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Experimental identification of small non-coding RNAs in the model marine bacterium Ruegeria pomeroyi DSS-3

ABSTRACT: Experimental identification of small non-coding RNAs in the model marine bacterium Ruegeria pomeroyi DSS-3

PROVIDER: PRJEB12772 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR1276340.fastq.gz	Fastqsanger.gz
	ERR1276341.fastq.gz	Fastqsanger.gz
	ERR1276342.fastq.gz	Fastqsanger.gz
	ERR1276343.fastq.gz	Fastqsanger.gz
	ERR1276344.fastq.gz	Fastqsanger.gz

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Ruegeria pomeroyi DSS-3

Project description:Ruegeria pomeroyi DSS-3 Mutation Accumulation

| PRJNA320454 | ENA

Experimental identification of small non-coding RNAs in the model marine bacterium Ruegeria pomeroyi DSS-3

Project description:In oligotrophic ocean waters where bacteria are often subjected to chronic nutrient limitation, community transcriptome sequencing has pointed to the presence of highly abundant small RNAs (sRNAs). The role of sRNAs in regulating response to nutrient stress was investigated in a model heterotrophic marine bacterium Ruegeria pomeroyi grown in continuous culture under carbon and nitrogen limitation. RNAseq analysis identified 98 sRNAs, of which 69 were cis-encoded and located antisense to their target genes, and 30 were trans-encoded and linked to predicted target genes through complementarity analysis. The most prevalent functional roles of target genes were transport, cell-cell interactions, signal transduction, and transcriptional regulation. Thirty-two percent of the sRNAs had been identified in a previous study of R. pomeroyi growth on organic sulfur compounds, and may be constitutively expressed, while 69% were not identified in previous studies. Eighty-six percent and were transcribed equally under both carbon and nutrient limitation, and may be involved in a general stress response; 14% were differentially regulated under carbon versus nitrogen stress, and may respond to specific nutrient limitations. A network analysis of the predicted target genes of the R. pomeroyi sRNAs indicated that they average fewer connections than typical protein-encoding genes, and appear to be more important in peripheral or niche-defining functions encoded in the pan genome rather than central metabolism encoded in the core genome.

2016-02-27 | E-MTAB-4468 | biostudies-arrayexpress

Ruegeria pomeroyi DSS-3

Project description:Ruegeria pomeroyi DSS-3 Mutation Accumulation Project

| PRJNA320442 | ENA

Ruegeria pomeroyi DSS-3 isolate:ATCC 700808

Project description:Ruegeria pomeroyi DSS-3 Transposon Mutagenesis - T0_B other

| PRJNA501643 | ENA

Ruegeria pomeroyi DSS-3 isolate:ATCC 700808

Project description:Ruegeria pomeroyi DSS-3 Transposon Mutagenesis - T6_LowN_B other

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Ruegeria pomeroyi DSS-3 isolate:ATCC 700808

Project description:Ruegeria pomeroyi DSS-3 Transposon Mutagenesis - T8_LowN_A other

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Ruegeria pomeroyi DSS-3 isolate:ATCC 700808

Project description:Ruegeria pomeroyi DSS-3 Transposon Mutagenesis - T8_LowP_A other

| PRJNA501663 | ENA

Ruegeria pomeroyi DSS-3 isolate:ATCC 700808

Project description:Ruegeria pomeroyi DSS-3 Transposon Mutagenesis - T8_LowP_B other

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Ruegeria pomeroyi DSS-3 isolate:ATCC 700808

Project description:Ruegeria pomeroyi DSS-3 Transposon Mutagenesis - T8_LowP_C other

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Ruegeria pomeroyi DSS-3 isolate:ATCC 700808

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