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Crystal structure of HypA, a nickel-binding metallochaperone for [NiFe] hydrogenase maturation. J Mol Biol 2009; 394:448-59. [PMID: 19769985 DOI: 10.1016/j.jmb.2009.09.030] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2009] [Revised: 08/27/2009] [Accepted: 09/14/2009] [Indexed: 11/23/2022]
Abstract
HypA is one of the auxiliary proteins involved in the maturation of [NiFe] hydrogenases. By an unknown mechanism, HypA functions as a metallochaperone in the insertion of the Ni atom into hydrogenases. We have determined the crystal structures of HypA from Thermococcus kodakaraensis KOD1 in both monomeric and dimeric states. The structure of the HypA monomer consists of Ni- and Zn-binding domains. The relative arrangement of the two metal-binding domains has been shown to be associated with local conformations of the conserved Ni-binding motif, suggesting a communication between the Ni- and Zn-binding sites. The HypA dimer has been shown to be stabilized by unexpected domain swapping through archaea-specific linker helices. In addition, the hexameric structure of HypA is formed in the crystal packing. Several hydrogen bonds and hydrophobic interactions stabilize the hexamer interface. These findings suggest the functional diversity of HypA proteins.
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Ghirardi ML, Posewitz MC, Maness PC, Dubini A, Yu J, Seibert M. Hydrogenases and hydrogen photoproduction in oxygenic photosynthetic organisms. ANNUAL REVIEW OF PLANT BIOLOGY 2007; 58:71-91. [PMID: 17150028 DOI: 10.1146/annurev.arplant.58.032806.103848] [Citation(s) in RCA: 186] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The photobiological production of H2 gas, using water as the only electron donor, is a property of two types of photosynthetic microorganisms: green algae and cyanobacteria. In these organisms, photosynthetic water splitting is functionally linked to H(2) production by the activity of hydrogenase enzymes. Interestingly, each of these organisms contains only one of two major types of hydrogenases, [FeFe] or [NiFe] enzymes, which are phylogenetically distinct but perform the same catalytic reaction, suggesting convergent evolution. This idea is supported by the observation that each of the two classes of hydrogenases has a different metallo-cluster, is encoded by entirely different sets of genes (apparently under the control of different promoter elements), and exhibits different maturation pathways. The genetics, biosynthesis, structure, function, and O2 sensitivity of these enzymes have been the focus of extensive research in recent years. Some of this effort is clearly driven by the potential for using these enzymes in future biological or biohybrid systems to produce renewable fuel or in fuel cell applications.
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Tamagnini P, Axelsson R, Lindberg P, Oxelfelt F, Wünschiers R, Lindblad P. Hydrogenases and hydrogen metabolism of cyanobacteria. Microbiol Mol Biol Rev 2002; 66:1-20, table of contents. [PMID: 11875125 PMCID: PMC120778 DOI: 10.1128/mmbr.66.1.1-20.2002] [Citation(s) in RCA: 375] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cyanobacteria may possess several enzymes that are directly involved in dihydrogen metabolism: nitrogenase(s) catalyzing the production of hydrogen concomitantly with the reduction of dinitrogen to ammonia, an uptake hydrogenase (encoded by hupSL) catalyzing the consumption of hydrogen produced by the nitrogenase, and a bidirectional hydrogenase (encoded by hoxFUYH) which has the capacity to both take up and produce hydrogen. This review summarizes our knowledge about cyanobacterial hydrogenases, focusing on recent progress since the first molecular information was published in 1995. It presents the molecular knowledge about cyanobacterial hupSL and hoxFUYH, their corresponding gene products, and their accessory genes before finishing with an applied aspect--the use of cyanobacteria in a biological, renewable production of the future energy carrier molecular hydrogen. In addition to scientific publications, information from three cyanobacterial genomes, the unicellular Synechocystis strain PCC 6803 and the filamentous heterocystous Anabaena strain PCC 7120 and Nostoc punctiforme (PCC 73102/ATCC 29133) is included.
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Affiliation(s)
- Paula Tamagnini
- Department of Botany, Institute for Molecular and Cell Biology, University of Porto, 4150-180 Porto, Portugal, Department of Physiological Botany, EBC, Uppsala University, SE-752 36 Uppsala, Sweden
| | - Rikard Axelsson
- Department of Botany, Institute for Molecular and Cell Biology, University of Porto, 4150-180 Porto, Portugal, Department of Physiological Botany, EBC, Uppsala University, SE-752 36 Uppsala, Sweden
| | - Pia Lindberg
- Department of Botany, Institute for Molecular and Cell Biology, University of Porto, 4150-180 Porto, Portugal, Department of Physiological Botany, EBC, Uppsala University, SE-752 36 Uppsala, Sweden
| | - Fredrik Oxelfelt
- Department of Botany, Institute for Molecular and Cell Biology, University of Porto, 4150-180 Porto, Portugal, Department of Physiological Botany, EBC, Uppsala University, SE-752 36 Uppsala, Sweden
| | - Röbbe Wünschiers
- Department of Botany, Institute for Molecular and Cell Biology, University of Porto, 4150-180 Porto, Portugal, Department of Physiological Botany, EBC, Uppsala University, SE-752 36 Uppsala, Sweden
| | - Peter Lindblad
- Department of Botany, Institute for Molecular and Cell Biology, University of Porto, 4150-180 Porto, Portugal, Department of Physiological Botany, EBC, Uppsala University, SE-752 36 Uppsala, Sweden
- Corresponding author. Mailing address: Department of Physiological Botany, EBC, Uppsala University, Villavägen 6, SE-752 36 Uppsala, Sweden. Phone and fax: 46-18-471-28-26. E-mail:
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Hansel A, Axelsson R, Lindberg P, Troshina OY, Wünschiers R, Lindblad P. Cloning and characterisation of a hyp gene cluster in the filamentous cyanobacterium Nostoc sp. strain PCC 73102. FEMS Microbiol Lett 2001; 201:59-64. [PMID: 11445168 DOI: 10.1111/j.1574-6968.2001.tb10733.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Maturation of [NiFe]-hydrogenases requires the action of several groups of accessory genes. Homologues of one group of these genes, the so-called hyp genes, putatively encoding proteins participating in the formation of an active uptake hydrogenase in the filamentous, heterocyst-forming cyanobacterium Nostoc PCC 73102, were cloned. The cluster, consisting of hypF, hypC, hypD, hypE, hypA, and hypB, is located 3.8 kb upstream from the uptake hydrogenase-encoding hupSL. Gene expression analyses show that these hyp genes are, like hupL, transcribed under N(2)-fixing but not under non-N(2)-fixing growth conditions. Furthermore, the six hyp genes are transcribed together with an open reading frame upstream of hypF, as a single mRNA. Analysis of the DNA region upstream of the experimentally determined transcriptional start site revealed putative -10 and -35 sequence elements and putative binding sites for the global nitrogen regulator NtcA.
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Affiliation(s)
- A Hansel
- Department of Physiological Botany, EBC, Uppsala University, Sweden
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Teplova M, Tereshko V, Sanishvili R, Joachimiak A, Bushueva T, Anderson WF, Egli M. The structure of the yrdC gene product from Escherichia coli reveals a new fold and suggests a role in RNA binding. Protein Sci 2000; 9:2557-66. [PMID: 11206077 PMCID: PMC2144518 DOI: 10.1110/ps.9.12.2557] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The yrdC family of genes codes for proteins that occur both independently and as a domain in proteins that have been implicated in regulation. An example for the latter case is the sua5 gene from yeast. SuaS was identified as a suppressor of a translation initiation defect in cytochrome c and is required for normal growth in yeast (Na JG, Pinto I, Hampsey M, 1992, Genetics 11:791-801). However, the function of the Sua5 protein remains unknown; Sua5 could act either at the transcriptional or the posttranscriptional levels to compensate for an aberrant translation start codon in the cyc gene. To potentially learn more about the function of YrdC and proteins featuring this domain, the crystal structure of the YrdC protein from Escherichia coli was determined at a resolution of 2.0 A. YrdC adopts a new fold with no obvious similarity to those of other proteins with known three-dimensional (3D) structure. The protein features a large concave surface on one side that exhibits a positive electrostatic potential. The dimensions of this depression, its curvature, and the fact that conserved basic amino acids are located at its floor suggest that YrdC may be a nucleic acid binding protein. An investigation of YrdC's binding affinities for single- and double-stranded RNA and DNA fragments as well as tRNAs demonstrates that YrdC binds preferentially to double-stranded RNA. Our work provides evidence that 3D structures of functionally uncharacterized gene products with unique sequences can yield novel folds and functional insights.
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Affiliation(s)
- M Teplova
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235, USA
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Van Soom C, Lerouge I, Vanderleyden J, Ruiz-Argüeso T, Palacios JM. Identification and characterization of hupT, a gene involved in negative regulation of hydrogen oxidation in Bradyrhizobium japonicum. J Bacteriol 1999; 181:5085-9. [PMID: 10438783 PMCID: PMC94000 DOI: 10.1128/jb.181.16.5085-5089.1999] [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
The Bradyrhizobium japonicum hupT gene was sequenced, and its gene product was found to be homologous to NtrB-like histidine kinases. A hupT mutant expresses higher levels of hydrogenase activity than the wild-type strain under hydrogenase-inducing conditions (i.e., microaerobiosis plus hydrogen, or symbiosis), whereas in noninduced hupT cells, hupSL expression is derepressed but does not lead to hydrogenase activity. We conclude that HupT is involved in the repression of HupSL synthesis at the transcriptional level but that enzymatic activation requires inducing conditions.
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Affiliation(s)
- C Van Soom
- F. A. Janssens Laboratory of Genetics, Katholieke Universiteit Leuven, B-3001 Heverlee, Belgium
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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.
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Affiliation(s)
- M Rousset
- Unité de Bioénergétique et Ingénierie des Protéines, IBSM, CNRS, 13402 Marseille Cedex 20, France
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