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Song WS, Kim JH, Namgung B, Cho HY, Shin H, Oh HB, Ha NC, Yoon SI. Complementary hydrophobic interaction of the redox enzyme maturation protein NarJ with the signal peptide of the respiratory nitrate reductase NarG. Int J Biol Macromol 2024; 262:129620. [PMID: 38262549 DOI: 10.1016/j.ijbiomac.2024.129620] [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: 07/24/2023] [Revised: 01/08/2024] [Accepted: 01/18/2024] [Indexed: 01/25/2024]
Abstract
In bacteria, NarJ plays an essential role as a redox enzyme maturation protein in the assembly of the nitrate reductase NarGHI by interacting with the N-terminal signal peptide of NarG to facilitate cofactor incorporation into NarG. The purpose of our research was to elucidate the exact mechanism of NarG signal peptide recognition by NarJ. We determined the structures of NarJ alone and in complex with the signal peptide of NarG via X-ray crystallography and verified the NarJ-NarG interaction through mutational, binding, and molecular dynamics simulation studies. NarJ adopts a curved α-helix bundle structure with a U-shaped hydrophobic groove on its concave side. This groove accommodates the signal peptide of NarG via a dual binding mode in which the left and right parts of the NarJ groove each interact with two consecutive hydrophobic residues from the N- and C-terminal regions of the NarG signal peptide, respectively, through shape and chemical complementarity. This binding is accompanied by unwinding of the helical structure of the NarG signal peptide and by stabilization of the NarG-binding loop of NarJ. We conclude that NarJ recognizes the NarG signal peptide through a complementary hydrophobic interaction mechanism that mediates a structural rearrangement.
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Affiliation(s)
- Wan Seok Song
- Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Jee-Hyeon Kim
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Byeol Namgung
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Hye Yeon Cho
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Hyunwoo Shin
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Han Byeol Oh
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Nam-Chul Ha
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Sung-Il Yoon
- Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon 24341, Republic of Korea; Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea.
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2
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Magalon A. History of Maturation of Prokaryotic Molybdoenzymes-A Personal View. Molecules 2023; 28:7195. [PMID: 37894674 PMCID: PMC10609526 DOI: 10.3390/molecules28207195] [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: 09/25/2023] [Revised: 10/11/2023] [Accepted: 10/17/2023] [Indexed: 10/29/2023] Open
Abstract
In prokaryotes, the role of Mo/W enzymes in physiology and bioenergetics is widely recognized. It is worth noting that the most diverse family of Mo/W enzymes is exclusive to prokaryotes, with the probable existence of several of them from the earliest forms of life on Earth. The structural organization of these enzymes, which often include additional redox centers, is as diverse as ever, as is their cellular localization. The most notable observation is the involvement of dedicated chaperones assisting with the assembly and acquisition of the metal centers, including Mo/W-bisPGD, one of the largest organic cofactors in nature. This review seeks to provide a new understanding and a unified model of Mo/W enzyme maturation.
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Affiliation(s)
- Axel Magalon
- Aix Marseille Université, CNRS, Laboratoire de Chimie Bactérienne (UMR7283), IMM, IM2B, 13402 Marseille, France
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3
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Bageshwar UK, DattaGupta A, Musser SM. Influence of the TorD signal peptide chaperone on Tat-dependent protein translocation. PLoS One 2021; 16:e0256715. [PMID: 34499687 PMCID: PMC8428690 DOI: 10.1371/journal.pone.0256715] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 07/28/2021] [Indexed: 11/18/2022] Open
Abstract
The twin-arginine translocation (Tat) pathway transports folded proteins across energetic membranes. Numerous Tat substrates contain co-factors that are inserted before transport with the assistance of redox enzyme maturation proteins (REMPs), which bind to the signal peptide of precursor proteins. How signal peptides are transferred from a REMP to a binding site on the Tat receptor complex remains unknown. Since the signal peptide mediates both interactions, possibilities include: i) a coordinated hand-off mechanism; or ii) a diffusional search after REMP dissociation. We investigated the binding interaction between substrates containing the TorA signal peptide (spTorA) and its cognate REMP, TorD, and the effect of TorD on the in vitro transport of such substrates. We found that Escherichia coli TorD is predominantly a monomer at low micromolar concentrations (dimerization KD > 50 μM), and this monomer binds reversibly to spTorA (KD ≈ 1 μM). While TorD binds to membranes (KD ≈ 100 nM), it has no apparent affinity for Tat translocons and it inhibits binding of a precursor substrate to the membrane. TorD has a minimal effect on substrate transport by the Tat system, being mildly inhibitory at high concentrations. These data are consistent with a model in which the REMP-bound signal peptide is shielded from recognition by the Tat translocon, and spontaneous dissociation of the REMP allows the substrate to engage the Tat machinery. Thus, the REMP does not assist with targeting to the Tat translocon, but rather temporarily shields the signal peptide.
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Affiliation(s)
- Umesh K. Bageshwar
- Department of Molecular and Cellular Medicine, Texas A&M University, College of Medicine, The Texas A&M Health Science Center, TX, United States of America
| | - Antara DattaGupta
- Department of Molecular and Cellular Medicine, Texas A&M University, College of Medicine, The Texas A&M Health Science Center, TX, United States of America
| | - Siegfried M. Musser
- Department of Molecular and Cellular Medicine, Texas A&M University, College of Medicine, The Texas A&M Health Science Center, TX, United States of America
- * E-mail:
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4
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Staicu LC, Barton LL. Selenium respiration in anaerobic bacteria: Does energy generation pay off? J Inorg Biochem 2021; 222:111509. [PMID: 34118782 DOI: 10.1016/j.jinorgbio.2021.111509] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/18/2021] [Accepted: 05/30/2021] [Indexed: 01/03/2023]
Abstract
Selenium (Se) respiration in bacteria was revealed for the first time at the end of 1980s. Although thermodynamically-favorable, energy-dense and documented in phylogenetically-diverse bacteria, this metabolic process appears to be accompanied by a number of challenges and numerous unanswered questions. Selenium oxyanions, SeO42- and SeO32-, are reduced to elemental Se (Se0) through anaerobic respiration, the end product being solid and displaying a considerable size (up to 500 nm) at the bacterial scale. Compared to other electron acceptors used in anaerobic respiration (e.g. N, S, Fe, Mn, and As), Se is one of the few elements whose end product is solid. Furthermore, unlike other known bacterial intracellular accumulations such as volutin (inorganic polyphosphate), S0, glycogen or magnetite, Se0 has not been shown to play a nutritional or ecological role for its host. In the context of anaerobic respiration of Se oxyanions, biogenic Se0 appears to be a by-product, a waste that needs proper handling, and this raises the question of the evolutionary implications of this process. Why would bacteria use a respiratory substrate that is useful, in the first place, and then highly detrimental? Interestingly, in certain artificial ecosystems (e.g. upflow bioreactors) Se0 might help bacterial cells to increase their density and buoyancy and thus avoid biomass wash-out, ensuring survival. This review article provides an in-depth analysis of selenium respiration (model selenium respiring bacteria, thermodynamics, respiratory enzymes, and genetic determinants), complemented by an extensive discussion about the evolutionary implications and the properties of biogenic Se0 using published and original/unpublished results.
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Affiliation(s)
- Lucian C Staicu
- Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland.
| | - Larry L Barton
- Department of Biology, University of New Mexico, MSCO3 2020, Albuquerque, NM 87131, USA
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5
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Niedzialkowska E, Mrugała B, Rugor A, Czub MP, Skotnicka A, Cotelesage JJH, George GN, Szaleniec M, Minor W, Lewiński K. Optimization of overexpression of a chaperone protein of steroid C25 dehydrogenase for biochemical and biophysical characterization. Protein Expr Purif 2017; 134:47-62. [PMID: 28343996 DOI: 10.1016/j.pep.2017.03.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 03/02/2017] [Accepted: 03/21/2017] [Indexed: 11/27/2022]
Abstract
Molybdenum is an essential nutrient for metabolism in plant, bacteria, and animals. Molybdoenzymes are involved in nitrogen assimilation and oxidoreductive detoxification, and bioconversion reactions of environmental, industrial, and pharmaceutical interest. Molybdoenzymes contain a molybdenum cofactor (Moco), which is a pyranopterin heterocyclic compound that binds a molybdenum atom via a dithiolene group. Because Moco is a large and complex compound deeply buried within the protein, molybdoenzymes are accompanied by private chaperone proteins responsible for the cofactor's insertion into the enzyme and the enzyme's maturation. An efficient recombinant expression and purification of both Moco-free and Moco-containing molybdoenzymes and their chaperones is of paramount importance for fundamental and applied research related to molybdoenzymes. In this work, we focused on a D1 protein annotated as a chaperone of steroid C25 dehydrogenase (S25DH) from Sterolibacterium denitrificans Chol-1S. The D1 protein is presumably involved in the maturation of S25DH engaged in oxygen-independent oxidation of sterols. As this chaperone is thought to be a crucial element that ensures the insertion of Moco into the enzyme and consequently, proper folding of S25DH optimization of the chaperon's expression is the first step toward the development of recombinant expression and purification methods for S25DH. We have identified common E. coli strains and conditions for both expression and purification that allow us to selectively produce Moco-containing and Moco-free chaperones. We have also characterized the Moco-containing chaperone by EXAFS and HPLC analysis and identified conditions that stabilize both forms of the protein. The protocols presented here are efficient and result in protein quantities sufficient for biochemical studies.
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Affiliation(s)
- Ewa Niedzialkowska
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30239 Krakow, Poland.
| | - Beata Mrugała
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30239 Krakow, Poland
| | - Agnieszka Rugor
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30239 Krakow, Poland
| | - Mateusz P Czub
- Faculty of Chemistry, Jagiellonian University, Ingardena 3, Krakow 30060, Poland; Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA
| | - Anna Skotnicka
- Faculty of Agriculture and Economics, University of Agriculture in Krakow, Mickiewicza 21, 31120 Krakow, Poland
| | - Julien J H Cotelesage
- Molecular and Environmental Sciences Group, Department of Geological Sciences, University of Saskatchewan, Saskatoon, SK S7N 5E2, Canada
| | - Graham N George
- Molecular and Environmental Sciences Group, Department of Geological Sciences, University of Saskatchewan, Saskatoon, SK S7N 5E2, Canada
| | - Maciej Szaleniec
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30239 Krakow, Poland
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA
| | - Krzysztof Lewiński
- Faculty of Chemistry, Jagiellonian University, Ingardena 3, Krakow 30060, Poland
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Connelly KRS, Stevenson C, Kneuper H, Sargent F. Biosynthesis of selenate reductase in Salmonella enterica: critical roles for the signal peptide and DmsD. MICROBIOLOGY-SGM 2016; 162:2136-2146. [PMID: 27902441 PMCID: PMC5203670 DOI: 10.1099/mic.0.000381] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Salmonella enterica serovar Typhimurium is a Gram-negative bacterium with a flexible respiratory capability. Under anaerobic conditions, S. enterica can utilize a range of terminal electron acceptors, including selenate, to sustain respiratory electron transport. The S. enterica selenate reductase is a membrane-bound enzyme encoded by the ynfEFGH-dmsD operon. The active enzyme is predicted to comprise at least three subunits where YnfE is a molybdenum-containing catalytic subunit. The YnfE protein is synthesized with an N-terminal twin-arginine signal peptide and biosynthesis of the enzyme is coordinated by a signal peptide binding chaperone called DmsD. In this work, the interaction between S. enterica DmsD and the YnfE signal peptide has been studied by chemical crosslinking. These experiments were complemented by genetic approaches, which identified the DmsD binding epitope within the YnfE signal peptide. YnfE signal peptide residues L24 and A28 were shown to be important for assembly of an active selenate reductase. Conversely, a random genetic screen identified the DmsD V16 residue as being important for signal peptide recognition and selenate reductase assembly.
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Affiliation(s)
| | - Calum Stevenson
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Holger Kneuper
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Frank Sargent
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
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7
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Cherak SJ, Turner RJ. Influence of GTP on system specific chaperone - Twin arginine signal peptide interaction. Biochem Biophys Res Commun 2015; 465:753-7. [PMID: 26299930 DOI: 10.1016/j.bbrc.2015.08.079] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 08/18/2015] [Indexed: 11/30/2022]
Abstract
Many bacterial respiratory redox enzymes depend on the twin-arginine translocase (Tat) system for translocation and membrane insertion. Tat substrates contain an N-terminal twin-arginine (SRRxFLK) motif serving as the targeting signal towards the translocon. Many Tat substrates have a system specific chaperone - redox enzyme maturation protein (REMP) - for final folding and assembly prior to Tat binding. The REMP DmsD strongly interacts with the twin-arginine motif of the DmsA signal sequence of dimethyl sulfoxide (DMSO) reductase. In this study, we have utilized the in vitro protein-protein interaction technique of an affinity pull down assay, as well as protein thermal stability measurement via differential scanning fluorimetry (DSF) to investigate the interaction of guanosine nucleotides (GNPs) with DmsD. Here we have shown highly cooperative binding of DmsD with GTP. A dissociative ligand-binding style isotherm was generated upon GTP titration into the DmsD:DmsAL interaction, yielding sigmoidal release of DmsD with a Hill coefficient of 2.09 and a dissociation constant of 0.99 mM. DSF further illustrated the change in thermal stability upon DmsD interaction with DmsAL and GTP. These results imply the possibility of DmsD detection and binding of GTP during the DMSO protein maturation mechanism, from ribosomal translation to membrane targeting and final assembly. Conceivably, GTP is shown to act as a molecular regulator in the biochemical pathway.
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Affiliation(s)
- Stephana J Cherak
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
| | - Raymond J Turner
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada.
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8
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Bay DC, Chan CS, Turner RJ. NarJ subfamily system specific chaperone diversity and evolution is directed by respiratory enzyme associations. BMC Evol Biol 2015; 15:110. [PMID: 26067063 PMCID: PMC4464133 DOI: 10.1186/s12862-015-0412-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 06/04/2015] [Indexed: 12/04/2022] Open
Abstract
Background Redox enzyme maturation proteins (REMPs) describe a diverse family of prokaryotic chaperones involved in the biogenesis of anaerobic complex iron sulfur molybdoenzyme (CISM) respiratory systems. Many REMP family studies have focused on NarJ subfamily members from Escherichia coli: NarJ, NarW, DmsD, TorD and YcdY. The aim of this bioinformatics study was to expand upon the evolution, distribution and genetic association of these 5 REMP members within 130 genome sequenced taxonomically diverse species representing 324 Prokaryotic sequences. NarJ subfamily member diversity was examined at the phylum-species level and at the amino acid/nucleotide level to determine how close their genetic associations were between their respective CISM systems within phyla. Results This study revealed that NarJ members possessed unique motifs that distinguished Gram-negative from Gram-positive/Archaeal species and identified a strict genetic association with its nitrate reductase complex (narGHI) operon compared to all other members. NarW appears to be found specifically in Gammaproteobacteria. DmsD also showed close associations with the dimethylsulfoxide reductase (dmsABC) operon compared to TorD. Phylogenetic analysis revealed that YcdY has recently evolved from DmsD and that YcdY has likely diverged into 2 subfamilies linked to Zn- dependent alkaline phosphatase (ycdX) operons and a newly identified operon containing part of Zn-metallopeptidase FtsH complex component (hflC) and NADH-quinone dehydrogenase (mdaB). TorD demonstrated the greatest diversity in operon association. TorD was identifed within operons from either trimethylamine-N-oxide reductase (torAC) or formate dehydrogenase (fdhGHI), where each type of TorD had a unique motif. Additionally a subgroup of dmsD and torD members were also linked to operons with biotin sulfoxide (bisC) and polysulfide reductase (nrfD) indicating a potential role in the maturation of diverse CISM. Conclusion Examination of diverse prokaryotic NarJ subfamily members demonstrates that the evolution and genetic association of each member is uniquely biased by its CISM operon association. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0412-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Denice C Bay
- Department of Biological Sciences, University of Calgary, Rm 156 Biological Science Bldg., 2500 University Dr. NW, Calgary, T2N 1 N4, AB, Canada.
| | - Catherine S Chan
- Department of Biological Sciences, University of Calgary, Rm 156 Biological Science Bldg., 2500 University Dr. NW, Calgary, T2N 1 N4, AB, Canada.
| | - Raymond J Turner
- Department of Biological Sciences, University of Calgary, Rm 156 Biological Science Bldg., 2500 University Dr. NW, Calgary, T2N 1 N4, AB, Canada.
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9
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Winstone TML, Turner RJ. Thermodynamic Characterization of the DmsD Binding Site for the DmsA Twin-Arginine Motif. Biochemistry 2015; 54:2040-51. [DOI: 10.1021/bi500891d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tara M. L. Winstone
- Department of Biological
Sciences, University of Calgary, 2500 University Drive Northwest, Calgary, AB, Canada T2N 1N4
| | - Raymond J. Turner
- Department of Biological
Sciences, University of Calgary, 2500 University Drive Northwest, Calgary, AB, Canada T2N 1N4
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10
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Abstract
The transition element molybdenum (Mo) is of primordial importance for biological systems, because it is required by enzymes catalyzing key reactions in the global carbon, sulfur, and nitrogen metabolism. To gain biological activity, Mo has to be complexed by a special cofactor. With the exception of bacterial nitrogenase, all Mo-dependent enzymes contain a unique pyranopterin-based cofactor coordinating a Mo atom at their catalytic site. Various types of reactions are catalyzed by Mo-enzymes in prokaryotes including oxygen atom transfer, sulfur or proton transfer, hydroxylation, or even nonredox reactions. Mo-enzymes are widespread in prokaryotes and many of them were likely present in the Last Universal Common Ancestor. To date, more than 50--mostly bacterial--Mo-enzymes are described in nature. In a few eubacteria and in many archaea, Mo is replaced by tungsten bound to the same unique pyranopterin. How Mo-cofactor is synthesized in bacteria is reviewed as well as the way until its insertion into apo-Mo-enzymes.
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11
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‘Come into the fold’: A comparative analysis of bacterial redox enzyme maturation protein members of the NarJ subfamily. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:2971-2984. [DOI: 10.1016/j.bbamem.2014.08.020] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 07/24/2014] [Accepted: 08/15/2014] [Indexed: 11/19/2022]
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12
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Rivardo F, Leach TGH, Chan CS, Winstone TML, Ladner CL, Sarfo KJ, Turner RJ. Unique Photobleaching Phenomena of the Twin-Arginine Translocase Respiratory Enzyme Chaperone DmsD. Open Biochem J 2014; 8:1-11. [PMID: 24497893 PMCID: PMC3912628 DOI: 10.2174/1874091x01408010001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2013] [Revised: 11/27/2013] [Accepted: 12/01/2013] [Indexed: 11/22/2022] Open
Abstract
DmsD is a chaperone of the redox enzyme maturation protein family specifically required for biogenesis of DMSO reductase in Escherichia coli. It exists in multiple folding forms, all of which are capable of binding its known substrate, the twin-arginine leader sequence of the DmsA catalytic subunit. It is important for maturation of the reductase and targeting to the cytoplasmic membrane for translocation. Here, we demonstrate that DmsD exhibits an irreversible photobleaching phenomenon upon 280 nm excitation irradiation. The phenomenon is due to quenching of the tryptophan residues in DmsD and is dependent on its folding and conformation. We also show that a tryptophan residue involved in DmsA signal peptide binding (W87) is important for photobleaching of DmsD. Mutation of W87, or binding of the DmsA twin-arginine signal peptide to DmsD in the pocket that includes W72, W80, and W91 significantly affects the degree of photobleaching. This study highlights the advantage of a photobleaching phenomenon to study protein folding and conformation changes within a protein that was once considered unusable in fluorescence spectroscopy.
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Affiliation(s)
- Fabrizio Rivardo
- BI 156, Department of Biological Sciences, University of Calgary, 2500 University Dr NW, Calgary, Alberta, Canada T2N 1N4
| | - Thorin G H Leach
- BI 156, Department of Biological Sciences, University of Calgary, 2500 University Dr NW, Calgary, Alberta, Canada T2N 1N4
| | - Catherine S Chan
- BI 156, Department of Biological Sciences, University of Calgary, 2500 University Dr NW, Calgary, Alberta, Canada T2N 1N4
| | - Tara M L Winstone
- BI 156, Department of Biological Sciences, University of Calgary, 2500 University Dr NW, Calgary, Alberta, Canada T2N 1N4
| | - Carol L Ladner
- BI 156, Department of Biological Sciences, University of Calgary, 2500 University Dr NW, Calgary, Alberta, Canada T2N 1N4
| | - Kwabena J Sarfo
- BI 156, Department of Biological Sciences, University of Calgary, 2500 University Dr NW, Calgary, Alberta, Canada T2N 1N4
| | - Raymond J Turner
- BI 156, Department of Biological Sciences, University of Calgary, 2500 University Dr NW, Calgary, Alberta, Canada T2N 1N4
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13
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Abstract
The Tat (twin-arginine translocation) system is a protein targeting pathway utilized by prokaryotes and chloroplasts. Tat substrates are produced with distinctive N-terminal signal peptides and are translocated as fully folded proteins. In Escherichia coli, Tat-dependent proteins often contain redox cofactors that must be loaded before translocation. Trimethylamine N-oxide reductase (TorA) is a model bacterial Tat substrate and is a molybdenum cofactor-dependent enzyme. Co-ordination of cofactor loading and translocation of TorA is directed by the TorD protein, which is a cytoplasmic chaperone known to interact physically with the TorA signal peptide. In the present study, a pre-export TorAD complex has been characterized using biochemical and biophysical techniques, including SAXS (small-angle X-ray scattering). A stable, cofactor-free TorAD complex was isolated, which revealed a 1:1 binding stoichiometry. Surprisingly, a TorAD complex with similar architecture can be isolated in the complete absence of the 39-residue TorA signal peptide. The present study demonstrates that two high-affinity binding sites for TorD are present on TorA, and that a single TorD protein binds both of those simultaneously. Further characterization suggested that the C-terminal ‘Domain IV’ of TorA remained solvent-exposed in the cofactor-free pre-export TorAD complex. It is possible that correct folding of Domain IV upon cofactor loading is the trigger for TorD release and subsequent export of TorA.
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14
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Lorenzi M, Sylvi L, Gerbaud G, Mileo E, Halgand F, Walburger A, Vezin H, Belle V, Guigliarelli B, Magalon A. Conformational selection underlies recognition of a molybdoenzyme by its dedicated chaperone. PLoS One 2012. [PMID: 23185350 PMCID: PMC3501500 DOI: 10.1371/journal.pone.0049523] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Molecular recognition is central to all biological processes. Understanding the key role played by dedicated chaperones in metalloprotein folding and assembly requires the knowledge of their conformational ensembles. In this study, the NarJ chaperone dedicated to the assembly of the membrane-bound respiratory nitrate reductase complex NarGHI, a molybdenum-iron containing metalloprotein, was taken as a model of dedicated chaperone. The combination of two techniques ie site-directed spin labeling followed by EPR spectroscopy and ion mobility mass spectrometry, was used to get information about the structure and conformational dynamics of the NarJ chaperone upon binding the N-terminus of the NarG metalloprotein partner. By the study of singly spin-labeled proteins, the E119 residue present in a conserved elongated hydrophobic groove of NarJ was shown to be part of the interaction site. Moreover, doubly spin-labeled proteins studied by pulsed double electron-electron resonance (DEER) spectroscopy revealed a large and composite distribution of inter-label distances that evolves into a single preexisting one upon complex formation. Additionally, ion mobility mass spectrometry experiments fully support these findings by revealing the existence of several conformers in equilibrium through the distinction of different drift time curves and the selection of one of them upon complex formation. Taken together our work provides a detailed view of the structural flexibility of a dedicated chaperone and suggests that the exquisite recognition and binding of the N-terminus of the metalloprotein is governed by a conformational selection mechanism.
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Affiliation(s)
- Magali Lorenzi
- Unité de Bioénergétique et Ingénierie des Protéines (UMR7281), Institut de Microbiologie de la Méditerranée, CNRS & Aix-Marseille Univ, Marseille, France
| | - Léa Sylvi
- Laboratoire de Chimie Bactérienne (UMR7283), Institut de Microbiologie de la Méditerranée, CNRS & Aix-Marseille Univ, Marseille, France
| | - Guillaume Gerbaud
- Unité de Bioénergétique et Ingénierie des Protéines (UMR7281), Institut de Microbiologie de la Méditerranée, CNRS & Aix-Marseille Univ, Marseille, France
| | - Elisabetta Mileo
- Unité de Bioénergétique et Ingénierie des Protéines (UMR7281), Institut de Microbiologie de la Méditerranée, CNRS & Aix-Marseille Univ, Marseille, France
| | - Frédéric Halgand
- Unité de Bioénergétique et Ingénierie des Protéines (UMR7281), Institut de Microbiologie de la Méditerranée, CNRS & Aix-Marseille Univ, Marseille, France
| | - Anne Walburger
- Laboratoire de Chimie Bactérienne (UMR7283), Institut de Microbiologie de la Méditerranée, CNRS & Aix-Marseille Univ, Marseille, France
| | - Hervé Vezin
- Laboratoire de Spectrochimie Infrarouge et Raman (UMR8516), Villeneuve d'Ascq, France
| | - Valérie Belle
- Unité de Bioénergétique et Ingénierie des Protéines (UMR7281), Institut de Microbiologie de la Méditerranée, CNRS & Aix-Marseille Univ, Marseille, France
- * E-mail: (VB); (AM)
| | - Bruno Guigliarelli
- Unité de Bioénergétique et Ingénierie des Protéines (UMR7281), Institut de Microbiologie de la Méditerranée, CNRS & Aix-Marseille Univ, Marseille, France
| | - Axel Magalon
- Laboratoire de Chimie Bactérienne (UMR7283), Institut de Microbiologie de la Méditerranée, CNRS & Aix-Marseille Univ, Marseille, France
- * E-mail: (VB); (AM)
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Magalon A, Fedor JG, Walburger A, Weiner JH. Molybdenum enzymes in bacteria and their maturation. Coord Chem Rev 2011. [DOI: 10.1016/j.ccr.2010.12.031] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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Abstract
Proteins that reside partially or completely outside the bacterial cytoplasm require specialized pathways to facilitate their localization. Globular proteins that function in the periplasm must be translocated across the hydrophobic barrier of the inner membrane. While the Sec pathway transports proteins in a predominantly unfolded conformation, the Tat pathway exports folded protein substrates. Protein transport by the Tat machinery is powered solely by the transmembrane proton gradient, and there is no requirement for nucleotide triphosphate hydrolysis. Proteins are targeted to the Tat machinery by N-terminal signal peptides that contain a consensus twin arginine motif. In Escherichia coli and Salmonella there are approximately thirty proteins with twin arginine signal peptides that are transported by the Tat pathway. The majority of these bind complex redox cofactors such as iron sulfur clusters or the molybdopterin cofactor. Here we describe what is known about Tat substrates in E. coli and Salmonella, the function and mechanism of Tat protein export, and how the cofactor insertion step is coordinated to ensure that only correctly assembled substrates are targeted to the Tat machinery.
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17
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Zakian S, Lafitte D, Vergnes A, Pimentel C, Sebban-Kreuzer C, Toci R, Claude JB, Guerlesquin F, Magalon A. Basis of recognition between the NarJ chaperone and the N-terminus of the NarG subunit from Escherichia coli nitrate reductase. FEBS J 2010; 277:1886-95. [DOI: 10.1111/j.1742-4658.2010.07611.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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18
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Guymer D, Maillard J, Agacan MF, Brearley CA, Sargent F. Intrinsic GTPase activity of a bacterial twin-arginine translocation proofreading chaperone induced by domain swapping. FEBS J 2010; 277:511-25. [PMID: 20064164 DOI: 10.1111/j.1742-4658.2009.07507.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The bacterial twin-arginine translocation (Tat) system is a protein targeting pathway dedicated to the transport of folded proteins across the cytoplasmic membrane. Proteins transported on the Tat pathway are synthesised as precursors with N-terminal signal peptides containing a conserved amino acid motif. In Escherichia coli, many Tat substrates contain prosthetic groups and undergo cytoplasmic assembly processes prior to the translocation event. A pre-export 'Tat proofreading' process, mediated by signal peptide-binding chaperones, is considered to prevent premature export of some Tat-targeted proteins until all other assembly processes are complete. TorD is a paradigm Tat proofreading chaperone and co-ordinates the maturation and export of the periplasmic respiratory enzyme trimethylamine N-oxide reductase (TorA). Although it is well established that TorD binds directly to the TorA signal peptide, the mechanism of regulation or control of binding is not understood. Previous structural analyses of TorD homologues showed that these proteins can exist as monomeric and domain-swapped dimeric forms. In the present study, we demonstrate that isolated recombinant TorD exhibits a magnesium-dependent GTP hydrolytic activity, despite the absence of classical nucleotide-binding motifs in the protein. TorD GTPase activity is shown to be present only in the domain-swapped homodimeric form of the protein, thus defining a biochemical role for the oligomerisation. Site-directed mutagenesis identified one TorD side-chain (D68) that was important in substrate selectivity. A D68W variant TorD protein was found to exhibit an ATPase activity not observed for native TorD, and an in vivo assay established that this variant was defective in the Tat proofreading process.
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Affiliation(s)
- David Guymer
- College of Life Sciences, University of Dundee, Dundee, UK
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19
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Shao X, Lu J, Hu Y, Xia B, Jin C. Solution structure of the Escherichia coli HybE reveals a novel fold. Proteins 2009; 75:1051-6. [PMID: 19291739 DOI: 10.1002/prot.22391] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Xuan Shao
- Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing 100871, China
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20
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Ramasamy SK, Clemons WM. Structure of the twin-arginine signal-binding protein DmsD from Escherichia coli. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:746-50. [PMID: 19652330 DOI: 10.1107/s1744309109023811] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2009] [Accepted: 06/21/2009] [Indexed: 11/10/2022]
Abstract
The translocation of folded proteins via the twin-arginine translocation (Tat) pathway is regulated to prevent the futile export of inactive substrate. DmsD is part of a class of cytoplasmic chaperones that play a role in preventing certain redox proteins from premature transport. DmsD from Escherichia coli has been crystallized in space group P4(1)2(1)2, with unit-cell parameters a = b = 97.45, c = 210.04 A, in the presence of a small peptide. The structure has been solved by molecular replacement to a resolution of 2.4 A and refined to an R factor of 19.4%. There are four molecules in the asymmetric unit that may mimic a higher order structure in vivo. There appears to be density for the peptide in a predicted binding pocket, which lends support to its role as the signal-recognition surface for this class of proteins.
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Affiliation(s)
- Suresh Kumar Ramasamy
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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21
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Sippl MJ. Fold space unlimited. Curr Opin Struct Biol 2009; 19:312-20. [DOI: 10.1016/j.sbi.2009.03.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2009] [Revised: 02/16/2009] [Accepted: 03/16/2009] [Indexed: 11/25/2022]
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22
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Guymer D, Maillard J, Sargent F. A genetic analysis of in vivo selenate reduction by Salmonella enterica serovar Typhimurium LT2 and Escherichia coli K12. Arch Microbiol 2009; 191:519-28. [DOI: 10.1007/s00203-009-0478-7] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2009] [Revised: 04/01/2009] [Accepted: 04/06/2009] [Indexed: 11/28/2022]
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23
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Stevens CM, Winstone TML, Turner RJ, Paetzel M. Structural analysis of a monomeric form of the twin-arginine leader peptide binding chaperone Escherichia coli DmsD. J Mol Biol 2009; 389:124-33. [PMID: 19361518 DOI: 10.1016/j.jmb.2009.03.069] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2009] [Revised: 03/27/2009] [Accepted: 03/31/2009] [Indexed: 11/20/2022]
Abstract
The redox enzyme maturation proteins play an essential role in the proofreading and membrane targeting of protein substrates to the twin-arginine translocase. Functionally, the most thoroughly characterized redox enzyme maturation protein to date is Escherichia coli DmsD (EcDmsD). Herein, we present the X-ray crystal structure of the monomeric form of the EcDmsD refined to 2.0 A resolution, with clear electron density present for each of its 204 amino acid residues. The structural data presented here complement the biochemical data previously generated regarding the function of these twin-arginine translocase leader peptide binding chaperone proteins. Docking and molecular dynamics simulation experiments were used to provide a proposed model for how this chaperone is able to recognize the leader peptide of its substrate DmsA. The interactions observed in the model are in agreement with previous biochemical data and suggest intimate interactions between the conserved twin-arginine motif of the leader peptide of E. coli DmsA and the most conserved regions on the surface of EcDmsD.
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Affiliation(s)
- Charles M Stevens
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
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Buchanan G, Maillard J, Nabuurs SB, Richardson DJ, Palmer T, Sargent F. Features of a twin-arginine signal peptide required for recognition by a Tat proofreading chaperone. FEBS Lett 2008; 582:3979-84. [DOI: 10.1016/j.febslet.2008.10.049] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2008] [Revised: 10/17/2008] [Accepted: 10/20/2008] [Indexed: 10/21/2022]
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25
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The twin-arginine signal peptide of Bacillus subtilis YwbN can direct either Tat- or Sec-dependent secretion of different cargo proteins: secretion of active subtilisin via the B. subtilis Tat pathway. Appl Environ Microbiol 2008; 74:7507-13. [PMID: 18931290 DOI: 10.1128/aem.01401-08] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Proteins that are produced for commercial purposes in Bacillus subtilis are commonly secreted via the Sec pathway. Despite its high secretion capacity, the secretion of heterologous proteins via the Sec pathway is often unsuccessful. Alternative secretion routes, like the Tat pathway, are therefore of interest. Two parallel Tat pathways with distinct specificities have previously been discovered in B. subtilis. To explore the application potential of these Tat pathways, several commercially relevant or heterologous model proteins were fused to the signal peptides of the known B. subtilis Tat substrates YwbN and PhoD. Remarkably, the YwbN signal peptide directed secretion of active subtilisin, a typical Sec substrate, via the B. subtilis TatAyCy route. In contrast, the same signal peptide directed Tat-independent secretion of the Bacillus licheniformis alpha-amylase (AmyL). Moreover, the YwbN signal peptide directed secretion of SufI, an Escherichia coli Tat substrate, in a Tat-independent manner, most likely via Sec. Our results suggest that cytoplasmic protein folding prior to translocation is probably a major determinant of Tat-dependent protein secretion in B. subtilis, as is the case with E. coli. We conclude that future applications for the Tat system of B. subtilis will most likely involve commercially interesting proteins that are Sec incompatible.
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