Gammaproteobacteria and Bacilli
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA817577 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Carbapenem-Resistant Klebsiella pneumoniae Causing Nosocomial Bloodstream Infections in Nanjing, China
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Project description:The evolution of gene order rearrangements within bacterial chromosomes is a fast process. Closely related species can have almost no conservation in long-range gene order. A prominent exception to this rule is a >40 kb long cluster of five core operons (secE-rpoBC-str-S10-spc-alpha) and three variable adjacent operons (cysS, tufB, and ecf) that together contain 57 genes of the transcriptional and translational machinery. Previous studies have indicated that at least part of this operon cluster might have been present in the last common ancestor of bacteria and archaea. Using 204 whole genome sequences, ∼2 Gy of evolution of the operon cluster were reconstructed back to the last common ancestors of the Gammaproteobacteria and of the Bacilli. A total of 163 independent evolutionary events were identified in which the operon cluster was altered. Further examination showed that the process of disconnecting two operons generally follows the same pattern. Initially, a small number of genes is inserted between the operons breaking the concatenation followed by a second event that fully disconnects the operons. While there is a general trend for loss of gene synteny over time, there are examples of increased alteration rates at specific branch points or within specific bacterial orders. This indicates the recurrence of relaxed selection on the gene order within bacterial chromosomes. The analysis of the alternation events indicates that segmental genome duplications and/or transposon-directed recombination play a crucial role in rearrangements of the operon cluster.
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Project description:Confirmation of nosocomial infections using whole-genome sequencing
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Project description:Genome sequencing of gram-negative bacteria collected in Japan (JARBS-GNR project)
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Project description:Marinoagarivorans rongchengensis genome sequencing and assembly
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Project description:Pseudomonas aeruginosa, a facultative human pathogen causing nosocomial infections, has complex regulatory systems involving many transcriptional regulators. The LTTR family (LysR-Type Transcriptional Regulators) consists of proteins involved in regulation of various processes including stress response, motility, virulence or amino acid metabolism. The aim of this study was characterization of the LysR-type regulator BsrA (PA2121), identified previously as a negative regulator of biofilm formation in P. aeruginosa. To identify the BsrA binding sites in P. aeruginosa the ChIP-seq analysis was performed. It revealed 765 BsrA binding sites in P. aeruginosa PAO1161 genome, among them 367 was localized in the intergenic regions. Parallel transcriptomic analysis identified altered expression of 157 genes in response to BsrA excess, among them 35 had a BsrA binding site in the corresponding promoter regions, indicating direct influence of BsrA on expression of these genes. BsrA-repressed loci encompass genes encoding proteins engaged in key metabolic pathways including the tricarboxylic acid cycle. A group of directly activated genes by BsrA, consists of several loci encoding proteins involved in pili/fimbriae assembly as well as secretion and transport systems. Results also confirmed that BsrA acts as an autorepressor. Presented data uncover the regulon of BsrA protein with its role as transcriptional regulator of genes engaged in vital cellular processes in P. aeruginosa.
2021-06-17 | GSE163233 | GEO
Project description:Stenotrophomonas maltophilia is an emerging opportunistic multidrug-resistant pathogen frequently co-isolated with other relevant nosocomial pathogens in respiratory tract infections. S. maltophilia uses the endogenous DSF quorum sensing (QS) system to regulate virulence processes but can also respond to exogenous AHL signals produced by neighboring bacteria. A whole-transcriptome sequencing analysis was performed for S. maltophilia strain K279a in the exponential and stationary phases and in exponential cultures after a treatment with exogenous DSF or AHLs. Among the common top upregulated genes, the putative TetR-like regulator Smlt2053 was selected for functional characterization. This regulator was found to sense long-chain fatty acids, including the QS signal DSF, and activate a β-oxidation catabolic pathway.
2023-05-16 | GSE206554 | GEO