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Streptosporangium roseum

ABSTRACT: Soil bacterium

PROVIDER: PRJNA60919 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
		Other
	SRR017622.fastq.gz	Fastqsanger.gz
	SRR017623.fastq.gz	Fastqsanger.gz
	SRR017624.fastq.gz	Fastqsanger.gz
	SRR017625.fastq.gz	Fastqsanger.gz

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Complete genome sequence of Streptosporangium roseum type strain (NI 9100).

Project description:Streptosporangium roseum Crauch 1955 is the type strain of the species which is the type species of the genus Streptosporangium. The 'pinkish coiled Streptomyces-like organism with a spore case' was isolated from vegetable garden soil in 1955. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a member of the family Streptosporangiaceae, and the second largest microbial genome sequence ever deciphered. The 10,369,518 bp long genome with its 9421 protein-coding and 80 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

| S-EPMC3035251 | biostudies-literature

Streptosporangium roseum DSM 43021

Project description:Soil actinomycete

| PRJNA21083 | ENA

An F-type lectin domain directs the activity of Streptosporangium roseum alpha-l-fucosidase.

Project description:F-type lectins are phylogenetically widespread but selectively distributed fucose-binding lectins with L-fucose- and calcium-binding sequence motifs and an F-type lectin fold. Bacterial F-type lectin domains frequently occur in tandem with various protein domains in diverse architectures, indicating a possible role in directing enzyme activities or other biological functions to distinct fucosylated niches. Here, we report the biochemical characterization of a Streptosporangium roseum protein containing an F-type lectin domain in tandem with an NPCBM-associated domain and a family GH 29A alpha-l-fucosidase domain. We show that the F-type lectin domain of this protein recognizes fucosylated glycans in both α and β linkages but has high affinity for a Fuc-α-1,2-Gal motif and that the alpha-l-fucosidase domain displays hydrolytic activity on glycan substrates with α1-2 and α1-4 linked fucose. We also show that the F-type lectin domain does not have any effect on the activity of the cis-positioned alpha-l-fucosidase domain with the synthetic substrate, 4-Methylumbelliferyl-alpha-l-fucopyranoside or on inhibition of this activity by l-fucose or deoxyfuconojirimycin hydrochloride. However, the F-type lectin domain together with the NPCBM-associated domain enhances the activity of the cis-positioned alpha-l-fucosidase domain for soluble fucosylated oligosaccharide substrates. While there are many reports of glycoside hydrolase activity towards insoluble and soluble polysaccharides being enhanced by cis-positioned carbohydrate binding modules on the polypeptide, this is the first report, to our knowledge, of enhancement of activity towards aqueous, freely diffusible, small oligosaccharides. We propose a model involving structural stabilization and a bind-and-jump action mediated by the F-type lectin domain to rationalize our findings.

| S-EPMC6455950 | biostudies-literature

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

Streptosporangium

Project description:Streptosporangium sp. overview

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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

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

Proteomic analysis of Flavobacterium johnsoniae

Project description:The soil bacterium Flavobacterium johnsoniae was grown on agar plates with or without pectin,bacteria were harvested, lysed, and subjected to LC-MS/MS analysis

2021-04-12 | PXD023649 | Pride

Transcriptome analysis of Arthrobacter in the phyllosphere

Project description:Arthrobacter chlorophenolicus A6 is a 4-chlorophenol degrading soil bacterium with high phyllosphere colonization capacity. Till now the genetic basis for the phyllosphere competency of Arthrobacter or other pollutant-degrading bacteria is uncertain. We investigated global gene expression profile of A. chlorophenolicus grown in the phyllosphere of common bean (Phaseolus vulgaris) compared to growth on agar surfaces.

2013-06-21 | GSE48198 | GEO

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