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Hsieh YC, Chia TS, Fun HK, Chen CJ. Crystal structure of dimeric flavodoxin from Desulfovibrio gigas suggests a potential binding region for the electron-transferring partner. Int J Mol Sci 2013; 14:1667-83. [PMID: 23322018 PMCID: PMC3565340 DOI: 10.3390/ijms14011667] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Revised: 12/03/2012] [Accepted: 12/25/2012] [Indexed: 11/16/2022] Open
Abstract
Flavodoxins, which exist widely in microorganisms, have been found in various pathways with multiple physiological functions. The flavodoxin (Fld) containing the cofactor flavin mononucleotide (FMN) from sulfur-reducing bacteria Desulfovibrio gigas (D. gigas) is a short-chain enzyme that comprises 146 residues with a molecular mass of 15 kDa and plays important roles in the electron-transfer chain. To investigate its structure, we purified this Fld directly from anaerobically grown D. gigas cells. The crystal structure of Fld, determined at resolution 1.3 Å, is a dimer with two FMN packing in an orientation head to head at a distance of 17 Å, which generates a long and connected negatively charged region. Two loops, Thr59-Asp63 and Asp95-Tyr100, are located in the negatively charged region and between two FMN, and are structurally dynamic. An analysis of each monomer shows that the structure of Fld is in a semiquinone state; the positions of FMN and the surrounding residues in the active site deviate. The crystal structure of Fld from D. gigas agrees with a dimeric form in the solution state. The dimerization area, dynamic characteristics and structure variations between monomers enable us to identify a possible binding area for its functional partners.
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Affiliation(s)
- Yin-Cheng Hsieh
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan; E-Mail:
| | - Tze Shyang Chia
- X-ray Crystallography Unit, School of Physics, Universiti Sains Malaysia, 11800 USM, Penang, Malaysia; E-Mails: (T.S.C.); (H.-K.F.)
| | - Hoong-Kun Fun
- X-ray Crystallography Unit, School of Physics, Universiti Sains Malaysia, 11800 USM, Penang, Malaysia; E-Mails: (T.S.C.); (H.-K.F.)
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia; E-Mail:
| | - Chun-Jung Chen
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan; E-Mail:
- Department of Physics, National Tsing Hua University, Hsinchu 30043, Taiwan
- Institute of Biotechnology, National Cheng Kung University, Tainan City 70101, Taiwan
- University Center for Bioscience and Biotechnology, National Cheng Kung University, Tainan City 70101, Taiwan
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +886-3-5780281 (ext. 7330); Fax: +886-3-5783813
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Broco M, Marques A, Oliveira S, Rodrigues-Pousada C. Characterisation of the 11 Kb DNA region adjacent to the gene encodingDesulfovibrio gigasflavoredoxin. ACTA ACUST UNITED AC 2009; 16:207-16. [PMID: 16147877 DOI: 10.1080/10425170500088296] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Flavoredoxin is an FMN binding protein that functions as an electron carrier in the sulphate metabolism of Desulfovibrio gigas. The neighbouring DNA regions of the gene encoding flavoredoxin were sequenced and characterised. Transcript analysis of the flavoredoxin gene resulted in a positive band corresponding to the size of the coding region, suggesting that flavoredoxin is encoded by a monocystronic unit, as previously suggested by sequence analysis. Analysis of the adjacent DNA regions revealed several interesting genes. The sequenced DNA regions contain nine open reading frames (ORFs) organised in two polycystronic and two monocystronic units. These genes encode proteins involved in different metabolic pathways, namely in DNA methylation, tRNA and rRNA modification, mRNA metabolism, cell division, CoA synthesis and lipoprotein transport across the membrane.
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Affiliation(s)
- Manuela Broco
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida República (EAN), Oeiras, Portugal
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Pauleta SR, Duarte AG, Carepo MS, Pereira AS, Tavares P, Moura I, Moura JJG. NMR assignment of the apo-form of a Desulfovibrio gigas protein containing a novel Mo-Cu cluster. Biomol NMR Assign 2007; 1:81-83. [PMID: 19636833 DOI: 10.1007/s12104-007-9022-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2007] [Accepted: 05/06/2007] [Indexed: 05/28/2023]
Abstract
We report the 98% assignment of the apo-form of an orange protein, containing a novel Mo-Cu cluster isolated from Desulfovibrio gigas. This protein presents a region where backbone amide protons exchange fast with bulk solvent becoming undetectable. These residues were assigned using 13C-detection experiments.
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Affiliation(s)
- Sofia R Pauleta
- REQUIMTE/CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica 2829-516, Portugal.
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Félix R, Rodrigues R, Machado P, Oliveira S, Rodrigues-Pousada C. A chemotaxis operon in the bacterium Desulfovibrio gigas is induced under several growth conditions. ACTA ACUST UNITED AC 2006; 17:56-64. [PMID: 16753818 DOI: 10.1080/10425170500412488] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
The chemosensory system of bacteria controls their motility and behaviour in different environments. In the present study, we report the identification of the first chemotaxis operon in Desulfovibrio gigas. Amino acid sequence analysis revealed seven coding regions for polypeptides with a high similarity to chemotaxis proteins from other organisms. D. gigas chemotaxis operon has a similar genetic organisation to chemotaxis operons found in the sequenced genomes of Desulfovibrio desulfuricans and Desulfovibrio vulgaris. Control of gene expression was assessed by real-time reverse transcription-PCR in cells grown under different conditions. mRNA levels were enhanced in the presence of thiosulfate and sulfite and decreased upon exposure to NO. No effect was observed in the presence of O2, NaNO2, pyruvate or fumarate. These results show that the expression of the chemotaxis operon is enhanced in the presence of thiosulfate and sulfite indicating that under these compounds a chemotactic response seems to be triggered in D. gigas.
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Affiliation(s)
- Rute Félix
- Instituto de Tecnologia Química e Biológica, Apartado 127, Oeiras, 2780-901, Portugal
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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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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Affiliation(s)
- Rute Rodrigues
- Instituto de Tecnologia Química e Biológica, Apartado 127, 2780-901 Oeiras, Portugal
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Machado P, Félix R, Rodrigues R, Oliveira S, Rodrigues-Pousada C. Characterization and expression analysis of the cytochrome bd oxidase operon from Desulfovibrio gigas. Curr Microbiol 2006; 52:274-81. [PMID: 16550467 DOI: 10.1007/s00284-005-0165-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2005] [Accepted: 11/14/2005] [Indexed: 11/27/2022]
Abstract
Although classified as anaerobic, Desulfovibrio gigas contains a functional canonical membrane respiratory chain, including a cytochrome bd quinol oxidase as its terminal element. In the present study, we report the identification of the operon cydAB encoding the two subunits of cytochrome bd from this bacterium. Two hypothetical promoter regions and sequences resembling transcriptional regulators-binding sites have been identified. Amino acid sequence analysis revealed a high similarity to cytochrome bd from other organisms, presenting the conserved residues typical from these proteins. Reverse transcription polymerase chain reaction (RT-PCR) and Northern blot analysis confirmed the operon transcription. Gene expression was assessed by real-time RT-PCR in cells grown in different media and under exposure to oxygen and nitric oxide. mRNA levels were slightly enhanced in the presence of 150 microM: NO. However, in the presence of 10 microM: NO, a decrease was observed of the steady-state population of cydAB mRNA. No considerable effect was observed in the presence of fumarate/sulfate medium, 60 microM: O2 or 10 microM: NO.
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Affiliation(s)
- Patrícia Machado
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Apartado 127, 2780-901, Oeiras, Portugal
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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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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
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Bursakov SA, Gavel OY, Di Rocco G, Lampreia J, Calvete J, Pereira AS, Moura JJG, Moura I. Antagonists Mo and Cu in a heterometallic cluster present on a novel protein (orange protein) isolated from Desulfovibrio gigas. J Inorg Biochem 2005; 98:833-40. [PMID: 15134929 DOI: 10.1016/j.jinorgbio.2003.12.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2003] [Revised: 11/14/2003] [Accepted: 12/02/2003] [Indexed: 10/26/2022]
Abstract
An orange-coloured protein (ORP) isolated from Desulfovibrio gigas, a sulphate reducer, has been previously shown by extended X-ray absorption fine structure (EXAFS) to contain a novel mixed-metal sulphide cluster of the type [S(2)MoS(2)CuS(2)MoS(2)] [J. Am. Chem. Soc. 122 (2000) 8321]. We report here the purification and the biochemical/spectroscopic characterisation of this novel protein. ORP is a soluble monomeric protein (11.8 kDa). The cluster is non-covalently bound to the polypeptide chain. The presence of a MoS(4)(2-) moiety in the structure of the cofactor contributes with a quite characteristic UV-Vis spectra, exhibiting an orange colour, with intense absorption peaks at 480 and 338 nm. Pure ORP reveals an Abs(480)/Abs(338) ratio of 0.535. The gene sequence coding for ORP as well as the amino acid sequence was determined. The putative biological function of ORP is discussed.
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Affiliation(s)
- S A Bursakov
- REQUIMTE, Departamento de Química, Centro de Química Fina e Biotecnologia, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica 2829-516, Portugal.
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Abstract
Despite their high sequence homology, rubredoxins from Desulfovibrio gigas and D. desulfuricans are stabilized to very different extents by compatible solutes such as diglycerol phosphate, the major osmolyte in the hyperthermophilic archaeon Archaeoglobus fulgidus[Lamosa P, Burke A, Peist R, Huber R, Liu M Y, Silva G, Rodrigues-Pousada C, LeGall J, Maycock C and Santos H (2000) Appl Environ Microbiol66, 1974-1979]. The principal structural difference between these two proteins is the absence of the hairpin loop in the rubredoxin from D. desulfuricans. Therefore, mutants of D. gigas rubredoxin bearing deletions in the loop region were constructed to investigate the importance of this structural feature on protein intrinsic stability, as well as on its capacity to undergo stabilization by compatible solutes. The three-dimensional structure of the mutant bearing the largest deletion, Delta17/29, was determined by 1H-NMR, demonstrating that, despite the drastic deletion, the main structural features were preserved. The dependence of the NH chemical shifts on temperature and solute concentration (diglycerol phosphate or mannosylglycerate) provide evidence of subtle conformational changes induced by the solute. The kinetic stability (as assessed from the absorption decay at 494 nm) of six mutant rubredoxins was determined at 90 degrees C and the stabilizing effect exerted by both solutes was assessed. The extent of protection conferred by each solute was highly dependent on the specific mutant examined: while the half-life for iron release in the wild-type D. gigas rubredoxin increased threefold in the presence of 0.1 M diglycerol phosphate, mutant Delta23/29 was destabilized. This study provides evidence for solute-induced compaction of the protein structure and occurrence of weak, specific interactions with the protein surface. The relevance of these findings to our understanding of the molecular basis for protein stabilization is discussed.
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Affiliation(s)
- Tiago M Pais
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Portugal
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