1
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Vanyan L, Trchounian K. Glucose concentration is determinant for the functioning of hydrogenase 1 and hydrogenase 2 in regulating the proton and potassium fluxes in Escherichia coli at pH 7.5. Biochimie 2024:S0300-9084(24)00172-X. [PMID: 39038731 DOI: 10.1016/j.biochi.2024.07.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 07/17/2024] [Accepted: 07/19/2024] [Indexed: 07/24/2024]
Abstract
This study examines how FOF1-ATPase, hydrogenases (Hyd-1 and Hyd-2), and potassium transport systems (TrkA) interact to maintain the proton motive force (pmf) in E. coli during fermentation of different glucose concentrations (2 g L-1 and 8 g L-1). Our findings indicate that mutants lacking the hyaA-hyaC genes exhibited a 30 % increase in total proton flux compared to the wild type when grown with 2 g L-1 glucose. This has been observed during assays where similar glucose levels were supplemented. Disruptions in proton pumping, particularly in hyaB and hyaC single mutants, led to increased potassium uptake. The hyaB mutant showed a threefold increase in the contribution of FOF1-ATPase to proton flux, suggesting a significant role for Hyd-1 in proton translocation. In the hybC mutant grown in 2 g L-1 glucose conditions, DCCD-sensitive fluxes decreased by 70 %, indicating critical role of Hyd-2 in proton transport and FOF1 function. When cells were grown with 8 g L-1 glucose, the 2H+/1K+ ratio was significantly disturbed in both wild type and mutants. Despite these perturbances, mutants with disruptions in Hyd-1 and Hyd-2 maintained constant FOF1 function, suggesting that this enzyme remains stable in glucose-rich environments. These results provide valuable insights into how Hyd-1 and Hyd-2 contribute to the regulation of ion transport, particularly proton translocation, in response to glucose concentration. Our study uncovered potential complementary mechanisms between Hyd-1 and Hyd-2 subunits, suggesting a complex interplay between these enzymes via metabolic cross talk with FOF1 in response to glucose concentrations to maintain pmf.
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Affiliation(s)
- Liana Vanyan
- Department of Biochemistry, Microbiology and Biotechnology, Faculty of Biology, Yerevan State University, 1 A. Manoogian str., 0025, Yerevan, Armenia; Research Institute of Biology, Yerevan State University, 1 A. Manoogian str., 0025, Yerevan, Armenia; Microbial Biotechnologies and Biofuel Innovation Center, Yerevan State University, 1 A. Manoogian str., 0025, Yerevan, Armenia
| | - Karen Trchounian
- Department of Biochemistry, Microbiology and Biotechnology, Faculty of Biology, Yerevan State University, 1 A. Manoogian str., 0025, Yerevan, Armenia; Research Institute of Biology, Yerevan State University, 1 A. Manoogian str., 0025, Yerevan, Armenia; Microbial Biotechnologies and Biofuel Innovation Center, Yerevan State University, 1 A. Manoogian str., 0025, Yerevan, Armenia.
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2
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Evans R, Krahn N, Weiss J, Vincent KA, Söll D, Armstrong FA. Replacing a Cysteine Ligand by Selenocysteine in a [NiFe]-Hydrogenase Unlocks Hydrogen Production Activity and Addresses the Role of Concerted Proton-Coupled Electron Transfer in Electrocatalytic Reversibility. J Am Chem Soc 2024; 146:16971-16976. [PMID: 38747098 PMCID: PMC11212049 DOI: 10.1021/jacs.4c03489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 05/09/2024] [Accepted: 05/10/2024] [Indexed: 06/27/2024]
Abstract
Hydrogenases catalyze hydrogen/proton interconversion that is normally electrochemically reversible (having minimal overpotential requirement), a special property otherwise almost exclusive to platinum metals. The mechanism of [NiFe]-hydrogenases includes a long-range proton-coupled electron-transfer process involving a specific Ni-coordinated cysteine and the carboxylate of a nearby glutamate. A variant in which this cysteine has been exchanged for selenocysteine displays two distinct changes in electrocatalytic properties, as determined by protein film voltammetry. First, proton reduction, even in the presence of H2 (a strong product inhibitor), is greatly enhanced relative to H2 oxidation: this result parallels a characteristic of natural [NiFeSe]-hydrogenases which are superior H2 production catalysts. Second, an inflection (an S-shaped "twist" in the trace) appears around the formal potential, the small overpotentials introduced in each direction (oxidation and reduction) signaling a departure from electrocatalytic reversibility. Concerted proton-electron transfer offers a lower energy pathway compared to stepwise transfers. Given the much lower proton affinity of Se compared to that of S, the inflection provides compelling evidence that concerted proton-electron transfer is important in determining why [NiFe]-hydrogenases are reversible electrocatalysts.
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Affiliation(s)
- Rhiannon
M. Evans
- Department
of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Natalie Krahn
- Department
of Biochemistry and Molecular Biology, University
of Georgia, Athens, Georgia 30602, United
States
| | - Joshua Weiss
- Department
of Biochemistry and Molecular Biology, University
of Georgia, Athens, Georgia 30602, United
States
| | - Kylie A. Vincent
- Department
of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Dieter Söll
- Department
of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511, United States
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Fraser A. Armstrong
- Department
of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
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3
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Barco RA, Merino N, Lam B, Budnik B, Kaplan M, Wu F, Amend JP, Nealson KH, Emerson D. Comparative proteomics of a versatile, marine, iron-oxidizing chemolithoautotroph. Environ Microbiol 2024; 26:e16632. [PMID: 38861374 DOI: 10.1111/1462-2920.16632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 04/20/2024] [Indexed: 06/13/2024]
Abstract
This study conducted a comparative proteomic analysis to identify potential genetic markers for the biological function of chemolithoautotrophic iron oxidation in the marine bacterium Ghiorsea bivora. To date, this is the only characterized species in the class Zetaproteobacteria that is not an obligate iron-oxidizer, providing a unique opportunity to investigate differential protein expression to identify key genes involved in iron-oxidation at circumneutral pH. Over 1000 proteins were identified under both iron- and hydrogen-oxidizing conditions, with differentially expressed proteins found in both treatments. Notably, a gene cluster upregulated during iron oxidation was identified. This cluster contains genes encoding for cytochromes that share sequence similarity with the known iron-oxidase, Cyc2. Interestingly, these cytochromes, conserved in both Bacteria and Archaea, do not exhibit the typical β-barrel structure of Cyc2. This cluster potentially encodes a biological nanowire-like transmembrane complex containing multiple redox proteins spanning the inner membrane, periplasm, outer membrane, and extracellular space. The upregulation of key genes associated with this complex during iron-oxidizing conditions was confirmed by quantitative reverse transcription-PCR. These findings were further supported by electromicrobiological methods, which demonstrated negative current production by G. bivora in a three-electrode system poised at a cathodic potential. This research provides significant insights into the biological function of chemolithoautotrophic iron oxidation.
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Affiliation(s)
- Roman A Barco
- Department of Earth Sciences, University of Southern California, Los Angeles, California, USA
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, USA
| | - N Merino
- Department of Earth Sciences, University of Southern California, Los Angeles, California, USA
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
- Lawrence Livermore National Lab, Biosciences and Biotechnology Division, Livermore, California, USA
| | - B Lam
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - B Budnik
- Mass Spectrometry and Proteomics Resource Laboratory, Harvard University, Cambridge, Massachusetts, USA
| | - M Kaplan
- Department of Microbiology, University of Chicago, Chicago, Illinois, USA
| | - F Wu
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, Zhejiang, China
| | - J P Amend
- Department of Earth Sciences, University of Southern California, Los Angeles, California, USA
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - K H Nealson
- Department of Earth Sciences, University of Southern California, Los Angeles, California, USA
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - D Emerson
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, USA
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4
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Steiniger F, Sorokin DY, Deppenmeier U. Process of energy conservation in the extremely haloalkaliphilic methyl-reducing methanogen Methanonatronarchaeum thermophilum. FEBS J 2021; 289:549-563. [PMID: 34435454 DOI: 10.1111/febs.16165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/05/2021] [Accepted: 08/24/2021] [Indexed: 11/26/2022]
Abstract
The recently isolated methanogen Methanonatronarchaeum thermophilum is an extremely haloalkaliphilic and moderately thermophilic archaeon and belongs to the novel class Methanonatronarchaeia in the phylum Halobacteriota. The knowledge about the physiology and biochemistry of members of the class Methanonatronarchaeia is still limited. It is known that M. thermophilum performs hydrogen or formate-dependent methyl-reducing methanogenesis. Here, we show that the organism was able to grow on all tested C1 -methylated substrates (methanol, trimethylamine, dimethylamine, monomethylamine) in combination with formate or molecular hydrogen. A temporary accumulation of intermediates (dimethylamine or/and monomethylamine) in the medium occurred during the consumption of trimethylamine or dimethylamine. The energy conservation of M. thermophilum was dependent on a respiratory chain consisting of a hydrogenase (VhoGAC), a formate dehydrogenase (FdhGHI), and a heterodisulfide reductase (HdrDE) that were well adapted to the harsh physicochemical conditions in the natural habitat. The experiments revealed the presence of two variants of energy-conserving oxidoreductase systems in the membrane. These included the H2 : heterodisulfide oxidoreductase system, which has already been described in Methanosarcina species, as well as the novel formate: heterodisulfide oxidoreductase system. The latter electron transport chain, which was experimentally proven for the first time, distinguishes the organism from all other known methanogenic archaea and represents a unique feature of the class Methanonatronarchaeia. Experiments with 2-hydroxyphenazine and the inhibitor diphenyleneiodonium chloride indicated that a methanophenazine-like cofactor might function as an electron carrier between the hydrogenase/ formate dehydrogenase and the heterodisulfide reductase.
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Affiliation(s)
- Fabian Steiniger
- Institute of Microbiology and Biotechnology, University of Bonn, Bonn, Germany
| | - Dimitry Y Sorokin
- Research Centre of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia.,Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Uwe Deppenmeier
- Institute of Microbiology and Biotechnology, University of Bonn, Bonn, Germany
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5
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Genome-Wide Screening of Oxidizing Agent Resistance Genes in Escherichia coli. Antioxidants (Basel) 2021; 10:antiox10060861. [PMID: 34072091 PMCID: PMC8228696 DOI: 10.3390/antiox10060861] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 05/25/2021] [Accepted: 05/26/2021] [Indexed: 01/31/2023] Open
Abstract
The use of oxidizing agents is one of the most favorable approaches to kill bacteria in daily life. However, bacteria have been evolving to survive in the presence of different oxidizing agents. In this study, we aimed to obtain a comprehensive list of genes whose expression can make Escherichiacoli cells resistant to different oxidizing agents. For this purpose, we utilized the ASKA library and performed a genome-wide screening of ~4200 E. coli genes. Hydrogen peroxide (H2O2) and hypochlorite (HOCl) were tested as representative oxidizing agents in this study. To further validate our screening results, we used different E. coli strains as host cells to express or inactivate selected resistance genes individually. More than 100 genes obtained in this screening were not known to associate with oxidative stress responses before. Thus, this study is expected to facilitate both basic studies on oxidative stress and the development of antibacterial agents.
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6
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Liu G, Beaton SE, Grieve AG, Evans R, Rogers M, Strisovsky K, Armstrong FA, Freeman M, Exley RM, Tang CM. Bacterial rhomboid proteases mediate quality control of orphan membrane proteins. EMBO J 2020; 39:e102922. [PMID: 32337752 PMCID: PMC7232013 DOI: 10.15252/embj.2019102922] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 03/17/2020] [Accepted: 03/24/2020] [Indexed: 02/01/2023] Open
Abstract
Although multiprotein membrane complexes play crucial roles in bacterial physiology and virulence, the mechanisms governing their quality control remain incompletely understood. In particular, it is not known how unincorporated, orphan components of protein complexes are recognised and eliminated from membranes. Rhomboids, the most widespread and largest superfamily of intramembrane proteases, are known to play key roles in eukaryotes. In contrast, the function of prokaryotic rhomboids has remained enigmatic. Here, we show that the Shigella sonnei rhomboid proteases GlpG and the newly identified Rhom7 are involved in membrane protein quality control by specifically targeting components of respiratory complexes, with the metastable transmembrane domains (TMDs) of rhomboid substrates protected when they are incorporated into a functional complex. Initial cleavage by GlpG or Rhom7 allows subsequent degradation of the orphan substrate. Given the occurrence of this strategy in an evolutionary ancient organism and the presence of rhomboids in all domains of life, it is likely that this form of quality control also mediates critical events in eukaryotes and protects cells from the damaging effects of orphan proteins.
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Affiliation(s)
- Guangyu Liu
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Stephen E Beaton
- Inorganic Chemistry Laboratory, University of Oxford, Oxford, UK
| | - Adam G Grieve
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Rhiannon Evans
- Inorganic Chemistry Laboratory, University of Oxford, Oxford, UK
| | - Miranda Rogers
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Kvido Strisovsky
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Praha 6, Czech Republic
| | | | - Matthew Freeman
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Rachel M Exley
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Christoph M Tang
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
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7
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Benoit SL, Maier RJ, Sawers RG, Greening C. Molecular Hydrogen Metabolism: a Widespread Trait of Pathogenic Bacteria and Protists. Microbiol Mol Biol Rev 2020; 84:e00092-19. [PMID: 31996394 PMCID: PMC7167206 DOI: 10.1128/mmbr.00092-19] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Pathogenic microorganisms use various mechanisms to conserve energy in host tissues and environmental reservoirs. One widespread but often overlooked means of energy conservation is through the consumption or production of molecular hydrogen (H2). Here, we comprehensively review the distribution, biochemistry, and physiology of H2 metabolism in pathogens. Over 200 pathogens and pathobionts carry genes for hydrogenases, the enzymes responsible for H2 oxidation and/or production. Furthermore, at least 46 of these species have been experimentally shown to consume or produce H2 Several major human pathogens use the large amounts of H2 produced by colonic microbiota as an energy source for aerobic or anaerobic respiration. This process has been shown to be critical for growth and virulence of the gastrointestinal bacteria Salmonella enterica serovar Typhimurium, Campylobacter jejuni, Campylobacter concisus, and Helicobacter pylori (including carcinogenic strains). H2 oxidation is generally a facultative trait controlled by central regulators in response to energy and oxidant availability. Other bacterial and protist pathogens produce H2 as a diffusible end product of fermentation processes. These include facultative anaerobes such as Escherichia coli, S Typhimurium, and Giardia intestinalis, which persist by fermentation when limited for respiratory electron acceptors, as well as obligate anaerobes, such as Clostridium perfringens, Clostridioides difficile, and Trichomonas vaginalis, that produce large amounts of H2 during growth. Overall, there is a rich literature on hydrogenases in growth, survival, and virulence in some pathogens. However, we lack a detailed understanding of H2 metabolism in most pathogens, especially obligately anaerobic bacteria, as well as a holistic understanding of gastrointestinal H2 transactions overall. Based on these findings, we also evaluate H2 metabolism as a possible target for drug development or other therapies.
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Affiliation(s)
- Stéphane L Benoit
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - Robert J Maier
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - R Gary Sawers
- Institute of Microbiology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Chris Greening
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
- Department of Microbiology, Monash Biomedicine Discovery Institute, Clayton, VIC, Australia
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8
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The structure of hydrogenase-2 from Escherichia coli: implications for H 2-driven proton pumping. Biochem J 2018; 475:1353-1370. [PMID: 29555844 PMCID: PMC5902676 DOI: 10.1042/bcj20180053] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 03/12/2018] [Accepted: 03/16/2018] [Indexed: 01/19/2023]
Abstract
Under anaerobic conditions, Escherichia coli is able to metabolize molecular hydrogen via the action of several [NiFe]-hydrogenase enzymes. Hydrogenase-2, which is typically present in cells at low levels during anaerobic respiration, is a periplasmic-facing membrane-bound complex that functions as a proton pump to convert energy from hydrogen (H2) oxidation into a proton gradient; consequently, its structure is of great interest. Empirically, the complex consists of a tightly bound core catalytic module, comprising large (HybC) and small (HybO) subunits, which is attached to an Fe–S protein (HybA) and an integral membrane protein (HybB). To date, efforts to gain a more detailed picture have been thwarted by low native expression levels of Hydrogenase-2 and the labile interaction between HybOC and HybA/HybB subunits. In the present paper, we describe a new overexpression system that has facilitated the determination of high-resolution crystal structures of HybOC and, hence, a prediction of the quaternary structure of the HybOCAB complex.
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9
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Abstract
Numerous recent developments in the biochemistry, molecular biology, and physiology of formate and H2 metabolism and of the [NiFe]-hydrogenase (Hyd) cofactor biosynthetic machinery are highlighted. Formate export and import by the aquaporin-like pentameric formate channel FocA is governed by interaction with pyruvate formate-lyase, the enzyme that generates formate. Formate is disproportionated by the reversible formate hydrogenlyase (FHL) complex, which has been isolated, allowing biochemical dissection of evolutionary parallels with complex I of the respiratory chain. A recently identified sulfido-ligand attached to Mo in the active site of formate dehydrogenases led to the proposal of a modified catalytic mechanism. Structural analysis of the homologous, H2-oxidizing Hyd-1 and Hyd-5 identified a novel proximal [4Fe-3S] cluster in the small subunit involved in conferring oxygen tolerance to the enzymes. Synthesis of Salmonella Typhimurium Hyd-5 occurs aerobically, which is novel for an enterobacterial Hyd. The O2-sensitive Hyd-2 enzyme has been shown to be reversible: it presumably acts as a conformational proton pump in the H2-oxidizing mode and is capable of coupling reverse electron transport to drive H2 release. The structural characterization of all the Hyp maturation proteins has given new impulse to studies on the biosynthesis of the Fe(CN)2CO moiety of the [NiFe] cofactor. It is synthesized on a Hyp-scaffold complex, mainly comprising HypC and HypD, before insertion into the apo-large subunit. Finally, clear evidence now exists indicating that Escherichia coli can mature Hyd enzymes differentially, depending on metal ion availability and the prevailing metabolic state. Notably, Hyd-3 of the FHL complex takes precedence over the H2-oxidizing enzymes.
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10
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The dual-function chaperone HycH improves assembly of the formate hydrogenlyase complex. Biochem J 2017; 474:2937-2950. [PMID: 28718449 DOI: 10.1042/bcj20170431] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 07/11/2017] [Accepted: 07/17/2017] [Indexed: 11/17/2022]
Abstract
The assembly of multi-protein complexes requires the concerted synthesis and maturation of its components and subsequently their co-ordinated interaction. The membrane-bound formate hydrogenlyase (FHL) complex is the primary hydrogen-producing enzyme in Escherichia coli and is composed of seven subunits mostly encoded within the hycA-I operon for [NiFe]-hydrogenase-3 (Hyd-3). The HycH protein is predicted to have an accessory function and is not part of the final structural FHL complex. In this work, a mutant strain devoid of HycH was characterised and found to have significantly reduced FHL activity due to the instability of the electron transfer subunits. HycH was shown to interact specifically with the unprocessed species of HycE, the catalytic hydrogenase subunit of the FHL complex, at different stages during the maturation and assembly of the complex. Variants of HycH were generated with the aim of identifying interacting residues and those that influence activity. The R70/71/K72, the Y79, the E81 and the Y128 variant exchanges interrupt the interaction with HycE without influencing the FHL activity. In contrast, FHL activity, but not the interaction with HycE, was negatively influenced by H37 exchanges with polar residues. Finally, a HycH Y30 variant was unstable. Surprisingly, an overlapping function between HycH with its homologous counterpart HyfJ from the operon encoding [NiFe]-hydrogenase-4 (Hyd-4) was identified and this is the first example of sharing maturation machinery components between Hyd-3 and Hyd-4 complexes. The data presented here show that HycH has a novel dual role as an assembly chaperone for a cytoplasmic [NiFe]-hydrogenase.
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11
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Biosynthesis of Salmonella enterica [NiFe]-hydrogenase-5: probing the roles of system-specific accessory proteins. J Biol Inorg Chem 2016; 21:865-73. [PMID: 27566174 DOI: 10.1007/s00775-016-1385-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 08/04/2016] [Indexed: 10/21/2022]
Abstract
A subset of bacterial [NiFe]-hydrogenases have been shown to be capable of activating dihydrogen-catalysis under aerobic conditions; however, it remains relatively unclear how the assembly and activation of these enzymes is carried out in the presence of air. Acquiring this knowledge is important if a generic method for achieving production of O2-resistant [NiFe]-hydrogenases within heterologous hosts is to be developed. Salmonella enterica serovar Typhimurium synthesizes the [NiFe]-hydrogenase-5 (Hyd-5) enzyme under aerobic conditions. As well as structural genes, the Hyd-5 operon also contains several accessory genes that are predicted to be involved in different stages of biosynthesis of the enzyme. In this work, deletions in the hydF, hydG, and hydH genes have been constructed. The hydF gene encodes a protein related to Ralstonia eutropha HoxO, which is known to interact with the small subunit of a [NiFe]-hydrogenase. HydG is predicted to be a fusion of the R. eutropha HoxQ and HoxR proteins, both of which have been implicated in the biosynthesis of an O2-tolerant hydrogenase, and HydH is a homologue of R. eutropha HoxV, which is a scaffold for [NiFe] cofactor assembly. It is shown here that HydG and HydH play essential roles in Hyd-5 biosynthesis. Hyd-5 can be isolated and characterized from a ΔhydF strain, indicating that HydF may not play the same vital role as the orthologous HoxO. This study, therefore, emphasises differences that can be observed when comparing the function of hydrogenase maturases in different biological systems.
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12
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Abstract
[NiFe]-hydrogenases catalyze the reversible conversion of hydrogen gas into protons and electrons and are vital metabolic components of many species of bacteria and archaea. At the core of this enzyme is a sophisticated catalytic center comprising nickel and iron, as well as cyanide and carbon monoxide ligands, which is anchored to the large hydrogenase subunit through cysteine residues. The production of this multicomponent active site is accomplished by a collection of accessory proteins and can be divided into discrete stages. The iron component is fashioned by the proteins HypC, HypD, HypE, and HypF, which functionalize iron with cyanide and carbon monoxide. Insertion of the iron center signals to the metallochaperones HypA, HypB, and SlyD to selectively deliver the nickel to the active site. A specific protease recognizes the completed metal cluster and then cleaves the C-terminus of the large subunit, resulting in a conformational change that locks the active site in place. Finally, the large subunit associates with the small subunit, and the complete holoenzyme translocates to its final cellular position. Beyond this broad overview of the [NiFe]-hydrogenase maturation process, biochemical and structural studies are revealing the fundamental underlying molecular mechanisms. Here, we review recent work illuminating how the accessory proteins contribute to the maturation of [NiFe]-hydrogenase and discuss some of the outstanding questions that remain to be resolved.
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Affiliation(s)
- Michael J Lacasse
- Department of Chemistry, University of Toronto , Toronto, Ontario, Canada M5S 3H6
| | - Deborah B Zamble
- Department of Chemistry, University of Toronto , Toronto, Ontario, Canada M5S 3H6.,Department of Biochemistry, University of Toronto , Toronto, Ontario, Canada M5S 1A8
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13
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Abstract
In Escherichia coli, hydrogen metabolism plays a prominent role in anaerobic physiology. The genome contains the capability to produce and assemble up to four [NiFe]-hydrogenases, each of which are known, or predicted, to contribute to different aspects of cellular metabolism. In recent years, there have been major advances in the understanding of the structure, function, and roles of the E. coli [NiFe]-hydrogenases. The membrane-bound, periplasmically oriented, respiratory Hyd-1 isoenzyme has become one of the most important paradigm systems for understanding an important class of oxygen-tolerant enzymes, as well as providing key information on the mechanism of hydrogen activation per se. The membrane-bound, periplasmically oriented, Hyd-2 isoenzyme has emerged as an unusual, bidirectional redox valve able to link hydrogen oxidation to quinone reduction during anaerobic respiration, or to allow disposal of excess reducing equivalents as hydrogen gas. The membrane-bound, cytoplasmically oriented, Hyd-3 isoenzyme is part of the formate hydrogenlyase complex, which acts to detoxify excess formic acid under anaerobic fermentative conditions and is geared towards hydrogen production under those conditions. Sequence identity between some Hyd-3 subunits and those of the respiratory NADH dehydrogenases has led to hypotheses that the activity of this isoenzyme may be tightly coupled to the formation of transmembrane ion gradients. Finally, the E. coli genome encodes a homologue of Hyd-3, termed Hyd-4, however strong evidence for a physiological role for E. coli Hyd-4 remains elusive. In this review, the versatile hydrogen metabolism of E. coli will be discussed and the roles and potential applications of the spectrum of different types of [NiFe]-hydrogenases available will be explored.
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14
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Coordination of Synthesis and Assembly of a Modular Membrane-Associated [NiFe]-Hydrogenase Is Determined by Cleavage of the C-Terminal Peptide. J Bacteriol 2015; 197:2989-98. [PMID: 26170410 DOI: 10.1128/jb.00437-15] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 07/02/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED During biosynthesis of [NiFe]-hydrogenase 2 (Hyd-2) of Escherichia coli, a 15-amino-acid C-terminal peptide is cleaved from the catalytic large subunit precursor, pro-HybC. This peptide is removed only after NiFe(CN)2CO cofactor insertion by the Hyp accessory protein machinery has been completed, suggesting that it has a regulatory function during enzyme maturation. We show here that in hyp mutants that fail to synthesize and insert the NiFe cofactor, and therefore retain the peptide, the Tat (twin-arginine translocon) signal peptide on the small subunit HybO is not removed and the subunit is degraded. In a mutant lacking the large subunit, the Tat signal peptide was also not removed from pre-HybO, indicating that the mature large subunit must actively engage the small subunit to elicit Tat transport. We validated the proposed regulatory role of the C-terminal peptide in controlling enzyme assembly by genetically removing it from the precursor of HybC, which allowed assembly and Tat-dependent membrane association of a HybC-HybO heterodimer lacking the NiFe(CN)2CO cofactor. Finally, genetic transfer of the C-terminal peptide from pro-HyaB, the large subunit of Hyd-1, onto HybC did not influence its dependence on the accessory protein HybG, a HypC paralog, or the specific protease HybD. This indicates that the C-terminal peptide per se is not required for interaction with the Hyp machinery but rather suggests a role of the peptide in maintaining a conformation of the protein suitable for cofactor insertion. Together, our results demonstrate that the C-terminal peptide on the catalytic subunit controls biosynthesis, assembly, and membrane association of Hyd-2. IMPORTANCE [NiFe]-hydrogenases are multisubunit enzymes with a catalytic subunit containing a NiFe(CN)2CO cofactor. Results of previous studies suggested that after synthesis and insertion of the cofactor by the Hyp accessory proteins, this large subunit changes conformation upon proteolytic removal of a short peptide from its C terminus. We show that removal of this peptide is necessary to allow the cleavage of the Tat signal peptide from the small subunit with concomitant membrane association of the heterodimer to occur. Genetic removal of the C-terminal peptide from the large subunit allowed productive interaction with the small subunit and Tat-dependent membrane insertion of a NiFe cofactor-free enzyme. Results based on swapping of C-terminal peptides between hydrogenases suggest that this peptide governs enzyme assembly via a conformational switch.
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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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Efficient export of human growth hormone, interferon α2b and antibody fragments to the periplasm by the Escherichia coli Tat pathway in the absence of prior disulfide bond formation. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1853:756-63. [DOI: 10.1016/j.bbamcr.2014.12.027] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2014] [Revised: 12/18/2014] [Accepted: 12/20/2014] [Indexed: 11/19/2022]
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17
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An engineered genetic selection for ternary protein complexes inspired by a natural three-component hitchhiker mechanism. Sci Rep 2014; 4:7570. [PMID: 25531212 PMCID: PMC4273604 DOI: 10.1038/srep07570] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 12/02/2014] [Indexed: 12/29/2022] Open
Abstract
The bacterial twin-arginine translocation (Tat) pathway is well known to translocate correctly folded monomeric and dimeric proteins across the tightly sealed cytoplasmic membrane. We identified a naturally occurring heterotrimer, the Escherichia coli aldehyde oxidoreductase PaoABC, that is co-translocated by the Tat translocase according to a ternary “hitchhiker” mechanism. Specifically, the PaoB and PaoC subunits, each devoid of export signals, are escorted to the periplasm in a piggyback fashion by the Tat signal peptide-containing subunit PaoA. Moreover, export of PaoA was blocked when either PaoB or PaoC was absent, revealing a surprising interdependence for export that is not seen for classical secretory proteins. Inspired by this observation, we created a bacterial three-hybrid selection system that links the formation of ternary protein complexes with antibiotic resistance. As proof-of-concept, a bispecific antibody was employed as an adaptor that physically crosslinked one antigen fused to a Tat export signal with a second antigen fused to TEM-1 β-lactamase (Bla). The resulting non-covalent heterotrimer was exported in a Tat-dependent manner, delivering Bla to the periplasm where it hydrolyzed β-lactam antibiotics. Collectively, these results highlight the remarkable flexibility of the Tat system and its potential for studying and engineering ternary protein interactions in living bacteria.
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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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Affiliation(s)
- Wolfgang Lubitz
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Hideaki Ogata
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Olaf Rüdiger
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Edward Reijerse
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
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Engineering Hydrogenases for H2 Production: Bolts and Goals. MICROBIAL BIOENERGY: HYDROGEN PRODUCTION 2014. [DOI: 10.1007/978-94-017-8554-9_3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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Dow JM, Grahl S, Ward R, Evans R, Byron O, Norman DG, Palmer T, Sargent F. Characterization of a periplasmic nitrate reductase in complex with its biosynthetic chaperone. FEBS J 2013; 281:246-60. [PMID: 24314029 PMCID: PMC4159696 DOI: 10.1111/febs.12592] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 10/24/2013] [Accepted: 10/28/2013] [Indexed: 11/28/2022]
Abstract
Escherichia coli is a Gram‐negative bacterium that can use nitrate during anaerobic respiration. The catalytic subunit of the periplasmic nitrate reductase NapA contains two types of redox cofactor and is exported across the cytoplasmic membrane by the twin‐arginine protein transport pathway. NapD is a small cytoplasmic protein that is essential for the activity of the periplasmic nitrate reductase and binds tightly to the twin‐arginine signal peptide of NapA. Here we show, using spin labelling and EPR, that the isolated twin‐arginine signal peptide of NapA is structured in its unbound form and undergoes a small but significant conformational change upon interaction with NapD. In addition, a complex comprising the full‐length NapA protein and NapD could be isolated by engineering an affinity tag onto NapD only. Analytical ultracentrifugation demonstrated that the two proteins in the NapDA complex were present in a 1 : 1 molar ratio, and small angle X‐ray scattering analysis of the complex indicated that NapA was at least partially folded when bound by its NapD partner. A NapDA complex could not be isolated in the absence of the NapA Tat signal peptide. Taken together, this work indicates that the NapD chaperone binds primarily at the NapA signal peptide in this system and points towards a role for NapD in the insertion of the molybdenum cofactor. Structured digital abstract NapD and NapAbind by x ray scattering (View interaction) NapA and NapD physically interact by molecular sieving (View interaction) NapA and NapDbind by electron paramagnetic resonance (View interaction)
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Affiliation(s)
- Jennifer M Dow
- Division of Molecular Microbiology, College of Life Sciences, University of Dundee, UK
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Abstract
AIM To investigate the biological activity of the H. pylori SlyD in vitro. METHODS Helicobacter pylori (H.pylori) slyD prokaryotic expression vector was carried out in Escherichia coli (E.coli), and recombination SlyD (rSlyD) was purified by immobilized metal affinity chromatography. The proliferation, apoptosis, invasion, transformation effects of rSlyD on AGS cells was detected by CCK-8, cell cycle, caspase-3 activity, matrigel invasion assay, and double-deck soft agar colony forming efficiency. In addition, the expressions of PCNA, KI-67, caspase-3, and MMP-9 were detected by western blot and immunofluorescence assay, respectively. RESULTS The CCK-8 assay revealed that cell proliferation was increased in a time and dose-dependent manner in AGS + rSlyD group compared with that of AGS or AGS + PBS group (p < .05). There are significant difference of PCNA and KI67 expressions among AGS, AGS + PBS, AGS + rSlyD groups (p < .05). Soft agar colony formation assay revealed the colony number (foci>100 μm) in AGS + rSlyD group was 26.3 ± 7.09, whereas 5.6 ± 1.15 in AGS and 5.0 ± 1.0 in AGS + PBS groups, respectively (p < .01). Colorimetric enzyme assay revealed the activity of caspase-3 was decreased to 31.45 ± 0.49 after treatment with rSlyD, whereas 55.5 ± 0.43 in AGS and 55.1 ± 0.25 in AGS + PBS group, respectively (p < .001). Similar caspase-3 expression also was confirmed by Western blot. The number of invasive cells in transwell chambers assay is 196.66 ± 40.41 in AGS + rSlyD group higher than 85 ± 22.9 in AGS or 81.66 ± 15.27 in AGS + PBS group, respectively (p < .001). The MMP-9 expression in AGS + rSlyD group was also higher than that of AGS or AGS + PBS group. CONCLUSION These results suggest that the HpSlyD may play an important role in disturbing cell proliferation, apoptosis, and enhancing cell transformation and invasion in the AGS cell line. HpSlyD might contribute to gastric pathogenicity in H.pylori-associated diseases.
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Affiliation(s)
- Dan Kang
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Affiliated Hospital of China Medical University, Shenyang, China
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Bowman L, Palmer T, Sargent F. A regulatory domain controls the transport activity of a twin-arginine signal peptide. FEBS Lett 2013; 587:3365-70. [PMID: 24036452 DOI: 10.1016/j.febslet.2013.09.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Revised: 09/02/2013] [Accepted: 09/03/2013] [Indexed: 11/25/2022]
Abstract
The twin-arginine translocation (Tat) pathway is used by bacteria for the transmembrane transport of folded proteins. Proteins are targeted to the Tat translocase by signal peptides that have common tripartite structures consisting of polar n-regions, hydrophobic h-regions, and polar c-regions. In this work, the signal peptide of [NiFe] hydrogenase-1 from Escherichia coli has been studied. The hydrogenase-1 signal peptide contains an extended n-region that has a conserved primary structure. Genetic and biochemical approaches reveal that the signal peptide n-region is essential for hydrogenase assembly and acts as a regulatory domain controlling transport activity of the signal peptide.
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Affiliation(s)
- Lisa Bowman
- College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
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Kudva R, Denks K, Kuhn P, Vogt A, Müller M, Koch HG. Protein translocation across the inner membrane of Gram-negative bacteria: the Sec and Tat dependent protein transport pathways. Res Microbiol 2013; 164:505-34. [DOI: 10.1016/j.resmic.2013.03.016] [Citation(s) in RCA: 122] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 03/11/2013] [Indexed: 11/28/2022]
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25
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Kim JYH, Cha HJ. Recent progress in hydrogenase and its biotechnological application for viable hydrogen technology. KOREAN J CHEM ENG 2013. [DOI: 10.1007/s11814-012-0208-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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26
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Waraho-Zhmayev D, Gkogka L, Yu TY, DeLisa MP. A microbial sensor for discovering structural probes of protein misfolding and aggregation. Prion 2013; 7:151-6. [PMID: 23357829 DOI: 10.4161/pri.23328] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
In all cell types, protein homeostasis, or "proteostasis," is maintained by sophisticated quality control networks that regulate protein synthesis, folding, trafficking, aggregation, disaggregation, and degradation. In one notable example, Escherichia coli employ a proteostasis system that determines whether substrates of the twin-arginine translocation (Tat) pathway are correctly folded and thus suitable for transport across the tightly sealed cytoplasmic membrane. Herein, we review growing evidence that the Tat translocase itself discriminates folded proteins from those that are misfolded and/or aggregated, preferentially exporting only the former. Genetic suppressors that inactivate this mechanism have recently been isolated and provide direct evidence for the participation of the Tat translocase in structural proofreading of its protein substrates. We also discuss how this discriminatory "folding sensor" has been exploited for the discovery of structural probes (e.g., sequence mutations, pharmacologic chaperones, intracellular antibodies) that modulate the folding and solubility of virtually any protein-of-interest, including those associated with aggregation diseases (e.g., α-synuclein, amyloid-β protein). Taken together, these studies highlight the utility of engineered bacteria for rapidly and inexpensively uncovering potent anti-aggregation factors.
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Fröbel J, Rose P, Müller M. Twin-arginine-dependent translocation of folded proteins. Philos Trans R Soc Lond B Biol Sci 2012; 367:1029-46. [PMID: 22411976 PMCID: PMC3297433 DOI: 10.1098/rstb.2011.0202] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Twin-arginine translocation (Tat) denotes a protein transport pathway in bacteria, archaea and plant chloroplasts, which is specific for precursor proteins harbouring a characteristic twin-arginine pair in their signal sequences. Many Tat substrates receive cofactors and fold prior to translocation. For a subset of them, proofreading chaperones coordinate maturation and membrane-targeting. Tat translocases comprise two kinds of membrane proteins, a hexahelical TatC-type protein and one or two members of the single-spanning TatA protein family, called TatA and TatB. TatC- and TatA-type proteins form homo- and hetero-oligomeric complexes. The subunits of TatABC translocases are predominantly recovered from two separate complexes, a TatBC complex that might contain some TatA, and a homomeric TatA complex. TatB and TatC coordinately recognize twin-arginine signal peptides and accommodate them in membrane-embedded binding pockets. Advanced binding of the signal sequence to the Tat translocase requires the proton-motive force (PMF) across the membranes and might involve a first recruitment of TatA. When targeted in this manner, folded twin-arginine precursors induce homo-oligomerization of TatB and TatA. Ultimately, this leads to the formation of a transmembrane protein conduit that possibly consists of a pore-like TatA structure. The translocation step again is dependent on the PMF.
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Affiliation(s)
- Julia Fröbel
- Institute of Biochemistry and Molecular Biology, ZBMZ, University of Freiburg, Stefan-Meier-Strasse 17, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, Schänzle-Strasse 1, 79104 Freiburg, Germany
| | - Patrick Rose
- Institute of Biochemistry and Molecular Biology, ZBMZ, University of Freiburg, Stefan-Meier-Strasse 17, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, Schänzle-Strasse 1, 79104 Freiburg, Germany
| | - Matthias Müller
- Institute of Biochemistry and Molecular Biology, ZBMZ, University of Freiburg, Stefan-Meier-Strasse 17, 79104 Freiburg, Germany
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Parkin A, Sargent F. The hows and whys of aerobic H2 metabolism. Curr Opin Chem Biol 2012; 16:26-34. [PMID: 22366384 DOI: 10.1016/j.cbpa.2012.01.012] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Revised: 01/16/2012] [Accepted: 01/25/2012] [Indexed: 01/08/2023]
Abstract
The bacterial [NiFe]-hydrogenases have been classified as either 'standard' or 'O2-tolerant' based on their ability to function in the presence of O2. Typically, these enzymes contain four redox-active metal centers: a Ni-Fe-CO-2CN- active site and three electron-transferring Fe-S clusters. Recent research suggests that, rather than differences at the catalytic active site, it is a novel Fe-S cluster electron transfer (ET) relay that controls how [NiFe]-hydrogenases recover from O2 attack. In light of recent structural data and mutagenic studies this article reviews the molecular mechanism of O2-tolerance in [NiFe]-hydrogenases and discusses the biosynthesis of the unique Fe-S relay.
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Affiliation(s)
- Alison Parkin
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, Oxford OX1 3QR, UK
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29
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Hou B, Brüser T. The Tat-dependent protein translocation pathway. Biomol Concepts 2011; 2:507-23. [DOI: 10.1515/bmc.2011.040] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Accepted: 08/05/2011] [Indexed: 11/15/2022] Open
Abstract
AbstractThe twin-arginine translocation (Tat) pathway is found in bacteria, archaea, and plant chloroplasts, where it is dedicated to the transmembrane transport of fully folded proteins. These proteins contain N-terminal signal peptides with a specific Tat-system binding motif that is recognized by the transport machinery. In contrast to other protein transport systems, the Tat system consists of multiple copies of only two or three usually small (∼8–30 kDa) membrane proteins that oligomerize to two large complexes that transiently interact during translocation. Only one of these complexes includes a polytopic membrane protein, TatC. The other complex consists of TatA. Tat systems of plants, proteobacteria, and several other phyla contain a third component, TatB. TatB is evolutionarily and structurally related to TatA and usually forms tight complexes with TatC. Minimal two-component Tat systems lacking TatB are found in many bacterial and archaeal phyla. They consist of a ‘bifunctional’ TatA that also covers TatB functionalities, and a TatC. Recent insights into the structure and interactions of the Tat proteins have various important implications.
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Affiliation(s)
- Bo Hou
- Institute of Microbiology, Leibniz University Hannover, Schneiderberg 50, D-30167 Hannover, Germany
| | - Thomas Brüser
- Institute of Microbiology, Leibniz University Hannover, Schneiderberg 50, D-30167 Hannover, Germany
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Cheng T, Li H, Xia W, Sun H. Multifaceted SlyD from Helicobacter pylori: implication in [NiFe] hydrogenase maturation. J Biol Inorg Chem 2011; 17:331-43. [PMID: 22045417 PMCID: PMC3292732 DOI: 10.1007/s00775-011-0855-y] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Accepted: 10/07/2011] [Indexed: 12/31/2022]
Abstract
SlyD belongs to the FK506-binding protein (FKBP) family with both peptidylprolyl isomerase (PPIase) and chaperone activities, and is considered to be a ubiquitous cytosolic protein-folding facilitator in bacteria. It possesses a histidine- and cysteine-rich C-terminus binding to selected divalent metal ions (e.g., Ni2+, Zn2+), which is important for its involvement in the maturation processes of metalloenzymes. We have determined the solution structure of C-terminus-truncated SlyD from Helicobacter pylori (HpSlyDΔC). HpSlyDΔC folds into two well-separated, orientation-independent domains: the PPIase-active FKBP domain and the chaperone-active insert-in-flap (IF) domain. The FKBP domain consists of a four-stranded antiparallel β-sheet with an α-helix on one side, whereas the IF domain folds into a four-stranded antiparallel β-sheet accompanied by a short α-helix. Intact H. pylori SlyD binds both Ni2+ and Zn2+, with dissociation constants of 2.74 and 3.79 μM respectively. Intriguingly, binding of Ni2+ instead of Zn2+ induces protein conformational changes around the active sites of the FKBP domain, implicating a regulatory role of nickel. The twin-arginine translocation (Tat) signal peptide from the small subunit of [NiFe] hydrogenase (HydA) binds the protein at the IF domain. Nickel binding and the recognition of the Tat signal peptide by the protein suggest that SlyD participates in [NiFe] hydrogenase maturation processes.
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Affiliation(s)
- Tianfan Cheng
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, People’s Republic of China
| | - Hongyan Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, People’s Republic of China
| | - Wei Xia
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, People’s Republic of China
| | - Hongzhe Sun
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, People’s Republic of China
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Chan Chung KC, Zamble DB. Protein interactions and localization of the Escherichia coli accessory protein HypA during nickel insertion to [NiFe] hydrogenase. J Biol Chem 2011; 286:43081-90. [PMID: 22016389 DOI: 10.1074/jbc.m111.290726] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Nickel delivery during maturation of Escherichia coli [NiFe] hydrogenase 3 includes the accessory proteins HypA, HypB, and SlyD. Although the isolated proteins have been characterized, little is known about how they interact with each other and the hydrogenase 3 large subunit, HycE. In this study the complexes of HypA and HycE were investigated after modification with the Strep-tag II. Multiprotein complexes containing HypA, HypB, SlyD, and HycE were observed, consistent with the assembly of a single nickel insertion cluster. An interaction between HypA and HycE did not require the other nickel insertion proteins, but HypB was not found with the large subunit in the absence of HypA. The HypA-HycE complex was not detected in the absence of the HypC or HypD proteins, involved in the preceding iron insertion step, and this interaction is enhanced by nickel brought into the cell by the NikABCDE membrane transporter. Furthermore, without the hydrogenase 1, 2, and 3 large subunits, complexes between HypA, HypB, and SlyD were observed. These results support the hypothesis that HypA acts as a scaffold for assembly of the nickel insertion proteins with the hydrogenase precursor protein after delivery of the iron center. At different stages of the hydrogenase maturation process, HypA was observed at or near the cell membrane by using fluorescence confocal microscopy, as was HycE, suggesting membrane localization of the nickel insertion event.
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Affiliation(s)
- Kim C Chan Chung
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
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Kim JYH, Jo BH, Cha HJ. Production of biohydrogen by heterologous expression of oxygen-tolerant Hydrogenovibrio marinus [NiFe]-hydrogenase in Escherichia coli. J Biotechnol 2011; 155:312-9. [PMID: 21794837 DOI: 10.1016/j.jbiotec.2011.07.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Revised: 07/05/2011] [Accepted: 07/11/2011] [Indexed: 11/15/2022]
Abstract
Oxygen sensitivity of hydrogenase is a critical issue in efficient biological hydrogen production. In the present study, oxygen-tolerant [NiFe]-hydrogenase from the marine bacterium, Hydrogenovibrio marinus, was heterologously expressed in Escherichia coli, for the first time. Recombinant E. coli BL21 expressing H. marinus [NiFe]-hydrogenase actively produced hydrogen, but the parent strain did not. Recombinant H. marinus hydrogenase required both nickel and iron for biological activity. Compared to the recombinant E. coli [NiFe]-hydrogenase 1 described in our previous report, recombinant H. marinus [NiFe]-hydrogenase displayed 1.6- to 1.7-fold higher hydrogen production activity in vitro. Importantly, H. marinus [NiFe]-hydrogenase exhibited relatively good oxygen tolerance in analyses involving changes of surface aeration and oxygen proportion within a gas mixture. Specifically, recombinant H. marinus [NiFe]-hydrogenase produced ∼7- to 9-fold more hydrogen than did E. coli [NiFe]-hydrogenase 1 in a gaseous environment containing 5-10% (v/v) oxygen. In addition, purified H. marinus [NiFe]-hydrogenase displayed a hydrogen evolution activity of ∼28.8 nmol H₂/(minmg protein) under normal aerobic purification conditions. Based on these results, we suggest that oxygen-tolerant H. marinus [NiFe]-hydrogenase can be employed for in vivo and in vitro biohydrogen production without requirement for strictly anaerobic facilities.
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Affiliation(s)
- Jaoon Y H Kim
- Department of Chemical Engineering, Pohang University of Science and Technology, Pohang 790-784, Republic of Korea
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The maturation factors HoxR and HoxT contribute to oxygen tolerance of membrane-bound [NiFe] hydrogenase in Ralstonia eutropha H16. J Bacteriol 2011; 193:2487-97. [PMID: 21441514 DOI: 10.1128/jb.01427-10] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The membrane-bound [NiFe] hydrogenase (MBH) of Ralstonia eutropha H16 undergoes a complex maturation process comprising cofactor assembly and incorporation, subunit oligomerization, and finally twin-arginine-dependent membrane translocation. Due to its outstanding O(2) and CO tolerance, the MBH is of biotechnological interest and serves as a molecular model for a robust hydrogen catalyst. Adaptation of the enzyme to oxygen exposure has to take into account not only the catalytic reaction but also biosynthesis of the intricate redox cofactors. Here, we report on the role of the MBH-specific accessory proteins HoxR and HoxT, which are key components in MBH maturation at ambient O(2) levels. MBH-driven growth on H(2) is inhibited or retarded at high O(2) partial pressure (pO(2)) in mutants inactivated in the hoxR and hoxT genes. The ratio of mature and nonmature forms of the MBH small subunit is shifted toward the precursor form in extracts derived from the mutant cells grown at high pO(2). Lack of hoxR and hoxT can phenotypically be restored by providing O(2)-limited growth conditions. Analysis of copurified maturation intermediates leads to the conclusion that the HoxR protein is a constituent of a large transient protein complex, whereas the HoxT protein appears to function at a final stage of MBH maturation. UV-visible spectroscopy of heterodimeric MBH purified from hoxR mutant cells points to alterations of the Fe-S cluster composition. Thus, HoxR may play a role in establishing a specific Fe-S cluster profile, whereas the HoxT protein seems to be beneficial for cofactor stability under aerobic conditions.
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Chung KCC, Zamble DB. The Escherichia coli metal-binding chaperone SlyD interacts with the large subunit of [NiFe]-hydrogenase 3. FEBS Lett 2010; 585:291-4. [PMID: 21185288 DOI: 10.1016/j.febslet.2010.12.024] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Revised: 12/10/2010] [Accepted: 12/14/2010] [Indexed: 11/30/2022]
Abstract
The multi-step biosynthesis of the [NiFe]-hydrogenase enzyme involves a variety of accessory proteins. To further understand this process, a Strep-tag II variant of the large subunit of Escherichia coli hydrogenase 3, HycE, was constructed to enable isolation of protein complexes. A complex with SlyD, a chaperone protein implicated in hydrogenase production through association with the nickel-binding accessory protein HypB, was observed. A SlyD-HycE interaction preceding both iron and nickel insertion to the enzyme was detected, mediated by the chaperone domain of SlyD, and independent of HypB. These results support a model of several roles for SlyD during hydrogenase maturation.
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Affiliation(s)
- Kim C Chan Chung
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
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Chan CS, Chang L, Winstone TML, Turner RJ. Comparing system-specific chaperone interactions with their Tat dependent redox enzyme substrates. FEBS Lett 2010; 584:4553-8. [PMID: 20974141 DOI: 10.1016/j.febslet.2010.10.043] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2010] [Revised: 09/16/2010] [Accepted: 10/17/2010] [Indexed: 12/01/2022]
Abstract
Redox enzyme substrates of the twin-arginine translocation (Tat) system contain a RR-motif in their leader peptide and require the assistance of chaperones, redox enzyme maturation proteins (REMPs). Here various regions of the RR-containing oxidoreductase subunit (leader peptide, full preprotein with and without a leader cleavage site, mature protein) were assayed for interaction with their REMPs. All REMPs bound their preprotein substrates independent of the cleavage site. Some showed binding to either the leader or mature region, whereas in one case only the preprotein bound its REMP. The absence of Tat also influenced the amount of chaperone-substrate interaction.
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Affiliation(s)
- Catherine S Chan
- Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, Alberta, Canada
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36
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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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37
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Calusinska M, Happe T, Joris B, Wilmotte A. The surprising diversity of clostridial hydrogenases: a comparative genomic perspective. MICROBIOLOGY-SGM 2010; 156:1575-1588. [PMID: 20395274 DOI: 10.1099/mic.0.032771-0] [Citation(s) in RCA: 132] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Among the large variety of micro-organisms capable of fermentative hydrogen production, strict anaerobes such as members of the genus Clostridium are the most widely studied. They can produce hydrogen by a reversible reduction of protons accumulated during fermentation to dihydrogen, a reaction which is catalysed by hydrogenases. Sequenced genomes provide completely new insights into the diversity of clostridial hydrogenases. Building on previous reports, we found that [FeFe] hydrogenases are not a homogeneous group of enzymes, but exist in multiple forms with different modular structures and are especially abundant in members of the genus Clostridium. This unusual diversity seems to support the central role of hydrogenases in cell metabolism. In particular, the presence of multiple putative operons encoding multisubunit [FeFe] hydrogenases highlights the fact that hydrogen metabolism is very complex in this genus. In contrast with [FeFe] hydrogenases, their [NiFe] hydrogenase counterparts, widely represented in other bacteria and archaea, are found in only a few clostridial species. Surprisingly, a heteromultimeric Ech hydrogenase, known to be an energy-converting [NiFe] hydrogenase and previously described only in methanogenic archaea and some sulfur-reducing bacteria, was found to be encoded by the genomes of four cellulolytic strains: Clostridum cellulolyticum, Clostridum papyrosolvens, Clostridum thermocellum and Clostridum phytofermentans.
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Affiliation(s)
- Magdalena Calusinska
- Center for Protein Engineering, University of Liège, Allée de la Chimie 3, B4000 Liège, Belgium
| | - Thomas Happe
- Lehrstuhl für Biochemie der Pflanzen, AG, Photobiotechnologie, Ruhr - Universität Bochum, 44780 Bochum, Germany
| | - Bernard Joris
- Center for Protein Engineering, University of Liège, Allée de la Chimie 3, B4000 Liège, Belgium
| | - Annick Wilmotte
- Center for Protein Engineering, University of Liège, Allée de la Chimie 3, B4000 Liège, Belgium
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38
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Requirements for construction of a functional hybrid complex of photosystem I and [NiFe]-hydrogenase. Appl Environ Microbiol 2010; 76:2641-51. [PMID: 20154103 DOI: 10.1128/aem.02700-09] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The development of cellular systems in which the enzyme hydrogenase is efficiently coupled to the oxygenic photosynthesis apparatus represents an attractive avenue to produce H(2) sustainably from light and water. Here we describe the molecular design of the individual components required for the direct coupling of the O(2)-tolerant membrane-bound hydrogenase (MBH) from Ralstonia eutropha H16 to the acceptor site of photosystem I (PS I) from Synechocystis sp. PCC 6803. By genetic engineering, the peripheral subunit PsaE of PS I was fused to the MBH, and the resulting hybrid protein was purified from R. eutropha to apparent homogeneity via two independent affinity chromatographical steps. The catalytically active MBH-PsaE (MBH(PsaE)) hybrid protein could be isolated only from the cytoplasmic fraction. This was surprising, since the MBH is a substrate of the twin-arginine translocation system and was expected to reside in the periplasm. We conclude that the attachment of the additional PsaE domain to the small, electron-transferring subunit of the MBH completely abolished the export competence of the protein. Activity measurements revealed that the H(2) production capacity of the purified MBH(PsaE) fusion protein was very similar to that of wild-type MBH. In order to analyze the specific interaction of MBH(PsaE) with PS I, His-tagged PS I lacking the PsaE subunit was purified via Ni-nitrilotriacetic acid affinity and subsequent hydrophobic interaction chromatography. Formation of PS I-hydrogenase supercomplexes was demonstrated by blue native gel electrophoresis. The results indicate a vital prerequisite for the quantitative analysis of the MBH(PsaE)-PS I complex formation and its light-driven H(2) production capacity by means of spectroelectrochemistry.
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Price CE, Driessen AJM. Biogenesis of membrane bound respiratory complexes in Escherichia coli. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2010; 1803:748-66. [PMID: 20138092 DOI: 10.1016/j.bbamcr.2010.01.019] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2009] [Revised: 01/21/2010] [Accepted: 01/27/2010] [Indexed: 11/19/2022]
Abstract
Escherichia coli is one of the preferred bacteria for studies on the energetics and regulation of respiration. Respiratory chains consist of primary dehydrogenases and terminal reductases or oxidases linked by quinones. In order to assemble this complex arrangement of protein complexes, synthesis of the subunits occurs in the cytoplasm followed by assembly in the cytoplasm and/or membrane, the incorporation of metal or organic cofactors and the anchoring of the complex to the membrane. In the case of exported metalloproteins, synthesis, assembly and incorporation of metal cofactors must be completed before translocation across the cytoplasmic membrane. Coordination data on these processes is, however, scarce. In this review, we discuss the various processes that respiratory proteins must undergo for correct assembly and functional coupling to the electron transport chain in E. coli. Targeting to and translocation across the membrane together with cofactor synthesis and insertion are discussed in a general manner followed by a review of the coordinated biogenesis of individual respiratory enzyme complexes. Lastly, we address the supramolecular organization of respiratory enzymes into supercomplexes and their localization to specialized domains in the membrane.
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Affiliation(s)
- Claire E Price
- Department of Molecular Microbiology, University of Groningen, 9751 NN Haren, The Netherlands
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40
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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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41
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Bageshwar UK, Whitaker N, Liang FC, Musser SM. Interconvertibility of lipid- and translocon-bound forms of the bacterial Tat precursor pre-SufI. Mol Microbiol 2009; 74:209-226. [PMID: 19732346 DOI: 10.1111/j.1365-2958.2009.06862.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Signal peptides target protein cargos for secretion from the bacterial cytoplasm. These signal peptides contain a tri-partite structure consisting of a central hydrophobic domain (h-domain), and two flanking polar domains. Using a recently developed in vitro transport assay, we report here that a central h-domain position (C17) of the twin arginine translocation (Tat) substrate pre-SufI is especially sensitive to amino acid hydrophobicity. The C17I mutant is transported more efficiently than wild type, whereas charged substitutions completely block transport. Transport efficiency is well-correlated with Tat translocon binding efficiency. The precursor protein also binds to non-Tat components of the membrane, presumably to the lipids. This lipid-bound precursor can be chased through the Tat translocons under conditions of high proton motive force. Thus, the non-Tat bound form of the precursor is a functional intermediate in the transport cycle. This intermediate appears to directly equilibrate with the translocon-bound form of the precursor.
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Affiliation(s)
- Umesh K Bageshwar
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M Health Science Center, College Station, TX 77843, USA
| | - Neal Whitaker
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M Health Science Center, College Station, TX 77843, USA
| | - Fu-Cheng Liang
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M Health Science Center, College Station, TX 77843, USA
| | - Siegfried M Musser
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M Health Science Center, College Station, TX 77843, USA
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42
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Affiliation(s)
- Yanjie Li
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
| | - Deborah B. Zamble
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
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43
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Ruffell D. Featuring… Frank Sargent. FEBS Lett 2009; 583:1654-5. [DOI: 10.1016/j.febslet.2009.04.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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44
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Shao X, Lu J, Xia B, Jin C. 1H, 13C and 15N resonance assignments of the chaperone HybE of hydrogenase-2 from Escherichia coli. BIOMOLECULAR NMR ASSIGNMENTS 2009; 3:129-131. [PMID: 19636963 DOI: 10.1007/s12104-009-9157-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2008] [Accepted: 03/23/2009] [Indexed: 05/28/2023]
Abstract
Escherichia coli HybE is a chaperone of hydrogenase-2 and plays a critical role in coordinating the assembly and export of the HybO and HybC subunits of hydrogenase-2. Previous studies indicated that the quality-control during the assembly and export of the HybO-HybC by the Tat pathway was putatively performed by HybE. However, the molecular basis of the biological function of HybE remains unknown. The structural information is essential in order to obtain functional insights of HybE. Here we report the backbone and sidechain resonance assignments of (1)H, (13)C and (15) N atoms in E. coli HybE.
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Affiliation(s)
- Xuan Shao
- Beijing Nuclear Magnetic Resonance Center, Peking University, 100871, Beijing, China
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45
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Holzapfel E, Moser M, Schiltz E, Ueda T, Betton JM, Müller M. Twin-Arginine-Dependent Translocation of SufI in the Absence of Cytosolic Helper Proteins. Biochemistry 2009; 48:5096-105. [DOI: 10.1021/bi900520d] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Eva Holzapfel
- Institute of Biochemistry and Molecular Biology, ZBMZ, University of Freiburg, Stefan-Meier-Strasse 17, D-79104 Freiburg, Germany
| | - Michael Moser
- Institute of Biochemistry and Molecular Biology, ZBMZ, University of Freiburg, Stefan-Meier-Strasse 17, D-79104 Freiburg, Germany
| | - Emile Schiltz
- Institute of Biochemistry and Molecular Biology, ZBMZ, University of Freiburg, Stefan-Meier-Strasse 17, D-79104 Freiburg, Germany
- Institute of Organic Chemistry and Biochemistry, University of Freiburg, Albert-Strasse 21, D-79104 Freiburg, Germany
| | - Takuya Ueda
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
| | - Jean-Michel Betton
- Unité Biochimie Structurale, CNRS URA 2185, Institut Pasteur, 75724 Paris cedex 15, France
| | - Matthias Müller
- Institute of Biochemistry and Molecular Biology, ZBMZ, University of Freiburg, Stefan-Meier-Strasse 17, D-79104 Freiburg, Germany
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46
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Differential Interactions between Tat-specific redox enzyme peptides and their chaperones. J Bacteriol 2009; 191:2091-101. [PMID: 19151138 DOI: 10.1128/jb.00949-08] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The twin-arginine translocase (Tat) system is used by many bacteria to move proteins across the cytoplasmic membrane. Tat substrates are prefolded and contain a conserved SRRxFLK twin-arginine (RR) motif at their N termini. Many Tat substrates in Escherichia coli are cofactor-containing redox enzymes that have specific chaperones called redox enzyme maturation proteins (REMPs). Here we characterized the interactions between 10 REMPs and 15 RR peptides of known and predicted Tat-specific redox enzyme subunits. A combination of in vitro and in vivo experiments demonstrated that some REMPs were specific to a redox enzyme(s) of similar function, whereas others were less specific and bound peptides of unrelated enzymes. Results from Biacore surface plasmon resonance (SPR) and bacterial two-hybrid experiments identified interactions in addition to those found in far-Western experiments, suggesting that conformational freedom and/or other cellular factors may be required. Furthermore, we show that the interaction of the two prevents both from being proteolytically degraded in vivo, and kinetic data from SPR show up to 10-fold-tighter binding to the expected RR substrate when multiple binding partners existed. Investigations using full-length sequences of the RR proteins showed that the mature portion for some redox enzyme subunits is required for detection of the interactions. Sequence alignments among the REMPs and RR peptides indicated that homology between the REMPs and the hydrophobic regions following the RR motifs in the peptides correlates to cross-recognition.
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47
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Parish D, Benach J, Liu G, Singarapu KK, Xiao R, Acton T, Su M, Bansal S, Prestegard JH, Hunt J, Montelione GT, Szyperski T. Protein chaperones Q8ZP25_SALTY from Salmonella typhimurium and HYAE_ECOLI from Escherichia coli exhibit thioredoxin-like structures despite lack of canonical thioredoxin active site sequence motif. JOURNAL OF STRUCTURAL AND FUNCTIONAL GENOMICS 2008; 9:41-9. [PMID: 19039680 PMCID: PMC2850599 DOI: 10.1007/s10969-008-9050-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2008] [Accepted: 11/10/2008] [Indexed: 10/21/2022]
Abstract
The structure of the 142-residue protein Q8ZP25_SALTY encoded in the genome of Salmonella typhimurium LT2 was determined independently by NMR and X-ray crystallography, and the structure of the 140-residue protein HYAE_ECOLI encoded in the genome of Escherichia coli was determined by NMR. The two proteins belong to Pfam (Finn et al. 34:D247-D251, 2006) PF07449, which currently comprises 50 members, and belongs itself to the 'thioredoxin-like clan'. However, protein HYAE_ECOLI and the other proteins of Pfam PF07449 do not contain the canonical Cys-X-X-Cys active site sequence motif of thioredoxin. Protein HYAE_ECOLI was previously classified as a [NiFe] hydrogenase-1 specific chaperone interacting with the twin-arginine translocation (Tat) signal peptide. The structures presented here exhibit the expected thioredoxin-like fold and support the view that members of Pfam family PF07449 specifically interact with Tat signal peptides.
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Affiliation(s)
- David Parish
- David Parish · Gaohua Liu · Kiran Kumar Singarapu · Thomas Szyperski, Department of Chemistry, Northeast Structural Genomics Consortium, The State University of New York at Buffalo, Buffalo, NY 14260,
- Jordi Benach · Min Su · John F. Hunt, Department of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, NY 10027
- Rong Xiao · Thomas Acton · Gaetano T. Montelione, The Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Northeast Structural Genomics Consortium, Rutgers University and Robert Wood Johnson Medical School, Piscataway, NJ 08854
- Sonal Bansal · James H. Prestegard, Complex Carbohydrate Research Center and Department of Chemistry, University of Georgia, Athens, Georgia, 30602-4712
| | - Jordi Benach
- David Parish · Gaohua Liu · Kiran Kumar Singarapu · Thomas Szyperski, Department of Chemistry, Northeast Structural Genomics Consortium, The State University of New York at Buffalo, Buffalo, NY 14260,
- Jordi Benach · Min Su · John F. Hunt, Department of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, NY 10027
- Rong Xiao · Thomas Acton · Gaetano T. Montelione, The Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Northeast Structural Genomics Consortium, Rutgers University and Robert Wood Johnson Medical School, Piscataway, NJ 08854
- Sonal Bansal · James H. Prestegard, Complex Carbohydrate Research Center and Department of Chemistry, University of Georgia, Athens, Georgia, 30602-4712
| | - Goahua Liu
- David Parish · Gaohua Liu · Kiran Kumar Singarapu · Thomas Szyperski, Department of Chemistry, Northeast Structural Genomics Consortium, The State University of New York at Buffalo, Buffalo, NY 14260,
- Jordi Benach · Min Su · John F. Hunt, Department of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, NY 10027
- Rong Xiao · Thomas Acton · Gaetano T. Montelione, The Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Northeast Structural Genomics Consortium, Rutgers University and Robert Wood Johnson Medical School, Piscataway, NJ 08854
- Sonal Bansal · James H. Prestegard, Complex Carbohydrate Research Center and Department of Chemistry, University of Georgia, Athens, Georgia, 30602-4712
| | - Kiran Kumar Singarapu
- David Parish · Gaohua Liu · Kiran Kumar Singarapu · Thomas Szyperski, Department of Chemistry, Northeast Structural Genomics Consortium, The State University of New York at Buffalo, Buffalo, NY 14260,
- Jordi Benach · Min Su · John F. Hunt, Department of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, NY 10027
- Rong Xiao · Thomas Acton · Gaetano T. Montelione, The Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Northeast Structural Genomics Consortium, Rutgers University and Robert Wood Johnson Medical School, Piscataway, NJ 08854
- Sonal Bansal · James H. Prestegard, Complex Carbohydrate Research Center and Department of Chemistry, University of Georgia, Athens, Georgia, 30602-4712
| | - Rong Xiao
- David Parish · Gaohua Liu · Kiran Kumar Singarapu · Thomas Szyperski, Department of Chemistry, Northeast Structural Genomics Consortium, The State University of New York at Buffalo, Buffalo, NY 14260,
- Jordi Benach · Min Su · John F. Hunt, Department of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, NY 10027
- Rong Xiao · Thomas Acton · Gaetano T. Montelione, The Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Northeast Structural Genomics Consortium, Rutgers University and Robert Wood Johnson Medical School, Piscataway, NJ 08854
- Sonal Bansal · James H. Prestegard, Complex Carbohydrate Research Center and Department of Chemistry, University of Georgia, Athens, Georgia, 30602-4712
| | - Thomas Acton
- David Parish · Gaohua Liu · Kiran Kumar Singarapu · Thomas Szyperski, Department of Chemistry, Northeast Structural Genomics Consortium, The State University of New York at Buffalo, Buffalo, NY 14260,
- Jordi Benach · Min Su · John F. Hunt, Department of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, NY 10027
- Rong Xiao · Thomas Acton · Gaetano T. Montelione, The Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Northeast Structural Genomics Consortium, Rutgers University and Robert Wood Johnson Medical School, Piscataway, NJ 08854
- Sonal Bansal · James H. Prestegard, Complex Carbohydrate Research Center and Department of Chemistry, University of Georgia, Athens, Georgia, 30602-4712
| | - Min Su
- David Parish · Gaohua Liu · Kiran Kumar Singarapu · Thomas Szyperski, Department of Chemistry, Northeast Structural Genomics Consortium, The State University of New York at Buffalo, Buffalo, NY 14260,
- Jordi Benach · Min Su · John F. Hunt, Department of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, NY 10027
- Rong Xiao · Thomas Acton · Gaetano T. Montelione, The Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Northeast Structural Genomics Consortium, Rutgers University and Robert Wood Johnson Medical School, Piscataway, NJ 08854
- Sonal Bansal · James H. Prestegard, Complex Carbohydrate Research Center and Department of Chemistry, University of Georgia, Athens, Georgia, 30602-4712
| | - Sonal Bansal
- David Parish · Gaohua Liu · Kiran Kumar Singarapu · Thomas Szyperski, Department of Chemistry, Northeast Structural Genomics Consortium, The State University of New York at Buffalo, Buffalo, NY 14260,
- Jordi Benach · Min Su · John F. Hunt, Department of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, NY 10027
- Rong Xiao · Thomas Acton · Gaetano T. Montelione, The Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Northeast Structural Genomics Consortium, Rutgers University and Robert Wood Johnson Medical School, Piscataway, NJ 08854
- Sonal Bansal · James H. Prestegard, Complex Carbohydrate Research Center and Department of Chemistry, University of Georgia, Athens, Georgia, 30602-4712
| | - James H. Prestegard
- David Parish · Gaohua Liu · Kiran Kumar Singarapu · Thomas Szyperski, Department of Chemistry, Northeast Structural Genomics Consortium, The State University of New York at Buffalo, Buffalo, NY 14260,
- Jordi Benach · Min Su · John F. Hunt, Department of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, NY 10027
- Rong Xiao · Thomas Acton · Gaetano T. Montelione, The Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Northeast Structural Genomics Consortium, Rutgers University and Robert Wood Johnson Medical School, Piscataway, NJ 08854
- Sonal Bansal · James H. Prestegard, Complex Carbohydrate Research Center and Department of Chemistry, University of Georgia, Athens, Georgia, 30602-4712
| | - John Hunt
- David Parish · Gaohua Liu · Kiran Kumar Singarapu · Thomas Szyperski, Department of Chemistry, Northeast Structural Genomics Consortium, The State University of New York at Buffalo, Buffalo, NY 14260,
- Jordi Benach · Min Su · John F. Hunt, Department of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, NY 10027
- Rong Xiao · Thomas Acton · Gaetano T. Montelione, The Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Northeast Structural Genomics Consortium, Rutgers University and Robert Wood Johnson Medical School, Piscataway, NJ 08854
- Sonal Bansal · James H. Prestegard, Complex Carbohydrate Research Center and Department of Chemistry, University of Georgia, Athens, Georgia, 30602-4712
| | - Gaetano T. Montelione
- David Parish · Gaohua Liu · Kiran Kumar Singarapu · Thomas Szyperski, Department of Chemistry, Northeast Structural Genomics Consortium, The State University of New York at Buffalo, Buffalo, NY 14260,
- Jordi Benach · Min Su · John F. Hunt, Department of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, NY 10027
- Rong Xiao · Thomas Acton · Gaetano T. Montelione, The Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Northeast Structural Genomics Consortium, Rutgers University and Robert Wood Johnson Medical School, Piscataway, NJ 08854
- Sonal Bansal · James H. Prestegard, Complex Carbohydrate Research Center and Department of Chemistry, University of Georgia, Athens, Georgia, 30602-4712
| | - Thomas Szyperski
- David Parish · Gaohua Liu · Kiran Kumar Singarapu · Thomas Szyperski, Department of Chemistry, Northeast Structural Genomics Consortium, The State University of New York at Buffalo, Buffalo, NY 14260,
- Jordi Benach · Min Su · John F. Hunt, Department of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, NY 10027
- Rong Xiao · Thomas Acton · Gaetano T. Montelione, The Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Northeast Structural Genomics Consortium, Rutgers University and Robert Wood Johnson Medical School, Piscataway, NJ 08854
- Sonal Bansal · James H. Prestegard, Complex Carbohydrate Research Center and Department of Chemistry, University of Georgia, Athens, Georgia, 30602-4712
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Price CE, Driessen AJ. YidC Is Involved in the Biogenesis of Anaerobic Respiratory Complexes in the Inner Membrane of Escherichia coli. J Biol Chem 2008; 283:26921-7. [DOI: 10.1074/jbc.m804490200] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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49
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The twin-arginine transport system: moving folded proteins across membranes. Biochem Soc Trans 2008; 35:835-47. [PMID: 17956229 DOI: 10.1042/bst0350835] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The Tat (twin-arginine transport) pathway is a protein-targeting system dedicated to the transmembrane translocation of fully folded proteins. This system is highly prevalent in the cytoplasmic membranes of bacteria and archaea, and is also found in the thylakoid membranes of plant chloroplasts and possibly also in the inner membrane of plant mitochondria. Proteins are targeted to a membrane-embedded Tat translocase by specialized N-terminal twin-arginine signal peptides bearing an SRRXFLK amino acid motif. The genes encoding components of the Tat translocase were discovered approx. 10 years ago, and, since then, research in this area has expanded on a global scale. In this review, the key discoveries in this field are summarized, and recent studies of bacterial twin-arginine signal-peptide-binding proteins are discussed.
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Vignais PM, Billoud B. Occurrence, Classification, and Biological Function of Hydrogenases: An Overview. Chem Rev 2007; 107:4206-72. [PMID: 17927159 DOI: 10.1021/cr050196r] [Citation(s) in RCA: 1026] [Impact Index Per Article: 60.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Paulette M. Vignais
- CEA Grenoble, Laboratoire de Biochimie et Biophysique des Systèmes Intégrés, UMR CEA/CNRS/UJF 5092, Institut de Recherches en Technologies et Sciences pour le Vivant (iRTSV), 17 rue des Martyrs, 38054 Grenoble cedex 9, France, and Atelier de BioInformatique Université Pierre et Marie Curie (Paris 6), 12 rue Cuvier, 75005 Paris, France
| | - Bernard Billoud
- CEA Grenoble, Laboratoire de Biochimie et Biophysique des Systèmes Intégrés, UMR CEA/CNRS/UJF 5092, Institut de Recherches en Technologies et Sciences pour le Vivant (iRTSV), 17 rue des Martyrs, 38054 Grenoble cedex 9, France, and Atelier de BioInformatique Université Pierre et Marie Curie (Paris 6), 12 rue Cuvier, 75005 Paris, France
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