Divergence in gene regulation in Shewanella baltica strains
Ontology highlight
ABSTRACT:
ORGANISM(S): Shewanella baltica
PROVIDER: GSE100228 | GEO | 2017/12/15
SECONDARY ACCESSION(S): PRJNA391129
REPOSITORIES: GEO
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Project description:CGH of 46 Shewanella baltica strains using customized oligonucleotide microarrays
2019-03-31 | GSE123978 | GEO
Project description:Shewanella spp. possess a broad respiratory versatility, which contributes to the occupation of hypoxic/anoxic environmental or host-associated niches. Here we observed a strain-specific induction of biofilm formation in response to supplementation with the anaerobic electron acceptors dimethyl sulfoxide (DMSO) and nitrate in a panel of Shewanella algae isolates. The respiration-driven biofilm response is not observed in DMSO and nitrate reductase deletion mutants of the type strain S. algae CECT 5071, and can be restored upon complementation with the corresponding reductase operon(s) but not by an operon containing a catalytically inactive nitrate reductase. The distinct transcriptional changes, proportional to the effect of these compounds on biofilm formation, include cyclic di-GMP (c-di-GMP) turnover genes. In support, ectopic expression of the c-di-GMP phosphodiesterase YhjH of Salmonella Typhimurium but not its catalytically inactive variant decreased biofilm formation. The respiration-dependent biofilm response of S. algae may permit differential colonization of environmental or host niches.
2020-12-05 | GSE133627 | GEO
Project description:Comparisson of expression profiling of a etrA deletion mutant strain (experimental sample) with that of the wild type Shewanella oneidensis MR-1 strain to assess global direct/indirect genetic regulation EtrA in Shewanella oneidensis MR-1 shares 73.6% and 50.8% amino acid sequence identity with the oxygen-sensing regulator Fnr in E. coli and Anr in Pseudomonas aeruginosa, respectively; however, its regulatory role of anaerobic metabolism in Shewanella spp. is complex and not well understood. Whole-genome expression profiling using a etrA gene deletion mutant as the experimental sample and the wild type strain as the reference, determine that EtrA fine-tunes the expression of genes involved in various anaerobic metabolic pathways, including nitrate, fumarate and dimethyl sulfoxide reduction. Moreover, genes involved in prophage activation and and genes implicated in aerobic metabolism were also differentially expressed. In contrast to previous studies that attributed a minor regulatory role to EtrA in Shewanella spp., this study demonstrates that EtrA acts as a global transcriptional regulator and cofers physiological advantages to the strain under certain growth conditions.
2011-01-29 | GSE26935 | GEO
Project description:Niche partitioning and sequence evolution drive genomic and phenotypic divergence, which ultimately leads to bacterial diversification. This study investigated the genomic composition of two Shewanella baltica clades previously identified through multilocus sequencing typing and recovered from the redox transition zone in the central Baltic Sea. Comparative genomic analysis revealed significantly higher interclade than intraclade genomic dissimilarity and that a subset of genes present in clade A were associated with potential adaptation to respiration of sulfur compounds present in the redox transition zone. The transcriptomic divergence between two representative strains of clades A and D, OS185 and OS195, was also characterized and revealed marked regulatory differences. We found that both the transcriptional divergence of shared genes and expression of strain-specific genes led to differences in regulatory patterns between strains that correlate with environmental redox niches. For instance, under anoxic conditions of respiratory nitrate ammonification, OS185-the strain isolated from a nitrate-rich environment-upregulated nearly twice the number of shared genes upregulated by OS195-the strain isolated from an H2S-containing anoxic environment. Conversely, OS195 showed stronger induction of strain-specific genes, especially those associated with sulfur compound respiration, under thiosulfate-reducing conditions. A positive association between the level of transcriptional divergence and the level of sequence divergence for shared genes was also noted. Our results provide further support for the hypothesis that genomic changes impacting transcriptional regulation play an important role in the diversification of ecologically distinct populations.IMPORTANCE This study examined potential mechanisms through which co-occurring Shewanella baltica strains diversified to form ecologically distinct populations. At the time of isolation, the strains studied composed the major fraction of culturable nitrate-reducing communities in the Baltica Sea. Analysis of genomic content of 13 S. baltica strains from two clades representing different ecotypes demonstrated that one clade specifically possesses a number of genes that could favor successful adaptation to respire sulfur compounds in the portion of the water column from which these strains were isolated. In addition, transcriptional profiling of fully sequenced strains representative of these two clades, OS185 and OS195, under oxygen-, nitrate-, and thiosulfate-respiring conditions demonstrated that the strains exhibit relatively similar transcriptional responses during aerobic growth but more-distinct transcriptional responses under nitrate- and thiosulfate-respiring conditions. Results from this study provide insights into how genomic and gene regulatory diversification together impacted the redox specialization of the S. baltica strains.
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Project description:Anaerobic respiration in the metal reducer Shewanella oneidensis MR-1, unlike other bacteria, is regulated by the cAMP receptor protein, CRP. Three putative genes, cyaA, cyaB, and cyaC, predicted to encode class I, class IV, and class III adenylate cyclases respectively, have been identified in the genome sequence of this bacterium. Functional validation through complementation of an E. coli cya mutant confirmed that these genes encode proteins with adenylate cyclase activities. Chromosomal deletion of either cyaA or cyaB did not affect anaerobic respiration with fumarate, DMSO, or Fe(III), whereas the deletion of cyaC caused deficiencies in respiration with DMSO and Fe(III), and to a lesser extent with fumarate. A phenotype similar to that of a crp mutant, which lacks the ability to grow anaerobically with DMSO, fumarate, and Fe(III), was obtained when both cyaA and cyaC were deleted. Microarray analysis of gene expression in the crp and the cyaC mutants revealed the involvement of both genes in the regulation of key respiratory pathways that include DMSO, fumarate, and Fe(III) reduction. Additionally, several genes associated with plasmid replication, flagella biosynthesis, and electron transport, were differentially expressed in the cyaC mutant, but not in the crp mutant. Our results indicated that CyaC plays a major role in regulating anaerobic respiration, and may contribute to additional signaling pathways independent of CRP. To explore the roles of CyaC and CRP in the regulation of anaerobic respiration in Shewanella oneidensis MR-1, the genome-wide transcriptome profiles of ÎcyaC and Îcrp mutants were compared to those of the wild type. Given the growth deficiencies displayed by Îcrp and ÎcyaC under anaerobic conditions, all strains were cultured in chemostats under O2 limitation. Since both Îcrp and ÎcyaC strains are not impaired in aerobic respiration, oxygen-limited conditions provided the means to maintain equal growth rates (0.06 h-1) among the mutant and wild-type strains thus eliminating the effect of growth on the overall transcriptome profiles. At the same time, while growing aerobically, the cells decreased dissolved O2 concentration in the medium below the detection threshold (DOTâ¤1%) allowing for the expression of anaerobic respiratory genes. The latter was confirmed by the reduction of fumarate by the wild-type culture which produced stoichiometric amounts of succinate under O2-limited conditions. The optical density (OD600) of the wild type, ÎcyaC, and Îcrp chemostat cultures used for transcriptome profiling was 0.50, 0.45 and 0.40, respectively. All the experiments were carried out in duplicate.
2010-06-19 | E-GEOD-15657 | biostudies-arrayexpress
Project description:Anaerobic respiration in the metal reducer Shewanella oneidensis MR-1, unlike other bacteria, is regulated by the cAMP receptor protein, CRP. Three putative genes, cyaA, cyaB, and cyaC, predicted to encode class I, class IV, and class III adenylate cyclases respectively, have been identified in the genome sequence of this bacterium. Functional validation through complementation of an E. coli cya mutant confirmed that these genes encode proteins with adenylate cyclase activities. Chromosomal deletion of either cyaA or cyaB did not affect anaerobic respiration with fumarate, DMSO, or Fe(III), whereas the deletion of cyaC caused deficiencies in respiration with DMSO and Fe(III), and to a lesser extent with fumarate. A phenotype similar to that of a crp mutant, which lacks the ability to grow anaerobically with DMSO, fumarate, and Fe(III), was obtained when both cyaA and cyaC were deleted. Microarray analysis of gene expression in the crp and the cyaC mutants revealed the involvement of both genes in the regulation of key respiratory pathways that include DMSO, fumarate, and Fe(III) reduction. Additionally, several genes associated with plasmid replication, flagella biosynthesis, and electron transport, were differentially expressed in the cyaC mutant, but not in the crp mutant. Our results indicated that CyaC plays a major role in regulating anaerobic respiration, and may contribute to additional signaling pathways independent of CRP.
2009-04-15 | GSE15657 | GEO
Project description:Whole genome sequence of Shewanella baltica 128
| PRJNA438860 | ENA
Project description:Divergence in gene regulation in Shewanella baltica strains
| PRJNA391129 | ENA
Project description:Purpose: The goal is to study the regulatory role of ferric uptake regulator (Fur) during anaerobic respiration in Shewanella piezotolerans WP3
2016-06-10 | GSE47773 | GEO