The Ca-2LIM belongs to PLIM and GLIM (XLIM) was found highly expressed in floral tissue. Others showed ubiquitous expression pattern with their dominance in stem. Under hormonal and pathogenic conditions these LIMs were found to up-regulate during salicylic acid, abscisic acid and Ascochyta rabiei treatment or infection; and down-regulated in response to jasmonic acid treatment. The findings of this work, particularly in terms of modulation of LIM genes under biotic stress will open up the way to further explore and establish the role of chickpea LIMs in plant defense response.
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Affiliation(s)
- Vikas Srivastava
- Plant Immunity Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Praveen Kumar Verma
- Plant Immunity Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
- * E-mail:
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Nizam S, Gazara RK, Verma S, Singh K, Verma PK. Comparative structural modeling of six old yellow enzymes (OYEs) from the necrotrophic fungus Ascochyta rabiei: insight into novel OYE classes with differences in cofactor binding, organization of active site residues and stereopreferences. PLoS One 2014; 9:e95989. [PMID: 24776850 PMCID: PMC4002455 DOI: 10.1371/journal.pone.0095989] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 04/02/2014] [Indexed: 11/29/2022] Open
Abstract
Old Yellow Enzyme (OYE1) was the first flavin-dependent enzyme identified and characterized in detail by the entire range of physical techniques. Irrespective of this scrutiny, true physiological role of the enzyme remains a mystery. In a recent study, we systematically identified OYE proteins from various fungi and classified them into three classes viz. Class I, II and III. However, there is no information about the structural organization of Class III OYEs, eukaryotic Class II OYEs and Class I OYEs of filamentous fungi. Ascochyta rabiei, a filamentous phytopathogen which causes Ascochyta blight (AB) in chickpea possesses six OYEs (ArOYE1-6) belonging to the three OYE classes. Here we carried out comparative homology modeling of six ArOYEs representing all the three classes to get an in depth idea of structural and functional aspects of fungal OYEs. The predicted 3D structures of A. rabiei OYEs were refined and evaluated using various validation tools for their structural integrity. Analysis of FMN binding environment of Class III OYE revealed novel residues involved in interaction. The ligand para-hydroxybenzaldehyde (PHB) was docked into the active site of the enzymes and interacting residues were analyzed. We observed a unique active site organization of Class III OYE in comparison to Class I and II OYEs. Subsequently, analysis of stereopreference through structural features of ArOYEs was carried out, suggesting differences in R/S selectivity of these proteins. Therefore, our comparative modeling study provides insights into the FMN binding, active site organization and stereopreference of different classes of ArOYEs and indicates towards functional differences of these enzymes. This study provides the basis for future investigations towards the biochemical and functional characterization of these enigmatic enzymes.
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Affiliation(s)
- Shadab Nizam
- Plant Immunity Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Rajesh Kumar Gazara
- Plant Immunity Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Sandhya Verma
- Plant Immunity Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Kunal Singh
- Plant Immunity Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Praveen Kumar Verma
- Plant Immunity Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
- * E-mail:
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