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Conexibacter woesei

ABSTRACT: Soil bacterium

PROVIDER: PRJNA60925 | ENA |

REPOSITORIES: ENA

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Dataset's files

Source:

			Action	DRS
		Other
	AUKG01.dat.gz	Other
	AUKG01.fasta.gz	Fasta.gz
	AUKG01.master.dat	Other
	SRR017626.fastq.gz	Fastqsanger.gz

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Conexibacter woesei DSM 14684

Project description:Soil bacterium

| PRJNA20745 | ENA

Complete genome sequence of Conexibacter woesei type strain (ID131577).

Project description:The genus Conexibacter (Monciardini et al. 2003) represents the type genus of the family Conexibacteraceae (Stackebrandt 2005, emend. Zhi et al. 2009) with Conexibacter woesei as the type species of the genus. C. woesei is a representative of a deep evolutionary line of descent within the class Actinobacteria. Strain ID131577(T) was originally isolated from temperate forest soil in Gerenzano (Italy). Cells are small, short rods that are motile by peritrichous flagella. They may form aggregates after a longer period of growth and, then as a typical characteristic, an undulate structure is formed by self-aggregation of flagella with entangled bacterial cells. Here we describe the features of the organism, together with the complete sequence and annotation. The 6,359,369 bp long genome of C. woesei contains 5,950 protein-coding and 48 RNA genes and is part of the Genomic Encyclopedia of Bacteria and Archaea project.

| S-EPMC3035278 | biostudies-literature

Conexibacter woesei Iso977N

Project description:Conexibacter woesei Iso977N Genome sequencing and assembly

| PRJNA186462 | ENA

A proposal to rename the hyperthermophile Pyrococcus woesei as Pyrococcus furiosus subsp. woesei.

Project description:Pyrococcus species are hyperthermophilic members of the order Thermococcales, with optimal growth temperatures approaching 100 degrees C. All species grow heterotrophically and produce H2 or, in the presence of elemental sulfur (S(o)), H2S. Pyrococcus woesei and P. furiosus were isolated from marine sediments at the same Vulcano Island beach site and share many morphological and physiological characteristics. We report here that the rDNA operons of these strains have identical sequences, including their intergenic spacer regions and part of the 23S rRNA. Both species grow rapidly and produce H2 in the presence of 0.1% maltose and 10-100 microM sodium tungstate in S(o)-free medium. However, P. woesei shows more extensive autolysis than P. furiosus in the stationary phase. Pyrococcus furiosus and P. woesei share three closely related families of insertion sequences (ISs). A Southern blot performed with IS probes showed extensive colinearity between the genomes of P. woesei and P. furiosus. Cloning and sequencing of ISs that were in different contexts in P. woesei and P. furiosus revealed that the napA gene in P. woesei is disrupted by a type III IS element, whereas in P. furiosus, this gene is intact. A type I IS element, closely linked to the napA gene, was observed in the same context in both P. furiosus and P. woesei genomes. Our results suggest that the IS elements are implicated in genomic rearrangements and reshuffling in these closely related strains. We propose to rename P. woesei a subspecies of P. furiosus based on their identical rDNA operon sequences, many common IS elements that are shared genomic markers, and the observation that all P. woesei nucleotide sequences deposited in GenBank to date are > 99% identical to P. furiosus sequences.

| S-EPMC2685572 | biostudies-literature

Conexibacter

Project description:Conexibacter sp. overview

| PRJNA445331 | ENA

Lsr2 and its novel paralogue mediate the adjustment of Mycobacterium smegmatis to unfavorable environmental conditions

Project description:In this study, we analyze the role of Lsr2 as a transcription factor in M. smegmatis, a saprophytic bacterium whose natural habitat (soil and water) substantially differs from that of the obligatory mycobacterial pathogens. In summary, the combined RNA-seq and ChIP-seq data revealed that Lsr2 controls gene expression either directly by binding their promoter regions or indirectly through DNA loop formation.

2021-04-22 | GSE164708 | GEO

Transcription profiling of Sinorhizobium meliloti after exposure to elevated concentrations of the heavy metals cadmium and zinc to analyze stress responses

Project description:The stress response of the soil bacterium Sinorhizobium meliloti towards elevated concentrations of the heavy metals cadmium and zinc was analyzed via transcriptional profiling.

2008-03-15 | E-MTAB-13 | biostudies-arrayexpress

Methanobrevibacter woesei

Project description:Methanobrevibacter woesei overview

| PRJNA436606 | ENA

Heavy metal resistance in Cupriavidus metallidurans CH34 is governed by an intricate transcriptional network

Project description:Background: The high number of heavy metal resistance genes in the soil bacterium Cupriavidus metallidurans CH34 makes it an interesting model organism to study microbial responses to heavy metals. Results: In this study the transcriptional response of this bacterium was measured after challenging it to a wide range of sub-lethal concentrations of various essential or toxic metals. Considering the global transcriptional responses for each challenge as well as by identifying the overlap in upregulated genes between different metal responses, the sixteen metals could be clustered in three different groups. Additionally, next to the assessment of the transcriptional response of already known metal resistance genes, new metal response gene clusters were identified. The majority of the metal response loci showed similar expression profiles when cells were exposed to different metals, suggesting complex cross-talk at transcriptional level between the different metal responses. The highly redundant nature of these metal resistant regions – illustrated by the large number of paralogous genes – combined with the phylogenetic distribution of these metal response regions within evolutionary related and other metal resistant bacteria, provides important insights on the recent evolution of this naturally soil dwelling bacterium towards a highly metal-resistant strain found in harsh and anthropogenic environments. Conclusions: The metal-resistant soil bacterium Cupriavidus metallidurans CH34 displays myriads of gene expression patterns when exposed to a wide range of heavy metals at non-lethal concentrations. The interplay between the different gene expression clusters points towards a complex cross-regulated regulatory network governing heavy metal resistance in C. metallidurans CH34. Keywords: Cupriavidus metallidurans CH34, transcriptional regulation, heavy metal resistance

2011-06-28 | GSE23876 | GEO

Proteomics of Nitrospirae - Rice paddy Nitrospirae encode and express genes related to sulfate respiration: proposal of the new genus Candidatus Sulfobium

Project description:We present the draft genome of Nitrospirae bacterium Nbg-4 as a representative of this clade and couple this to in situ protein expression under sulfate-enriched and sulfate-depleted conditions in rice paddy soil. The proteins were extracted from the soil and analysed via LC-MS/MS measurements.

2018-01-08 | PXD007817 | Pride

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