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Hasnat MA, Leimkühler S. Shared functions of Fe-S cluster assembly and Moco biosynthesis. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119731. [PMID: 38631442 DOI: 10.1016/j.bbamcr.2024.119731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/29/2024] [Accepted: 04/04/2024] [Indexed: 04/19/2024]
Abstract
Molybdenum cofactor (Moco) biosynthesis is a complex process that involves the coordinated function of several proteins. In the recent years it has become evident that the availability of Fe-S clusters play an important role for the biosynthesis of Moco. First, the MoaA protein binds two [4Fe-4S] clusters per monomer. Second, the expression of the moaABCDE and moeAB operons is regulated by FNR, which senses the availability of oxygen via a functional [4Fe-4S] cluster. Finally, the conversion of cyclic pyranopterin monophosphate to molybdopterin requires the availability of the L-cysteine desulfurase IscS, which is an enzyme involved in the transfer of sulfur to various acceptor proteins with a main role in the assembly of Fe-S clusters. In this review, we dissect the dependence of the production of active molybdoenzymes in detail, starting from the regulation of gene expression and further explaining sulfur delivery and Fe-S cluster insertion into target enzymes. Further, Fe-S cluster assembly is also linked to iron availability. While the abundance of selected molybdoenzymes is largely decreased under iron-limiting conditions, we explain that the expression of the genes is dependent on an active FNR protein. FNR is a very important transcription factor that represents the master-switch for the expression of target genes in response to anaerobiosis. Moco biosynthesis is further directly dependent on the presence of ArcA and also on an active Fur protein.
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Affiliation(s)
- Muhammad Abrar Hasnat
- University of Potsdam, Institute of Biochemistry and Biology, Department of Molecular Enzymology, Karl-Liebknecht Str. 24-25, 14476 Potsdam-Golm, Germany
| | - Silke Leimkühler
- University of Potsdam, Institute of Biochemistry and Biology, Department of Molecular Enzymology, Karl-Liebknecht Str. 24-25, 14476 Potsdam-Golm, Germany.
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Zhu J, Zhao H, Yang Z. Genetic Analysis of the ts-Lethal Mutant Δpa0665/ pTS-pa0665 Reveals Its Role in Cell Morphology and Oxidative Phosphorylation in Pseudomonas aeruginosa. Genes (Basel) 2024; 15:590. [PMID: 38790219 PMCID: PMC11120684 DOI: 10.3390/genes15050590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 05/01/2024] [Accepted: 05/03/2024] [Indexed: 05/26/2024] Open
Abstract
Pa0665 in Pseudomonas aeruginosa shares homologous sequences with that of the essential A-type iron-sulfur (Fe-S) cluster insertion protein ErpA in Escherichia coli. However, its essentiality in P. aeruginosa and its complementation with E. coli erpA has not been experimentally examined. To fulfill this task, we constructed plasmid-based ts-mutant Δpa0665/pTS-pa0665 using a three-step protocol. The mutant displayed growth defects at 42 °C, which were complemented by expressing ec.erpA. Microscopic observations indicated a petite cell phenotype for Δpa0665/pTS-pa0665 at 42 °C, correlated with the downregulation of the oprG gene. RNA sequencing revealed significant transcriptional changes in genes associated with the oxidative phosphorylation (OXPHOS) system, aligning with reduced ATP levels in Δpa0665/pTS-pa0665 under 42 °C. Additionally, the ts-mutant showed heightened sensitivity to H2O2 at 42 °C. Overall, our study demonstrates the essential role of pa0665 for OXPHOS function and is complemented by ec.erpA. We propose that the plasmid-based ts-allele is useful for genetic analysis of essential genes of interest in P. aeruginosa.
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Affiliation(s)
| | | | - Zhili Yang
- Systems Biology, School for Marine Science and Technology, Zhejiang Ocean University, Zhoushan 316022, China; (J.Z.); (H.Z.)
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Niemand Wolhuter N, Ngakane L, de Wet TJ, Warren RM, Williams MJ. The Mycobacterium smegmatis HesB Protein, MSMEG_4272, Is Required for In Vitro Growth and Iron Homeostasis. Microorganisms 2023; 11:1573. [PMID: 37375075 DOI: 10.3390/microorganisms11061573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/07/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
A-type carrier (ATC) proteins are proposed to function in the biogenesis of Fe-S clusters, although their exact role remains controversial. The genome of Mycobacterium smegmatis encodes a single ATC protein, MSMEG_4272, which belongs to the HesB/YadR/YfhF family of proteins. Attempts to generate an MSMEG_4272 deletion mutant by two-step allelic exchange were unsuccessful, suggesting that the gene is essential for in vitro growth. CRISPRi-mediated transcriptional knock-down of MSMEG_4272 resulted in a growth defect under standard culture conditions, which was exacerbated in mineral-defined media. The knockdown strain displayed reduced intracellular iron levels under iron-replete conditions and increased susceptibility to clofazimine, 2,3-dimethoxy-1,4-naphthoquinone (DMNQ), and isoniazid, while the activity of the Fe-S containing enzymes, succinate dehydrogenase, and aconitase were not affected. This study suggests that MSMEG_4272 plays a role in the regulation of intracellular iron levels and is required for in vitro growth of M. smegmatis, particularly during exponential growth.
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Affiliation(s)
- Nandi Niemand Wolhuter
- NRF/DSI Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa
| | - Lerato Ngakane
- NRF/DSI Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa
| | - Timothy J de Wet
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, Department of Pathology, University of Cape Town, Cape Town 7925, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town 7925, South Africa
| | - Robin M Warren
- NRF/DSI Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa
| | - Monique J Williams
- NRF/DSI Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town 7700, South Africa
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Molecular Biology and Genetic Tools to Investigate Functional Redundancy Among Fe-S Cluster Carriers in E. coli. Methods Mol Biol 2021. [PMID: 34292541 DOI: 10.1007/978-1-0716-1605-5_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Iron-sulfur (Fe-S) clusters are among the oldest protein cofactors, and Fe-S cluster-based chemistry has shaped the cellular metabolism of all living organisms. Over the last 30 years, thanks to molecular biology and genetic approaches, numerous actors for Fe-S cluster assembly and delivery to apotargets have been uncovered. In prokaryotes, Escherichia coli is the best-studied for its convenience of growth and its genetic amenability. During evolution, redundant ways to secure the supply of Fe-S clusters to the client proteins have emerged in E. coli. Disrupting gene expression is essential for gene function exploration, but redundancy can blur the interpretations as it can mask the role of important biogenesis components. This chapter describes molecular biology and genetic strategies that have permitted to reveal the E. coli Fe-S cluster conveying component network, composition, organization, and plasticity. In this chapter, we will describe the following genetic methods to investigate the importance of E. coli Fe-S cluster carriers: one-step inactivation of chromosomal genes in E. coli using polymerase chain reaction (PCR) products, P1 transduction, arabinose-inducible expression system, mevalonate (MVA) genetic by-pass, sensitivity tests to oxidative stress and iron starvation, β-galactosidase assay, gentamicin survival test, and Hot Fusion cloning method.
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A-type carrier proteins are involved in [4Fe-4S] cluster insertion into the radical SAM protein MoaA for the synthesis of active molybdoenzymes. J Bacteriol 2021; 203:e0008621. [PMID: 33782054 DOI: 10.1128/jb.00086-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Iron sulfur (Fe-S) clusters are important biological cofactors present in proteins with crucial biological functions, from photosynthesis to DNA repair, gene expression and bioenergetic processes. For the insertion of Fe-S clusters into proteins, A-type carrier proteins have been identified. So far, three of them were characterized in detail in Escherichia coli, namely IscA, SufA and ErpA, which were shown to partially replace each other in their roles in [4Fe-4S] cluster insertion into specific target proteins. To further expand the knowledge of [4Fe-4S] cluster insertion into proteins, we analyzed the complex Fe-S cluster dependent network for the synthesis of the molybdenum cofactor (Moco) and the expression of genes encoding nitrate reductase in E. coli Our studies include the identification of the A-type carrier proteins ErpA and IscA involved in [4Fe-4S] cluster insertion into the S-adenosyl-methionine dependent radical SAM protein MoaA. We show that ErpA and IscA can partially replace each other in their role to provide [4Fe-4S] clusters for MoaA. Since most genes expressing molybdoenzymes are regulated by the transcriptional regulator for fumarate and nitrate reduction (FNR) under anaerobic conditions, we also identified the proteins that are crucial to obtain an active FNR under conditions of nitrate respiration. We show that ErpA is essential for the FNR-dependent expression of the narGHJI operon, a role that cannot be compensated by IscA under the growth conditions tested. SufA does not have a role in Fe-S cluster insertion into MoaA or FNR under anaerobic growth of nitrate respiration, based on low gene expression levels.IMPORTANCEUnderstanding the assembly of iron-sulfur (Fe-S) proteins is relevant to many fields, including nitrogen fixation, photosynthesis, bioenergetics and gene regulation. Still remaining critical gaps in our knowledge are how Fe-S clusters are transferred to their target proteins and how the specificity in this process is achieved, since different forms of Fe-S clusters need to be delivered to structurally highly diverse target proteins. Numerous Fe-S carrier proteins have been identified in prokaryotes like Escherichia coli, including ErpA, IscA, SusA and NfuA. In addition, the diverse Fe-S cluster delivery proteins and their target proteins underlie a complex regulatory network of expression, to ensure that both proteins are synthesized under particular growth conditions.
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Gerstel A, Zamarreño Beas J, Duverger Y, Bouveret E, Barras F, Py B. Oxidative stress antagonizes fluoroquinolone drug sensitivity via the SoxR-SUF Fe-S cluster homeostatic axis. PLoS Genet 2020; 16:e1009198. [PMID: 33137124 PMCID: PMC7671543 DOI: 10.1371/journal.pgen.1009198] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 11/17/2020] [Accepted: 10/15/2020] [Indexed: 11/18/2022] Open
Abstract
The level of antibiotic resistance exhibited by bacteria can vary as a function of environmental conditions. Here, we report that phenazine-methosulfate (PMS), a redox-cycling compound (RCC) enhances resistance to fluoroquinolone (FQ) norfloxacin. Genetic analysis showed that E. coli adapts to PMS stress by making Fe-S clusters with the SUF machinery instead of the ISC one. Based upon phenotypic analysis of soxR, acrA, and micF mutants, we showed that PMS antagonizes fluoroquinolone toxicity by SoxR-mediated up-regulation of the AcrAB drug efflux pump. Subsequently, we showed that despite the fact that SoxR could receive its cluster from either ISC or SUF, only SUF is able to sustain efficient SoxR maturation under exposure to prolonged PMS period or high PMS concentrations. This study furthers the idea that Fe-S cluster homeostasis acts as a sensor of environmental conditions, and because its broad influence on cell metabolism, modifies the antibiotic resistance profile of E. coli. Our study investigates how phenazine compounds, which are widely present in the environment, impact antibiotic resistance of the Gram-negative bacteria Escherichia coli. The paucity of new antibacterial molecules fuels concern in the wake of increased antibiotic resistance among pathogens. Equally worrying is the realization that environmental conditions can have a drastic influence on the efficiency of antibacterial compounds. Here we report that phenazine, a member of the redox-cycling molecule family, is antagonistic to norfloxacin, a well-known and routinely used fluoroquinolone antibiotic. We show that the mechanism E. coli is using for synthesizing Fe-S clusters controls the phenazine/fluoroquinolone antagonism. Indeed, upon exposure to phenazine, E. coli switches from making Fe-S clusters with the ISC Fe-S biogenesis system to making them with SUF, a consequence of which is the activation of the SoxR transcriptional activator, up-regulation of the AcrAB efflux pump, and efflux of fluoroquinolone out of the cell. This study illustrates the major influence that environmental conditions play in setting antibiotic level resistance and further highlights the major contribution of Fe-S cluster homeostasis in antibiotic susceptibility.
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Affiliation(s)
- Audrey Gerstel
- Laboratoire de Chimie Bactérienne, Aix-Marseille Université-CNRS UMR7283, Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Jordi Zamarreño Beas
- Laboratoire de Chimie Bactérienne, Aix-Marseille Université-CNRS UMR7283, Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Yohann Duverger
- Laboratoire de Chimie Bactérienne, Aix-Marseille Université-CNRS UMR7283, Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Emmanuelle Bouveret
- SAMe Unit, Département de Microbiologie, Institut Pasteur, CNRS UMR IMM 2001, Paris, France
| | - Frédéric Barras
- Laboratoire de Chimie Bactérienne, Aix-Marseille Université-CNRS UMR7283, Institut de Microbiologie de la Méditerranée, Marseille, France
- SAMe Unit, Département de Microbiologie, Institut Pasteur, CNRS UMR IMM 2001, Paris, France
- * E-mail: (FB); (BP)
| | - Béatrice Py
- Laboratoire de Chimie Bactérienne, Aix-Marseille Université-CNRS UMR7283, Institut de Microbiologie de la Méditerranée, Marseille, France
- * E-mail: (FB); (BP)
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The Requirement of Inorganic Fe-S Clusters for the Biosynthesis of the Organometallic Molybdenum Cofactor. INORGANICS 2020. [DOI: 10.3390/inorganics8070043] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Iron-sulfur (Fe-S) clusters are essential protein cofactors. In enzymes, they are present either in the rhombic [2Fe-2S] or the cubic [4Fe-4S] form, where they are involved in catalysis and electron transfer and in the biosynthesis of metal-containing prosthetic groups like the molybdenum cofactor (Moco). Here, we give an overview of the assembly of Fe-S clusters in bacteria and humans and present their connection to the Moco biosynthesis pathway. In all organisms, Fe-S cluster assembly starts with the abstraction of sulfur from l-cysteine and its transfer to a scaffold protein. After formation, Fe-S clusters are transferred to carrier proteins that insert them into recipient apo-proteins. In eukaryotes like humans and plants, Fe-S cluster assembly takes place both in mitochondria and in the cytosol. Both Moco biosynthesis and Fe-S cluster assembly are highly conserved among all kingdoms of life. Moco is a tricyclic pterin compound with molybdenum coordinated through its unique dithiolene group. Moco biosynthesis begins in the mitochondria in a Fe-S cluster dependent step involving radical/S-adenosylmethionine (SAM) chemistry. An intermediate is transferred to the cytosol where the dithiolene group is formed, to which molybdenum is finally added. Further connections between Fe-S cluster assembly and Moco biosynthesis are discussed in detail.
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Iron-Dependent Regulation of Molybdenum Cofactor Biosynthesis Genes in Escherichia coli. J Bacteriol 2019; 201:JB.00382-19. [PMID: 31235512 DOI: 10.1128/jb.00382-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 06/15/2019] [Indexed: 01/15/2023] Open
Abstract
Molybdenum cofactor (Moco) biosynthesis is a complex process that involves the coordinated function of several proteins. In recent years it has become obvious that the availability of iron plays an important role in the biosynthesis of Moco. First, the MoaA protein binds two [4Fe-4S] clusters per monomer. Second, the expression of the moaABCDE and moeAB operons is regulated by FNR, which senses the availability of oxygen via a functional [4Fe-4S] cluster. Finally, the conversion of cyclic pyranopterin monophosphate to molybdopterin requires the availability of the l-cysteine desulfurase IscS, which is a shared protein with a main role in the assembly of Fe-S clusters. In this report, we investigated the transcriptional regulation of the moaABCDE operon by focusing on its dependence on cellular iron availability. While the abundance of selected molybdoenzymes is largely decreased under iron-limiting conditions, our data show that the regulation of the moaABCDE operon at the level of transcription is only marginally influenced by the availability of iron. Nevertheless, intracellular levels of Moco were decreased under iron-limiting conditions, likely based on an inactive MoaA protein in addition to lower levels of the l-cysteine desulfurase IscS, which simultaneously reduces the sulfur availability for Moco production.IMPORTANCE FNR is a very important transcriptional factor that represents the master switch for the expression of target genes in response to anaerobiosis. Among the FNR-regulated operons in Escherichia coli is the moaABCDE operon, involved in Moco biosynthesis. Molybdoenzymes have essential roles in eukaryotic and prokaryotic organisms. In bacteria, molybdoenzymes are crucial for anaerobic respiration using alternative electron acceptors. This work investigates the connection of iron availability to the biosynthesis of Moco and the production of active molybdoenzymes.
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Bai Y, Chen T, Happe T, Lu Y, Sawyer A. Iron-sulphur cluster biogenesis via the SUF pathway. Metallomics 2019; 10:1038-1052. [PMID: 30019043 DOI: 10.1039/c8mt00150b] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Iron-sulphur (Fe-S) clusters are versatile cofactors, which are essential for key metabolic processes in cells, such as respiration and photosynthesis, and which may have also played a crucial role in establishing life on Earth. They can be found in almost all living organisms, from unicellular prokaryotes and archaea to multicellular animals and plants, and exist in diverse forms. This review focuses on the most ancient Fe-S cluster assembly system, the sulphur utilization factor (SUF) mechanism, which is crucial in bacteria for cell survival under stress conditions such as oxidation and iron starvation, and which is also present in the chloroplasts of green microalgae and plants, where it is responsible for plastidial Fe-S protein maturation. We explain the SUF Fe-S cluster assembly process, the proteins involved, their regulation and provide evolutionary insights. We specifically focus on examples from Fe-S cluster synthesis in the model organisms Escherichia coli and Arabidopsis thaliana and discuss in an in vivo context the assembly of the [FeFe]-hydrogenase H-cluster from Chlamydomonas reinhardtii.
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Affiliation(s)
- Y Bai
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.
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Pinske C. The Ferredoxin-Like Proteins HydN and YsaA Enhance Redox Dye-Linked Activity of the Formate Dehydrogenase H Component of the Formate Hydrogenlyase Complex. Front Microbiol 2018; 9:1238. [PMID: 29942290 PMCID: PMC6004506 DOI: 10.3389/fmicb.2018.01238] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 05/23/2018] [Indexed: 12/30/2022] Open
Abstract
Formate dehydrogenase H (FDH-H) and [NiFe]-hydrogenase 3 (Hyd-3) form the catalytic components of the hydrogen-producing formate hydrogenlyase (FHL) complex, which disproportionates formate to H2 and CO2 during mixed acid fermentation in enterobacteria. FHL comprises minimally seven proteins and little is understood about how this complex is assembled. Early studies identified a ferredoxin-like protein, HydN, as being involved in FDH-H assembly into the FHL complex. In order to understand how FDH-H and its small subunit HycB, which is also a ferredoxin-like protein, attach to the FHL complex, the possible roles of HydN and its paralogue, YsaA, in FHL complex stability and assembly were investigated. Deletion of the hycB gene reduced redox dye-mediated FDH-H activity to approximately 10%, abolished FHL-dependent H2-production, and reduced Hyd-3 activity. These data are consistent with HycB being an essential electron transfer component of the FHL complex. The FDH-H activity of the hydN and the ysaA deletion strains was reduced to 59 and 57% of the parental, while the double deletion reduced activity of FDH-H to 28% and the triple deletion with hycB to 1%. Remarkably, and in contrast to the hycB deletion, the absence of HydN and YsaA was without significant effect on FHL-dependent H2-production or total Hyd-3 activity; FDH-H protein levels were also unaltered. This is the first description of a phenotype for the E. coli ysaA deletion strain and identifies it as a novel factor required for optimal redox dye-linked FDH-H activity. A ysaA deletion strain could be complemented for FDH-H activity by hydN and ysaA, but the hydN deletion strain could not be complemented. Introduction of these plasmids did not affect H2 production. Bacterial two-hybrid interactions showed that YsaA, HydN, and HycB interact with each other and with the FDH-H protein. Further novel anaerobic cross-interactions of 10 ferredoxin-like proteins in E. coli were also discovered and described. Together, these data indicate that FDH-H activity measured with the redox dye benzyl viologen is the sum of the FDH-H protein interacting with three independent small subunits and suggest that FDH-H can associate with different redox-protein complexes in the anaerobic cell to supply electrons from formate oxidation.
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Affiliation(s)
- Constanze Pinske
- Institute for Biology/Microbiology, Martin-Luther University Halle-Wittenberg, Halle, Germany
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Jaroschinsky M, Pinske C, Gary Sawers R. Differential effects of isc operon mutations on the biosynthesis and activity of key anaerobic metalloenzymes in Escherichia coli. MICROBIOLOGY-SGM 2017. [PMID: 28640740 DOI: 10.1099/mic.0.000481] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Escherichia coli has two machineries for the synthesis of FeS clusters, namely Isc (iron-sulfur cluster) and Suf (sulfur formation). The Isc machinery, encoded by the iscRSUA-hscBA-fdx-iscXoperon, plays a crucial role in the biogenesis of FeS clusters for the oxidoreductases of aerobic metabolism. Less is known, however, about the role of ISC in the maturation of key multi-subunit metalloenzymes of anaerobic metabolism. Here, we determined the contribution of each iscoperon gene product towards the functionality of the major anaerobic oxidoreductases in E. coli, including three [NiFe]-hydrogenases (Hyd), two respiratory formate dehydrogenases (FDH) and nitrate reductase (NAR). Mutants lacking the cysteine desulfurase, IscS, lacked activity of all six enzymes, as well as the activity of fumaratereductase, and this was due to deficiencies in enzyme biosynthesis, maturation or FeS cluster insertion into electron-transfer components. Notably, based on anaerobic growth characteristics and metabolite patterns, the activity of the radical-S-adenosylmethionine enzyme pyruvate formate-lyase activase was independent of IscS, suggesting that FeS biogenesis for this ancient enzyme has different requirements. Mutants lacking either the scaffold protein IscU, the ferredoxin Fdx or the chaperones HscA or HscB had similar enzyme phenotypes: five of the oxidoreductases were essentially inactive, with the exception being the Hyd-3 enzyme, which formed part of the H2-producing formate hydrogenlyase (FHL) complex. Neither the frataxin-homologue CyaY nor the IscX protein was essential for synthesis of the three Hyd enzymes. Thus, while IscS is essential for H2 production in E. coli, the other ISC components are non-essential.
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Affiliation(s)
- Monique Jaroschinsky
- Institute for Biology/Microbiology, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Str 3, 06120 Halle (Saale), Germany.,Present address: ICP Analytik GmbH & Co. KG, Brandenburger Platz 1, 24211 Preetz, Germany
| | - Constanze Pinske
- Institute for Biology/Microbiology, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Str 3, 06120 Halle (Saale), Germany
| | - R Gary Sawers
- Institute for Biology/Microbiology, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Str 3, 06120 Halle (Saale), Germany
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Sawyer A, Bai Y, Lu Y, Hemschemeier A, Happe T. Compartmentalisation of [FeFe]-hydrogenase maturation in Chlamydomonas reinhardtii. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:1134-1143. [PMID: 28295776 DOI: 10.1111/tpj.13535] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 03/01/2017] [Accepted: 03/06/2017] [Indexed: 06/06/2023]
Abstract
Molecular hydrogen (H2 ) can be produced in green microalgae by [FeFe]-hydrogenases as a direct product of photosynthesis. The Chlamydomonas reinhardtii hydrogenase HYDA1 contains a catalytic site comprising a classic [4Fe4S] cluster linked to a unique 2Fe sub-cluster. From in vitro studies it appears that the [4Fe4S] cluster is incorporated first by the housekeeping FeS cluster assembly machinery, followed by the 2Fe sub-cluster, whose biosynthesis requires the specific maturases HYDEF and HYDG. To investigate the maturation process in vivo, we expressed HYDA1 from the C. reinhardtii chloroplast and nuclear genomes (with and without a chloroplast transit peptide) in a hydrogenase-deficient mutant strain, and examined the cellular enzymatic hydrogenase activity, as well as in vivo H2 production. The transformants expressing HYDA1 from the chloroplast genome displayed levels of H2 production comparable to the wild type, as did the transformants expressing full-length HYDA1 from the nuclear genome. In contrast, cells equipped with cytoplasm-targeted HYDA1 produced inactive enzyme, which could only be activated in vitro after reconstitution of the [4Fe4S] cluster. This indicates that the HYDA1 FeS cluster can only be built by the chloroplastic FeS cluster assembly machinery. Further, the expression of a bacterial hydrogenase gene, CPI, from the C. reinhardtii chloroplast genome resulted in H2 -producing strains, demonstrating that a hydrogenase with a very different structure can fulfil the role of HYDA1 in vivo and that overexpression of foreign hydrogenases in C. reinhardtii is possible. All chloroplast transformants were stable and no toxic effects were seen from HYDA1 or CPI expression.
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Affiliation(s)
- Anne Sawyer
- AG Photobiotechnologie, Lehrstuhl für Biochemie der Pflanzen, Fakultät für Biologie und Biotechnologie, Ruhr-Universität Bochum, 44801, Bochum, Germany
| | - Yu Bai
- AG Photobiotechnologie, Lehrstuhl für Biochemie der Pflanzen, Fakultät für Biologie und Biotechnologie, Ruhr-Universität Bochum, 44801, Bochum, Germany
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Yinghua Lu
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Anja Hemschemeier
- AG Photobiotechnologie, Lehrstuhl für Biochemie der Pflanzen, Fakultät für Biologie und Biotechnologie, Ruhr-Universität Bochum, 44801, Bochum, Germany
| | - Thomas Happe
- AG Photobiotechnologie, Lehrstuhl für Biochemie der Pflanzen, Fakultät für Biologie und Biotechnologie, Ruhr-Universität Bochum, 44801, Bochum, Germany
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13
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Barupala DP, Dzul SP, Riggs-Gelasco PJ, Stemmler TL. Synthesis, delivery and regulation of eukaryotic heme and Fe-S cluster cofactors. Arch Biochem Biophys 2016; 592:60-75. [PMID: 26785297 PMCID: PMC4784227 DOI: 10.1016/j.abb.2016.01.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 01/13/2016] [Accepted: 01/14/2016] [Indexed: 11/25/2022]
Abstract
In humans, the bulk of iron in the body (over 75%) is directed towards heme- or Fe-S cluster cofactor synthesis, and the complex, highly regulated pathways in place to accomplish biosynthesis have evolved to safely assemble and load these cofactors into apoprotein partners. In eukaryotes, heme biosynthesis is both initiated and finalized within the mitochondria, while cellular Fe-S cluster assembly is controlled by correlated pathways both within the mitochondria and within the cytosol. Iron plays a vital role in a wide array of metabolic processes and defects in iron cofactor assembly leads to human diseases. This review describes progress towards our molecular-level understanding of cellular heme and Fe-S cluster biosynthesis, focusing on the regulation and mechanistic details that are essential for understanding human disorders related to the breakdown in these essential pathways.
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Affiliation(s)
- Dulmini P Barupala
- Departments of Biochemistry and Molecular Biology, and Pharmaceutical Sciences, Wayne State University, Detroit, MI 48201, USA
| | - Stephen P Dzul
- Departments of Biochemistry and Molecular Biology, and Pharmaceutical Sciences, Wayne State University, Detroit, MI 48201, USA
| | | | - Timothy L Stemmler
- Departments of Biochemistry and Molecular Biology, and Pharmaceutical Sciences, Wayne State University, Detroit, MI 48201, USA.
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14
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Blanc B, Gerez C, Ollagnier de Choudens S. Assembly of Fe/S proteins in bacterial systems: Biochemistry of the bacterial ISC system. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1853:1436-47. [PMID: 25510311 DOI: 10.1016/j.bbamcr.2014.12.009] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Revised: 11/20/2014] [Accepted: 12/08/2014] [Indexed: 12/26/2022]
Abstract
Iron/sulfur clusters are key cofactors in proteins involved in a large number of conserved cellular processes, including gene expression, DNA replication and repair, ribosome biogenesis, tRNA modification, central metabolism and respiration. Fe/S proteins can perform a wide range of functions, from electron transfer to redox and non-redox catalysis. In all living organisms, Fe/S proteins are first synthesized in an apo-form. However, as the Fe/S prosthetic group is required for correct folding and/or protein stability, Fe/S clusters are inserted co-translationally or immediately after translation by specific assembly machineries. These systems have been extensively studied over the last decade, both in prokaryotes and eukaryotes. The present review covers the basic principles of the bacterial housekeeping Fe/S biogenesis ISC system, and related recent molecular advances. Some of the most exciting recent highlights relating to this system include structural and functional characterization of binary and ternary complexes involved in Fe/S cluster formation on the scaffold protein IscU. These advances enhance our understanding of the Fe/S cluster assembly mechanism by revealing essential interactions that could never be determined with isolated proteins and likely are closer to an in vivo situation. Much less is currently known about the molecular mechanism of the Fe/S transfer step, but a brief account of the protein-protein interactions involved is given. This article is part of a Special Issue entitled: Fe/S proteins: Analysis, structure, function, biogenesis and diseases.
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Affiliation(s)
- B Blanc
- Université Grenoble Alpes, LCBM, 38054 Grenoble, France; CEA, DSV, iRTSV, LCBM, Biocatalyse, 38054 Grenoble, France; CNRS UMR5249, LCBM, 38054 Grenoble, France
| | - C Gerez
- Université Grenoble Alpes, LCBM, 38054 Grenoble, France; CEA, DSV, iRTSV, LCBM, Biocatalyse, 38054 Grenoble, France; CNRS UMR5249, LCBM, 38054 Grenoble, France
| | - S Ollagnier de Choudens
- Université Grenoble Alpes, LCBM, 38054 Grenoble, France; CEA, DSV, iRTSV, LCBM, Biocatalyse, 38054 Grenoble, France; CNRS UMR5249, LCBM, 38054 Grenoble, France.
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15
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Yee N, Choi J, Porter AW, Carey S, Rauschenbach I, Harel A. Selenate reductase activity inEscherichia colirequires Isc iron-sulfur cluster biosynthesis genes. FEMS Microbiol Lett 2014; 361:138-43. [DOI: 10.1111/1574-6968.12623] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 09/29/2014] [Accepted: 10/07/2014] [Indexed: 11/29/2022] Open
Affiliation(s)
- Nathan Yee
- School of Environmental and Biological Sciences; Rutgers, The State University of New Jersey; New Brunswick NJ USA
| | - Jessica Choi
- School of Environmental and Biological Sciences; Rutgers, The State University of New Jersey; New Brunswick NJ USA
| | - Abigail W. Porter
- School of Environmental and Biological Sciences; Rutgers, The State University of New Jersey; New Brunswick NJ USA
| | - Sean Carey
- School of Environmental and Biological Sciences; Rutgers, The State University of New Jersey; New Brunswick NJ USA
| | - Ines Rauschenbach
- School of Environmental and Biological Sciences; Rutgers, The State University of New Jersey; New Brunswick NJ USA
| | - Arye Harel
- School of Environmental and Biological Sciences; Rutgers, The State University of New Jersey; New Brunswick NJ USA
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16
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Zorn M, Ihling CH, Golbik R, Sawers RG, Sinz A. Mapping Cell Envelope and Periplasm Protein Interactions of Escherichia coli Respiratory Formate Dehydrogenases by Chemical Cross-Linking and Mass Spectrometry. J Proteome Res 2014; 13:5524-35. [DOI: 10.1021/pr5004906] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Michael Zorn
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, D-06120 Halle (Saale), Germany
| | - Christian H. Ihling
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, D-06120 Halle (Saale), Germany
| | | | | | - Andrea Sinz
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, D-06120 Halle (Saale), Germany
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17
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Yokoyama K, Leimkühler S. The role of FeS clusters for molybdenum cofactor biosynthesis and molybdoenzymes in bacteria. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1853:1335-49. [PMID: 25268953 DOI: 10.1016/j.bbamcr.2014.09.021] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 09/19/2014] [Accepted: 09/22/2014] [Indexed: 11/29/2022]
Abstract
The biosynthesis of the molybdenum cofactor (Moco) has been intensively studied, in addition to its insertion into molybdoenzymes. In particular, a link between the assembly of molybdoenzymes and the biosynthesis of FeS clusters has been identified in the recent years: 1) the synthesis of the first intermediate in Moco biosynthesis requires an FeS-cluster containing protein, 2) the sulfurtransferase for the dithiolene group in Moco is also involved in the synthesis of FeS clusters, thiamin and thiolated tRNAs, 3) the addition of a sulfido-ligand to the molybdenum atom in the active site additionally involves a sulfurtransferase, and 4) most molybdoenzymes in bacteria require FeS clusters as redox active cofactors. In this review we will focus on the biosynthesis of the molybdenum cofactor in bacteria, its modification and insertion into molybdoenzymes, with an emphasis to its link to FeS cluster biosynthesis and sulfur transfer.
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Affiliation(s)
- Kenichi Yokoyama
- Department of Biochemistry, Duke University Medical Center, Durham, NC, USA
| | - Silke Leimkühler
- Department of Molecular Enzymology, Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany.
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18
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Global identification of genes affecting iron-sulfur cluster biogenesis and iron homeostasis. J Bacteriol 2014; 196:1238-49. [PMID: 24415728 DOI: 10.1128/jb.01160-13] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Iron-sulfur (Fe-S) clusters are ubiquitous cofactors that are crucial for many physiological processes in all organisms. In Escherichia coli, assembly of Fe-S clusters depends on the activity of the iron-sulfur cluster (ISC) assembly and sulfur mobilization (SUF) apparatus. However, the underlying molecular mechanisms and the mechanisms that control Fe-S cluster biogenesis and iron homeostasis are still poorly defined. In this study, we performed a global screen to identify the factors affecting Fe-S cluster biogenesis and iron homeostasis using the Keio collection, which is a library of 3,815 single-gene E. coli knockout mutants. The approach was based on radiolabeling of the cells with [2-(14)C]dihydrouracil, which entirely depends on the activity of an Fe-S enzyme, dihydropyrimidine dehydrogenase. We identified 49 genes affecting Fe-S cluster biogenesis and/or iron homeostasis, including 23 genes important only under microaerobic/anaerobic conditions. This study defines key proteins associated with Fe-S cluster biogenesis and iron homeostasis, which will aid further understanding of the cellular mechanisms that coordinate the processes. In addition, we applied the [2-(14)C]dihydrouracil-labeling method to analyze the role of amino acid residues of an Fe-S cluster assembly scaffold (IscU) as a model of the Fe-S cluster assembly apparatus. The analysis showed that Cys37, Cys63, His105, and Cys106 are essential for the function of IscU in vivo, demonstrating the potential of the method to investigate in vivo function of proteins involved in Fe-S cluster assembly.
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Abstract
Small RNAs (sRNAs) constitute a large and heterogeneous class of bacterial gene expression regulators. Much like eukaryotic microRNAs, these sRNAs typically target multiple mRNAs through short seed pairing, thereby acting as global posttranscriptional regulators. In some bacteria, evidence for hundreds to possibly more than 1,000 different sRNAs has been obtained by transcriptome sequencing. However, the experimental identification of possible targets and, therefore, their confirmation as functional regulators of gene expression has remained laborious. Here, we present a strategy that integrates phylogenetic information to predict sRNA targets at the genomic scale and reconstructs regulatory networks upon functional enrichment and network analysis (CopraRNA, for Comparative Prediction Algorithm for sRNA Targets). Furthermore, CopraRNA precisely predicts the sRNA domains for target recognition and interaction. When applied to several model sRNAs, CopraRNA revealed additional targets and functions for the sRNAs CyaR, FnrS, RybB, RyhB, SgrS, and Spot42. Moreover, the mRNAs gdhA, lrp, marA, nagZ, ptsI, sdhA, and yobF-cspC were suggested as regulatory hubs targeted by up to seven different sRNAs. The verification of many previously undetected targets by CopraRNA, even for extensively investigated sRNAs, demonstrates its advantages and shows that CopraRNA-based analyses can compete with experimental target prediction approaches. A Web interface allows high-confidence target prediction and efficient classification of bacterial sRNAs.
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20
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Reprint of: Iron/sulfur proteins biogenesis in prokaryotes: formation, regulation and diversity. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:923-37. [PMID: 23660107 DOI: 10.1016/j.bbabio.2013.05.001] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Revised: 12/21/2012] [Accepted: 12/27/2012] [Indexed: 12/15/2022]
Abstract
Iron/sulfur centers are key cofactors of proteins intervening in multiple conserved cellular processes, such as gene expression, DNA repair, RNA modification, central metabolism and respiration. Mechanisms allowing Fe/S centers to be assembled, and inserted into polypeptides have attracted much attention in the last decade, both in eukaryotes and prokaryotes. Basic principles and recent advances in our understanding of the prokaryotic Fe/S biogenesis ISC and SUF systems are reviewed in the present communication. Most studies covered stem from investigations in Escherichia coli and Azotobacter vinelandii. Remarkable insights were brought about by complementary structural, spectroscopic, biochemical and genetic studies. Highlights of the recent years include scaffold mediated assembly of Fe/S cluster, A-type carriers mediated delivery of clusters and regulatory control of Fe/S homeostasis via a set of interconnected genetic regulatory circuits. Also, the importance of Fe/S biosynthesis systems in mediating soft metal toxicity was documented. A brief account of the Fe/S biosynthesis systems diversity as present in current databases is given here. Moreover, Fe/S biosynthesis factors have themselves been the object of molecular tailoring during evolution and some examples are discussed here. An effort was made to provide, based on the E. coli system, a general classification associating a given domain with a given function such as to help next search and annotation of genomes. This article is part of a Special Issue entitled: Metals in Bioenergetics and Biomimetics Systems.
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21
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Stripp ST, Soboh B, Lindenstrauss U, Braussemann M, Herzberg M, Nies DH, Sawers RG, Heberle J. HypD is the scaffold protein for Fe-(CN)2CO cofactor assembly in [NiFe]-hydrogenase maturation. Biochemistry 2013; 52:3289-96. [PMID: 23597401 DOI: 10.1021/bi400302v] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
[NiFe]-hydrogenases bind a NiFe-(CN)2CO cofactor in their catalytic large subunit. The iron-sulfur protein HypD and the small accessory protein HypC play a central role in the generation of the CO and CN(-) ligands. Infrared spectroscopy identified signatures on an anaerobically isolated HypCD complex that are reminiscent of those in the hydrogenase active site, suggesting that this complex is the assembly site of the Fe-(CN)2CO moiety of the cofactor prior to its transfer to the hydrogenase large subunit. Here, we report that HypD isolated in the absence of HypC shows infrared bands at 1956 cm(-1), 2072 cm(-1), and 2092 cm(-1) that can be assigned to CO, CN(1), and CN(2), respectively, and which are indistinguishable from those observed for the HypCD complex. HypC could not be isolated with CO or CN(-) ligand contribution. Treatment of HypD with EDTA led to the concomitant loss of Fe and the CO and CN(-) signatures, while oxidation by H2O2 resulted in a positive shift of the CO and CN(-) bands by 35 cm(-1) and 20 cm(-1), respectively, indicative of the ferrous iron as an immediate ligation site for the diatomic ligands. Analysis of HypD amino acid variants identified cysteines 41, 69, and 72 to be essential for maturation of the cofactor. We propose a refined model for the ligation of Fe-(CN)2CO to HypD and the role of HypC in [NiFe]-hydrogenase maturation.
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Affiliation(s)
- Sven T Stripp
- Experimental Molecular Biophysics, Freie Universität Berlin , Arnimalle 14, 14195 Berlin, Germany
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22
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Pinske C, Jaroschinsky M, Sawers RG. Levels of control exerted by the Isc iron-sulfur cluster system on biosynthesis of the formate hydrogenlyase complex. MICROBIOLOGY-SGM 2013; 159:1179-1189. [PMID: 23558265 DOI: 10.1099/mic.0.066142-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The membrane-associated formate hydrogenlyase (FHL) complex of bacteria like Escherichia coli is responsible for the disproportionation of formic acid into the gaseous products carbon dioxide and dihydrogen. It comprises minimally seven proteins including FdhF and HycE, the catalytic subunits of formate dehydrogenase H and hydrogenase 3, respectively. Four proteins of the FHL complex have iron-sulphur cluster ([Fe-S]) cofactors. Biosynthesis of [Fe-S] is principally catalysed by the Isc or Suf systems and each comprises proteins for assembly and for delivery of [Fe-S]. This study demonstrates that the Isc system is essential for biosynthesis of an active FHL complex. In the absence of the IscU assembly protein no hydrogen production or activity of FHL subcomponents was detected. A deletion of the iscU gene also resulted in reduced intracellular formate levels partially due to impaired synthesis of pyruvate formate-lyase, which is dependent on the [Fe-S]-containing regulator FNR. This caused reduced expression of the formate-inducible fdhF gene. The A-type carrier (ATC) proteins IscA and ErpA probably deliver [Fe-S] to specific apoprotein components of the FHL complex because mutants lacking either protein exhibited strongly reduced hydrogen production. Neither ATC protein could compensate for the lack of the other, suggesting that they had independent roles in [Fe-S] delivery to complex components. Together, the data indicate that the Isc system modulates FHL complex biosynthesis directly by provision of [Fe-S] as well as indirectly by influencing gene expression through the delivery of [Fe-S] to key regulators and enzymes that ultimately control the generation and oxidation of formate.
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Affiliation(s)
- Constanze Pinske
- Division of Molecular Microbiology, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK.,Institute of Biology/Microbiology, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120 Halle (Saale), Germany
| | - Monique Jaroschinsky
- Institute of Biology/Microbiology, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120 Halle (Saale), Germany
| | - R Gary Sawers
- Institute of Biology/Microbiology, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120 Halle (Saale), Germany
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23
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Boutigny S, Saini A, Baidoo EEK, Yeung N, Keasling JD, Butland G. Physical and functional interactions of a monothiol glutaredoxin and an iron sulfur cluster carrier protein with the sulfur-donating radical S-adenosyl-L-methionine enzyme MiaB. J Biol Chem 2013; 288:14200-14211. [PMID: 23543739 DOI: 10.1074/jbc.m113.460360] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The biosynthesis of iron sulfur (FeS) clusters, their trafficking from initial assembly on scaffold proteins via carrier proteins to final incorporation into FeS apoproteins, is a highly coordinated process enabled by multiprotein systems encoded in iscRSUAhscBAfdx and sufABCDSE operons in Escherichia coli. Although these systems are believed to encode all factors required for initial cluster assembly and transfer to FeS carrier proteins, accessory factors such as monothiol glutaredoxin, GrxD, and the FeS carrier protein NfuA are located outside of these defined systems. These factors have been suggested to function both as shuttle proteins acting to transfer clusters between scaffold and carrier proteins and in the final stages of FeS protein assembly by transferring clusters to client FeS apoproteins. Here we implicate both of these factors in client protein interactions. We demonstrate specific interactions between GrxD, NfuA, and the methylthiolase MiaB, a radical S-adenosyl-L-methionine-dependent enzyme involved in the maturation of a subset of tRNAs. We show that GrxD and NfuA physically interact with MiaB with affinities compatible with an in vivo function. We furthermore demonstrate that NfuA is able to transfer its cluster in vitro to MiaB, whereas GrxD is unable to do so. The relevance of these interactions was demonstrated by linking the activity of MiaB with GrxD and NfuA in vivo. We observe a severe defect in in vivo MiaB activity in cells lacking both GrxD and NfuA, suggesting that these proteins could play complementary roles in maturation and repair of MiaB.
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Affiliation(s)
- Sylvain Boutigny
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Avneesh Saini
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Edward E K Baidoo
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720; Joint BioEnergy Institute, Emeryville, California 94608
| | - Natasha Yeung
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Jay D Keasling
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720; Joint BioEnergy Institute, Emeryville, California 94608; Department of Chemical Engineering, University of California, Berkeley, California 94720; Department of Bioengineering, University of California, Berkeley, California 94720
| | - Gareth Butland
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720.
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24
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Vinella D, Loiseau L, de Choudens SO, Fontecave M, Barras F. In vivo[Fe-S] cluster acquisition by IscR and NsrR, two stress regulators inEscherichia coli. Mol Microbiol 2013; 87:493-508. [DOI: 10.1111/mmi.12135] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/17/2012] [Indexed: 11/30/2022]
Affiliation(s)
- Daniel Vinella
- Laboratoire de Chimie Bactérienne; UMR 7283 (Aix-Marseille Université-CNRS); Institut de Microbiologie de la Méditerranée; 31 Chemin Joseph Aiguier; 13009; Marseille; France
| | - Laurent Loiseau
- Laboratoire de Chimie Bactérienne; UMR 7283 (Aix-Marseille Université-CNRS); Institut de Microbiologie de la Méditerranée; 31 Chemin Joseph Aiguier; 13009; Marseille; France
| | - Sandrine Ollagnier de Choudens
- Laboratoire de Chimie et Biologie des Métaux; UMR 5249 (CEA-Université Grenoble I-CNRS); 17 Rue des Martyrs; 38054; Grenoble Cedex; France
| | | | - Frédéric Barras
- Laboratoire de Chimie Bactérienne; UMR 7283 (Aix-Marseille Université-CNRS); Institut de Microbiologie de la Méditerranée; 31 Chemin Joseph Aiguier; 13009; Marseille; France
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25
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Roche B, Aussel L, Ezraty B, Mandin P, Py B, Barras F. Iron/sulfur proteins biogenesis in prokaryotes: formation, regulation and diversity. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:455-69. [PMID: 23298813 DOI: 10.1016/j.bbabio.2012.12.010] [Citation(s) in RCA: 212] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Revised: 12/21/2012] [Accepted: 12/27/2012] [Indexed: 12/17/2022]
Abstract
Iron/sulfur centers are key cofactors of proteins intervening in multiple conserved cellular processes, such as gene expression, DNA repair, RNA modification, central metabolism and respiration. Mechanisms allowing Fe/S centers to be assembled, and inserted into polypeptides have attracted much attention in the last decade, both in eukaryotes and prokaryotes. Basic principles and recent advances in our understanding of the prokaryotic Fe/S biogenesis ISC and SUF systems are reviewed in the present communication. Most studies covered stem from investigations in Escherichia coli and Azotobacter vinelandii. Remarkable insights were brought about by complementary structural, spectroscopic, biochemical and genetic studies. Highlights of the recent years include scaffold mediated assembly of Fe/S cluster, A-type carriers mediated delivery of clusters and regulatory control of Fe/S homeostasis via a set of interconnected genetic regulatory circuits. Also, the importance of Fe/S biosynthesis systems in mediating soft metal toxicity was documented. A brief account of the Fe/S biosynthesis systems diversity as present in current databases is given here. Moreover, Fe/S biosynthesis factors have themselves been the object of molecular tailoring during evolution and some examples are discussed here. An effort was made to provide, based on the E. coli system, a general classification associating a given domain with a given function such as to help next search and annotation of genomes. This article is part of a Special Issue entitled: Metals in Bioenergetics and Biomimetics Systems.
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Affiliation(s)
- Béatrice Roche
- Institut de Microbiologie de la Méditerranée, Marseille, France
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26
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Partow S, Siewers V, Daviet L, Schalk M, Nielsen J. Reconstruction and evaluation of the synthetic bacterial MEP pathway in Saccharomyces cerevisiae. PLoS One 2012; 7:e52498. [PMID: 23285068 PMCID: PMC3532213 DOI: 10.1371/journal.pone.0052498] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2012] [Accepted: 11/19/2012] [Indexed: 12/03/2022] Open
Abstract
Isoprenoids, which are a large group of natural and chemical compounds with a variety of applications as e.g. fragrances, pharmaceuticals and potential biofuels, are produced via two different metabolic pathways, the mevalonate (MVA) pathway and the 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway. Here, we attempted to replace the endogenous MVA pathway in Saccharomyces cerevisiae by a synthetic bacterial MEP pathway integrated into the genome to benefit from its superior properties in terms of energy consumption and productivity at defined growth conditions. It was shown that the growth of a MVA pathway deficient S. cerevisiae strain could not be restored by the heterologous MEP pathway even when accompanied by the co-expression of genes erpA, hISCA1 and CpIscA involved in the Fe-S trafficking routes leading to maturation of IspG and IspH and E. coli genes fldA and fpr encoding flavodoxin and flavodoxin reductase believed to be responsible for electron transfer to IspG and IspH.
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Affiliation(s)
- Siavash Partow
- Department of Chemical and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
| | - Verena Siewers
- Department of Chemical and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
| | - Laurent Daviet
- Firmenich SA, Corporate R&D Division, Geneva, Switzerland
| | - Michel Schalk
- Firmenich SA, Corporate R&D Division, Geneva, Switzerland
| | - Jens Nielsen
- Department of Chemical and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
- * E-mail:
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27
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Brennan FP, Grant J, Botting CH, O'Flaherty V, Richards KG, Abram F. Insights into the low-temperature adaptation and nutritional flexibility of a soil-persistentEscherichia coli. FEMS Microbiol Ecol 2012; 84:75-85. [DOI: 10.1111/1574-6941.12038] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Revised: 10/23/2012] [Accepted: 10/24/2012] [Indexed: 01/14/2023] Open
Affiliation(s)
- Fiona P. Brennan
- Ecological Sciences Group; The James Hutton Institute; Craigiebucker, Aberdeen; Scotland
| | - Jim Grant
- Ashtown Research Centre; Teagasc; Dublin; Ireland
| | - Catherine H. Botting
- Biomedical Sciences Research Complex; University of St. Andrews; St. Andrews; Fife; UK
| | - Vincent O'Flaherty
- Microbial Ecology Laboratory; Department of Microbiology; School of Natural Sciences and Ryan Institute; National University of Ireland, Galway; Galway; Ireland
| | | | - Florence Abram
- Functional Environmental Microbiology; Department of Microbiology; School of Natural Sciences; National University of Ireland, Galway; Galway; Ireland
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28
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Py B, Gerez C, Angelini S, Planel R, Vinella D, Loiseau L, Talla E, Brochier-Armanet C, Garcia Serres R, Latour JM, Ollagnier-de Choudens S, Fontecave M, Barras F. Molecular organization, biochemical function, cellular role and evolution of NfuA, an atypical Fe-S carrier. Mol Microbiol 2012; 86:155-71. [PMID: 22966982 DOI: 10.1111/j.1365-2958.2012.08181.x] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Biosynthesis of iron-sulphur (Fe-S) proteins is catalysed by multi-protein systems, ISC and SUF. However, 'non-ISC, non-SUF' Fe-S biosynthesis factors have been described, both in prokaryotes and eukaryotes. Here we report in vitro and in vivo investigations of such a 'non-ISC, non SUF' component, the Nfu proteins. Phylogenomic analysis allowed us to define four subfamilies. Escherichia coli NfuA is within subfamily II. Most members of this subfamily have a Nfu domain fused to a 'degenerate' A-type carrier domain (ATC*) lacking Fe-S cluster co-ordinating Cys ligands. The Nfu domain binds a [4Fe-4S] cluster while the ATC* domain interacts with NuoG (a complex I subunit) and aconitase B (AcnB). In vitro, holo-NfuA promotes maturation of AcnB. In vivo, NfuA is necessary for full activity of complex I under aerobic growth conditions, and of AcnB in the presence of superoxide. NfuA receives Fe-S clusters from IscU/HscBA and SufBCD scaffolds and eventually transfers them to the ATCs IscA and SufA. This study provides significant information on one of the Fe-S biogenesis factors that has been often used as a building block by ISC and/or SUF synthesizing organisms, including bacteria, plants and animals.
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Affiliation(s)
- Béatrice Py
- Laboratoire de Chimie Bactérienne, UMR 7283 Aix-Marseille Université-CNRS, Institut de Microbiologie de la Méditerranée, 31 Chemin Joseph Aiguier, 13009 Marseille, France
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Zymographic differentiation of [NiFe]-hydrogenases 1, 2 and 3 of Escherichia coli K-12. BMC Microbiol 2012; 12:134. [PMID: 22769583 PMCID: PMC3431244 DOI: 10.1186/1471-2180-12-134] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2012] [Accepted: 06/25/2012] [Indexed: 11/10/2022] Open
Abstract
Background When grown under anaerobic conditions, Escherichia coli K-12 is able to synthesize three active [NiFe]-hydrogenases (Hyd1-3). Two of these hydrogenases are respiratory enzymes catalysing hydrogen oxidation, whereby Hyd-1 is oxygen-tolerant and Hyd-2 is considered a standard oxygen-sensitive hydrogenase. Hyd-3, together with formate dehydrogenase H (Fdh-H), forms the formate hydrogenlyase (FHL) complex, which is responsible for H2 evolution by intact cells. Hydrogen oxidation activity can be assayed for all three hydrogenases using benzyl viologen (BV; Eo′ = -360 mV) as an artificial electron acceptor; however ascribing activities to specific isoenzymes is not trivial. Previously, an in-gel assay could differentiate Hyd-1 and Hyd-2, while Hyd-3 had long been considered too unstable to be visualized on such native gels. This study identifies conditions allowing differentiation of all three enzymes using simple in-gel zymographic assays. Results Using a modified in-gel assay hydrogen-dependent BV reduction catalyzed by Hyd-3 has been described for the first time. High hydrogen concentrations facilitated visualization of Hyd-3 activity. The activity was membrane-associated and although not essential for visualization of Hyd-3, the activity was maximal in the presence of a functional Fdh-H enzyme. Furthermore, through the use of nitroblue tetrazolium (NBT; Eo′ = -80 mV) it was demonstrated that Hyd-1 reduces this redox dye in a hydrogen-dependent manner, while neither Hyd-2 nor Hyd-3 could couple hydrogen oxidation to NBT reduction. Hydrogen-dependent reduction of NBT was also catalysed by an oxygen-sensitive variant of Hyd-1 that had a supernumerary cysteine residue at position 19 of the small subunit substituted for glycine. This finding suggests that tolerance toward oxygen is not the main determinant that governs electron donation to more redox-positive electron acceptors such as NBT. Conclusions The utilization of particular electron acceptors at different hydrogen concentrations and redox potentials correlates with the known physiological functions of the respective hydrogenase. The ability to rapidly distinguish between oxygen-tolerant and standard [NiFe]-hydrogenases provides a facile new screen for the discovery of novel enzymes. A reliable assay for Hyd-3 will reinvigorate studies on the characterisation of the hydrogen-evolving FHL complex.
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Soboh B, Kuhns M, Braussemann M, Waclawek M, Muhr E, Pierik AJ, Sawers RG. Evidence for an oxygen-sensitive iron–sulfur cluster in an immature large subunit species of Escherichia coli [NiFe]-hydrogenase 2. Biochem Biophys Res Commun 2012; 424:158-63. [DOI: 10.1016/j.bbrc.2012.06.096] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Accepted: 06/19/2012] [Indexed: 11/24/2022]
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Pinske C, Sawers RG. Delivery of iron-sulfur clusters to the hydrogen-oxidizing [NiFe]-hydrogenases in Escherichia coli requires the A-type carrier proteins ErpA and IscA. PLoS One 2012; 7:e31755. [PMID: 22363723 PMCID: PMC3283652 DOI: 10.1371/journal.pone.0031755] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Accepted: 01/12/2012] [Indexed: 11/19/2022] Open
Abstract
During anaerobic growth Escherichia coli synthesizes two membrane-associated hydrogen-oxidizing [NiFe]-hydrogenases, termed hydrogenase 1 and hydrogenase 2. Each enzyme comprises a catalytic subunit containing the [NiFe] cofactor, an electron-transferring small subunit with a particular complement of [Fe-S] (iron-sulfur) clusters and a membrane-anchor subunit. How the [Fe-S] clusters are delivered to the small subunit of these enzymes is unclear. A-type carrier (ATC) proteins of the Isc (iron-sulfur-cluster) and Suf (sulfur mobilization) [Fe-S] cluster biogenesis pathways are proposed to traffic pre-formed [Fe-S] clusters to apoprotein targets. Mutants that could not synthesize SufA had active hydrogenase 1 and hydrogenase 2 enzymes, thus demonstrating that the Suf machinery is not required for hydrogenase maturation. In contrast, mutants devoid of the IscA, ErpA or IscU proteins of the Isc machinery had no detectable hydrogenase 1 or 2 activities. Lack of activity of both enzymes correlated with the absence of the respective [Fe-S]-cluster-containing small subunit, which was apparently rapidly degraded. During biosynthesis the hydrogenase large subunits receive their [NiFe] cofactor from the Hyp maturation machinery. Subsequent to cofactor insertion a specific C-terminal processing step occurs before association of the large subunit with the small subunit. This processing step is independent of small subunit maturation. Using western blotting experiments it could be shown that although the amount of each hydrogenase large subunit was strongly reduced in the iscA and erpA mutants, some maturation of the large subunit still occurred. Moreover, in contrast to the situation in Isc-proficient strains, these processed large subunits were not membrane-associated. Taken together, our findings demonstrate that both IscA and ErpA are required for [Fe-S] cluster delivery to the small subunits of the hydrogen-oxidizing hydrogenases; however, delivery of the Fe atom to the active site might have different requirements.
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Affiliation(s)
- Constanze Pinske
- Institute for Biology/Microbiology, Martin-Luther University Halle-Wittenberg, Halle (Saale) Germany
| | - R. Gary Sawers
- Institute for Biology/Microbiology, Martin-Luther University Halle-Wittenberg, Halle (Saale) Germany
- * E-mail:
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