The dcr gene family of Desulfovibrio: Implications from the sequence of dcrH and phylogenetic comparison with other mcp genes

Deckers, Harm M.; Voordouw, Gerrit

doi:10.1007/bf00393566

Cited by 15 publications

(13 citation statements)

References 39 publications

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“…M. tuberculosis also encodes a putative receptor-type cyclase, similar in topology to the eukaryotic receptor guanylyl cyclases, implying the ability to sense an extracellular signal. The extracellular domain of this protein (Rv2435c) has homology to a chemotaxis receptor in Desulfovibrio vulgaris for which the ligand is unknown (Deckers and Voordouw 1996). Also present in M. tuberculosis were putative integral membrane cyclases similar in topology to the multicellular eukaryotic adenylyl cyclases.…”

Section: Tuberculosismentioning

confidence: 99%

Functional Classification of cNMP-binding Proteins and Nucleotide Cyclases with Implications for Novel Regulatory Pathways in Mycobacterium tuberculosis

McCue¹,

McDonough²,

Lawrence³

2000

Genome Res.

133

162

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We have analyzed the cyclic nucleotide (cNMP)-binding protein and nucleotide cyclase superfamilies using Bayesian computational methods of protein family identification and classification. In addition to the known cNMP-binding proteins (cNMP-dependent kinases, cNMP-gated channels, cAMP-guanine nucleotide exchange factors, and bacterial cAMP-dependent transcription factors), new functional groups of cNMP-binding proteins were identified, including putative ABC-transporter subunits, translocases, and esterases. Classification of the nucleotide cyclases revealed subtle differences in sequence conservation of the active site that distinguish the five classes of cyclases: the multicellular eukaryotic adenylyl cyclases, the eukaryotic receptor-type guanylyl cyclases, the eukaryotic soluble guanylyl cyclases, the unicellular eukaryotic and prokaryotic adenylyl cyclases, and the putative prokaryotic guanylyl cyclases. Phylogenetic distribution of the cNMP-binding proteins and cyclases was analyzed, with particular attention to the 22 complete archaeal and eubacterial genome sequences. Mycobacterium tuberculosis H37Rv and Synechocystis PCC6803 were each found to encode several more putative cNMP-binding proteins than other prokaryotes; many of these proteins are of unknown function. M. tuberculosis also encodes several more putative nucleotide cyclases than other prokaryotic species.Signal transduction pathways control many critical cellular processes, including chemotaxis, differentiation, proliferation, and apoptosis. For example, signal transduction pathways are necessary for bacterial pathogens to sense and respond to host environments, cellular differentiation during embryogenesis, conductance of nerve impulses, and cell cycle control. Disruption of these pathways can result in neoplasia, arteriosclerosis, neurological and developmental abnormalities, and cell death. The most common mechanisms of signal transduction include the phosphorylation or dephosphorylation of effector proteins by kinases and phosphatases, respectively, and the production of second messengers. Cyclic nucleotides were first recognized as second messengers 40 years ago. Such diverse molecules as (p)ppGpp, Ca 2+ , inositol triphosphate, and diacylglycerol have also been recognized as second messengers since then.The cyclic nucleotides adenosine 3Ј,5Ј-cyclic monophosphate (cAMP) and guanosine 3Ј,5Ј-cyclic monophosphate (cGMP) are key universal second messengers, mediating cellular functions in organisms as phylogenetically diverse as Escherichia coli and Homo sapiens. Intracellular concentrations of cyclic nucleotides (cNMPs) are controlled by regulation of their relative rates of synthesis, excretion, and degradation (Botsford and Harman 1992;). The nucleotide cyclases (adenylyl and guanylyl cyclase), the cNMP phosphodiesterases, and the cyclic nucleotide effector proteins (cNMP-binding proteins) have been particularly intense areas of signal transduction research, providing detailed studies of these proteins (for reviews, see Kolb et

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Section: Tuberculosismentioning

confidence: 99%

Functional Classification of cNMP-binding Proteins and Nucleotide Cyclases with Implications for Novel Regulatory Pathways in Mycobacterium tuberculosis

McCue¹,

McDonough²,

Lawrence³

2000

Genome Res.

133

162

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“…Furthermore, the D. vulgaris genome encodes a family of genes for methyl-accepting chemotaxis proteins (MCPs) (Deckers and Voordouw 1996), including those for DcrA (DVU3182) (Fu et al 1994) and DcrH (DVU3155) (Xiong et al 2000), proposed to be involved in sensing the oxygen concentration or redox potential of the environment (Dolla et al 1992;Fu et al 1994). …”

Section: Introductionmentioning

confidence: 99%

Transcriptional response of Desulfovibrio vulgaris Hildenborough to oxidative stress mimicking environmental conditions

Pereira

Xavier

et al. 2007

Arch Microbiol

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Sulphate-reducing bacteria are anaerobes readily found in oxic-anoxic interfaces. Multiple defence pathways against oxidative conditions were identified in these organisms and proposed to be differentially expressed under different concentrations of oxygen, contributing to their ability to survive oxic conditions. In this study, Desulfovibrio vulgaris Hildenborough cells were exposed to the highest concentration of oxygen that sulphate-reducing bacteria are likely to encounter in natural habitats, and the global transcriptomic response was determined. 307 genes were responsive, with cellular roles in energy metabolism, protein fate, cell envelope and regulatory functions, including multiple genes encoding heat shock proteins, peptidases and proteins with heat shock promoters. Of the oxygen reducing mechanisms of D. vulgaris only the periplasmic hydrogen-dependent mechanism is up-regulated, involving the [NiFeSe] hydrogenase, formate dehydrogenase(s) and the Hmc membrane complex. The oxidative defence response concentrates on damage repair by metal-free enzymes. . These data, together with the down regulation of the Fur operon, which restricts the availability of iron, and the lack of response of the PerR operon, suggest that a major effect of this oxygen stress is the inactivation and/or degradation of multiple metalloproteins present in D. vulgaris as a consequence of oxidative damage to their metal clusters.

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“…Whether one or both of these putative promoters function in the cell under different growth conditions remains to be seen. In the case of another chemolithotrophic bacterium, D. vulgaris Hildenborough, which possesses two completely described genes coding for MCPs, dcrA and dcrH, a putative 70 promoter upstream of the first AUG codon rather than a 28 -type promoter has been reported (12,13,15). On the other hand, the mcp and che genes from E. coli possess only a 28 promoter (6,21,32).…”

Section: Discussionmentioning

confidence: 99%

“…Anomalous migrations have also been observed for HtrI, an MCP from Halobacterium salinarium with an acidic nature and a slower migration under similar SDS-PAGE conditions (50). Nevertheless, the molecular mass of LcrI is in the size range described for most MCPs, since they possess between 512 and 668 residues, except protein DcrH from D. vulgaris Hildenborough, which contains 959 amino acids (13).…”

Section: Sequence Of the Lcri Gene And Properties Of The Lcri Proteinmentioning

confidence: 91%

Molecular Cloning, Sequencing, and Expression of a Chemoreceptor Gene from Leptospirillum ferrooxidans

Delgado¹,

Toledo

Jerez³

1998

Appl Environ Microbiol

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We have cloned and sequenced a 2,262-bp chromosomal DNA fragment from the chemolithoautotrophic acidophilic bacteriumLeptospirillum ferrooxidans. This DNA contained an open reading frame for a 577-amino-acid protein showing several characteristics of the bacterial chemoreceptors and, therefore, we named this gene lcrI for Leptospirillumchemotaxis receptor I. This is the first sequence reported for a gene from L. ferrooxidans encoding a protein. ThelcrI gene showed both ς28-like and ς70-like putative promoters. The LcrI deduced protein contained two hydrophobic regions most likely corresponding to the two transmembrane regions present in all of the methyl-accepting chemotaxis proteins (MCPs) which make them fold with both periplasmic and cytoplasmic domains. We have proposed a cytoplasmic domain for LcrI, which also contains the highly conserved domain (HCD region), present in all of the chemotactic receptors, and two probable methylation sites. The in vitro expression of a DNA plasmid containing the 2,262-bp fragment showed the synthesis of a 58-kDa protein which was immunoprecipitated by antibodies against the Tar protein (an MCP fromEscherichia coli), confirming some degree of antigenic conservation. In addition, this 58-kDa protein was expressed inE. coli, being associated with its cytoplasmic membrane fraction. It was not possible to determine a chemotactic receptor function for LcrI expressed in E. coli. This was most likely due to the fact that the periplasmic pH of E. coli, which differs by 3 to 4 pH units from that of acidophilic chemolithotrophs, does not allow the right conformation for the LcrI periplasmic domain.

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The dcr gene family of Desulfovibrio: Implications from the sequence of dcrH and phylogenetic comparison with other mcp genes

Cited by 15 publications

References 39 publications

Functional Classification of cNMP-binding Proteins and Nucleotide Cyclases with Implications for Novel Regulatory Pathways in Mycobacterium tuberculosis

Functional Classification of cNMP-binding Proteins and Nucleotide Cyclases with Implications for Novel Regulatory Pathways in Mycobacterium tuberculosis

Transcriptional response of Desulfovibrio vulgaris Hildenborough to oxidative stress mimicking environmental conditions

Molecular Cloning, Sequencing, and Expression of a Chemoreceptor Gene from Leptospirillum ferrooxidans

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