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Tossounian MA, Zhao Y, Yu BYK, Markey SA, Malanchuk O, Zhu Y, Cain A, Gout I. Low-molecular-weight thiol transferases in redox regulation and antioxidant defence. Redox Biol 2024; 71:103094. [PMID: 38479221 PMCID: PMC10950700 DOI: 10.1016/j.redox.2024.103094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 02/08/2024] [Accepted: 02/18/2024] [Indexed: 03/24/2024] Open
Abstract
Low-molecular-weight (LMW) thiols are produced in all living cells in different forms and concentrations. Glutathione (GSH), coenzyme A (CoA), bacillithiol (BSH), mycothiol (MSH), ergothioneine (ET) and trypanothione T(SH)2 are the main LMW thiols in eukaryotes and prokaryotes. LMW thiols serve as electron donors for thiol-dependent enzymes in redox-mediated metabolic and signaling processes, protect cellular macromolecules from oxidative and xenobiotic stress, and participate in the reduction of oxidative modifications. The level and function of LMW thiols, their oxidized disulfides and mixed disulfide conjugates in cells and tissues is tightly controlled by dedicated oxidoreductases, such as peroxiredoxins, glutaredoxins, disulfide reductases and LMW thiol transferases. This review provides the first summary of the current knowledge of structural and functional diversity of transferases for LMW thiols, including GSH, BSH, MSH and T(SH)2. Their role in maintaining redox homeostasis in single-cell and multicellular organisms is discussed, focusing in particular on the conjugation of specific thiols to exogenous and endogenous electrophiles, or oxidized protein substrates. Advances in the development of new research tools, analytical methodologies, and genetic models for the analysis of known LMW thiol transferases will expand our knowledge and understanding of their function in cell growth and survival under oxidative stress, nutrient deprivation, and during the detoxification of xenobiotics and harmful metabolites. The antioxidant function of CoA has been recently discovered and the breakthrough in defining the identity and functional characteristics of CoA S-transferase(s) is soon expected.
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Affiliation(s)
- Maria-Armineh Tossounian
- Department of Structural and Molecular Biology, University College London, London, WC1E 6BT, United Kingdom
| | - Yuhan Zhao
- Department of Structural and Molecular Biology, University College London, London, WC1E 6BT, United Kingdom
| | - Bess Yi Kun Yu
- Department of Structural and Molecular Biology, University College London, London, WC1E 6BT, United Kingdom
| | - Samuel A Markey
- Department of Structural and Molecular Biology, University College London, London, WC1E 6BT, United Kingdom
| | - Oksana Malanchuk
- Department of Structural and Molecular Biology, University College London, London, WC1E 6BT, United Kingdom; Department of Cell Signaling, Institute of Molecular Biology and Genetics, Kyiv, 143, Ukraine
| | - Yuejia Zhu
- Department of Structural and Molecular Biology, University College London, London, WC1E 6BT, United Kingdom
| | - Amanda Cain
- Department of Structural and Molecular Biology, University College London, London, WC1E 6BT, United Kingdom
| | - Ivan Gout
- Department of Structural and Molecular Biology, University College London, London, WC1E 6BT, United Kingdom; Department of Cell Signaling, Institute of Molecular Biology and Genetics, Kyiv, 143, Ukraine.
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Bech PK, Jarmusch SA, Rasmussen JA, Limborg MT, Gram L, Henriksen NNSE. Succession of microbial community composition and secondary metabolism during marine biofilm development. ISME COMMUNICATIONS 2024; 4:ycae006. [PMID: 38390522 PMCID: PMC10881302 DOI: 10.1093/ismeco/ycae006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 01/15/2024] [Accepted: 01/17/2024] [Indexed: 02/24/2024]
Abstract
In nature, secondary metabolites mediate interactions between microorganisms residing in complex microbial communities. However, the degree to which community dynamics can be linked to secondary metabolite potential remains largely unknown. In this study, we address the relationship between community succession and secondary metabolism variation. We used 16S and 18S rRNA gene and adenylation domain amplicon sequencing, genome-resolved metagenomics, and untargeted metabolomics to track the taxons, biosynthetic gene clusters, and metabolome dynamics in situ of microorganisms during marine biofilm succession over 113 days. Two phases were identified during the community succession, with a clear shift around Day 29, where the alkaloid secondary metabolites, pseudanes, were also detected. The microbial secondary metabolite potential changed between the phases, and only a few community members, including Myxococotta spp., were responsible for the majority of the biosynthetic gene cluster potential in the early succession phase. In the late phase, bryozoans and benthic copepods were detected, and the microbial nonribosomal peptide potential drastically decreased in association with a reduction in the relative abundance of the prolific secondary metabolite producers. Conclusively, this study provides evidence that the early succession of the marine biofilm community favors prokaryotes with high nonribosomal peptide synthetase potential. In contrast, the late succession is dominated by multicellular eukaryotes and a reduction in bacterial nonribosomal peptide synthetase potential.
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Affiliation(s)
- Pernille Kjersgaard Bech
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, DK-2800, Denmark
| | - Scott A Jarmusch
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, DK-2800, Denmark
| | - Jacob Agerbo Rasmussen
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen K, DK-1014, Denmark
| | - Morten Tønsberg Limborg
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen K, DK-1014, Denmark
| | - Lone Gram
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, DK-2800, Denmark
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Keller LML, Flattich K, Weber-Ban E. Novel WYL domain-containing transcriptional activator acts in response to genotoxic stress in rapidly growing mycobacteria. Commun Biol 2023; 6:1222. [PMID: 38042942 PMCID: PMC10693628 DOI: 10.1038/s42003-023-05592-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 11/15/2023] [Indexed: 12/04/2023] Open
Abstract
The WYL domain is a nucleotide-sensing module that controls the activity of transcription factors involved in the regulation of DNA damage response and phage defense mechanisms in bacteria. In this study, we investigated a WYL domain-containing transcription factor in Mycobacterium smegmatis that we termed stress-involved WYL domain-containing regulator (SiwR). We found that SiwR controls adjacent genes that belong to the DinB/YfiT-like putative metalloenzymes superfamily by upregulating their expression in response to various genotoxic stress conditions, including upon exposure to H2O2 or the natural antibiotic zeocin. We show that SiwR binds different forms of single-stranded DNA (ssDNA) with high affinity, primarily through its characteristic WYL domain. In combination with complementation studies of a M. smegmatis siwR deletion strain, our findings support a role of the WYL domains as signal-sensing activity switches of WYL domain-containing transcription factors (WYL TFs). Our study provides evidence that WYL TFs are involved in the adaptation of bacteria to changing environments and encountered stress conditions.
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Affiliation(s)
| | - Kim Flattich
- Institute of Molecular Biology and Biophysics, ETH Zurich, 8093, Zurich, Switzerland
| | - Eilika Weber-Ban
- Institute of Molecular Biology and Biophysics, ETH Zurich, 8093, Zurich, Switzerland.
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Naowarojna N, Irani S, Hu W, Cheng R, Zhang L, Li X, Chen J, Zhang YJ, Liu P. Crystal Structure of the Ergothioneine Sulfoxide Synthase from Candidatus Chloracidobacterium thermophilum and Structure-Guided Engineering To Modulate Its Substrate Selectivity. ACS Catal 2019; 9:6955-6961. [PMID: 32257583 DOI: 10.1021/acscatal.9b02054] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Ergothioneine is a thiohistidine derivative with potential benefits on many aging-related diseases. The central step of aerobic ergothioneine biosynthesis is the oxidative C-S bond formation reaction catalyzed by mononuclear nonheme iron sulfoxide synthases (EgtB and Egt1). Thus far, only the Mycobacterium thermoresistibile EgtB (EgtB Mth ) crystal structure is available, while the structural information for the more industrially attractive Egt1 enzyme is not. Herein, we reported the crystal structure of the ergothioneine sulfoxide synthase (EgtB Cth ) from Candidatus Chloracidobacterium thermophilum. EgtB Cth has both EgtB- and Egt1-type of activities. Guided by the structural information, we conducted Rosetta Enzyme Design calculations, and we biochemically demonstrated that EgtB Cth can be engineered more toward Egt1-type of activity. This study provides information regarding the factors governing the substrate selectivity in Egt1- and EgtB-catalysis and lays the groundwork for future sulfoxide synthase engineering toward the development of an effective ergothioneine process through a synthetic biology approach.
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Affiliation(s)
- Nathchar Naowarojna
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Seema Irani
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, United States
| | - Weiyao Hu
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
- School of Chemistry and Chemical Engineering, Shanghai JiaoTong University, Shanghai 200240, China
| | - Ronghai Cheng
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Li Zhang
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Xinhao Li
- School of Chemistry and Chemical Engineering, Shanghai JiaoTong University, Shanghai 200240, China
| | - Jiesheng Chen
- School of Chemistry and Chemical Engineering, Shanghai JiaoTong University, Shanghai 200240, China
| | - Yan Jessie Zhang
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, United States
| | - Pinghua Liu
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
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Zhang J, Zhao L, Seo HS, Jung JH, Choi JI, Kim MK, Lim S. Crystal structure of the highly radiation-inducible DinB/YfiT superfamily protein DR0053 from Deinococcus radiodurans R1. Biochem Biophys Res Commun 2019; 513:354-359. [PMID: 30961930 DOI: 10.1016/j.bbrc.2019.03.209] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 03/30/2019] [Indexed: 12/11/2022]
Abstract
Deinococcus radiodurans is an extremophilic bacterium well-known for its extraordinary resistance to ionizing radiation and other DNA damage- and oxidative stress-generating agents. In addition to its efficient DNA damage repair and oxidative stress resistance mechanisms, protein family expansions and stress-induced genes/proteins are also regarded as important components that add to the robustness of this bacterium. D. radiodurans encodes specific expansions of 13 DinB/YfiT homologs, which is a relatively large number when compared to those found in Gram-positive bacteria. In this study, we investigated the expression profiles of 13 dinB genes after γ-irradiation, mitomycin C and H2O2 treatment. dr0053 had the highest expression levels after DNA-damage inducing γ-irradiation and MMC treatment, increasing ∼200-fold and ∼16-fold, respectively. We also determined the crystal structure of DR0053 at 2.07 Å resolution. DR0053 adopted a typical four-helix bundle structure that is characteristic of DinB/YfiT proteins. A putative metal binding site was occupied by zinc even though the highly conserved His triad of DinB/YfiT proteins was replaced by Glu-Asn-His.
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Affiliation(s)
- Jing Zhang
- Biotechnology Research Division, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea; Department of Biotechnology and Bioengineering, Interdisciplinary Program for Bioenergy and Biomaterials, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Lei Zhao
- Biotechnology Research Division, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea; Department of Biotechnology and Bioengineering, Interdisciplinary Program for Bioenergy and Biomaterials, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Ho Seong Seo
- Biotechnology Research Division, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea; Department of Radiation Science and Technology, University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Jong-Hyun Jung
- Biotechnology Research Division, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea; Department of Radiation Science and Technology, University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Jong-Il Choi
- Department of Biotechnology and Bioengineering, Interdisciplinary Program for Bioenergy and Biomaterials, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Min-Kyu Kim
- Biotechnology Research Division, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea; Department of Radiation Science and Technology, University of Science and Technology, Daejeon, 34113, Republic of Korea.
| | - Sangyong Lim
- Biotechnology Research Division, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea; Department of Radiation Science and Technology, University of Science and Technology, Daejeon, 34113, Republic of Korea.
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