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Sánchez Pérez LDC, Zubillaga RA, García-Gutiérrez P, Landa A. Sigma-Class Glutathione Transferases (GSTσ): A New Target with Potential for Helminth Control. Trop Med Infect Dis 2024; 9:85. [PMID: 38668546 PMCID: PMC11053550 DOI: 10.3390/tropicalmed9040085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 04/10/2024] [Accepted: 04/12/2024] [Indexed: 04/29/2024] Open
Abstract
Glutathione transferases (GSTs EC 2.5.1.18) are critical components of phase II metabolism, instrumental in xenobiotics' metabolism. Their primary function involves conjugating glutathione to both endogenous and exogenous toxic compounds, which increases their solubility and enables their ejection from cells. They also play a role in the transport of non-substrate compounds and immunomodulation, aiding in parasite establishment within its host. The cytosolic GST subfamily is the most abundant and diverse in helminths, and sigma-class GST (GSTσ) belongs to it. This review focuses on three key functions of GSTσ: serving as a detoxifying agent that provides drug resistance, functioning as an immune system modulator through its involvement in prostaglandins synthesis, and acting as a vaccine antigen.
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Affiliation(s)
| | - Rafael A. Zubillaga
- Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa, Mexico City C.P. 09310, Mexico; (L.d.C.S.P.); (P.G.-G.)
| | - Ponciano García-Gutiérrez
- Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa, Mexico City C.P. 09310, Mexico; (L.d.C.S.P.); (P.G.-G.)
| | - Abraham Landa
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad Universitaria, Mexico City C.P. 04510, Mexico
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2
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Wang SY, Wang YX, Yue SS, Shi XC, Lu FY, Wu SQ, Herrera-Balandrano DD, Laborda P. G-site residue S67 is involved in the fungicide-degrading activity of a tau class glutathione S-transferase from Carica papaya. J Biol Chem 2024; 300:107123. [PMID: 38417796 PMCID: PMC10958117 DOI: 10.1016/j.jbc.2024.107123] [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: 10/12/2023] [Revised: 02/13/2024] [Accepted: 02/22/2024] [Indexed: 03/01/2024] Open
Abstract
Thiram is a toxic fungicide extensively used for the management of pathogens in fruits. Although it is known that thiram degrades in plant tissues, the key enzymes involved in this process remain unexplored. In this study, we report that a tau class glutathione S-transferase (GST) from Carica papaya can degrade thiram. This enzyme was easily obtained by heterologous expression in Escherichia coli, showed low promiscuity toward other thiuram disulfides, and catalyzed thiram degradation under physiological reaction conditions. Site-directed mutagenesis indicated that G-site residue S67 shows a key influence for the enzymatic activity toward thiram, while mutation of residue S13, which reduced the GSH oxidase activity, did not significantly affect the thiram-degrading activity. The formation of dimethyl dithiocarbamate, which was subsequently converted into carbon disulfide, and dimethyl dithiocarbamoylsulfenic acid as the thiram degradation products suggested that thiram undergoes an alkaline hydrolysis that involves the rupture of the disulfide bond. Application of the GST selective inhibitor 4-chloro-7-nitro-2,1,3-benzoxadiazole reduced papaya peel thiram-degrading activity by 95%, indicating that this is the main degradation route of thiram in papaya. GST from Carica papaya also catalyzed the degradation of the fungicides chlorothalonil and thiabendazole, with residue S67 showing again a key influence for the enzymatic activity. These results fill an important knowledge gap in understanding the catalytic promiscuity of plant GSTs and reveal new insights into the fate and degradation products of thiram in fruits.
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Affiliation(s)
- Su-Yan Wang
- School of Life Sciences, Nantong University, Nantong, China
| | - Yan-Xia Wang
- School of Life Sciences, Nantong University, Nantong, China
| | - Sheng-Shuo Yue
- School of Life Sciences, Nantong University, Nantong, China
| | - Xin-Chi Shi
- School of Life Sciences, Nantong University, Nantong, China
| | - Feng-Yi Lu
- School of Life Sciences, Nantong University, Nantong, China
| | - Si-Qi Wu
- School of Life Sciences, Nantong University, Nantong, China
| | | | - Pedro Laborda
- School of Life Sciences, Nantong University, Nantong, China.
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3
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Win SY, Seo H, Horio F, Fujisawa S, Sato J, Motai Y, Sato T, Oishi E, Taneno A, Htun LL, Bawm S, Okagawa T, Maekawa N, Konnai S, Ohashi K, Murata S. In Vivo Characterization of the Anti-Glutathione S-Transferase Antibody Using an In Vitro Mite Feeding Model. Vaccines (Basel) 2024; 12:148. [PMID: 38400132 PMCID: PMC10892040 DOI: 10.3390/vaccines12020148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/25/2024] [Accepted: 01/29/2024] [Indexed: 02/25/2024] Open
Abstract
Poultry red mites (Dermanyssus gallinae, PRMs), tropical fowl mites (Ornithonyssus bursa, TFMs), and northern fowl mites (O. sylviarum, NFMs) are blood-feeding pests that debilitate poultry worldwide. Glutathione S-transferase (GST) plays an important role in the detoxification and drug metabolism of mites. However, research on avian mite GSTs as vaccine antigens is still lacking. Therefore, we aimed to evaluate the potential of avian mite GSTs for vaccine development. We identified GST genes from TFMs and NFMs. We prepared recombinant GST (rGST) from TFMs, NFMs, and PRMs, and assessed their protein functions. Moreover, we evaluated the cross-reactivity and acaricidal effect of immune plasma against each rGST on TFMs, NFMs, and PRMs. The deduced amino acid sequences of GSTs from TFMs and NFMs were 80% similar to those of the PRMs. The rGSTs exhibited catalytic activity in conjugating glutathione to the 1-chloro-2,4-dinitrobenzene substrate. Immune plasma against each rGST showed cross-reactivity with rGST from different mite species. Moreover, the survival rate of PRMs fed with immune plasma against the rGST of TFMs and NFMs was significantly lower than that of the control plasma. These results demonstrate the potential application of GST as an antigen for the development of a broad-spectrum vaccine against avian mites.
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Affiliation(s)
- Shwe Yee Win
- Laboratory of Infectious Diseases, Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, Kita-18, Nishi-9, Kita-ku, Sapporo 060-0818, Japan
| | - Hikari Seo
- Laboratory of Infectious Diseases, Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, Kita-18, Nishi-9, Kita-ku, Sapporo 060-0818, Japan
| | - Fumiya Horio
- Laboratory of Infectious Diseases, Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, Kita-18, Nishi-9, Kita-ku, Sapporo 060-0818, Japan
| | - Sotaro Fujisawa
- Laboratory of Infectious Diseases, Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, Kita-18, Nishi-9, Kita-ku, Sapporo 060-0818, Japan
| | - Jumpei Sato
- Laboratory of Infectious Diseases, Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, Kita-18, Nishi-9, Kita-ku, Sapporo 060-0818, Japan
| | - Yoshinosuke Motai
- Laboratory of Infectious Diseases, Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, Kita-18, Nishi-9, Kita-ku, Sapporo 060-0818, Japan
| | - Takumi Sato
- Vaxxinova Japan K.K., 1-24-8 Hamamatsucho, Minato-ku, Tokyo 105-0013, Japan
| | - Eiji Oishi
- Vaxxinova Japan K.K., 1-24-8 Hamamatsucho, Minato-ku, Tokyo 105-0013, Japan
| | - Akira Taneno
- Vaxxinova Japan K.K., 1-24-8 Hamamatsucho, Minato-ku, Tokyo 105-0013, Japan
| | - Lat Lat Htun
- Department of Pharmacology and Parasitology, University of Veterinary Science, Yezin, Nay Pyi Taw 15013, Myanmar
| | - Saw Bawm
- Department of Pharmacology and Parasitology, University of Veterinary Science, Yezin, Nay Pyi Taw 15013, Myanmar
- Department of Livestock and Aquaculture Research, Ministry of Agriculture, Livestock and Irrigation, Nay Pyi Taw 15013, Myanmar
| | - Tomohiro Okagawa
- Department of Advanced Pharmaceutics, Faculty of Veterinary Medicine, Hokkaido University, Kita-18, Nishi-9, Kita-ku, Sapporo 060-0818, Japan
| | - Naoya Maekawa
- Department of Advanced Pharmaceutics, Faculty of Veterinary Medicine, Hokkaido University, Kita-18, Nishi-9, Kita-ku, Sapporo 060-0818, Japan
| | - Satoru Konnai
- Laboratory of Infectious Diseases, Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, Kita-18, Nishi-9, Kita-ku, Sapporo 060-0818, Japan
- Department of Advanced Pharmaceutics, Faculty of Veterinary Medicine, Hokkaido University, Kita-18, Nishi-9, Kita-ku, Sapporo 060-0818, Japan
- Institute for Vaccine Research and Development (GU-IVReD), Hokkaido University, Sapporo 060-0818, Japan
| | - Kazuhiko Ohashi
- Laboratory of Infectious Diseases, Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, Kita-18, Nishi-9, Kita-ku, Sapporo 060-0818, Japan
- Department of Advanced Pharmaceutics, Faculty of Veterinary Medicine, Hokkaido University, Kita-18, Nishi-9, Kita-ku, Sapporo 060-0818, Japan
- International Affairs Office, Faculty of Veterinary Medicine, Hokkaido University, Kita-18, Nishi-9, Kita-ku, Sapporo 060-0818, Japan
| | - Shiro Murata
- Laboratory of Infectious Diseases, Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, Kita-18, Nishi-9, Kita-ku, Sapporo 060-0818, Japan
- Department of Advanced Pharmaceutics, Faculty of Veterinary Medicine, Hokkaido University, Kita-18, Nishi-9, Kita-ku, Sapporo 060-0818, Japan
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Ribeiro AJM, Riziotis IG, Borkakoti N, Thornton JM. Enzyme function and evolution through the lens of bioinformatics. Biochem J 2023; 480:1845-1863. [PMID: 37991346 PMCID: PMC10754289 DOI: 10.1042/bcj20220405] [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: 07/20/2023] [Revised: 11/09/2023] [Accepted: 11/14/2023] [Indexed: 11/23/2023]
Abstract
Enzymes have been shaped by evolution over billions of years to catalyse the chemical reactions that support life on earth. Dispersed in the literature, or organised in online databases, knowledge about enzymes can be structured in distinct dimensions, either related to their quality as biological macromolecules, such as their sequence and structure, or related to their chemical functions, such as the catalytic site, kinetics, mechanism, and overall reaction. The evolution of enzymes can only be understood when each of these dimensions is considered. In addition, many of the properties of enzymes only make sense in the light of evolution. We start this review by outlining the main paradigms of enzyme evolution, including gene duplication and divergence, convergent evolution, and evolution by recombination of domains. In the second part, we overview the current collective knowledge about enzymes, as organised by different types of data and collected in several databases. We also highlight some increasingly powerful computational tools that can be used to close gaps in understanding, in particular for types of data that require laborious experimental protocols. We believe that recent advances in protein structure prediction will be a powerful catalyst for the prediction of binding, mechanism, and ultimately, chemical reactions. A comprehensive mapping of enzyme function and evolution may be attainable in the near future.
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Affiliation(s)
- Antonio J. M. Ribeiro
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, U.K
| | - Ioannis G. Riziotis
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, U.K
| | - Neera Borkakoti
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, U.K
| | - Janet M. Thornton
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, U.K
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5
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Zmich A, Perkins LJ, Bingman C, Acheson JF, Buller AR. Multiplexed Assessment of Promiscuous Non-Canonical Amino Acid Synthase Activity in a Pyridoxal Phosphate-Dependent Protein Family. ACS Catal 2023; 13:11644-11655. [PMID: 37720819 PMCID: PMC10501158 DOI: 10.1021/acscatal.3c02498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/19/2023]
Abstract
Pyridoxal phosphate (PLP)-dependent enzymes afford access to a variety of non-canonical amino acids (ncAAs), which are premier buildings blocks for the construction of complex bioactive molecules. The vinylglycine ketimine (VGK) subfamily of PLP-dependent enzymes plays a critical role in sulfur metabolism and is home to a growing set of secondary metabolic enzymes that synthesize γ-substituted ncAAs. Identification of VGK enzymes for biocatalysis faces a distinct challenge because the subfamily contains both desirable synthases as well as lyases that break down ncAAs. Some enzymes have both activities, which may contribute to pervasive mis-annotation. To navigate this complex functional landscape, we used a substrate multiplexed screening approach to rapidly measure the substrate promiscuity of 40 homologs in the VGK subfamily. We found that enzymes involved in transsulfuration are less likely to have promiscuous activities and often possess undesirable lyase activity. Enzymes from direct sulfuration and secondary metabolism generally had a high degree of substrate promiscuity. From this cohort, we identified an exemplary γ-synthase from Caldicellulosiruptor hydrothermalis (CahyGS). This enzyme is thermostable and has high expression (~400 mg protein per L culture), enabling preparative scale synthesis of thioether containing ncAAs. When assayed with l-allylglycine, CahyGS catalyzes a stereoselective γ-addition reaction to afford access to a unique set of γ-methyl branched ncAAs. We determined high-resolution crystal structures of this enzyme that define an open-close transition associated with ligand binding and set the stage for future engineering within this enzyme subfamily.
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Affiliation(s)
- Anna Zmich
- Department of Biochemistry, University of Wisconsin−Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Lydia J. Perkins
- Department of Chemistry, University of Wisconsin−Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Craig Bingman
- Department of Biochemistry, University of Wisconsin−Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Justin F Acheson
- Department of Biochemistry, University of Wisconsin−Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Andrew R. Buller
- Department of Biochemistry, University of Wisconsin−Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
- Department of Chemistry, University of Wisconsin−Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
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6
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Buda K, Miton CM, Fan XC, Tokuriki N. Molecular determinants of protein evolvability. Trends Biochem Sci 2023; 48:751-760. [PMID: 37330341 DOI: 10.1016/j.tibs.2023.05.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/18/2023] [Accepted: 05/23/2023] [Indexed: 06/19/2023]
Abstract
The plethora of biological functions that sustain life is rooted in the remarkable evolvability of proteins. An emerging view highlights the importance of a protein's initial state in dictating evolutionary success. A deeper comprehension of the mechanisms that govern the evolvability of these initial states can provide invaluable insights into protein evolution. In this review, we describe several molecular determinants of protein evolvability, unveiled by experimental evolution and ancestral sequence reconstruction studies. We further discuss how genetic variation and epistasis can promote or constrain functional innovation and suggest putative underlying mechanisms. By establishing a clear framework for these determinants, we provide potential indicators enabling the forecast of suitable evolutionary starting points and delineate molecular mechanisms in need of deeper exploration.
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Affiliation(s)
- Karol Buda
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
| | - Charlotte M Miton
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
| | - Xingyu Cara Fan
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
| | - Nobuhiko Tokuriki
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada.
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Hornung BVH, Terrapon N. An objective criterion to evaluate sequence-similarity networks helps in dividing the protein family sequence space. PLoS Comput Biol 2023; 19:e1010881. [PMID: 37585436 PMCID: PMC10461819 DOI: 10.1371/journal.pcbi.1010881] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 08/28/2023] [Accepted: 01/18/2023] [Indexed: 08/18/2023] Open
Abstract
The deluge of genomic data raises various challenges for computational protein annotation. The definition of superfamilies, based on conserved folds, or of families, showing more recent homology signatures, allow a first categorization of the sequence space. However, for precise functional annotation or the identification of the unexplored parts within a family, a division into subfamilies is essential. As curators of an expert database, the Carbohydrate Active Enzymes database (CAZy), we began, more than 15 years ago, to manually define subfamilies based on phylogeny reconstruction. However, facing the increasing amount of sequence and functional data, we required more scalable and reproducible methods. The recently popularized sequence similarity networks (SSNs), allows to cope with very large families and computation of many subfamily schemes. Still, the choice of the optimal SSN subfamily scheme only relies on expert knowledge so far, without any data-driven guidance from within the network. In this study, we therefore decided to investigate several network properties to determine a criterion which can be used by curators to evaluate the quality of subfamily assignments. The performance of the closeness centrality criterion, a network property to indicate the connectedness within the network, shows high similarity to the decisions of expert curators from eight distinct protein families. Closeness centrality also suggests that in some cases multiple levels of subfamilies could be possible, depending on the granularity of the research question, while it indicates when no subfamily emerged in some family evolution. We finally used closeness centrality to create subfamilies in four families of the CAZy database, providing a finer functional annotation and highlighting subfamilies without biochemically characterized members for potential future discoveries.
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Affiliation(s)
| | - Nicolas Terrapon
- Aix Marseille Université, CNRS, UMR 7257 AFMB, Marseille, France
- INRAE, USC 1408 AFMB, Marseille, France
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8
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Mocchetti E, Morette L, Mulliert G, Mathiot S, Guillot B, Dehez F, Chauvat F, Cassier-Chauvat C, Brochier-Armanet C, Didierjean C, Hecker A. Biochemical and Structural Characterization of Chi-Class Glutathione Transferases: A Snapshot on the Glutathione Transferase Encoded by sll0067 Gene in the Cyanobacterium Synechocystis sp. Strain PCC 6803. Biomolecules 2022; 12:biom12101466. [PMID: 36291676 PMCID: PMC9599700 DOI: 10.3390/biom12101466] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 09/30/2022] [Accepted: 10/05/2022] [Indexed: 11/24/2022] Open
Abstract
Glutathione transferases (GSTs) constitute a widespread superfamily of enzymes notably involved in detoxification processes and/or in specialized metabolism. In the cyanobacterium Synechocsytis sp. PCC 6803, SynGSTC1, a chi-class GST (GSTC), is thought to participate in the detoxification process of methylglyoxal, a toxic by-product of cellular metabolism. A comparative genomic analysis showed that GSTCs were present in all orders of cyanobacteria with the exception of the basal order Gloeobacterales. These enzymes were also detected in some marine and freshwater noncyanobacterial bacteria, probably as a result of horizontal gene transfer events. GSTCs were shorter of about 30 residues compared to most cytosolic GSTs and had a well-conserved SRAS motif in the active site (10SRAS13 in SynGSTC1). The crystal structure of SynGSTC1 in complex with glutathione adopted the canonical GST fold with a very open active site because the α4 and α5 helices were exceptionally short. A transferred multipolar electron-density analysis allowed a fine description of the solved structure. Unexpectedly, Ser10 did not have an electrostatic influence on glutathione as usually observed in serinyl-GSTs. The S10A variant was only slightly less efficient than the wild-type and molecular dynamics simulations suggested that S10 was a stabilizer of the protein backbone rather than an anchor site for glutathione.
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Affiliation(s)
- Eva Mocchetti
- Université de Lorraine, CNRS, CRM2, F-54000 Nancy, France
| | - Laura Morette
- Université de Lorraine, INRAE, IAM, F-54000 Nancy, France
| | | | | | - Benoît Guillot
- Université de Lorraine, CNRS, CRM2, F-54000 Nancy, France
| | - François Dehez
- Université de Lorraine, CNRS, LPCT, F-54000 Nancy, France
| | - Franck Chauvat
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), F-91190 Gif-sur-Yvette, France
| | - Corinne Cassier-Chauvat
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), F-91190 Gif-sur-Yvette, France
| | | | - Claude Didierjean
- Université de Lorraine, CNRS, CRM2, F-54000 Nancy, France
- Correspondence: (C.D.); (A.H.)
| | - Arnaud Hecker
- Université de Lorraine, INRAE, IAM, F-54000 Nancy, France
- Correspondence: (C.D.); (A.H.)
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9
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Genomic and functional insights into the diversification of the elongation factor eEF1Bγ in fungi. FUNGAL BIOL REV 2022. [DOI: 10.1016/j.fbr.2022.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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10
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Hackmann TJ. Redefining the coenzyme A transferase superfamily with a large set of manually-annotated proteins. Protein Sci 2022; 31:864-881. [PMID: 35049101 PMCID: PMC8927868 DOI: 10.1002/pro.4277] [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: 09/14/2021] [Revised: 12/07/2021] [Accepted: 01/13/2022] [Indexed: 10/19/2022]
Abstract
The coenzyme A (CoA) transferases are a superfamily of proteins central to the metabolism of acetyl-CoA and other CoA thioesters. They are diverse group, catalyzing over a hundred biochemical reactions and spanning all three domains of life. A deeply rooted idea, proposed two decades ago, is these enzymes fall into three families (I, II, III). Here we find they fall into different families, which we achieve by analyzing all CoA transferases characterized to date. We manually annotated 94 CoA transferases with functional information (including rates of catalysis for 208 reactions) from 97 publications. This represents all enzymes we could find in the primary literature, and it is double the number annotated in four protein databases (BRENDA, KEGG, MetaCyc, UniProt). We found family I transferases are not closely related to each other in terms of sequence, structure, and reactions catalyzed. This family is not even monophyletic. These problems are solved by regrouping the three families into six, including one family with many non-CoA transferases. The problem (and solution) became apparent only by analyzing our large set of manually-annotated proteins. It would have been missed if we had used the small number of proteins annotated in UniProt and other databases. Our work is important to understanding the biology of CoA transferases. It also warns investigators doing phylogenetic analyses of proteins to go beyond information in databases. This article is protected by copyright. All rights reserved.
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Strom SA, Hager AG, Concepcion JCT, Seiter NJ, Davis AS, Morris JA, Kaundun SS, Riechers DE. Metabolic Pathways for S-Metolachlor Detoxification Differ Between Tolerant Corn and Multiple-Resistant Waterhemp. PLANT & CELL PHYSIOLOGY 2021; 62:1770-1785. [PMID: 34453831 PMCID: PMC8664635 DOI: 10.1093/pcp/pcab132] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 08/27/2021] [Indexed: 05/04/2023]
Abstract
Herbicide resistance in weeds can be conferred by target-site and/or non-target-site mechanisms, such as rapid metabolic detoxification. Resistance to the very-long-chain fatty acid-inhibiting herbicide, S-metolachlor, in multiple herbicide-resistant populations (CHR and SIR) of waterhemp (Amaranthus tuberculatus) is conferred by rapid metabolism compared with sensitive populations. However, enzymatic pathways for S-metolachlor metabolism in waterhemp are unknown. Enzyme assays using S-metolachlor were developed to determine the specific activities of glutathione S-transferases (GSTs) and cytochrome P450 monooxygenases (P450s) from CHR and SIR seedlings to compare with tolerant corn and sensitive waterhemp (WUS). GST activities were greater (∼2-fold) in CHR and SIR compared to WUS but much less than corn. In contrast, P450s in microsomal extracts from CHR and SIR formed O-demethylated S-metolachlor, and their NADPH-dependent specific activities were greater (>20-fold) than corn or WUS. Metabolite profiles of S-metolachlor generated via untargeted and targeted liquid chromatography-mass spectrometry from CHR and SIR differed from WUS, with greater relative abundances of O-demethylated S-metolachlor and O-demethylated S-metolachlor-glutathione conjugates formed by CHR and SIR. In summary, our results demonstrate that S-metolachlor metabolism in resistant waterhemp involves Phase I and Phase II metabolic activities acting in concert, but the initial O-demethylation reaction confers resistance.
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Affiliation(s)
| | - Aaron G Hager
- Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA
| | | | - Nicholas J Seiter
- Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA
| | - Adam S Davis
- Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA
| | - James A Morris
- Jealott’s Hill International Research Centre, Syngenta UK Ltd, Bracknell, Berkshire RG42, UK
| | - Shiv S Kaundun
- Jealott’s Hill International Research Centre, Syngenta UK Ltd, Bracknell, Berkshire RG42, UK
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12
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Markin CJ, Mokhtari DA, Sunden F, Appel MJ, Akiva E, Longwell SA, Sabatti C, Herschlag D, Fordyce PM. Revealing enzyme functional architecture via high-throughput microfluidic enzyme kinetics. Science 2021; 373:373/6553/eabf8761. [PMID: 34437092 DOI: 10.1126/science.abf8761] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 05/24/2021] [Indexed: 12/21/2022]
Abstract
Systematic and extensive investigation of enzymes is needed to understand their extraordinary efficiency and meet current challenges in medicine and engineering. We present HT-MEK (High-Throughput Microfluidic Enzyme Kinetics), a microfluidic platform for high-throughput expression, purification, and characterization of more than 1500 enzyme variants per experiment. For 1036 mutants of the alkaline phosphatase PafA (phosphate-irrepressible alkaline phosphatase of Flavobacterium), we performed more than 670,000 reactions and determined more than 5000 kinetic and physical constants for multiple substrates and inhibitors. We uncovered extensive kinetic partitioning to a misfolded state and isolated catalytic effects, revealing spatially contiguous regions of residues linked to particular aspects of function. Regions included active-site proximal residues but extended to the enzyme surface, providing a map of underlying architecture not possible to derive from existing approaches. HT-MEK has applications that range from understanding molecular mechanisms to medicine, engineering, and design.
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Affiliation(s)
- C J Markin
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - D A Mokhtari
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - F Sunden
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - M J Appel
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - E Akiva
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA
| | - S A Longwell
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - C Sabatti
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA.,Department of Statistics, Stanford University, Stanford, CA 94305, USA
| | - D Herschlag
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA. .,Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA.,ChEM-H Institute, Stanford University, Stanford, CA 94305, USA
| | - P M Fordyce
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA. .,ChEM-H Institute, Stanford University, Stanford, CA 94305, USA.,Department of Genetics, Stanford University, Stanford, CA 94305, USA.,Chan Zuckerberg Biohub; San Francisco, CA 94110, USA
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13
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Repecka D, Jauniskis V, Karpus L, Rembeza E, Rokaitis I, Zrimec J, Poviloniene S, Laurynenas A, Viknander S, Abuajwa W, Savolainen O, Meskys R, Engqvist MKM, Zelezniak A. Expanding functional protein sequence spaces using generative adversarial networks. NAT MACH INTELL 2021. [DOI: 10.1038/s42256-021-00310-5] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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14
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Diversity of Omega Glutathione Transferases in mushroom-forming fungi revealed by phylogenetic, transcriptomic, biochemical and structural approaches. Fungal Genet Biol 2021; 148:103506. [PMID: 33450403 DOI: 10.1016/j.fgb.2020.103506] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 12/20/2020] [Accepted: 12/22/2020] [Indexed: 01/20/2023]
Abstract
The Omega class of glutathione transferases (GSTs) forms a distinct class within the cytosolic GST superfamily because most of them possess a catalytic cysteine residue. The human GST Omega 1 isoform was first characterized twenty years ago, but it took years of work to clarify the roles of the human isoforms. Concerning the kingdom of fungi, little is known about the cellular functions of Omega glutathione transferases (GSTOs), although they are widely represented in some of these organisms. In this study, we re-assess the phylogeny and the classification of GSTOs based on 240 genomes of mushroom-forming fungi (Agaricomycetes). We observe that the number of GSTOs is not only extended in the order of Polyporales but also in other orders such as Boletales. Our analysis leads to a new classification in which the fungal GSTOs are divided into two Types A and B. The catalytic residue of Type-A is either cysteine or serine, while that of Type-B is cysteine. The present study focuses on Trametes versicolor GSTO isoforms that possess a catalytic cysteine residue. Transcriptomic data show that Type-A GSTOs are constitutive enzymes while Type-B are inducible ones. The crystallographic analysis reveals substantial structural differences between the two types while they have similar biochemical profiles in the tested conditions. Additionally, these enzymes have the ability to bind antioxidant molecules such as wood polyphenols in two possible binding sites as observed from X-ray structures. The multiplication of GSTOs could allow fungal organisms to adapt more easily to new environments.
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15
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Hernández Estévez I, Rodríguez Hernández M. “Plant Glutathione S-transferases: An overview”. ACTA ACUST UNITED AC 2020. [DOI: 10.1016/j.plgene.2020.100233] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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16
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Rawat M, Maupin-Furlow JA. Redox and Thiols in Archaea. Antioxidants (Basel) 2020; 9:antiox9050381. [PMID: 32380716 PMCID: PMC7278568 DOI: 10.3390/antiox9050381] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/30/2020] [Accepted: 05/02/2020] [Indexed: 12/11/2022] Open
Abstract
Low molecular weight (LMW) thiols have many functions in bacteria and eukarya, ranging from redox homeostasis to acting as cofactors in numerous reactions, including detoxification of xenobiotic compounds. The LMW thiol, glutathione (GSH), is found in eukaryotes and many species of bacteria. Analogues of GSH include the structurally different LMW thiols: bacillithiol, mycothiol, ergothioneine, and coenzyme A. Many advances have been made in understanding the diverse and multiple functions of GSH and GSH analogues in bacteria but much less is known about distribution and functions of GSH and its analogues in archaea, which constitute the third domain of life, occupying many niches, including those in extreme environments. Archaea are able to use many energy sources and have many unique metabolic reactions and as a result are major contributors to geochemical cycles. As LMW thiols are major players in cells, this review explores the distribution of thiols and their biochemistry in archaea.
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Affiliation(s)
- Mamta Rawat
- Biology Department, California State University, Fresno, CA 93740, USA
- Correspondence: (M.R.); (J.A.M.-F.)
| | - Julie A. Maupin-Furlow
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL 32611, USA
- Correspondence: (M.R.); (J.A.M.-F.)
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17
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Koiwai K, Inaba K, Morohashi K, Enya S, Arai R, Kojima H, Okabe T, Fujikawa Y, Inoue H, Yoshino R, Hirokawa T, Kato K, Fukuzawa K, Shimada-Niwa Y, Nakamura A, Yumoto F, Senda T, Niwa R. An integrated approach to unravel a crucial structural property required for the function of the insect steroidogenic Halloween protein Noppera-bo. J Biol Chem 2020; 295:7154-7167. [PMID: 32241910 PMCID: PMC7242711 DOI: 10.1074/jbc.ra119.011463] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 03/23/2020] [Indexed: 12/16/2022] Open
Abstract
Ecdysteroids are the principal steroid hormones essential for insect development and physiology. In the last 18 years, several enzymes responsible for ecdysteroid biosynthesis encoded by Halloween genes were identified and genetically and biochemically characterized. However, the tertiary structures of these proteins have not yet been characterized. Here, we report the results of an integrated series of in silico, in vitro, and in vivo analyses of the Halloween GST protein Noppera-bo (Nobo). We determined crystal structures of Drosophila melanogaster Nobo (DmNobo) complexed with GSH and 17β-estradiol, a DmNobo inhibitor. 17β-Estradiol almost fully occupied the putative ligand-binding pocket and a prominent hydrogen bond formed between 17β-estradiol and Asp-113 of DmNobo. We found that Asp-113 is essential for 17β-estradiol–mediated inhibition of DmNobo enzymatic activity, as 17β-estradiol did not inhibit and physically interacted less with the D113A DmNobo variant. Asp-113 is highly conserved among Nobo proteins, but not among other GSTs, implying that this residue is important for endogenous Nobo function. Indeed, a homozygous nobo allele with the D113A substitution exhibited embryonic lethality and an undifferentiated cuticle structure, a phenocopy of complete loss-of-function nobo homozygotes. These results suggest that the nobo family of GST proteins has acquired a unique amino acid residue that appears to be essential for binding an endogenous sterol substrate to regulate ecdysteroid biosynthesis. To the best of our knowledge, ours is the first study describing the structural characteristics of insect steroidogenic Halloween proteins. Our findings provide insights relevant for applied entomology to develop insecticides that specifically inhibit ecdysteroid biosynthesis.
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Affiliation(s)
- Kotaro Koiwai
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Kazue Inaba
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan.,Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Kana Morohashi
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Sora Enya
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Reina Arai
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Hirotatsu Kojima
- Drug Discovery Initiative, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takayoshi Okabe
- Drug Discovery Initiative, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yuuta Fujikawa
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Hideshi Inoue
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Ryunosuke Yoshino
- Graduate School of Comprehensive Human Sciences Majors of Medical Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Takatsugu Hirokawa
- Transborder Medical Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan.,Division of Biomedical Science, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan.,Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Koichiro Kato
- Mizuho Information & Research Institute, Inc., 2-3 Kanda Nishiki-cho, Chiyoda-ku, Tokyo 101-8443, Japan
| | - Kaori Fukuzawa
- School of Pharmacy and Pharmaceutical Sciences, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo 142-8501, Japan
| | - Yuko Shimada-Niwa
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Akira Nakamura
- Institute of Molecular Embryology and Genetics, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto 860-0811, Japan
| | - Fumiaki Yumoto
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Toshiya Senda
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan.,School of High Energy Accelerator Science, Sokendai University, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan.,Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Ibaraki 305-8571, Japan
| | - Ryusuke Niwa
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan .,Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
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18
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Fisher B, Snodgrass HM, Jones KA, Andorfer MC, Lewis JC. Site-Selective C-H Halogenation Using Flavin-Dependent Halogenases Identified via Family-Wide Activity Profiling. ACS CENTRAL SCIENCE 2019; 5:1844-1856. [PMID: 31807686 PMCID: PMC6891866 DOI: 10.1021/acscentsci.9b00835] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Indexed: 05/19/2023]
Abstract
Enzymes are powerful catalysts for site-selective C-H bond functionalization. Identifying suitable enzymes for this task and for biocatalysis in general remains challenging, however, due to the fundamental difficulty of predicting catalytic activity from sequence information. In this study, family-wide activity profiling was used to obtain sequence-function information on flavin-dependent halogenases (FDHs). This broad survey provided a number of insights into FDH activity, including halide specificity and substrate preference, that were not apparent from the more focused studies reported to date. Regions of FDH sequence space that are most likely to contain enzymes suitable for halogenating small-molecule substrates were also identified. FDHs with novel substrate scope and complementary regioselectivity on large, three-dimensionally complex compounds were characterized and used for preparative-scale late-stage C-H functionalization. In many cases, these enzymes provide activities that required several rounds of directed evolution to accomplish in previous efforts, highlighting that this approach can achieve significant time savings for biocatalyst identification and provide advanced starting points for further evolution.
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Affiliation(s)
- Brian
F. Fisher
- Department
of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Harrison M. Snodgrass
- Department
of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Krysten A. Jones
- Department
of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | - Mary C. Andorfer
- Department
of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Jared C. Lewis
- Department
of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
- E-mail:
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19
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Si M, Che C, Li G, Li X, Gong Z, Liu J, Yang G, Chen C. Characterization of Xi-class mycothiol S-transferase from Corynebacterium glutamicum and its protective effects in oxidative stress. Microb Cell Fact 2019; 18:182. [PMID: 31655587 PMCID: PMC6815410 DOI: 10.1186/s12934-019-1232-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Accepted: 10/12/2019] [Indexed: 01/17/2023] Open
Abstract
Background Oxidative stress caused by inevitable hostile conditions during fermentative process was the most serious threat to the survival of the well-known industrial microorganism Corynebacterium glutamicum. To survive, C. glutamicum developed several antioxidant defenses including millimolar concentrations of mycothiol (MSH) and protective enzymes. Glutathione (GSH) S-transferases (GSTs) with essentially defensive role in oxidative stress have been well defined in numerous microorganisms, while their physiological and biochemical functions remained elusive in C. glutamicum thus far. Results In the present study, we described protein NCgl1216 belonging to a novel MSH S-transferase Xi class (MstX), considered as the equivalent of GST Xi class (GSTX). MstX had a characteristic conserved catalytic motif (Cys-Pro-Trp-Ala, C-P-W-A). MstX was active as thiol transferase, dehydroascorbate reductase, mycothiolyl-hydroquinone reductase and MSH peroxidase, while it showed null activity toward canonical GSTs substrate as 1-chloro-2,4-dinitrobenzene (CDNB) and GST Omega’s specific substance glutathionyl-acetophenones, indicating MstX had some biochemical characteristics related with mycoredoxin (Mrx). Site-directed mutagenesis showed that, among the two cysteine residues of the molecule, only the residue at position 67 was required for the activity. Moreover, the residues adjacent to the active Cys67 were also important for activity. These results indicated that the thiol transferase of MstX operated through a monothiol mechanism. In addition, we found MstX played important role in various stress resistance. The lack of C. glutamicum mstX gene resulted in significant growth inhibition and increased sensitivity under adverse stress condition. The mstX expression was induced by stress. Conclusion Corynebacterium glutamicum MstX might be critically involved in response to oxidative conditions, thereby giving new insight in how C. glutamicum survived oxidative stressful conditions.
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Affiliation(s)
- Meiru Si
- College of Life Sciences, Qufu Normal University, Qufu, 273165, Shandong, China
| | - Chengchuan Che
- College of Life Sciences, Qufu Normal University, Qufu, 273165, Shandong, China
| | - Guanxi Li
- College of Life Sciences, Qufu Normal University, Qufu, 273165, Shandong, China
| | - Xiaona Li
- College of Life Sciences, Qufu Normal University, Qufu, 273165, Shandong, China
| | - Zhijin Gong
- College of Life Sciences, Qufu Normal University, Qufu, 273165, Shandong, China
| | - Jinfeng Liu
- College of Life Sciences, Qufu Normal University, Qufu, 273165, Shandong, China
| | - Ge Yang
- College of Life Sciences, Qufu Normal University, Qufu, 273165, Shandong, China.
| | - Can Chen
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, 466001, Henan, China.
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20
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Senneby E, Sunnerhagen T, Hallström B, Lood R, Malmström J, Karlsson C, Rasmussen M. Identification of two abundant Aerococcus urinae cell wall-anchored proteins. Int J Med Microbiol 2019; 309:151325. [PMID: 31257068 DOI: 10.1016/j.ijmm.2019.06.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 06/16/2019] [Accepted: 06/23/2019] [Indexed: 02/06/2023] Open
Abstract
Aerococcus urinae is an emerging pathogen that causes urinary tract infections, bacteremia and infective endocarditis. The mechanisms through which A. urinae cause infection are largely unknown. The aims of this study were to describe the surface proteome of A. urinae and to analyse A. urinae genomes in search for genes encoding surface proteins. Two proteins, denoted Aerococcal surface protein (Asp) 1 and 2, were through the use of mass spectrometry based proteomics found to quantitatively dominate the aerococcal surface. The presence of these proteins on the surface was also shown using ELISA with serum from rabbits immunized with the recombinant Asp. These proteins had a signal sequence in the amino-terminal end and a cell wall-sorting region in the carboxy-terminal end, which contained an LPATG-motif, a hydrophobic domain and a positively charged tail. Twenty-three additional A. urinae genomes were sequenced using Illumina HiSeq technology. Six different variants of asp genes were found (denoted asp1-6). All isolates had either one or two of these asp-genes located in a conserved locus, designated Locus encoding Aerococcal Surface Proteins (LASP). The 25 genomes had in median 13 genes encoding LPXTG-proteins (range 6-24). For other Gram-positive bacteria, cell wall-anchored surface proteins with an LPXTG-motif play a key role for virulence. Thus, it will be of great interest to explore the function of the Asp proteins of A. urinae to establish a better understanding of the molecular mechanisms by which A. urinae cause disease.
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Affiliation(s)
- Erik Senneby
- Division of Infection Medicine, Department of Clinical Sciences, BMC B14, 221 85, Lund University, Lund, Sweden.
| | - Torgny Sunnerhagen
- Division of Infection Medicine, Department of Clinical Sciences, BMC B14, 221 85, Lund University, Lund, Sweden.
| | - Björn Hallström
- Centre for Translational Genomics, Division of Clinical Genetics, BMC B10, 221 85, Lund University, Lund, Sweden.
| | - Rolf Lood
- Division of Infection Medicine, Department of Clinical Sciences, BMC B14, 221 85, Lund University, Lund, Sweden.
| | - Johan Malmström
- Division of Infection Medicine, Department of Clinical Sciences, BMC B14, 221 85, Lund University, Lund, Sweden.
| | - Christofer Karlsson
- Division of Infection Medicine, Department of Clinical Sciences, BMC B14, 221 85, Lund University, Lund, Sweden.
| | - Magnus Rasmussen
- Division of Infection Medicine, Department of Clinical Sciences, BMC B14, 221 85, Lund University, Lund, Sweden.
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21
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Exploring the sequence, function, and evolutionary space of protein superfamilies using sequence similarity networks and phylogenetic reconstructions. Methods Enzymol 2019; 620:315-347. [PMID: 31072492 DOI: 10.1016/bs.mie.2019.03.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Integrative computational methods can facilitate the discovery of new protein functions and enzymatic reactions by enabling the observation and investigation of complex sequence-structure-function and evolutionary relationships within protein superfamilies. Here, we highlight the use of sequence similarity networks (SSNs) and phylogenetic reconstructions to map the functional divergence and evolutionary history of protein superfamilies. We exemplify this approach using the nitroreductase (NTR) flavoenzyme superfamily, demonstrating that SSN investigations can provide a rapid and effective means to classify groups of proteins, expose sequence similarity relationships across the global scale of a protein superfamily, and efficiently support detailed phylogenetic analyses. Integration of such approaches with systematic experimental characterization will expand our understanding of the functional diversity of enzymes, their evolution, and their associated physiological roles.
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22
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Sylvestre-Gonon E, Law SR, Schwartz M, Robe K, Keech O, Didierjean C, Dubos C, Rouhier N, Hecker A. Functional, Structural and Biochemical Features of Plant Serinyl-Glutathione Transferases. FRONTIERS IN PLANT SCIENCE 2019; 10:608. [PMID: 31191562 PMCID: PMC6540824 DOI: 10.3389/fpls.2019.00608] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 04/25/2019] [Indexed: 05/04/2023]
Abstract
Glutathione transferases (GSTs) belong to a ubiquitous multigenic family of enzymes involved in diverse biological processes including xenobiotic detoxification and secondary metabolism. A canonical GST is formed by two domains, the N-terminal one adopting a thioredoxin (TRX) fold and the C-terminal one an all-helical structure. The most recent genomic and phylogenetic analysis based on this domain organization allowed the classification of the GST family into 14 classes in terrestrial plants. These GSTs are further distinguished based on the presence of the ancestral cysteine (Cys-GSTs) present in TRX family proteins or on its substitution by a serine (Ser-GSTs). Cys-GSTs catalyze the reduction of dehydroascorbate and deglutathionylation reactions whereas Ser-GSTs catalyze glutathione conjugation reactions and eventually have peroxidase activity, both activities being important for stress tolerance or herbicide detoxification. Through non-catalytic, so-called ligandin properties, numerous plant GSTs also participate in the binding and transport of small heterocyclic ligands such as flavonoids including anthocyanins, and polyphenols. So far, this function has likely been underestimated compared to the other documented roles of GSTs. In this review, we compiled data concerning the known enzymatic and structural properties as well as the biochemical and physiological functions associated to plant GSTs having a conserved serine in their active site.
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Affiliation(s)
- Elodie Sylvestre-Gonon
- Interactions Arbres-Microorganismes, Institut National de la Recherche Agronomique, Université de Lorraine, Nancy, France
| | - Simon R. Law
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
| | - Mathieu Schwartz
- Centre National de la Recherche Scientifique, Cristallographie, Résonance Magnétique et Modélisations, Université de Lorraine, Nancy, France
| | - Kevin Robe
- Biochimie et Physiologie Moléculaire des Plantes (BPMP), INRA, CNRS, SupAgro-M, Université de Montpellier, Montpellier, France
| | - Olivier Keech
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
| | - Claude Didierjean
- Centre National de la Recherche Scientifique, Cristallographie, Résonance Magnétique et Modélisations, Université de Lorraine, Nancy, France
| | - Christian Dubos
- Biochimie et Physiologie Moléculaire des Plantes (BPMP), INRA, CNRS, SupAgro-M, Université de Montpellier, Montpellier, France
| | - Nicolas Rouhier
- Interactions Arbres-Microorganismes, Institut National de la Recherche Agronomique, Université de Lorraine, Nancy, France
- *Correspondence: Nicolas Rouhier, Arnaud Hecker,
| | - Arnaud Hecker
- Interactions Arbres-Microorganismes, Institut National de la Recherche Agronomique, Université de Lorraine, Nancy, France
- *Correspondence: Nicolas Rouhier, Arnaud Hecker,
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23
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Kontur WS, Olmsted CN, Yusko LM, Niles AV, Walters KA, Beebe ET, Vander Meulen KA, Karlen SD, Gall DL, Noguera DR, Donohue TJ. A heterodimeric glutathione S-transferase that stereospecifically breaks lignin's β( R)-aryl ether bond reveals the diversity of bacterial β-etherases. J Biol Chem 2018; 294:1877-1890. [PMID: 30541921 PMCID: PMC6369299 DOI: 10.1074/jbc.ra118.006548] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Revised: 12/07/2018] [Indexed: 11/12/2022] Open
Abstract
Lignin is a heterogeneous polymer of aromatic subunits that is a major component of lignocellulosic plant biomass. Understanding how microorganisms deconstruct lignin is important for understanding the global carbon cycle and could aid in developing systems for processing plant biomass into valuable commodities. Sphingomonad bacteria use stereospecific glutathione S-transferases (GSTs) called β-etherases to cleave the β-aryl ether (β-O-4) bond, the most common bond between aromatic subunits in lignin. Previously characterized bacterial β-etherases are homodimers that fall into two distinct GST subclasses: LigE homologues, which cleave the β(R) stereoisomer of the bond, and LigF homologues, which cleave the β(S) stereoisomer. Here, we report on a heterodimeric β-etherase (BaeAB) from the sphingomonad Novosphingobium aromaticivorans that stereospecifically cleaves the β(R)-aryl ether bond of the di-aromatic compound β-(2-methoxyphenoxy)-γ-hydroxypropiovanillone (MPHPV). BaeAB's subunits are phylogenetically distinct from each other and from other β-etherases, although they are evolutionarily related to LigF, despite the fact that BaeAB and LigF cleave different β-aryl ether bond stereoisomers. We identify amino acid residues in BaeAB's BaeA subunit important for substrate binding and catalysis, including an asparagine that is proposed to activate the GSH cofactor. We also show that BaeAB homologues from other sphingomonads can cleave β(R)-MPHPV and that they may be as common in bacteria as LigE homologues. Our results suggest that the ability to cleave the β-aryl ether bond arose independently at least twice in GSTs and that BaeAB homologues may be important for cleaving the β(R)-aryl ether bonds of lignin-derived oligomers in nature.
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Affiliation(s)
- Wayne S Kontur
- From the Wisconsin Energy Institute.,the Department of Energy Great Lakes Bioenergy Research Center, and
| | - Charles N Olmsted
- From the Wisconsin Energy Institute.,the Department of Energy Great Lakes Bioenergy Research Center, and
| | - Larissa M Yusko
- From the Wisconsin Energy Institute.,the Department of Energy Great Lakes Bioenergy Research Center, and
| | - Alyssa V Niles
- From the Wisconsin Energy Institute.,the Department of Energy Great Lakes Bioenergy Research Center, and
| | - Kevin A Walters
- From the Wisconsin Energy Institute.,the Department of Energy Great Lakes Bioenergy Research Center, and
| | - Emily T Beebe
- From the Wisconsin Energy Institute.,the Department of Energy Great Lakes Bioenergy Research Center, and.,the Departments of Biochemistry
| | - Kirk A Vander Meulen
- From the Wisconsin Energy Institute.,the Department of Energy Great Lakes Bioenergy Research Center, and.,the Departments of Biochemistry
| | - Steven D Karlen
- From the Wisconsin Energy Institute.,the Department of Energy Great Lakes Bioenergy Research Center, and.,the Departments of Biochemistry
| | - Daniel L Gall
- From the Wisconsin Energy Institute.,the Department of Energy Great Lakes Bioenergy Research Center, and
| | - Daniel R Noguera
- From the Wisconsin Energy Institute.,the Department of Energy Great Lakes Bioenergy Research Center, and.,Civil and Environmental Engineering, and
| | - Timothy J Donohue
- From the Wisconsin Energy Institute, .,the Department of Energy Great Lakes Bioenergy Research Center, and.,Bacteriology, University of Wisconsin, Madison, Wisconsin 53706
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24
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Schwartz M, Perrot T, Deroy A, Roret T, Morel‐Rouhier M, Mulliert G, Gelhaye E, Favier F, Didierjean C. Trametes versicolor
glutathione transferase Xi 3, a dual Cys‐GST with catalytic specificities of both Xi and Omega classes. FEBS Lett 2018; 592:3163-3172. [DOI: 10.1002/1873-3468.13224] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 08/09/2018] [Accepted: 08/11/2018] [Indexed: 11/06/2022]
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25
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Copp JN, Akiva E, Babbitt PC, Tokuriki N. Revealing Unexplored Sequence-Function Space Using Sequence Similarity Networks. Biochemistry 2018; 57:4651-4662. [PMID: 30052428 DOI: 10.1021/acs.biochem.8b00473] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The rapidly expanding number of protein sequences found in public databases can improve our understanding of how protein functions evolve. However, our current knowledge of protein function likely represents a small fraction of the diverse repertoire that exists in nature. Integrative computational methods can facilitate the discovery of new protein functions and enzymatic reactions through the observation and investigation of the complex sequence-structure-function relationships within protein superfamilies. Here, we highlight the use of sequence similarity networks (SSNs) to identify previously unexplored sequence and function space. We exemplify this approach using the nitroreductase (NTR) superfamily. We demonstrate that SSN investigations can provide a rapid and effective means to classify groups of proteins, therefore exposing experimentally unexplored sequences that may exhibit novel functionality. Integration of such approaches with systematic experimental characterization will expand our understanding of the functional diversity of enzymes and their associated physiological roles.
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Affiliation(s)
- Janine N Copp
- Michael Smith Laboratories , University of British Columbia , 2185 East Mall , Vancouver , British Columbia V6T 1Z4 , Canada
| | - Eyal Akiva
- Department of Bioengineering and Therapeutic Sciences , University of California , San Francisco , California 94158 , United States.,Quantitative Biosciences Institute , University of California , San Francisco , California 94143 , United States
| | - Patricia C Babbitt
- Department of Bioengineering and Therapeutic Sciences , University of California , San Francisco , California 94158 , United States.,Quantitative Biosciences Institute , University of California , San Francisco , California 94143 , United States
| | - Nobuhiko Tokuriki
- Michael Smith Laboratories , University of British Columbia , 2185 East Mall , Vancouver , British Columbia V6T 1Z4 , Canada
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26
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Holliday GL, Akiva E, Meng EC, Brown SD, Calhoun S, Pieper U, Sali A, Booker SJ, Babbitt PC. Atlas of the Radical SAM Superfamily: Divergent Evolution of Function Using a "Plug and Play" Domain. Methods Enzymol 2018; 606:1-71. [PMID: 30097089 DOI: 10.1016/bs.mie.2018.06.004] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The radical SAM superfamily contains over 100,000 homologous enzymes that catalyze a remarkably broad range of reactions required for life, including metabolism, nucleic acid modification, and biogenesis of cofactors. While the highly conserved SAM-binding motif responsible for formation of the key 5'-deoxyadenosyl radical intermediate is a key structural feature that simplifies identification of superfamily members, our understanding of their structure-function relationships is complicated by the modular nature of their structures, which exhibit varied and complex domain architectures. To gain new insight about these relationships, we classified the entire set of sequences into similarity-based subgroups that could be visualized using sequence similarity networks. This superfamily-wide analysis reveals important features that had not previously been appreciated from studies focused on one or a few members. Functional information mapped to the networks indicates which members have been experimentally or structurally characterized, their known reaction types, and their phylogenetic distribution. Despite the biological importance of radical SAM chemistry, the vast majority of superfamily members have never been experimentally characterized in any way, suggesting that many new reactions remain to be discovered. In addition to 20 subgroups with at least one known function, we identified additional subgroups made up entirely of sequences of unknown function. Importantly, our results indicate that even general reaction types fail to track well with our sequence similarity-based subgroupings, raising major challenges for function prediction for currently identified and new members that continue to be discovered. Interactive similarity networks and other data from this analysis are available from the Structure-Function Linkage Database.
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Affiliation(s)
- Gemma L Holliday
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, United States.
| | - Eyal Akiva
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, United States
| | - Elaine C Meng
- Resource for Biocomputing, Visualization, and Informatics, Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA, United States
| | - Shoshana D Brown
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, United States
| | - Sara Calhoun
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, United States; Graduate Program in Biophysics, University of California, San Francisco, CA, United States
| | - Ursula Pieper
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, United States
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, United States; Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, United States; Quantitative Biosciences Institute, University of California, San Francisco, CA, United States
| | - Squire J Booker
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States; Department of Chemistry, The Pennsylvania State University, University Park, PA, United States; The Howard Hughes Medical Institute, The Pennsylvania State University, University Park, PA, United States
| | - Patricia C Babbitt
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, United States; Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, United States; Quantitative Biosciences Institute, University of California, San Francisco, CA, United States.
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27
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Ghodge SV, Raushel FM. Structure, Mechanism, and Substrate Profiles of the Trinuclear Metallophosphatases from the Amidohydrolase Superfamily. Methods Enzymol 2018; 607:187-216. [PMID: 30149858 DOI: 10.1016/bs.mie.2018.04.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The rate of reliable protein function annotation has not kept pace with the rapid advances in genome sequencing technology. This has created a gap between the number of available protein sequences, and an accurate determination of the respective physiological functions. This investigation has attempted to bridge the gap within the confines of members of the polymerase and histidinol phosphatase family of proteins in cog1387 and cog0613, which is related to the amidohydrolase superfamily. The adopted approach relies on using the mechanistic knowledge of a known enzymatic reaction, and discovering functions of closely related homologs using various tools including bioinformatics and rational library screening. The initial enzymatic reaction was that of L-histidinol phosphate phosphatase. Extensive structural, biochemical, and bioinformatic analysis of enzymes capable of hydrolyzing L-histidinol phosphate provided useful insights in predicting substrates and mechanistic studies of related enzymes. This led to the discovery of unprecedented catalytic functions such as a cyclic phosphate dihydrolase that specifically hydrolyzed a cyclic phosphodiester to inorganic phosphate and a vicinal diol; a phosphoesterase that hydrolyzes the 3'-phosphate of 3',5'-adenosine bisphosphate and similar nucleotides; and the first reported 5'-3' exonuclease for 5'-phosphorylated oligonucleotides from Escherichia coli and related organisms. This work provides a template for developing sequence-structure-function correlations within a family of enzymes that helps expedite new enzyme function discovery and more accurate annotations in protein databases.
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Affiliation(s)
- Swapnil V Ghodge
- Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Frank M Raushel
- Department of Chemistry, Texas A & M University, College Station, TX, United States.
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28
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Tossounian MA, Wahni K, Van Molle I, Vertommen D, Astolfi Rosado L, Messens J. Redox-regulated methionine oxidation of Arabidopsis thaliana glutathione transferase Phi9 induces H-site flexibility. Protein Sci 2018; 28:56-67. [PMID: 29732642 DOI: 10.1002/pro.3440] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 04/30/2018] [Accepted: 04/30/2018] [Indexed: 11/08/2022]
Abstract
Glutathione transferase enzymes help plants to cope with biotic and abiotic stress. They mainly catalyze the conjugation of glutathione (GSH) onto xenobiotics, and some act as glutathione peroxidase. With X-ray crystallography, kinetics, and thermodynamics, we studied the impact of oxidation on Arabidopsis thaliana glutathione transferase Phi 9 (GSTF9). GSTF9 has no cysteine in its sequence, and it adopts a universal GST structural fold characterized by a typical conserved GSH-binding site (G-site) and a hydrophobic co-substrate-binding site (H-site). At elevated H2 O2 concentrations, methionine sulfur oxidation decreases its transferase activity. This oxidation increases the flexibility of the H-site loop, which is reflected in lower activities for hydrophobic substrates. Determination of the transition state thermodynamic parameters shows that upon oxidation an increased enthalpic penalty is counterbalanced by a more favorable entropic contribution. All in all, to guarantee functionality under oxidative stress conditions, GSTF9 employs a thermodynamic and structural compensatory mechanism and becomes substrate of methionine sulfoxide reductases, making it a redox-regulated enzyme.
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Affiliation(s)
- Maria-Armineh Tossounian
- VIB-VUB Center for Structural Biology, Brussels, B-1050, Belgium.,Brussels Center for Redox Biology, Brussels, B-1050, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, B-1050, Belgium
| | - Khadija Wahni
- VIB-VUB Center for Structural Biology, Brussels, B-1050, Belgium.,Brussels Center for Redox Biology, Brussels, B-1050, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, B-1050, Belgium
| | - Inge Van Molle
- VIB-VUB Center for Structural Biology, Brussels, B-1050, Belgium.,Brussels Center for Redox Biology, Brussels, B-1050, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, B-1050, Belgium
| | - Didier Vertommen
- de Duve Institute, Université Catholique de Louvain, Brussels, B-1200, Belgium
| | - Leonardo Astolfi Rosado
- VIB-VUB Center for Structural Biology, Brussels, B-1050, Belgium.,Brussels Center for Redox Biology, Brussels, B-1050, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, B-1050, Belgium
| | - Joris Messens
- VIB-VUB Center for Structural Biology, Brussels, B-1050, Belgium.,Brussels Center for Redox Biology, Brussels, B-1050, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, B-1050, Belgium
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29
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Schwartz M, Perrot T, Aubert E, Dumarçay S, Favier F, Gérardin P, Morel-Rouhier M, Mulliert G, Saiag F, Didierjean C, Gelhaye E. Molecular recognition of wood polyphenols by phase II detoxification enzymes of the white rot Trametes versicolor. Sci Rep 2018; 8:8472. [PMID: 29855494 PMCID: PMC5981210 DOI: 10.1038/s41598-018-26601-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 05/04/2018] [Indexed: 11/09/2022] Open
Abstract
Wood decay fungi have complex detoxification systems that enable them to cope with secondary metabolites produced by plants. Although the number of genes encoding for glutathione transferases is especially expanded in lignolytic fungi, little is known about their target molecules. In this study, by combining biochemical, enzymatic and structural approaches, interactions between polyphenols and six glutathione transferases from the white-rot fungus Trametes versicolor have been demonstrated. Two isoforms, named TvGSTO3S and TvGSTO6S have been deeply studied at the structural level. Each isoform shows two distinct ligand-binding sites, a narrow L-site at the dimer interface and a peculiar deep hydrophobic H-site. In TvGSTO3S, the latter appears optimized for aromatic ligand binding such as hydroxybenzophenones. Affinity crystallography revealed that this H-site retains the flavonoid dihydrowogonin from a partially purified wild-cherry extract. Besides, TvGSTO6S binds two molecules of the flavonoid naringenin in the L-site. These data suggest that TvGSTO isoforms could interact with plant polyphenols released during wood degradation.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Fanny Saiag
- Université de Lorraine, INRA, IAM, Nancy, France
| | | | - Eric Gelhaye
- Université de Lorraine, INRA, IAM, Nancy, France.
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30
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Perner J, Kotál J, Hatalová T, Urbanová V, Bartošová-Sojková P, Brophy PM, Kopáček P. Inducible glutathione S-transferase (IrGST1) from the tick Ixodes ricinus is a haem-binding protein. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2018. [PMID: 29526768 DOI: 10.1016/j.ibmb.2018.02.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Blood-feeding parasites are inadvertently exposed to high doses of potentially cytotoxic haem liberated upon host blood digestion. Detoxification of free haem is a special challenge for ticks, which digest haemoglobin intracellularly. Ticks lack a haem catabolic mechanism, mediated by haem oxygenase, and need to dispose of vast majority of acquired haem via its accumulation in haemosomes. The knowledge of individual molecules involved in the maintenance of haem homeostasis in ticks is still rather limited. RNA-seq analyses of the Ixodes ricinus midguts from blood- and serum-fed females identified an abundant transcript of glutathione S-transferase (gst) to be substantially up-regulated in the presence of red blood cells in the diet. Here, we have determined the full sequence of this encoding gene, ir-gst1, and found that it is homologous to the delta-/epsilon-class of GSTs. Phylogenetic analyses across related chelicerates revealed that only one clear IrGST1 orthologue could be found in each available transcriptome from hard and soft ticks. These orthologues create a well-supported clade clearly separated from other ticks' or mites' delta-/epsilon-class GSTs and most likely evolved as an adaptation to tick blood-feeding life style. We have confirmed that IrGST1 expression is induced by dietary haem(oglobin), and not by iron or other components of host blood. Kinetic properties of recombinant IrGST1 were evaluated by model and natural GST substrates. The enzyme was also shown to bind haemin in vitro as evidenced by inhibition assay, VIS spectrophotometry, gel filtration, and affinity chromatography. In the native state, IrGST1 forms a dimer which further polymerises upon binding of excessive amount of haemin molecules. Due to susceptibility of ticks to haem as a signalling molecule, we speculate that the expression of IrGST1 in tick midgut functions as intracellular buffer of labile haem pool to ameliorate its cytotoxic effects upon haemoglobin intracellular hydrolysis.
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Affiliation(s)
- Jan Perner
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 370 05, České Budějovice, Czech Republic; Faculty of Science, University of South Bohemia, Branišovská 31, 370 05, České Budějovice, Czech Republic.
| | - Jan Kotál
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 370 05, České Budějovice, Czech Republic; Faculty of Science, University of South Bohemia, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - Tereza Hatalová
- Faculty of Science, University of South Bohemia, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - Veronika Urbanová
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - Pavla Bartošová-Sojková
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - Peter M Brophy
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, SY23 3DA, UK
| | - Petr Kopáček
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 370 05, České Budějovice, Czech Republic
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31
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Davidson R, Baas BJ, Akiva E, Holliday GL, Polacco BJ, LeVieux JA, Pullara CR, Zhang YJ, Whitman CP, Babbitt PC. A global view of structure-function relationships in the tautomerase superfamily. J Biol Chem 2018; 293:2342-2357. [PMID: 29184004 PMCID: PMC5818174 DOI: 10.1074/jbc.m117.815340] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 11/27/2017] [Indexed: 12/13/2022] Open
Abstract
The tautomerase superfamily (TSF) consists of more than 11,000 nonredundant sequences present throughout the biosphere. Characterized members have attracted much attention because of the unusual and key catalytic role of an N-terminal proline. These few characterized members catalyze a diverse range of chemical reactions, but the full scale of their chemical capabilities and biological functions remains unknown. To gain new insight into TSF structure-function relationships, we performed a global analysis of similarities across the entire superfamily and computed a sequence similarity network to guide classification into distinct subgroups. Our results indicate that TSF members are found in all domains of life, with most being present in bacteria. The eukaryotic members of the cis-3-chloroacrylic acid dehalogenase subgroup are limited to fungal species, whereas the macrophage migration inhibitory factor subgroup has wide eukaryotic representation (including mammals). Unexpectedly, we found that 346 TSF sequences lack Pro-1, of which 85% are present in the malonate semialdehyde decarboxylase subgroup. The computed network also enabled the identification of similarity paths, namely sequences that link functionally diverse subgroups and exhibit transitional structural features that may help explain reaction divergence. A structure-guided comparison of these linker proteins identified conserved transitions between them, and kinetic analysis paralleled these observations. Phylogenetic reconstruction of the linker set was consistent with these findings. Our results also suggest that contemporary TSF members may have evolved from a short 4-oxalocrotonate tautomerase-like ancestor followed by gene duplication and fusion. Our new linker-guided strategy can be used to enrich the discovery of sequence/structure/function transitions in other enzyme superfamilies.
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Affiliation(s)
| | - Bert-Jan Baas
- the Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy
| | - Eyal Akiva
- From the Department of Bioengineering and Therapeutic Sciences
| | | | | | | | - Collin R Pullara
- the Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy
| | - Yan Jessie Zhang
- the Department of Molecular Biosciences, and
- the Institute for Cellular and Molecular Biology, University of Texas, Austin, Texas 78712
| | - Christian P Whitman
- the Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy,
| | - Patricia C Babbitt
- From the Department of Bioengineering and Therapeutic Sciences,
- the Department of Pharmaceutical Chemistry, and
- the Quantitative Biosciences Institute, University of California, San Francisco, California 94143 and
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32
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Kontur WS, Bingman CA, Olmsted CN, Wassarman DR, Ulbrich A, Gall DL, Smith RW, Yusko LM, Fox BG, Noguera DR, Coon JJ, Donohue TJ. Novosphingobium aromaticivorans uses a Nu-class glutathione S-transferase as a glutathione lyase in breaking the β-aryl ether bond of lignin. J Biol Chem 2018; 293:4955-4968. [PMID: 29449375 PMCID: PMC5892560 DOI: 10.1074/jbc.ra117.001268] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 02/01/2018] [Indexed: 01/01/2023] Open
Abstract
As a major component of plant cell walls, lignin is a potential renewable source of valuable chemicals. Several sphingomonad bacteria have been identified that can break the β-aryl ether bond connecting most phenylpropanoid units of the lignin heteropolymer. Here, we tested three sphingomonads predicted to be capable of breaking the β-aryl ether bond of the dimeric aromatic compound guaiacylglycerol-β-guaiacyl ether (GGE) and found that Novosphingobium aromaticivorans metabolizes GGE at one of the fastest rates thus far reported. After the ether bond of racemic GGE is broken by replacement with a thioether bond involving glutathione, the glutathione moiety must be removed from the resulting two stereoisomers of the phenylpropanoid conjugate β-glutathionyl-γ-hydroxypropiovanillone (GS-HPV). We found that the Nu-class glutathione S-transferase NaGSTNu is the only enzyme needed to remove glutathione from both (R)- and (S)-GS-HPV in N. aromaticivorans We solved the crystal structure of NaGSTNu and used molecular modeling to propose a mechanism for the glutathione lyase (deglutathionylation) reaction in which an enzyme-stabilized glutathione thiolate attacks the thioether bond of GS-HPV, and the reaction proceeds through an enzyme-stabilized enolate intermediate. Three residues implicated in the proposed mechanism (Thr51, Tyr166, and Tyr224) were found to be critical for the lyase reaction. We also found that Nu-class GSTs from Sphingobium sp. SYK-6 (which can also break the β-aryl ether bond) and Escherichia coli (which cannot break the β-aryl ether bond) can also cleave (R)- and (S)-GS-HPV, suggesting that glutathione lyase activity may be common throughout this widespread but largely uncharacterized class of glutathione S-transferases.
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Affiliation(s)
- Wayne S Kontur
- From the Wisconsin Energy Institute.,the Department of Energy Great Lakes Bioenergy Research Center
| | - Craig A Bingman
- the Department of Energy Great Lakes Bioenergy Research Center.,the Departments of Biochemistry
| | - Charles N Olmsted
- From the Wisconsin Energy Institute.,the Department of Energy Great Lakes Bioenergy Research Center
| | - Douglas R Wassarman
- From the Wisconsin Energy Institute.,the Department of Energy Great Lakes Bioenergy Research Center
| | | | - Daniel L Gall
- From the Wisconsin Energy Institute.,the Department of Energy Great Lakes Bioenergy Research Center
| | - Robert W Smith
- the Department of Energy Great Lakes Bioenergy Research Center.,the Departments of Biochemistry
| | | | - Brian G Fox
- From the Wisconsin Energy Institute.,the Department of Energy Great Lakes Bioenergy Research Center.,the Departments of Biochemistry
| | - Daniel R Noguera
- From the Wisconsin Energy Institute.,the Department of Energy Great Lakes Bioenergy Research Center.,Civil and Environmental Engineering
| | - Joshua J Coon
- From the Wisconsin Energy Institute.,the Department of Energy Great Lakes Bioenergy Research Center.,Chemistry.,the Genome Center of Wisconsin, and.,Biomolecular Chemistry, and
| | - Timothy J Donohue
- From the Wisconsin Energy Institute, .,the Department of Energy Great Lakes Bioenergy Research Center.,Bacteriology, University of Wisconsin, Madison, Wisconsin 53706
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33
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Underground metabolism: network-level perspective and biotechnological potential. Curr Opin Biotechnol 2018; 49:108-114. [DOI: 10.1016/j.copbio.2017.07.015] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 07/20/2017] [Accepted: 07/21/2017] [Indexed: 12/18/2022]
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34
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.Newton MS, Arcus VL, Gerth ML, Patrick WM. Enzyme evolution: innovation is easy, optimization is complicated. Curr Opin Struct Biol 2018; 48:110-116. [DOI: 10.1016/j.sbi.2017.11.007] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 11/21/2017] [Indexed: 10/18/2022]
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35
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Holliday GL, Brown SD, Akiva E, Mischel D, Hicks MA, Morris JH, Huang CC, Meng EC, Pegg SCH, Ferrin TE, Babbitt PC. Biocuration in the structure-function linkage database: the anatomy of a superfamily. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2017; 2017:3074783. [PMID: 28365730 PMCID: PMC5467563 DOI: 10.1093/database/bax006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 01/23/2017] [Indexed: 12/11/2022]
Abstract
With ever-increasing amounts of sequence data available in both the primary literature and sequence repositories, there is a bottleneck in annotating molecular function to a sequence. This article describes the biocuration process and methods used in the structure-function linkage database (SFLD) to help address some of the challenges. We discuss how the hierarchy within the SFLD allows us to infer detailed functional properties for functionally diverse enzyme superfamilies in which all members are homologous, conserve an aspect of their chemical function and have associated conserved structural features that enable the chemistry. Also presented is the Enzyme Structure-Function Ontology (ESFO), which has been designed to capture the relationships between enzyme sequence, structure and function that underlie the SFLD and is used to guide the biocuration processes within the SFLD. Database URL:http://sfld.rbvi.ucsf.edu/
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Affiliation(s)
- Gemma L Holliday
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94143, USA
| | - Shoshana D Brown
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94143, USA
| | - Eyal Akiva
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94143, USA
| | - David Mischel
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94143, USA
| | - Michael A Hicks
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94143, USA.,Human Longevity, Inc, San Diego, CA 92121, USA
| | - John H Morris
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA 94143, USA
| | - Conrad C Huang
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA 94143, USA
| | - Elaine C Meng
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA 94143, USA
| | | | - Thomas E Ferrin
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA 94143, USA.,California Institute for Quantitative Biosciences, University of California, San Francisco, CA 94158, USA
| | - Patricia C Babbitt
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94143, USA.,Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA 94143, USA.,California Institute for Quantitative Biosciences, University of California, San Francisco, CA 94158, USA
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36
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Mitchell JB. Enzyme function and its evolution. Curr Opin Struct Biol 2017; 47:151-156. [PMID: 29107208 DOI: 10.1016/j.sbi.2017.10.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 08/29/2017] [Accepted: 10/02/2017] [Indexed: 01/10/2023]
Abstract
With rapid increases over recent years in the determination of protein sequence and structure, alongside knowledge of thousands of enzyme functions and hundreds of chemical mechanisms, it is now possible to combine breadth and depth in our understanding of enzyme evolution. Phylogenetics continues to move forward, though determining correct evolutionary family trees is not trivial. Protein function prediction has spawned a variety of promising methods that offer the prospect of identifying enzymes across the whole range of chemical functions and over numerous species. This knowledge is essential to understand antibiotic resistance, as well as in protein re-engineering and de novo enzyme design.
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Affiliation(s)
- John Bo Mitchell
- EaStCHEM School of Chemistry and Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Scotland KY16 9ST, United Kingdom
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37
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Evolutionary and molecular foundations of multiple contemporary functions of the nitroreductase superfamily. Proc Natl Acad Sci U S A 2017; 114:E9549-E9558. [PMID: 29078300 PMCID: PMC5692541 DOI: 10.1073/pnas.1706849114] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Functionally diverse enzyme superfamilies are sets of homologs that conserve a structural fold and mechanistic details but perform various distinct chemical reactions. What are the evolutionary routes by which ancestral proteins diverge to produce extant enzymes? We present an approach that combines experimental data with computational tools to trace these sequence–structure–function transitions in a model system, the functionally diverse flavin mononucleotide-dependent nitroreductases (NTRs). Our results suggest an evolutionary model in which contemporary NTR classes have diverged in a radial manner from a minimal flavin-binding scaffold via insertions at key positions and fixation of functional residues, yielding the reaction versatility of contemporary enzymes. These principles will facilitate rational design of NTRs and advance general approaches for delineating the emergence of functional diversity in enzyme superfamilies. Insight regarding how diverse enzymatic functions and reactions have evolved from ancestral scaffolds is fundamental to understanding chemical and evolutionary biology, and for the exploitation of enzymes for biotechnology. We undertook an extensive computational analysis using a unique and comprehensive combination of tools that include large-scale phylogenetic reconstruction to determine the sequence, structural, and functional relationships of the functionally diverse flavin mononucleotide-dependent nitroreductase (NTR) superfamily (>24,000 sequences from all domains of life, 54 structures, and >10 enzymatic functions). Our results suggest an evolutionary model in which contemporary subgroups of the superfamily have diverged in a radial manner from a minimal flavin-binding scaffold. We identified the structural design principle for this divergence: Insertions at key positions in the minimal scaffold that, combined with the fixation of key residues, have led to functional specialization. These results will aid future efforts to delineate the emergence of functional diversity in enzyme superfamilies, provide clues for functional inference for superfamily members of unknown function, and facilitate rational redesign of the NTR scaffold.
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38
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Evans AF, O'Brien SR, Ma R, Hager AG, Riggins CW, Lambert KN, Riechers DE. Biochemical characterization of metabolism-based atrazine resistance in Amaranthus tuberculatus and identification of an expressed GST associated with resistance. PLANT BIOTECHNOLOGY JOURNAL 2017; 15:1238-1249. [PMID: 28218978 PMCID: PMC5595711 DOI: 10.1111/pbi.12711] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Revised: 02/02/2017] [Accepted: 02/08/2017] [Indexed: 05/08/2023]
Abstract
Rapid detoxification of atrazine in naturally tolerant crops such as maize (Zea mays) and grain sorghum (Sorghum bicolor) results from glutathione S-transferase (GST) activity. In previous research, two atrazine-resistant waterhemp (Amaranthus tuberculatus) populations from Illinois, U.S.A. (designated ACR and MCR), displayed rapid formation of atrazine-glutathione (GSH) conjugates, implicating elevated rates of metabolism as the resistance mechanism. Our main objective was to utilize protein purification combined with qualitative proteomics to investigate the hypothesis that enhanced atrazine detoxification, catalysed by distinct GSTs, confers resistance in ACR and MCR. Additionally, candidate AtuGST expression was analysed in an F2 population segregating for atrazine resistance. ACR and MCR showed higher specific activities towards atrazine in partially purified ammonium sulphate and GSH affinity-purified fractions compared to an atrazine-sensitive population (WCS). One-dimensional electrophoresis of these fractions displayed an approximate 26-kDa band, typical of GST subunits. Several phi- and tau-class GSTs were identified by LC-MS/MS from each population, based on peptide similarity with GSTs from Arabidopsis. Elevated constitutive expression of one phi-class GST, named AtuGSTF2, correlated strongly with atrazine resistance in ACR and MCR and segregating F2 population. These results indicate that AtuGSTF2 may be linked to a metabolic mechanism that confers atrazine resistance in ACR and MCR.
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Affiliation(s)
- Anton F. Evans
- Department of Crop SciencesUniversity of Illinois at Urbana‐ChampaignUrbanaILUSA
| | - Sarah R. O'Brien
- Department of Crop SciencesUniversity of Illinois at Urbana‐ChampaignUrbanaILUSA
| | - Rong Ma
- Department of Crop SciencesUniversity of Illinois at Urbana‐ChampaignUrbanaILUSA
| | - Aaron G. Hager
- Department of Crop SciencesUniversity of Illinois at Urbana‐ChampaignUrbanaILUSA
| | - Chance W. Riggins
- Department of Crop SciencesUniversity of Illinois at Urbana‐ChampaignUrbanaILUSA
| | - Kris N. Lambert
- Department of Crop SciencesUniversity of Illinois at Urbana‐ChampaignUrbanaILUSA
| | - Dean E. Riechers
- Department of Crop SciencesUniversity of Illinois at Urbana‐ChampaignUrbanaILUSA
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Perperopoulou F, Pouliou F, Labrou NE. Recent advances in protein engineering and biotechnological applications of glutathione transferases. Crit Rev Biotechnol 2017; 38:511-528. [PMID: 28936894 DOI: 10.1080/07388551.2017.1375890] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Glutathione transferases (GSTs, EC 2.5.1.18) are a widespread family of enzymes that play a central role in the detoxification, metabolism, and transport or sequestration of endogenous or xenobiotic compounds. During the last two decades, delineation of the important structural and catalytic features of GSTs has laid the groundwork for engineering GSTs, involving both rational and random approaches, aiming to create new variants with new or altered properties. These approaches have expanded the usefulness of native GSTs, not only for understanding the fundamentals of molecular detoxification mechanisms, but also for the development medical, analytical, environmental, and agricultural applications. This review article attempts to summarize successful examples and current developments on GST engineering, highlighting in parallel the recent knowledge gained on their phylogenetic relationships, structural/catalytic features, and biotechnological applications.
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Affiliation(s)
- Fereniki Perperopoulou
- a Department of Biotechnology, Laboratory of Enzyme Technology , School of Food, Biotechnology and Development, Agricultural University of Athens , Athens , Greece
| | - Fotini Pouliou
- a Department of Biotechnology, Laboratory of Enzyme Technology , School of Food, Biotechnology and Development, Agricultural University of Athens , Athens , Greece
| | - Nikolaos E Labrou
- a Department of Biotechnology, Laboratory of Enzyme Technology , School of Food, Biotechnology and Development, Agricultural University of Athens , Athens , Greece
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Gerlt JA. Genomic Enzymology: Web Tools for Leveraging Protein Family Sequence-Function Space and Genome Context to Discover Novel Functions. Biochemistry 2017; 56:4293-4308. [PMID: 28826221 PMCID: PMC5569362 DOI: 10.1021/acs.biochem.7b00614] [Citation(s) in RCA: 136] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
![]()
The exponentially increasing number
of protein and nucleic acid
sequences provides opportunities to discover novel enzymes, metabolic
pathways, and metabolites/natural products, thereby adding to our
knowledge of biochemistry and biology. The challenge has evolved from
generating sequence information to mining the databases to integrating
and leveraging the available information, i.e., the availability of
“genomic enzymology” web tools. Web tools that allow
identification of biosynthetic gene clusters are widely used by the
natural products/synthetic biology community, thereby facilitating
the discovery of novel natural products and the enzymes responsible
for their biosynthesis. However, many novel enzymes with interesting
mechanisms participate in uncharacterized small-molecule metabolic
pathways; their discovery and functional characterization also can
be accomplished by leveraging information in protein and nucleic acid
databases. This Perspective focuses on two genomic enzymology web
tools that assist the discovery novel metabolic pathways: (1) Enzyme
Function Initiative-Enzyme Similarity Tool (EFI-EST) for generating
sequence similarity networks to visualize and analyze sequence–function
space in protein families and (2) Enzyme Function Initiative-Genome
Neighborhood Tool (EFI-GNT) for generating genome neighborhood networks
to visualize and analyze the genome context in microbial and fungal
genomes. Both tools have been adapted to other applications to facilitate
target selection for enzyme discovery and functional characterization.
As the natural products community has demonstrated, the enzymology
community needs to embrace the essential role of web tools that allow
the protein and genome sequence databases to be leveraged for novel
insights into enzymological problems.
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Affiliation(s)
- John A Gerlt
- Departments of Biochemistry and Chemistry, Institute for Genomic Biology, University of Illinois , Urbana-Champaign Urbana, Illinois 61801, United States
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Pégeot H, Mathiot S, Perrot T, Gense F, Hecker A, Didierjean C, Rouhier N. Structural plasticity among glutathione transferase Phi members: natural combination of catalytic residues confers dual biochemical activities. FEBS J 2017. [DOI: 10.1111/febs.14138] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Henri Pégeot
- UMR 1136 Interactions Arbres/Microorganismes; Faculté des Sciences et Technologies; Université de Lorraine/INRA; Vandoeuvre-lès-Nancy France
| | - Sandrine Mathiot
- UMR 7036 CRM2, Equipe BioMod; Faculté des Sciences et Technologies; Université de Lorraine/CNRS; Vandoeuvre-lès-Nancy France
| | - Thomas Perrot
- UMR 1136 Interactions Arbres/Microorganismes; Faculté des Sciences et Technologies; Université de Lorraine/INRA; Vandoeuvre-lès-Nancy France
| | - Frédéric Gense
- UMR 7036 CRM2, Equipe BioMod; Faculté des Sciences et Technologies; Université de Lorraine/CNRS; Vandoeuvre-lès-Nancy France
| | - Arnaud Hecker
- UMR 1136 Interactions Arbres/Microorganismes; Faculté des Sciences et Technologies; Université de Lorraine/INRA; Vandoeuvre-lès-Nancy France
| | - Claude Didierjean
- UMR 7036 CRM2, Equipe BioMod; Faculté des Sciences et Technologies; Université de Lorraine/CNRS; Vandoeuvre-lès-Nancy France
| | - Nicolas Rouhier
- UMR 1136 Interactions Arbres/Microorganismes; Faculté des Sciences et Technologies; Université de Lorraine/INRA; Vandoeuvre-lès-Nancy France
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42
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Chatzikonstantinou M, Vlachakis D, Chronopoulou E, Papageorgiou L, Papageorgiou AC, Labrou NE. The glutathione transferase family of Chlamydomonas reinhardtii: Identification and characterization of novel sigma class-like enzymes. ALGAL RES 2017. [DOI: 10.1016/j.algal.2017.03.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Knutson ST, Westwood BM, Leuthaeuser JB, Turner BE, Nguyendac D, Shea G, Kumar K, Hayden JD, Harper AF, Brown SD, Morris JH, Ferrin TE, Babbitt PC, Fetrow JS. An approach to functionally relevant clustering of the protein universe: Active site profile-based clustering of protein structures and sequences. Protein Sci 2017; 26:677-699. [PMID: 28054422 PMCID: PMC5368075 DOI: 10.1002/pro.3112] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Accepted: 12/22/2016] [Indexed: 01/11/2023]
Abstract
Protein function identification remains a significant problem. Solving this problem at the molecular functional level would allow mechanistic determinant identification-amino acids that distinguish details between functional families within a superfamily. Active site profiling was developed to identify mechanistic determinants. DASP and DASP2 were developed as tools to search sequence databases using active site profiling. Here, TuLIP (Two-Level Iterative clustering Process) is introduced as an iterative, divisive clustering process that utilizes active site profiling to separate structurally characterized superfamily members into functionally relevant clusters. Underlying TuLIP is the observation that functionally relevant families (curated by Structure-Function Linkage Database, SFLD) self-identify in DASP2 searches; clusters containing multiple functional families do not. Each TuLIP iteration produces candidate clusters, each evaluated to determine if it self-identifies using DASP2. If so, it is deemed a functionally relevant group. Divisive clustering continues until each structure is either a functionally relevant group member or a singlet. TuLIP is validated on enolase and glutathione transferase structures, superfamilies well-curated by SFLD. Correlation is strong; small numbers of structures prevent statistically significant analysis. TuLIP-identified enolase clusters are used in DASP2 GenBank searches to identify sequences sharing functional site features. Analysis shows a true positive rate of 96%, false negative rate of 4%, and maximum false positive rate of 4%. F-measure and performance analysis on the enolase search results and comparison to GEMMA and SCI-PHY demonstrate that TuLIP avoids the over-division problem of these methods. Mechanistic determinants for enolase families are evaluated and shown to correlate well with literature results.
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Affiliation(s)
- Stacy T. Knutson
- Department of PhysicsWake Forest UniversityWinston‐SalemNorth Carolina27106
- Department of Computer ScienceWake Forest UniversityWinston‐SalemNorth Carolina27106
| | - Brian M. Westwood
- Department of PhysicsWake Forest UniversityWinston‐SalemNorth Carolina27106
- Department of Computer ScienceWake Forest UniversityWinston‐SalemNorth Carolina27106
| | - Janelle B. Leuthaeuser
- Molecular Genetics and Genomics ProgramWake Forest School of MedicineWinston‐SalemNorth Carolina27157
| | - Brandon E. Turner
- Department of PhysicsWake Forest UniversityWinston‐SalemNorth Carolina27106
| | - Don Nguyendac
- Department of PhysicsWake Forest UniversityWinston‐SalemNorth Carolina27106
| | - Gabrielle Shea
- Department of PhysicsWake Forest UniversityWinston‐SalemNorth Carolina27106
| | - Kiran Kumar
- Department of PhysicsWake Forest UniversityWinston‐SalemNorth Carolina27106
| | - Julia D. Hayden
- Biochemistry Program, Dickinson CollegeCarlislePennsylvania17013
| | - Angela F. Harper
- Department of PhysicsWake Forest UniversityWinston‐SalemNorth Carolina27106
| | - Shoshana D. Brown
- Department of Pharmaceutical ChemistryUniversity of CaliforniaSan FranciscoCalifornia94158
| | - John H. Morris
- Department of Pharmaceutical ChemistryUniversity of CaliforniaSan FranciscoCalifornia94158
| | - Thomas E. Ferrin
- Department of Pharmaceutical ChemistryUniversity of CaliforniaSan FranciscoCalifornia94158
| | - Patricia C. Babbitt
- Department of Pharmaceutical ChemistryUniversity of CaliforniaSan FranciscoCalifornia94158
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44
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Integrative view of 2-oxoglutarate/Fe(II)-dependent oxygenase diversity and functions in bacteria. Biochim Biophys Acta Gen Subj 2017; 1861:323-334. [DOI: 10.1016/j.bbagen.2016.12.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 11/09/2016] [Accepted: 12/01/2016] [Indexed: 12/11/2022]
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45
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Direct Heme Uptake by Phytoplankton-Associated Roseobacter Bacteria. mSystems 2017; 2:mSystems00124-16. [PMID: 28083564 PMCID: PMC5225302 DOI: 10.1128/msystems.00124-16] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 12/09/2016] [Indexed: 01/19/2023] Open
Abstract
Ecosystem productivity in large regions of the surface ocean is fueled by iron that has been microbially regenerated from biomass. Currently, the specific microbes and molecules that mediate the transfer of recycled iron between microbial trophic levels remain largely unknown. We characterized a marine bacterial heme transporter and verified its role in acquiring heme, an abundant iron-containing enzyme cofactor. We present evidence that after host cell lysis, phytoplankton-associated bacteria directly extract heme and hemoproteins from algal cellular debris in order to fulfill their iron requirements and that the regulation of this process may be modulated by host cues. Direct heme transport, in contrast to multistep extracellular processing of hemoproteins, may allow certain phytoplankton-associated bacteria to rapidly extract iron from decaying phytoplankton, thus efficiently recycling cellular iron into the wider microbial loop. Iron is an essential micronutrient and can limit the growth of both marine phytoplankton and heterotrophic bacterioplankton. In this study, we investigated the molecular basis of heme transport, an organic iron acquisition pathway, in phytoplankton-associated Roseobacter bacteria and explored the potential role of bacterial heme uptake in the marine environment. We searched 153 Roseobacter genomes and found that nearly half contained putative complete heme transport systems with nearly the same synteny. We also examined a publicly available coculture transcriptome and found that Roseobacter strain Sulfitobacter sp. strain SA11 strongly downregulated a putative heme transport gene cluster during mutualistic growth with a marine diatom, suggesting that the regulation of heme transport might be influenced by host cues. We generated a mutant of phytoplankton-associated Roseobacter strain Ruegeria sp. strain TM1040 by insertionally inactivating its homolog of the TonB-dependent heme transporter hmuR and confirmed the role of this gene in the uptake of heme and hemoproteins. We performed competition experiments between iron-limited wild-type and mutant TM1040 strains and found that the wild type maintains a growth advantage when competing with the mutant for iron compounds derived solely from lysed diatom cells. Heme transport systems were largely absent from public marine metagenomes and metatranscriptomes, suggesting that marine bacteria with the potential for heme transport likely have small standing populations in the free-living bacterioplankton. Heme transport is likely a useful strategy for phytoplankton-associated bacteria because it provides direct access to components of the host intracellular iron pool after lysis. IMPORTANCE Ecosystem productivity in large regions of the surface ocean is fueled by iron that has been microbially regenerated from biomass. Currently, the specific microbes and molecules that mediate the transfer of recycled iron between microbial trophic levels remain largely unknown. We characterized a marine bacterial heme transporter and verified its role in acquiring heme, an abundant iron-containing enzyme cofactor. We present evidence that after host cell lysis, phytoplankton-associated bacteria directly extract heme and hemoproteins from algal cellular debris in order to fulfill their iron requirements and that the regulation of this process may be modulated by host cues. Direct heme transport, in contrast to multistep extracellular processing of hemoproteins, may allow certain phytoplankton-associated bacteria to rapidly extract iron from decaying phytoplankton, thus efficiently recycling cellular iron into the wider microbial loop.
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46
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Skopelitou K, Muleta AW, Papageorgiou AC, Chronopoulou EG, Pavli O, Flemetakis E, Skaracis GN, Labrou NE. Characterization and functional analysis of a recombinant tau class glutathione transferase GmGSTU2-2 from Glycine max. Int J Biol Macromol 2017; 94:802-812. [PMID: 27103493 DOI: 10.1016/j.ijbiomac.2016.04.044] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 03/12/2016] [Accepted: 04/15/2016] [Indexed: 01/31/2023]
Abstract
The plant tau class glutathione transferases (GSTs) perform diverse catalytic as well as non-catalytic roles in detoxification of xenobiotics, prevention of oxidative damage and endogenous metabolism. In the present work, the tau class isoenzyme GSTU2-2 from Glycine max (GmGSTU2-2) was characterized. Gene expression analysis of GmGSTU2 suggested a highly specific and selective induction pattern to osmotic stresses, indicating that gene expression is controlled by a specific mechanism. Purified, recombinant GmGSTU2-2 was shown to exhibit wide-range specificity towards xenobiotic compounds and ligand-binding properties, suggesting that the isoenzyme could provide catalytic flexibility in numerous metabolic conditions. Homology modeling and phylogenetic analysis suggested that the catalytic and ligand binding sites of GmGSTU2-2 are well conserved compared to other tau class GSTs. Structural analysis identified key amino acid residues in the hydrophobic binding site and provided insights into the substrate specificity of this enzyme. The results established that GmGSTU2-2 participates in a broad network of catalytic and regulatory functions involved in the plant stress response.
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Affiliation(s)
- Katholiki Skopelitou
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Food, Biotechnology and Development, Agricultural University of Athens, 75 Iera Odos Street, GR-11855 Athens, Greece
| | - Abdi W Muleta
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku 20521, Finland
| | | | - Evangelia G Chronopoulou
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Food, Biotechnology and Development, Agricultural University of Athens, 75 Iera Odos Street, GR-11855 Athens, Greece
| | - Ourania Pavli
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Athens, Greece
| | - Emmanouil Flemetakis
- Laboratory of Molecular Biology, Department of Biotechnology, School of Food, Biotechnology and Development, Agricultural University of Athens, Athens, Greece
| | - Georgios N Skaracis
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Athens, Greece
| | - Nikolaos E Labrou
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Food, Biotechnology and Development, Agricultural University of Athens, 75 Iera Odos Street, GR-11855 Athens, Greece.
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47
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Abstract
The Gene Ontology (GO) (Ashburner et al., Nat Genet 25(1):25-29, 2000) is a powerful tool in the informatics arsenal of methods for evaluating annotations in a protein dataset. From identifying the nearest well annotated homologue of a protein of interest to predicting where misannotation has occurred to knowing how confident you can be in the annotations assigned to those proteins is critical. In this chapter we explore what makes an enzyme unique and how we can use GO to infer aspects of protein function based on sequence similarity. These can range from identification of misannotation or other errors in a predicted function to accurate function prediction for an enzyme of entirely unknown function. Although GO annotation applies to any gene products, we focus here a describing our approach for hierarchical classification of enzymes in the Structure-Function Linkage Database (SFLD) (Akiva et al., Nucleic Acids Res 42(Database issue):D521-530, 2014) as a guide for informed utilisation of annotation transfer based on GO terms.
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Affiliation(s)
- Gemma L Holliday
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, 1700 4th Street, San Francisco, CA, 94158, USA.
| | - Rebecca Davidson
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, 1700 4th Street, San Francisco, CA, 94158, USA
| | - Eyal Akiva
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, 1700 4th Street, San Francisco, CA, 94158, USA
| | - Patricia C Babbitt
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, 1700 4th Street, San Francisco, CA, 94158, USA
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48
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Baier F, Copp JN, Tokuriki N. Evolution of Enzyme Superfamilies: Comprehensive Exploration of Sequence–Function Relationships. Biochemistry 2016; 55:6375-6388. [DOI: 10.1021/acs.biochem.6b00723] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- F. Baier
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - J. N. Copp
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - N. Tokuriki
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
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49
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Leuthaeuser JB, Morris JH, Harper AF, Ferrin TE, Babbitt PC, Fetrow JS. DASP3: identification of protein sequences belonging to functionally relevant groups. BMC Bioinformatics 2016; 17:458. [PMID: 27835946 PMCID: PMC5106842 DOI: 10.1186/s12859-016-1295-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 10/20/2016] [Indexed: 01/26/2023] Open
Abstract
Background Development of automatable processes for clustering proteins into functionally relevant groups is a critical hurdle as an increasing number of sequences are deposited into databases. Experimental function determination is exceptionally time-consuming and can’t keep pace with the identification of protein sequences. A tool, DASP (Deacon Active Site Profiler), was previously developed to identify protein sequences with active site similarity to a query set. Development of two iterative, automatable methods for clustering proteins into functionally relevant groups exposed algorithmic limitations to DASP. Results The accuracy and efficiency of DASP was significantly improved through six algorithmic enhancements implemented in two stages: DASP2 and DASP3. Validation demonstrated DASP3 provides greater score separation between true positives and false positives than earlier versions. In addition, DASP3 shows similar performance to previous versions in clustering protein structures into isofunctional groups (validated against manual curation), but DASP3 gathers and clusters protein sequences into isofunctional groups more efficiently than DASP and DASP2. Conclusions DASP algorithmic enhancements resulted in improved efficiency and accuracy of identifying proteins that contain active site features similar to those of the query set. These enhancements provide incremental improvement in structure database searches and initial sequence database searches; however, the enhancements show significant improvement in iterative sequence searches, suggesting DASP3 is an appropriate tool for the iterative processes required for clustering proteins into isofunctional groups. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-1295-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Janelle B Leuthaeuser
- Molecular Genetics and Genomics Program, Wake Forest University, Winston-Salem, NC, 27106, USA. .,Present address: University of Richmond, Gottwald Hall C302, Richmond, VA, 23173, USA.
| | - John H Morris
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Angela F Harper
- Department of Physics, Wake Forest University, Winston-Salem, NC, 27106, USA
| | - Thomas E Ferrin
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Patricia C Babbitt
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Jacquelyn S Fetrow
- Department of Chemistry, University of Richmond, Richmond, VA, 23173, USA
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50
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Crystal Structure of Saccharomyces cerevisiae ECM4, a Xi-Class Glutathione Transferase that Reacts with Glutathionyl-(hydro)quinones. PLoS One 2016; 11:e0164678. [PMID: 27736955 PMCID: PMC5063366 DOI: 10.1371/journal.pone.0164678] [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: 07/22/2016] [Accepted: 09/28/2016] [Indexed: 12/16/2022] Open
Abstract
Glutathionyl-hydroquinone reductases (GHRs) belong to the recently characterized Xi-class of glutathione transferases (GSTXs) according to unique structural properties and are present in all but animal kingdoms. The GHR ScECM4 from the yeast Saccharomyces cerevisiae has been studied since 1997 when it was found to be potentially involved in cell-wall biosynthesis. Up to now and in spite of biological studies made on this enzyme, its physiological role remains challenging. The work here reports its crystallographic study. In addition to exhibiting the general GSTX structural features, ScECM4 shows extensions including a huge loop which contributes to the quaternary assembly. These structural extensions are probably specific to Saccharomycetaceae. Soaking of ScECM4 crystals with GS-menadione results in a structure where glutathione forms a mixed disulfide bond with the cysteine 46. Solution studies confirm that ScECM4 has reductase activity for GS-menadione in presence of glutathione. Moreover, the high resolution structures allowed us to propose new roles of conserved residues of the active site to assist the cysteine 46 during the catalytic act.
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