1
|
Wall JD, Zane GM, Juba TR, Kuehl JV, Ray J, Chhabra SR, Trotter VV, Shatsky M, De León KB, Keller KL, Bender KS, Butland G, Arkin AP, Deutschbauer AM. Deletion Mutants, Archived Transposon Library, and Tagged Protein Constructs of the Model Sulfate-Reducing Bacterium Desulfovibrio vulgaris Hildenborough. Microbiol Resour Announc 2021; 10:e00072-21. [PMID: 33737356 PMCID: PMC7975874 DOI: 10.1128/mra.00072-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 02/17/2021] [Indexed: 11/20/2022] Open
Abstract
The dissimilatory sulfate-reducing deltaproteobacterium Desulfovibrio vulgaris Hildenborough (ATCC 29579) was chosen by the research collaboration ENIGMA to explore tools and protocols for bringing this anaerobe to model status. Here, we describe a collection of genetic constructs generated by ENIGMA that are available to the research community.
Collapse
Affiliation(s)
- Judy D Wall
- Biochemistry Division, University of Missouri, Columbia, Missouri, USA
| | - Grant M Zane
- Biochemistry Division, University of Missouri, Columbia, Missouri, USA
| | - Thomas R Juba
- Biochemistry Division, University of Missouri, Columbia, Missouri, USA
| | - Jennifer V Kuehl
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Jayashree Ray
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Swapnil R Chhabra
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Valentine V Trotter
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Maxim Shatsky
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Kara B De León
- Biochemistry Division, University of Missouri, Columbia, Missouri, USA
| | - Kimberly L Keller
- Biochemistry Division, University of Missouri, Columbia, Missouri, USA
| | - Kelly S Bender
- Biochemistry Division, University of Missouri, Columbia, Missouri, USA
| | - Gareth Butland
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Adam P Arkin
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Adam M Deutschbauer
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| |
Collapse
|
2
|
Genome Editing Method for the Anaerobic Magnetotactic Bacterium Desulfovibrio magneticus RS-1. Appl Environ Microbiol 2018; 84:AEM.01724-18. [PMID: 30194101 PMCID: PMC6210102 DOI: 10.1128/aem.01724-18] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 08/29/2018] [Indexed: 11/20/2022] Open
Abstract
Magnetotactic bacteria (MTB) are a group of organisms that form intracellular nanometer-scale magnetic crystals though a complex process involving lipid and protein scaffolds. These magnetic crystals and their lipid membranes, termed magnetosomes, are model systems for studying bacterial cell biology and biomineralization and are potential platforms for biotechnological applications. Due to a lack of genetic tools and unculturable representatives, the mechanisms of magnetosome formation in phylogenetically deeply branching MTB remain unknown. These MTB contain elongated bullet-/tooth-shaped magnetite and greigite crystals that likely form in a manner distinct from that of the cubooctahedral-shaped magnetite crystals of the genetically tractable MTB within the Alphaproteobacteria. Here, we present a method for genome editing in Desulfovibrio magneticus RS-1, a cultured representative of the deeply branching MTB of the class Deltaproteobacteria. This marks a crucial step in developing D. magneticus as a model for studying diverse mechanisms of magnetic particle formation by MTB. Magnetosomes are complex bacterial organelles that serve as model systems for studying bacterial cell biology, biomineralization, and global iron cycling. Magnetosome biogenesis is primarily studied in two closely related Alphaproteobacteria of the genus Magnetospirillum that form cubooctahedral-shaped magnetite crystals within a lipid membrane. However, chemically and structurally distinct magnetic particles have been found in physiologically and phylogenetically diverse bacteria. Due to a lack of molecular genetic tools, the mechanistic diversity of magnetosome formation remains poorly understood. Desulfovibrio magneticus RS-1 is an anaerobic sulfate-reducing deltaproteobacterium that forms bullet-shaped magnetite crystals. A recent forward genetic screen identified 10 genes in the conserved magnetosome gene island of D. magneticus that are essential for its magnetic phenotype. However, this screen likely missed mutants with defects in crystal size, shape, and arrangement. Reverse genetics to target the remaining putative magnetosome genes using standard genetic methods of suicide vector integration have not been feasible due to the low transconjugation efficiency. Here, we present a reverse genetic method for targeted mutagenesis in D. magneticus using a replicative plasmid. To test this method, we generated a mutant resistant to 5-fluorouracil by making a markerless deletion of the upp gene that encodes uracil phosphoribosyltransferase. We also used this method for targeted marker exchange mutagenesis by replacing kupM, a gene identified in our previous screen as a magnetosome formation factor, with a streptomycin resistance cassette. Overall, our results show that targeted mutagenesis using a replicative plasmid is effective in D. magneticus and may also be applied to other genetically recalcitrant bacteria. IMPORTANCE Magnetotactic bacteria (MTB) are a group of organisms that form intracellular nanometer-scale magnetic crystals though a complex process involving lipid and protein scaffolds. These magnetic crystals and their lipid membranes, termed magnetosomes, are model systems for studying bacterial cell biology and biomineralization and are potential platforms for biotechnological applications. Due to a lack of genetic tools and unculturable representatives, the mechanisms of magnetosome formation in phylogenetically deeply branching MTB remain unknown. These MTB contain elongated bullet-/tooth-shaped magnetite and greigite crystals that likely form in a manner distinct from that of the cubooctahedral-shaped magnetite crystals of the genetically tractable MTB within the Alphaproteobacteria. Here, we present a method for genome editing in Desulfovibrio magneticus RS-1, a cultured representative of the deeply branching MTB of the class Deltaproteobacteria. This marks a crucial step in developing D. magneticus as a model for studying diverse mechanisms of magnetic particle formation by MTB.
Collapse
|
3
|
Kpebe A, Benvenuti M, Guendon C, Rebai A, Fernandez V, Le Laz S, Etienne E, Guigliarelli B, García-Molina G, de Lacey AL, Baffert C, Brugna M. A new mechanistic model for an O 2-protected electron-bifurcating hydrogenase, Hnd from Desulfovibrio fructosovorans. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:1302-1312. [PMID: 30463674 DOI: 10.1016/j.bbabio.2018.09.364] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 08/22/2018] [Accepted: 09/16/2018] [Indexed: 10/28/2022]
Abstract
The genome of the sulfate-reducing and anaerobic bacterium Desulfovibrio fructosovorans encodes different hydrogenases. Among them is Hnd, a tetrameric cytoplasmic [FeFe] hydrogenase that has previously been described as an NADP-specific enzyme (Malki et al., 1995). In this study, we purified and characterized a recombinant Strep-tagged form of Hnd and demonstrated that it is an electron-bifurcating enzyme. Flavin-based electron-bifurcation is a mechanism that couples an exergonic redox reaction to an endergonic one allowing energy conservation in anaerobic microorganisms. One of the three ferredoxins of the bacterium, that was named FdxB, was also purified and characterized. It contains a low-potential (Em = -450 mV) [4Fe4S] cluster. We found that Hnd was not able to reduce NADP+, and that it catalyzes the simultaneous reduction of FdxB and NAD+. Moreover, Hnd is the first electron-bifurcating hydrogenase that retains activity when purified aerobically due to formation of an inactive state of its catalytic site protecting against O2 damage (Hinact). Hnd is highly active with the artificial redox partner (methyl viologen) and can perform the electron-bifurcation reaction to oxidize H2 with a specific activity of 10 μmol of NADH/min/mg of enzyme. Surprisingly, the ratio between NADH and reduced FdxB varies over the reaction with a decreasing amount of FdxB reduced per NADH produced, indicating a more complex mechanism than previously described. We proposed a new mechanistic model in which the ferredoxin is recycled at the hydrogenase catalytic subunit.
Collapse
Affiliation(s)
- Arlette Kpebe
- Aix Marseille Univ, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402, Marseille Cedex 09, France.
| | - Martino Benvenuti
- Aix Marseille Univ, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402, Marseille Cedex 09, France.
| | - Chloé Guendon
- Aix Marseille Univ, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402, Marseille Cedex 09, France.
| | - Amani Rebai
- Aix Marseille Univ, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402, Marseille Cedex 09, France
| | - Victoria Fernandez
- Aix Marseille Univ, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402, Marseille Cedex 09, France
| | - Sébastien Le Laz
- Aix Marseille Univ, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402, Marseille Cedex 09, France
| | - Emilien Etienne
- Aix Marseille Univ, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402, Marseille Cedex 09, France.
| | - Bruno Guigliarelli
- Aix Marseille Univ, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402, Marseille Cedex 09, France.
| | | | - Antonio L de Lacey
- Instituto de Catálisis y Petroleoquímica, CSIC, c/ Marie Curie 2, Madrid, Spain.
| | - Carole Baffert
- Aix Marseille Univ, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402, Marseille Cedex 09, France.
| | - Myriam Brugna
- Aix Marseille Univ, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402, Marseille Cedex 09, France.
| |
Collapse
|
4
|
Kinfu BM, Jahnke M, Janus M, Besirlioglu V, Roggenbuck M, Meurer R, Vojcic L, Borchert M, Schwaneberg U, Chow J, Streit WR. Recombinant RNA Polymerase from Geobacillus
sp. GHH01 as tool for rapid generation of metagenomic RNAs using in vitro technologies. Biotechnol Bioeng 2017; 114:2739-2752. [DOI: 10.1002/bit.26436] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 08/09/2017] [Accepted: 08/21/2017] [Indexed: 01/18/2023]
Affiliation(s)
- Birhanu M. Kinfu
- Microbiology and Biotechnology, Biocenter Klein Flottbek; University of Hamburg; Ohnhorststr Hamburg Germany
| | - Maike Jahnke
- Microbiology and Biotechnology, Biocenter Klein Flottbek; University of Hamburg; Ohnhorststr Hamburg Germany
| | - Mareike Janus
- Microbiology and Biotechnology, Biocenter Klein Flottbek; University of Hamburg; Ohnhorststr Hamburg Germany
| | | | | | | | | | | | | | - Jennifer Chow
- Microbiology and Biotechnology, Biocenter Klein Flottbek; University of Hamburg; Ohnhorststr Hamburg Germany
| | - Wolfgang R. Streit
- Microbiology and Biotechnology, Biocenter Klein Flottbek; University of Hamburg; Ohnhorststr Hamburg Germany
| |
Collapse
|
5
|
Le Laz S, kpebe A, Bauzan M, Lignon S, Rousset M, Brugna M. Expression of terminal oxidases under nutrient-starved conditions in Shewanella oneidensis: detection of the A-type cytochrome c oxidase. Sci Rep 2016; 6:19726. [PMID: 26815910 PMCID: PMC4728554 DOI: 10.1038/srep19726] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 12/17/2015] [Indexed: 11/12/2022] Open
Abstract
Shewanella species are facultative anaerobic bacteria that colonize redox-stratified habitats where O2 and nutrient concentrations fluctuate. The model species Shewanella oneidensis MR-1 possesses genes coding for three terminal oxidases that can perform O2 respiration: a bd-type quinol oxidase and cytochrome c oxidases of the cbb3-type and the A-type. Whereas the bd- and cbb3-type oxidases are routinely detected, evidence for the expression of the A-type enzyme has so far been lacking. Here, we investigated the effect of nutrient starvation on the expression of these terminal oxidases under different O2 tensions. Our results reveal that the bd-type oxidase plays a significant role under nutrient starvation in aerobic conditions. The expression of the cbb3-type oxidase is also modulated by the nutrient composition of the medium and increases especially under iron-deficiency in exponentially growing cells. Most importantly, under conditions of carbon depletion, high O2 and stationary-growth, we report for the first time the expression of the A-type oxidase in S. oneidensis, indicating that this terminal oxidase is not functionally lost. The physiological role of the A-type oxidase in energy conservation and in the adaptation of S. oneidensis to redox-stratified environments is discussed.
Collapse
Affiliation(s)
- Sébastien Le Laz
- CNRS, Aix-Marseille Université, Laboratoire de Bioénergétique et Ingénierie des Protéines, UMR 7281, IMM, 13402 Marseille Cedex 20, France
| | - Arlette kpebe
- CNRS, Aix-Marseille Université, Laboratoire de Bioénergétique et Ingénierie des Protéines, UMR 7281, IMM, 13402 Marseille Cedex 20, France
| | - Marielle Bauzan
- CNRS, Aix-Marseille Université, Unité de fermentation, FR3479, IMM, 13402 Marseille Cedex 20, France
| | - Sabrina Lignon
- CNRS, Aix-Marseille Université, Plate-forme Protéomique, FR3479, IMM, MaP IBiSA, 13402 Marseille Cedex 20, France
| | - Marc Rousset
- CNRS, Aix-Marseille Université, Laboratoire de Bioénergétique et Ingénierie des Protéines, UMR 7281, IMM, 13402 Marseille Cedex 20, France
| | - Myriam Brugna
- CNRS, Aix-Marseille Université, Laboratoire de Bioénergétique et Ingénierie des Protéines, UMR 7281, IMM, 13402 Marseille Cedex 20, France
| |
Collapse
|
6
|
Santos AA, Venceslau SS, Grein F, Leavitt WD, Dahl C, Johnston DT, Pereira IAC. A protein trisulfide couples dissimilatory sulfate reduction to energy conservation. Science 2016; 350:1541-5. [PMID: 26680199 DOI: 10.1126/science.aad3558] [Citation(s) in RCA: 139] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Microbial sulfate reduction has governed Earth's biogeochemical sulfur cycle for at least 2.5 billion years. However, the enzymatic mechanisms behind this pathway are incompletely understood, particularly for the reduction of sulfite-a key intermediate in the pathway. This critical reaction is performed by DsrAB, a widespread enzyme also involved in other dissimilatory sulfur metabolisms. Using in vitro assays with an archaeal DsrAB, supported with genetic experiments in a bacterial system, we show that the product of sulfite reduction by DsrAB is a protein-based trisulfide, in which a sulfite-derived sulfur is bridging two conserved cysteines of DsrC. Physiological studies also reveal that sulfate reduction rates are determined by cellular levels of DsrC. Dissimilatory sulfate reduction couples the four-electron reduction of the DsrC trisulfide to energy conservation.
Collapse
Affiliation(s)
- André A Santos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Sofia S Venceslau
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Fabian Grein
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - William D Leavitt
- Department of Earth and Planetary Science, Harvard University, Cambridge, MA, USA
| | - Christiane Dahl
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Germany
| | - David T Johnston
- Department of Earth and Planetary Science, Harvard University, Cambridge, MA, USA
| | - Inês A C Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
| |
Collapse
|
7
|
The Carbon Monoxide Dehydrogenase from Desulfovibrio vulgaris. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:1574-83. [DOI: 10.1016/j.bbabio.2015.08.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 07/29/2015] [Accepted: 08/04/2015] [Indexed: 11/21/2022]
|
8
|
da Silva SM, Amaral C, Neves SS, Santos C, Pimentel C, Rodrigues-Pousada C. An HcpR paralog of Desulfovibrio gigas provides protection against nitrosative stress. FEBS Open Bio 2015; 5:594-604. [PMID: 26273559 PMCID: PMC4534486 DOI: 10.1016/j.fob.2015.07.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 07/01/2015] [Indexed: 01/12/2023] Open
Abstract
Desulfovibrio gigas genome encodes two HcpR paralogs, HcpR1 and HcpR2. Cells lacking HcpR1 are less tolerant to NO. HcpR1 regulates the expression of several genes related to nitrogen metabolism. Phylogenetic analyses indicate that the presence of HcpR paralogs is a common finding among Desulfovibrio species.
Desulfovibrio gigas belongs to the group of sulfate reducing bacteria (SRB). These ubiquitous and metabolically versatile microorganisms are often exposed to reactive nitrogen species (RNS). Nonetheless, the mechanisms and regulatory elements involved in nitrosative stress protection are still poorly understood. The transcription factor HcpR has emerged as a putative regulator of nitrosative stress response among anaerobic bacteria. HcpR is known to orchestrate the expression of the hybrid cluster protein gene, hcp, proposed to be involved in cellular defense against RNS. According to phylogenetic analyses, the occurrence of hcpR paralog genes is a common feature among several Desulfovibrio species. Within the D. gigas genome we have identified two HcpR-related sequences. One of these sequences, hcpR1, was found in the close vicinity of the hcp gene and this finding prompted us to proceed with its functional characterization. We observed that the growth of a D. gigas strain lacking hcpR1 is severely impaired under nitrosative stress. An in silico search revealed several putative targets of HcpR1 that were experimentally validated. The fact that HcpR1 regulates several genes encoding proteins involved in nitrite and nitrate metabolism, together with the sensitive growth phenotype to NO displayed by an hcpR1 mutant strain, strongly supports a relevant role of this factor under nitrosative stress. Moreover, the finding that several Desulfovibrio species possess HcpR paralogs, which have been transmitted vertically in the evolution and diversification of the genus, suggests that these sequences may confer adaptive or survival advantage to these organisms, possibly by increasing their tolerance to nitrosative stress.
Collapse
Key Words
- BI, Bayesian inference
- BS, bootstrap
- CRP/FNR, cAMP receptor protein/fumarate and nitrate reductase regulatory protein
- Desulfovibrio
- Frdx, ferredoxin
- GSNO, S-nitrosoglutathione
- HGT, horizontal gene transfer
- Hcp, hybrid cluster protein
- HcpR
- ML, maximum likelihood
- MP, maximum parsimony
- Molecular phylogeny
- NO, nitric oxide
- Nitrosative stress
- PP, posterior probability
- RNS, reactive nitrogen species
- ROO, rubredoxin oxygen reductase
- SRB, sulfate reducing bacteria
- Sulfate reducing bacteria
- Transcription regulation
Collapse
Affiliation(s)
- Sofia M da Silva
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Catarina Amaral
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Susana S Neves
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Cátia Santos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Catarina Pimentel
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Claudina Rodrigues-Pousada
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| |
Collapse
|
9
|
Ramos AR, Grein F, Oliveira GP, Venceslau SS, Keller KL, Wall JD, Pereira IAC. The FlxABCD-HdrABC proteins correspond to a novel NADH dehydrogenase/heterodisulfide reductase widespread in anaerobic bacteria and involved in ethanol metabolism in Desulfovibrio vulgaris Hildenborough. Environ Microbiol 2015; 17:2288-305. [PMID: 25367508 DOI: 10.1111/1462-2920.12689] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2014] [Accepted: 10/23/2014] [Indexed: 11/29/2022]
Abstract
Flavin-based electron bifurcation (FBEB) is an important mechanism for the energy metabolism of anaerobes. A new family of NADH dehydrogenases, the flavin oxidoreductase (FlxABCD, previously called FloxABCD), was proposed to perform FBEB in sulphate-reducing organisms coupled with heterodisulfide reductase (HdrABC). We found that the hdrABC-flxABCD gene cluster is widespread among anaerobic bacteria, pointing to a general and important role in their bioenergetics. In this work, we studied FlxABCD of Desulfovibrio vulgaris Hildenborough. The hdr-flx genes are part of the same transcriptional unit and are increased in transcription during growth in ethanol-sulfate, and to a less extent during pyruvate fermentation. Two mutant strains were generated: one where expression of the hdr-flx genes was interrupted and another lacking the flxA gene. Both strains were unable to grow with ethanol-sulfate, whereas growth was restored in a flxA-complemented strain. The mutant strains also produced very reduced amounts of ethanol compared with the wild type during pyruvate fermentation. Our results show that in D. vulgaris, the FlxABCD-HdrABC proteins are essential for NADH oxidation during growth on ethanol, probably involving a FBEB mechanism that leads to reduction of ferredoxin and the small protein DsrC, while in fermentation they operate in reverse, reducing NAD(+) for ethanol production.
Collapse
Affiliation(s)
- Ana Raquel Ramos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, 2780-157, Portugal
| | - Fabian Grein
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, 2780-157, Portugal
| | - Gonçalo P Oliveira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, 2780-157, Portugal
| | - Sofia S Venceslau
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, 2780-157, Portugal
| | - Kimberly L Keller
- Biochemistry Department, University of Missouri, Columbia, MO, USA.,ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies), Berkeley, CA, USA
| | - Judy D Wall
- Biochemistry Department, University of Missouri, Columbia, MO, USA.,ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies), Berkeley, CA, USA
| | - Inês A C Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, 2780-157, Portugal
| |
Collapse
|
10
|
Rahn-Lee L, Byrne ME, Zhang M, Le Sage D, Glenn DR, Milbourne T, Walsworth RL, Vali H, Komeili A. A genetic strategy for probing the functional diversity of magnetosome formation. PLoS Genet 2015; 11:e1004811. [PMID: 25569806 PMCID: PMC4287615 DOI: 10.1371/journal.pgen.1004811] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 10/07/2014] [Indexed: 11/18/2022] Open
Abstract
Model genetic systems are invaluable, but limit us to understanding only a few organisms in detail, missing the variations in biological processes that are performed by related organisms. One such diverse process is the formation of magnetosome organelles by magnetotactic bacteria. Studies of model magnetotactic α-proteobacteria have demonstrated that magnetosomes are cubo-octahedral magnetite crystals that are synthesized within pre-existing membrane compartments derived from the inner membrane and orchestrated by a specific set of genes encoded within a genomic island. However, this model cannot explain all magnetosome formation, which is phenotypically and genetically diverse. For example, Desulfovibrio magneticus RS-1, a δ-proteobacterium for which we lack genetic tools, produces tooth-shaped magnetite crystals that may or may not be encased by a membrane with a magnetosome gene island that diverges significantly from those of the α-proteobacteria. To probe the functional diversity of magnetosome formation, we used modern sequencing technology to identify hits in RS-1 mutated with UV or chemical mutagens. We isolated and characterized mutant alleles of 10 magnetosome genes in RS-1, 7 of which are not found in the α-proteobacterial models. These findings have implications for our understanding of magnetosome formation in general and demonstrate the feasibility of applying a modern genetic approach to an organism for which classic genetic tools are not available.
Collapse
Affiliation(s)
- Lilah Rahn-Lee
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Meghan E. Byrne
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Manjing Zhang
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, United States of America
| | - David Le Sage
- Department of Physics, Harvard University, Cambridge, Massachusetts, United States of America
- Harvard-Smithsonian Center for Astrophysics, Cambridge, Massachusetts, United States of America
| | - David R. Glenn
- Department of Physics, Harvard University, Cambridge, Massachusetts, United States of America
- Harvard-Smithsonian Center for Astrophysics, Cambridge, Massachusetts, United States of America
- Center for Brain Science, Harvard University, Cambridge, Massachusetts, United States of America
| | - Timothy Milbourne
- Department of Physics, Harvard University, Cambridge, Massachusetts, United States of America
| | - Ronald L. Walsworth
- Department of Physics, Harvard University, Cambridge, Massachusetts, United States of America
- Harvard-Smithsonian Center for Astrophysics, Cambridge, Massachusetts, United States of America
- Center for Brain Science, Harvard University, Cambridge, Massachusetts, United States of America
| | - Hojatollah Vali
- Facility for Electron Microscopy Research, McGill University, Montreal, Quebec, Canada
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada
- Department of Earth and Planetary Sciences, McGill University, Montreal, Quebec, Canada
| | - Arash Komeili
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, United States of America
- * E-mail:
| |
Collapse
|
11
|
Ray J, Keller KL, Catena M, Juba TR, Zemla M, Rajeev L, Knierim B, Zane GM, Robertson JJ, Auer M, Wall JD, Mukhopadhyay A. Exploring the role of CheA3 in Desulfovibrio vulgaris Hildenborough motility. Front Microbiol 2014; 5:77. [PMID: 24639670 PMCID: PMC3944678 DOI: 10.3389/fmicb.2014.00077] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2013] [Accepted: 02/12/2014] [Indexed: 01/07/2023] Open
Abstract
Sulfate-reducing bacteria such as Desulfovibrio vulgaris Hildenborough are often found in environments with limiting growth nutrients. Using lactate as the electron donor and carbon source, and sulfate as the electron acceptor, wild type D. vulgaris shows motility on soft agar plates. We evaluated this phenotype with mutants resulting from insertional inactivation of genes potentially related to motility. Our study revealed that the cheA3 (DVU2072) kinase mutant was impaired in the ability to form motility halos. Insertions in two other cheA loci did not exhibit a loss in this phenotype. The cheA3 mutant was also non-motile in capillary assays. Complementation with a plasmid-borne copy of cheA3 restores wild type phenotypes. The cheA3 mutant displayed a flagellum as observed by electron microscopy, grew normally in liquid medium, and was motile in wet mounts. In the growth conditions used, the D. vulgaris ΔfliA mutant (DVU3229) for FliA, predicted to regulate flagella-related genes including cheA3, was defective both in flagellum formation and in forming the motility halos. In contrast, a deletion of the flp gene (DVU2116) encoding a pilin-related protein was similar to wild type. We conclude that wild type D. vulgaris forms motility halos on solid media that are mediated by flagella-related mechanisms via the CheA3 kinase. The conditions under which the CheA1 (DVU1594) and CheA2 (DVU1960) kinase function remain to be explored.
Collapse
Affiliation(s)
- Jayashree Ray
- Physical Biosciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | | | - Michela Catena
- Physical Biosciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Thomas R Juba
- Biochemistry Division, University of Missouri Columbia, MO, USA
| | - Marcin Zemla
- Life Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Lara Rajeev
- Physical Biosciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Bernhard Knierim
- Life Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Grant M Zane
- Biochemistry Division, University of Missouri Columbia, MO, USA
| | | | - Manfred Auer
- Life Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Judy D Wall
- Biochemistry Division, University of Missouri Columbia, MO, USA
| | - Aindrila Mukhopadhyay
- Physical Biosciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| |
Collapse
|
12
|
New model for electron flow for sulfate reduction in Desulfovibrio alaskensis G20. Appl Environ Microbiol 2013; 80:855-68. [PMID: 24242254 DOI: 10.1128/aem.02963-13] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To understand the energy conversion activities of the anaerobic sulfate-reducing bacteria, it is necessary to identify the components involved in electron flow. The importance of the abundant type I tetraheme cytochrome c3 (TpIc3) as an electron carrier during sulfate respiration was questioned by the previous isolation of a null mutation in the gene encoding TpIc3, cycA, in Desulfovibrio alaskensis G20. Whereas respiratory growth of the CycA mutant with lactate and sulfate was little affected, growth with pyruvate and sulfate was significantly impaired. We have explored the phenotype of the CycA mutant through physiological tests and transcriptomic and proteomic analyses. Data reported here show that electrons from pyruvate oxidation do not reach adenylyl sulfate reductase, the enzyme catalyzing the first redox reaction during sulfate reduction, in the absence of either CycA or the type I cytochrome c3:menaquinone oxidoreductase transmembrane complex, QrcABCD. In contrast to the wild type, the CycA and QrcA mutants did not grow with H2 or formate and sulfate as the electron acceptor. Transcriptomic and proteomic analyses of the CycA mutant showed that transcripts and enzymes for the pathway from pyruvate to succinate were strongly decreased in the CycA mutant regardless of the growth mode. Neither the CycA nor the QrcA mutant grew on fumarate alone, consistent with the omics results and a redox regulation of gene expression. We conclude that TpIc3 and the Qrc complex are D. alaskensis components essential for the transfer of electrons released in the periplasm to reach the cytoplasmic adenylyl sulfate reductase and present a model that may explain the CycA phenotype through confurcation of electrons.
Collapse
|
13
|
Pedrero Z, Bridou R, Mounicou S, Guyoneaud R, Monperrus M, Amouroux D. Transformation, localization, and biomolecular binding of Hg species at subcellular level in methylating and nonmethylating sulfate-reducing bacteria. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2012; 46:11744-11751. [PMID: 23050725 DOI: 10.1021/es302412q] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Microbial activity is recognized to play an important role on Hg methylation in aquatic ecosystems. However, the mechanism at the cellular level is still poorly understood. In this work subcellular partitioning and transformation of Hg species in two strains: Desulfovibrio sp. BerOc1 and Desulfovibrio desulfuricans G200 (which exhibit different Hg methylation potential) are studied as an approach to the elucidation of Hg methylation/demethylation processes. The incubation with isotopically labeled Hg species ((199)Hgi and Me(201)Hg) not only allows the determination of methylation and demethylation rates simultaneously, but also the comparison of the localization of the originally added and resulting species of such metabolic processes. A dissimilar Hg species distribution was observed. In general terms, monomethylmercury (MeHg) is preferentially localized in the extracellular fraction; meanwhile inorganic mercury (Hgi) is associated to the cells. The investigation of Hg binding biomolecules on the cytoplasmatic and extracellular fractions (size exclusion chromatography coupled to ICP-MS) revealed noticeable differences in the pattern corresponding to the Hg methylating and nonmethylating strains.
Collapse
Affiliation(s)
- Zoyne Pedrero
- Laboratoire de Chimie Analytique Bio-Inorganique et Environnement, Institut Pluridisciplinaire de Recherche sur l'Environnement et les Matériaux UMR 5254, CNRS Université de Pau et des Pays de l'Adour, 2 Avenue Pierre Angot, 64053 Pau, France.
| | | | | | | | | | | |
Collapse
|
14
|
Keller KL, Wall JD. Genetics and molecular biology of the electron flow for sulfate respiration in desulfovibrio. Front Microbiol 2011; 2:135. [PMID: 21747813 PMCID: PMC3129016 DOI: 10.3389/fmicb.2011.00135] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2011] [Accepted: 06/10/2011] [Indexed: 11/25/2022] Open
Abstract
Progress in the genetic manipulation of the Desulfovibrio strains has provided an opportunity to explore electron flow pathways during sulfate respiration. Most bacteria in this genus couple the oxidation of organic acids or ethanol with the reduction of sulfate, sulfite, or thiosulfate. Both fermentation of pyruvate in the absence of an alternative terminal electron acceptor, disproportionation of fumarate and growth on H2 with CO2 during sulfate reduction are exhibited by some strains. The ability to produce or consume H2 provides Desulfovibrio strains the capacity to participate as either partner in interspecies H2 transfer. Interestingly the mechanisms of energy conversion, pathways of electron flow and the parameters determining the pathways used remain to be elucidated. Recent application of molecular genetic tools for the exploration of the metabolism of Desulfovibrio vulgaris Hildenborough has provided several new datasets that might provide insights and constraints to the electron flow pathways. These datasets include (1) gene expression changes measured in microarrays for cells cultured with different electron donors and acceptors, (2) relative mRNA abundances for cells growing exponentially in defined medium with lactate as carbon source and electron donor plus sulfate as terminal electron acceptor, and (3) a random transposon mutant library selected on medium containing lactate plus sulfate supplemented with yeast extract. Studies of directed mutations eliminating apparent key components, the quinone-interacting membrane-bound oxidoreductase (Qmo) complex, the Type 1 tetraheme cytochrome c3 (Tp1-c3), or the Type 1 cytochrome c3:menaquinone oxidoreductase (Qrc) complex, suggest a greater flexibility in electron flow than previously considered. The new datasets revealed the absence of random transposons in the genes encoding an enzyme with homology to Coo membrane-bound hydrogenase. From this result, we infer that Coo hydrogenase plays an important role in D. vulgaris growth on lactate plus sulfate. These observations along with those reported previously have been combined in a model showing dual pathways of electrons from the oxidation of both lactate and pyruvate during sulfate respiration. Continuing genetic and biochemical analyses of key genes in Desulfovibrio strains will allow further clarification of a general model for sulfate respiration.
Collapse
Affiliation(s)
- Kimberly L Keller
- Department of Biochemistry, University of Missouri Columbia, MO, USA
| | | |
Collapse
|
15
|
Towards a rigorous network of protein-protein interactions of the model sulfate reducer Desulfovibrio vulgaris Hildenborough. PLoS One 2011; 6:e21470. [PMID: 21738675 PMCID: PMC3125180 DOI: 10.1371/journal.pone.0021470] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2011] [Accepted: 06/01/2011] [Indexed: 11/19/2022] Open
Abstract
Protein-protein interactions offer an insight into cellular processes beyond what may be obtained by the quantitative functional genomics tools of proteomics and transcriptomics. The aforementioned tools have been extensively applied to study Escherichia coli and other aerobes and more recently to study the stress response behavior of Desulfovibrio vulgaris Hildenborough, a model obligate anaerobe and sulfate reducer and the subject of this study. Here we carried out affinity purification followed by mass spectrometry to reconstruct an interaction network among 12 chromosomally encoded bait and 90 prey proteins based on 134 bait-prey interactions identified to be of high confidence. Protein-protein interaction data are often plagued by the lack of adequate controls and replication analyses necessary to assess confidence in the results, including identification of potential false positives. We addressed these issues through the use of biological replication, exponentially modified protein abundance indices, results from an experimental negative control, and a statistical test to assign confidence to each putative interacting pair applicable to small interaction data studies. We discuss the biological significance of metabolic features of D. vulgaris revealed by these protein-protein interaction data and the observed protein modifications. These include the distinct role of the putative carbon monoxide-induced hydrogenase, unique electron transfer routes associated with different oxidoreductases, and the possible role of methylation in regulating sulfate reduction.
Collapse
|
16
|
Keller KL, Wall JD, Chhabra S. Methods for Engineering Sulfate Reducing Bacteria of the Genus Desulfovibrio. Methods Enzymol 2011; 497:503-17. [DOI: 10.1016/b978-0-12-385075-1.00022-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
|
17
|
Zane GM, Yen HCB, Wall JD. Effect of the deletion of qmoABC and the promoter-distal gene encoding a hypothetical protein on sulfate reduction in Desulfovibrio vulgaris Hildenborough. Appl Environ Microbiol 2010; 76:5500-9. [PMID: 20581180 PMCID: PMC2918943 DOI: 10.1128/aem.00691-10] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2010] [Accepted: 06/18/2010] [Indexed: 12/24/2022] Open
Abstract
The pathway of electrons required for the reduction of sulfate in sulfate-reducing bacteria (SRB) is not yet fully characterized. In order to determine the role of a transmembrane protein complex suggested to be involved in this process, a deletion in Desulfovibrio vulgaris Hildenborough was created by marker exchange mutagenesis that eliminated four genes putatively encoding the QmoABC complex and a hypothetical protein (DVU0851). The Qmo (quinone-interacting membrane-bound oxidoreductase) complex is proposed to be responsible for transporting electrons to the dissimilatory adenosine-5'-phosphosulfate reductase in SRB. In support of the predicted role of this complex, the deletion mutant was unable to grow using sulfate as its sole electron acceptor with a range of electron donors. To explore a possible role for the hypothetical protein in sulfate reduction, a second mutant was constructed that had lost only the gene that codes for the DVU0851 protein. The second constructed mutant grew with sulfate as the sole electron acceptor; however, there was a lag that was not present with the wild-type or complemented strain. Neither deletion strain was significantly impaired for growth with sulfite or thiosulfate as the terminal electron acceptor. Complementation of the Delta(qmoABC-DVU0851) mutant with all four genes or only the qmoABC genes restored its ability to grow by sulfate respiration. These results confirmed the prediction that the Qmo complex is in the electron pathway for sulfate reduction and revealed that no other transmembrane complex could compensate when Qmo was lacking.
Collapse
Affiliation(s)
- Grant M. Zane
- University of Missouri, Columbia, Missouri, the Virtual Institute for Microbial Stress and Survival‡
| | - Huei-che Bill Yen
- University of Missouri, Columbia, Missouri, the Virtual Institute for Microbial Stress and Survival‡
| | - Judy D. Wall
- University of Missouri, Columbia, Missouri, the Virtual Institute for Microbial Stress and Survival‡
| |
Collapse
|
18
|
Relating diffusion along the substrate tunnel and oxygen sensitivity in hydrogenase. Nat Chem Biol 2009; 6:63-70. [DOI: 10.1038/nchembio.276] [Citation(s) in RCA: 159] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2009] [Accepted: 10/26/2009] [Indexed: 11/08/2022]
|
19
|
Development of a markerless genetic exchange system for Desulfovibrio vulgaris Hildenborough and its use in generating a strain with increased transformation efficiency. Appl Environ Microbiol 2009; 75:7682-91. [PMID: 19837844 DOI: 10.1128/aem.01839-09] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In recent years, the genetic manipulation of the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough has seen enormous progress. In spite of this progress, the current marker exchange deletion method does not allow for easy selection of multiple sequential gene deletions in a single strain because of the limited number of selectable markers available in D. vulgaris. To broaden the repertoire of genetic tools for manipulation, an in-frame, markerless deletion system has been developed. The counterselectable marker that makes this deletion system possible is the pyrimidine salvage enzyme, uracil phosphoribosyltransferase, encoded by upp. In wild-type D. vulgaris, growth was shown to be inhibited by the toxic pyrimidine analog 5-fluorouracil (5-FU), whereas a mutant bearing a deletion of the upp gene was resistant to 5-FU. When a plasmid containing the wild-type upp gene expressed constitutively from the aph(3')-II promoter (promoter for the kanamycin resistance gene in Tn5) was introduced into the upp deletion strain, sensitivity to 5-FU was restored. This observation allowed us to develop a two-step integration and excision strategy for the deletion of genes of interest. Since this in-frame deletion strategy does not retain an antibiotic cassette, multiple deletions can be generated in a single strain without the accumulation of genes conferring antibiotic resistances. We used this strategy to generate a deletion strain lacking the endonuclease (hsdR, DVU1703) of a type I restriction-modification system that we designated JW7035. The transformation efficiency of the JW7035 strain was found to be 100 to 1,000 times greater than that of the wild-type strain when stable plasmids were introduced via electroporation.
Collapse
|
20
|
Castañeda-Carrión IN, Whiteley M, Krumholz LR. Characterization of pNC1, a small and mobilizable plasmid for use in genetic manipulation of Desulfovibrio africanus. J Microbiol Methods 2009; 79:23-31. [PMID: 19631701 DOI: 10.1016/j.mimet.2009.07.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2009] [Revised: 07/13/2009] [Accepted: 07/14/2009] [Indexed: 10/20/2022]
Abstract
To develop a vector system that facilitates genetic manipulation in Desulfovibrio species, we screened native sulfate-reducing bacteria for small plasmids. A self-replicating plasmid was discovered in Desulfovibrio africanus SR-1. Sequence analysis of this 8568-bp plasmid (pNC1) revealed a G+C content of 47.2% and nine open reading frames. This plasmid has a copy number of six. Compatible hosts include D. africanus and Pseudomonas aeruginosa PA14. Genetic characterization of pNC1 revealed that 53.6% of the plasmid contains genes associated with replication, mobilization, and partitioning. The 1123-bp replicon is composed of a rep gene and four 22-bp iterons. The mobilization operon is composed of three genes with a putative 144-bp oriT. The partitioning operon is composed of parA and parB with a downstream parS. We report the construction of a small pNC1-based cloning vector which transforms D. africanus at high frequencies (approximately 1.5 x 10(3) CFU/microg DNA), is mobilizable at high transfer frequency (4.8 x 10(-4) transconjugants/donor), and is stably maintained under non-selective pressure. This study provides a potential host-vector system for Desulfovibrio gene functional analyses.
Collapse
|
21
|
Mikheenko IP, Rousset M, Dementin S, Macaskie LE. Bioaccumulation of palladium by Desulfovibrio fructosivorans wild-type and hydrogenase-deficient strains. Appl Environ Microbiol 2008; 74:6144-6. [PMID: 18689514 PMCID: PMC2565964 DOI: 10.1128/aem.02538-07] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2007] [Accepted: 08/01/2008] [Indexed: 11/20/2022] Open
Abstract
Wild-type Desulfovibrio fructosivorans and three hydrogenase-negative mutants reduced Pd(II) to Pd(0). The location of Pd(0) nanoparticles on the cytoplasmic membrane of the mutant retaining only cytoplasmic membrane-bound hydrogenase was strong evidence for the role of hydrogenases in Pd(0) deposition. Hydrogenase activity was retained at acidic pH, shown previously to favor Pd(0) deposition.
Collapse
Affiliation(s)
- I P Mikheenko
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, England, United Kingdom
| | | | | | | |
Collapse
|
22
|
Dementin S, Belle V, Bertrand P, Guigliarelli B, Adryanczyk-Perrier G, De Lacey AL, Fernandez VM, Rousset M, Léger C. Changing the ligation of the distal [4Fe4S] cluster in NiFe hydrogenase impairs inter- and intramolecular electron transfers. J Am Chem Soc 2007; 128:5209-18. [PMID: 16608357 DOI: 10.1021/ja060233b] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In NiFe hydrogenases, electrons are transferred from the active site to the redox partner via a chain of three Iron-Sulfur clusters, and the surface-exposed [4Fe4S] cluster has an unusual His(Cys)3 ligation. When this Histidine (H184 in Desulfovibrio fructosovorans) is changed into a cysteine or a glycine, a distal cubane is still assembled but the oxidative activity of the mutants is only 1.5 and 3% of that of the WT, respectively. We compared the activities of the WT and engineered enzymes for H2 oxidation, H+ reduction and H/D exchange, under various conditions: (i) either with the enzyme directly adsorbed onto an electrode or using soluble redox partners, and (ii) in the presence of exogenous ligands whose binding to the exposed Fe of H184G was expected to modulate the properties of the distal cluster. Protein film voltammetry proved particularly useful to unravel the effects of the mutations on inter and intramolecular electron transfer (ET). We demonstrate that changing the coordination of the distal cluster has no effect on cluster assembly, protein stability, active-site chemistry and proton transfer; however, it slows down the first-order rates of ET to and from the cluster. All-sulfur coordination is actually detrimental to ET, and intramolecular (uphill) ET is rate determining in the glycine variant. This demonstrates that although [4Fe4S] clusters are robust chemical constructs, the direct protein ligands play an essential role in imparting their ability to transfer electrons.
Collapse
Affiliation(s)
- Sébastien Dementin
- Laboratoire de Bioénergétique et Ingénierie des Protéines, CNRS UPR 9036, IBSM and Université de Provence, 31 chemin Joseph Aiguier, 13402 Marseille Cédex 20, France
| | | | | | | | | | | | | | | | | |
Collapse
|
23
|
Bender KS, Yen HCB, Hemme CL, Yang Z, He Z, He Q, Zhou J, Huang KH, Alm EJ, Hazen TC, Arkin AP, Wall JD. Analysis of a ferric uptake regulator (Fur) mutant of Desulfovibrio vulgaris Hildenborough. Appl Environ Microbiol 2007; 73:5389-400. [PMID: 17630305 PMCID: PMC2042090 DOI: 10.1128/aem.00276-07] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Previous experiments examining the transcriptional profile of the anaerobe Desulfovibrio vulgaris demonstrated up-regulation of the Fur regulon in response to various environmental stressors. To test the involvement of Fur in the growth response and transcriptional regulation of D. vulgaris, a targeted mutagenesis procedure was used for deleting the fur gene. Growth of the resulting Deltafur mutant (JW707) was not affected by iron availability, but the mutant did exhibit increased sensitivity to nitrite and osmotic stresses compared to the wild type. Transcriptional profiling of JW707 indicated that iron-bound Fur acts as a traditional repressor for ferrous iron uptake genes (feoAB) and other genes containing a predicted Fur binding site within their promoter. Despite the apparent lack of siderophore biosynthesis genes within the D. vulgaris genome, a large 12-gene operon encoding orthologs to TonB and TolQR also appeared to be repressed by iron-bound Fur. While other genes predicted to be involved in iron homeostasis were unaffected by the presence or absence of Fur, alternative expression patterns that could be interpreted as repression or activation by iron-free Fur were observed. Both the physiological and transcriptional data implicate a global regulatory role for Fur in the sulfate-reducing bacterium D. vulgaris.
Collapse
Affiliation(s)
- Kelly S Bender
- Department of Biochemistry, 117 Schweitzer Hall, Columbia, MO 65211, USA
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Kaneko R, Hayashi T, Tanahashi M, Naganuma T. Phylogenetic diversity and distribution of dissimilatory sulfite reductase genes from deep-sea sediment cores. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2007; 9:429-36. [PMID: 17497195 DOI: 10.1007/s10126-007-9003-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2006] [Accepted: 01/29/2007] [Indexed: 05/15/2023]
Abstract
The diversity and distribution of sulfate-reducing prokaryotes (SRP) was investigated in the Nankai Trough sediments of off-central Japan by exploring the diversity of a functional gene, dissimilatory sulfite reductase (dsrAB). Bulk DNAs were extracted from five piston-cored samples (up to 4.5 m long) with 41 vertical sections, and full-length dsrABgene sequences (ca. 1.9 kb) were PCR amplified and cloned. A total of 382 dsrAB clones yielded eight phylogenetic groups with an indigenous group forming a unique dsrAB lineage. The deltaproteobacterial dsrAB genes were found in almost all sediment samples, especially in the surface layer. One unique dsrAB clone group was also widespread in the dsrAB profiles of the studied sediments, and the percentage of its clones was generally shown gradual increase with sediment depth.
Collapse
Affiliation(s)
- Ryo Kaneko
- Graduate School of Biosphere Science, Hiroshima University, 1-4-4 Kagamiyama, Higashi-hiroshima, 739-8528, Japan
| | | | | | | |
Collapse
|
25
|
Importance of c-Type cytochromes for U(VI) reduction by Geobacter sulfurreducens. BMC Microbiol 2007; 7:16. [PMID: 17346345 PMCID: PMC1829397 DOI: 10.1186/1471-2180-7-16] [Citation(s) in RCA: 151] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2006] [Accepted: 03/08/2007] [Indexed: 11/10/2022] Open
Abstract
Background In order to study the mechanism of U(VI) reduction, the effect of deleting c-type cytochrome genes on the capacity of Geobacter sulfurreducens to reduce U(VI) with acetate serving as the electron donor was investigated. Results The ability of several c-type cytochrome deficient mutants to reduce U(VI) was lower than that of the wild type strain. Elimination of two confirmed outer membrane cytochromes and two putative outer membrane cytochromes significantly decreased (ca. 50–60%) the ability of G. sulfurreducens to reduce U(VI). Involvement in U(VI) reduction did not appear to be a general property of outer membrane cytochromes, as elimination of two other confirmed outer membrane cytochromes, OmcB and OmcC, had very little impact on U(VI) reduction. Among the periplasmic cytochromes, only MacA, proposed to transfer electrons from the inner membrane to the periplasm, appeared to play a significant role in U(VI) reduction. A subpopulation of both wild type and U(VI) reduction-impaired cells, 24–30%, accumulated amorphous uranium in the periplasm. Comparison of uranium-accumulating cells demonstrated a similar amount of periplasmic uranium accumulation in U(VI) reduction-impaired and wild type G. sulfurreducens. Assessment of the ability of the various suspensions to reduce Fe(III) revealed no correlation between the impact of cytochrome deletion on U(VI) reduction and reduction of Fe(III) hydroxide and chelated Fe(III). Conclusion This study indicates that c-type cytochromes are involved in U(VI) reduction by Geobacter sulfurreducens. The data provide new evidence for extracellular uranium reduction by G. sulfurreducens but do not rule out the possibility of periplasmic uranium reduction. Occurrence of U(VI) reduction at the cell surface is supported by the significant impact of elimination of outer membrane cytochromes on U(VI) reduction and the lack of correlation between periplasmic uranium accumulation and the capacity for uranium reduction. Periplasmic uranium accumulation may reflect the ability of uranium to penetrate the outer membrane rather than the occurrence of enzymatic U(VI) reduction. Elimination of cytochromes rarely had a similar impact on both Fe(III) and U(VI) reduction, suggesting that there are differences in the routes of electron transfer to U(VI) and Fe(III). Further studies are required to clarify the pathways leading to U(VI) reduction in G. sulfurreducens.
Collapse
|
26
|
Rodrigues R, Vicente JB, Félix R, Oliveira S, Teixeira M, Rodrigues-Pousada C. Desulfovibrio gigas flavodiiron protein affords protection against nitrosative stress in vivo. J Bacteriol 2006; 188:2745-51. [PMID: 16585735 PMCID: PMC1446983 DOI: 10.1128/jb.188.8.2745-2751.2006] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Desulfovibrio gigas flavodiiron protein (FDP), rubredoxin:oxygen oxidoreductase (ROO), was proposed to be the terminal oxidase of a soluble electron transfer chain coupling NADH oxidation to oxygen reduction. However, several members from the FDP family, to which ROO belongs, revealed nitric oxide (NO) reductase activity. Therefore, the protection afforded by ROO against the cytotoxic effects of NO was here investigated. The NO and oxygen reductase activities of recombinant ROO in vitro were tested by amperometric methods, and the enzyme was shown to effectively reduce NO and O(2). Functional complementation studies of an Escherichia coli mutant strain lacking the ROO homologue flavorubredoxin, an NO reductase, showed that ROO restores the anaerobic growth phenotype of cultures exposed to otherwise-toxic levels of exogenous NO. Additional studies in vivo using a D. gigas roo-deleted strain confirmed an increased sensitivity to NO of the mutant strain in comparison to the wild type. This effect is more pronounced when using the nitrosating agent S-nitrosoglutathione (GSNO), which effectively impairs the growth of the D. gigas Deltaroo strain. roo is constitutively expressed in D. gigas under all conditions tested. However, real-time reverse transcription-PCR analysis revealed a twofold induction of mRNA levels upon exposure to GSNO, suggesting regulation at the transcription level by NO. The newly proposed role of D. gigas ROO as an NO reductase combined with the O(2) reductase activity reveals a versatility which appears to afford protection to D. gigas at the onset of both oxidative and nitrosative stresses.
Collapse
Affiliation(s)
- Rute Rodrigues
- Instituto de Tecnologia Química e Biológica, Apartado 127, 2780-901 Oeiras, Portugal
| | | | | | | | | | | |
Collapse
|
27
|
Broco M, Rousset M, Oliveira S, Rodrigues-Pousada C. Deletion of flavoredoxin gene inDesulfovibrio gigasreveals its participation in thiosulfate reduction. FEBS Lett 2005; 579:4803-7. [PMID: 16099456 DOI: 10.1016/j.febslet.2005.07.044] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2005] [Revised: 07/14/2005] [Accepted: 07/25/2005] [Indexed: 11/25/2022]
Abstract
The gene encoding Desulfovibrio gigas flavoredoxin was deleted to elucidate its physiological role in the sulfate metabolism. Disruption of flr gene strongly inhibited the reduction of thiosulfate and exhibited a reduced growth in the presence of sulfite with lactate as electron donor. The growth with sulfate was not however affected by the lack of this protein. Additionally, flr mutant cells revealed a decrease of about 50% in the H2 consumption rate using thiosulfate as electron acceptor. Altogether, our results show in vivo that during sulfite respiration, trithionate and thiosulfate are produced and that flavoredoxin is specific for thiosulfate reduction.
Collapse
Affiliation(s)
- Manuela Broco
- Genomics and Stress Laboratory, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República (EAN), 2784-505 Oeiras, Portugal
| | | | | | | |
Collapse
|
28
|
Dementin S, Burlat B, De Lacey AL, Pardo A, Adryanczyk-Perrier G, Guigliarelli B, Fernandez VM, Rousset M. A Glutamate Is the Essential Proton Transfer Gate during the Catalytic Cycle of the [NiFe] Hydrogenase. J Biol Chem 2004; 279:10508-13. [PMID: 14688251 DOI: 10.1074/jbc.m312716200] [Citation(s) in RCA: 110] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Kinetic, EPR, and Fourier transform infrared spectroscopic analysis of Desulfovibrio fructosovorans [NiFe] hydrogenase mutants targeted to Glu-25 indicated that this amino acid participates in proton transfer between the active site and the protein surface during the catalytic cycle. Replacement of that glutamic residue by a glutamine did not modify the spectroscopic properties of the enzyme but cancelled the catalytic activity except the para-H(2)/ortho-H(2) conversion. This mutation impaired the fast proton transfer from the active site that allows high turnover numbers for the oxidation of hydrogen. Replacement of the glutamic residue by the shorter aspartic acid slowed down this proton transfer, causing a significant decrease of H(2) oxidation and hydrogen isotope exchange activities, but did not change the para-H(2)/ortho-H(2) conversion activity. The spectroscopic properties of this mutant were totally different, especially in the reduced state in which a non-photosensitive nickel EPR spectrum was obtained.
Collapse
Affiliation(s)
- Sébastien Dementin
- Unité de Bioénergétique et Ingénierie des Protéines, Institut de Biologie Structurale et Microbiologie, Marseille, France
| | | | | | | | | | | | | | | |
Collapse
|
29
|
Casalot L, De Luca G, Dermoun Z, Rousset M, de Philip P. Evidence for a fourth hydrogenase in Desulfovibrio fructosovorans. J Bacteriol 2002; 184:853-6. [PMID: 11790758 PMCID: PMC139505 DOI: 10.1128/jb.184.3.853-856.2002] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A strain devoid of the three hydrogenases characterized for Desulfovibrio fructosovorans was constructed using marker exchange mutagenesis. As expected, the H(2)-dependent methyl viologen reduction activity of the strain was null, but physiological studies showed no striking differences between the mutated and wild-type strains. The H(+)-D(2) exchange activity measured in the mutated strain indicates the presence of a fourth hydrogenase in D. fructosovorans.
Collapse
Affiliation(s)
- Laurence Casalot
- Laboratoire de Bioénergétique et Ingénierie des Protéines, UPR 9036-CNRS, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 09, France
| | | | | | | | | |
Collapse
|
30
|
Lloyd JR, Macaskie LE. Chapter 11 Biochemical basis of microbe-radionuclide interactions. RADIOACTIVITY IN THE ENVIRONMENT 2002. [DOI: 10.1016/s1569-4860(02)80040-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
31
|
Coppi MV, Leang C, Sandler SJ, Lovley DR. Development of a genetic system for Geobacter sulfurreducens. Appl Environ Microbiol 2001; 67:3180-7. [PMID: 11425739 PMCID: PMC92998 DOI: 10.1128/aem.67.7.3180-3187.2001] [Citation(s) in RCA: 313] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Members of the genus Geobacter are the dominant metal-reducing microorganisms in a variety of anaerobic subsurface environments and have been shown to be involved in the bioremediation of both organic and metal contaminants. To facilitate the study of the physiology of these organisms, a genetic system was developed for Geobacter sulfurreducens. The antibiotic sensitivity of this organism was characterized, and optimal conditions for plating it at high efficiency were established. A protocol for the introduction of foreign DNA into G. sulfurreducens by electroporation was also developed. Two classes of broad-host-range vectors, IncQ and pBBR1, were found to be capable of replication in G. sulfurreducens. In particular, the IncQ plasmid pCD342 was found to be a suitable expression vector for this organism. When the information and novel methods described above were utilized, the nifD gene of G. sulfurreducens was disrupted by the single-step gene replacement method. Insertional mutagenesis of this key gene in the nitrogen fixation pathway impaired the ability of G. sulfurreducens to grow in medium lacking a source of fixed nitrogen. Expression of the nifD gene in trans complemented this phenotype. This paper constitutes the first report of genetic manipulation of a member of the Geobacter genus.
Collapse
Affiliation(s)
- M V Coppi
- Department of Microbiology, University of Massachusetts at Amherst, Amherst, Massachusetts 01003, USA
| | | | | | | |
Collapse
|
32
|
Rapp-Giles BJ, Casalot L, English RS, Ringbauer JA, Dolla A, Wall JD. Cytochrome c(3) mutants of Desulfovibrio desulfuricans. Appl Environ Microbiol 2000; 66:671-7. [PMID: 10653734 PMCID: PMC91879 DOI: 10.1128/aem.66.2.671-677.2000] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To explore the physiological role of tetraheme cytochrome c(3) in the sulfate-reducing bacterium Desulfovibrio desulfuricans G20, the gene encoding the preapoprotein was cloned, sequenced, and mutated by plasmid insertion. The physical analysis of the DNA from the strain carrying the integrated plasmid showed that the insertion was successful. The growth rate of the mutant on lactate with sulfate was comparable to that of the wild type; however, mutant cultures did not achieve the same cell densities. Pyruvate, the oxidation product of lactate, served as a poor electron source for the mutant. Unexpectedly, the mutant was able to grow on hydrogen-sulfate medium. These data support a role for tetraheme cytochrome c(3) in the electron transport pathway from pyruvate to sulfate or sulfite in D. desulfuricans G20.
Collapse
Affiliation(s)
- B J Rapp-Giles
- Biochemistry Department, University of Missouri-Columbia, Columbia, Missouri 65211, USA
| | | | | | | | | | | |
Collapse
|
33
|
Rousset M, Montet Y, Guigliarelli B, Forget N, Asso M, Bertrand P, Fontecilla-Camps JC, Hatchikian EC. [3Fe-4S] to [4Fe-4S] cluster conversion in Desulfovibrio fructosovorans [NiFe] hydrogenase by site-directed mutagenesis. Proc Natl Acad Sci U S A 1998; 95:11625-30. [PMID: 9751716 PMCID: PMC21691 DOI: 10.1073/pnas.95.20.11625] [Citation(s) in RCA: 131] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The role of the high potential [3Fe-4S]1+,0 cluster of [NiFe] hydrogenase from Desulfovibrio species located halfway between the proximal and distal low potential [4Fe-4S]2+,1+ clusters has been investigated by using site-directed mutagenesis. Proline 238 of Desulfovibrio fructosovorans [NiFe] hydrogenase, which occupies the position of a potential ligand of the lacking fourth Fe-site of the [3Fe-4S] cluster, was replaced by a cysteine residue. The properties of the mutant enzyme were investigated in terms of enzymatic activity, EPR, and redox properties of the iron-sulfur centers and crystallographic structure. We have shown on the basis of both spectroscopic and x-ray crystallographic studies that the [3Fe-4S] cluster of D. fructosovorans hydrogenase was converted into a [4Fe-4S] center in the P238 mutant. The [3Fe-4S] to [4Fe-4S] cluster conversion resulted in a lowering of approximately 300 mV of the midpoint potential of the modified cluster, whereas no significant alteration of the spectroscopic and redox properties of the two native [4Fe-4S] clusters and the NiFe center occurred. The significant decrease of the midpoint potential of the intermediate Fe-S cluster had only a slight effect on the catalytic activity of the P238C mutant as compared with the wild-type enzyme. The implications of the results for the role of the high-potential [3Fe-4S] cluster in the intramolecular electron transfer pathway are discussed.
Collapse
Affiliation(s)
- M Rousset
- Unité de Bioénergétique et Ingéniérie des Protéines, Institut de Biologie Structurale et Microbiologie, Centre National de la Recherche Scientifique, 31, Chemin Joseph Aiguier, 13402 Marseille CDX 20, France
| | | | | | | | | | | | | | | |
Collapse
|
34
|
Rousset M, Magro V, Forget N, Guigliarelli B, Belaich JP, Hatchikian EC. Heterologous expression of the Desulfovibrio gigas [NiFe] hydrogenase in Desulfovibrio fructosovorans MR400. J Bacteriol 1998; 180:4982-6. [PMID: 9733707 PMCID: PMC107529 DOI: 10.1128/jb.180.18.4982-4986.1998] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The ability of Desulfovibrio fructosovorans MR400 DeltahynABC to express the heterologous cloned [NiFe] hydrogenase of Desulfovibrio gigas was investigated. The [NiFe] hydrogenase operon from D. gigas, hynABCD, was cloned, sequenced, and introduced into D. fructosovorans MR400. A portion of the recombinant heterologous [NiFe] hydrogenase was totally matured, exhibiting catalytic and spectroscopic properties identical to those of the native D. gigas protein. A chimeric operon containing hynAB from D. gigas and hynC from D. fructosovorans placed under the control of the D. fructosovorans hynAp promoter was constructed and expressed in D. fructosovorans MR400. Under these conditions, the same level of activity was obtained as with the D. gigas hydrogenase operon.
Collapse
Affiliation(s)
- M Rousset
- Unité de Bioénergétique et Ingénierie des Protéines, IBSM, CNRS, 13402 Marseille Cedex 20, France
| | | | | | | | | | | |
Collapse
|