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RNA-sequencing data from Pseudomonas putida KT2440 wild-type and Hfq-tagged strain form co-immunoprecipitation experiment

ABSTRACT: The RNA-chaperone Hfq is a global post-transcriptional regulator in Bacteria, important especially for the fine-tuning of the gene expression when the environmental conditions change. We looked into sRNAome during the growth of Pseudomonas putida KT2440 and compared it to a strain without Hfq protein. Numerous sRNAs were upregulated at a specific point during the growth and many were affected in the Hfq absence. Further we identified Hfq-binding RNA transcripts with co-immunoprecipitation and experimentally validated 17 sRNAs. Many novel Hfq-binding sRNAs were identified and are directly or indirectly regulated by Hfq. In addition 1870 mRNAs were found to bind to Hfq during the growth. Together, 202 antisense and 355 intergenic sRNAs have been detected in this study, several of them being 3’UTR- or 5’UTR-derived, and IS-related.

ORGANISM(S): Pseudomonas putida

PROVIDER: GSE85581 | GEO | 2017/01/01

SECONDARY ACCESSION(S): PRJNA338876

REPOSITORIES: GEO

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RNA-sequencing data from Pseudomonas putida KT2440 wild-type and Δhfq mutant

Project description:The RNA-chaperone Hfq is a global post-transcriptional regulator in Bacteria, important especially for the fine-tuning of the gene expression when the environmental conditions change. We looked into sRNAome during the growth of Pseudomonas putida KT2440 and compared it to a strain without Hfq protein. Numerous sRNAs were upregulated at a specific point during the growth and many were affected in the Hfq absence. Further we identified Hfq-binding RNA transcripts with co-immunoprecipitation and experimentally validated 17 sRNAs. Many novel Hfq-binding sRNAs were identified and are directly or indirectly regulated by Hfq. In addition 1870 mRNAs were found to bind to Hfq during the growth. Together, 202 antisense and 355 intergenic sRNAs have been detected in this study, several of them being 3’UTR- or 5’UTR-derived, and IS-related.

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Production of cis, cis-muconate from benzoate at high rate and yield by a mutant of P. putida KT2440

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Hfq CLASH uncovers sRNA-target interaction networks linked to nutrient availability adaptation [RNA-seq]

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KT2440 vs KT2440_NAH7

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2012-07-27 | E-MEXP-3412 | biostudies-arrayexpress

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