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

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: GSE85578 | GEO | 2017/01/01

SECONDARY ACCESSION(S): PRJNA338850

REPOSITORIES: GEO

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

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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Transcriptional network between pCAR1 and KT2440 chromosome

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

Project description:P. putida KT2440-JD1 was derived from P. putida KT2440 after NTG-mutagenesis and exposure to 3-fluorobenzoate. The strain was no longer able to grow with benzoate as a single source of carbon and energy. Instead, benzoate was co-metabolized to cis, cis-muconate, which accumulated in the culture medium while grown on glucose. During continuous cultivations with glucose as a growth substrate, benzoate was co-metabolized to cis, cis-muconate with a molar product yield (Y(P/S)) of 0.88 ±0.01 mol cis, cis-muconate/ mol benzoate and a specific production rate (qpm) of 0.18 ±0.03 g cis, cis-muconate/ (gDCW* h). During wash-out cultivation a maximum growth rate of 0.6 h-1 and a maximum qpm of 1.4 g cis, cis-muconate/ (gDCW* h) were obtained. Analysis of the transcriptome revealed that the cat operon was no longer induced in P. putida KT2440-JD1 in the presence of 5 mM benzoate. This was also confirmed on the proteomic level for CatA and CatB. A point mutation in catR in P. putida KT2440-JD1 changed the highly conserved Arg50 in the DNA binding domain to Cys50, resulting in the inactivation of the transcriptional regulator of the cat operon. A catechol 1,2-dioxygenase that is encoded by gene PP_3166 (catA2) on the ben operon is likely to convert catechol to cis, cis-muconate in P. putida KT2440-JD1.

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KT2440 vs. KT2440 _NAH7 Naphthalene

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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

Project description:Plasmid-free Pseudomonas putida KT2440 compared with the same strain harbouring NAH7 plasmid; all the cells were grown in minimal medium M9 with glucose

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

Hfq Globally Binds and Destabilizes sRNAs and mRNAs in Yersinia pestis

Project description:Hfq is a ubiquitous Sm-like RNA-binding protein in bacteria involved in physiological fitness and pathogenesis, while its in vivo binding nature remains elusive. Here we reported genome-wide Hfq-bound RNAs in Yersinia pestis, a causative agent of plague, by using cross-linking immunoprecipitation coupled with deep sequencing (CLIP-seq) approach. We show that the Hfq binding density is enriched in more than 80% mRNAs of Y. pestis and that Hfq also globally binds noncoding small RNAs (sRNAs) encoded by the intergenic, antisense, and 3′ regions of mRNAs. An Hfq U-rich stretch is highly enriched in sRNAs, while motifs partially complementary to AGAAUAA and GGGGAUUA are enriched in both mRNAs and sRNAs. Hfq-binding motifs are enriched at both terminal sites and in the gene body of mRNAs. Surprisingly, a large fraction of the sRNA and mRNA regions bound by Hfq and those downstream are destabilized, likely via a 5′P-activated RNase E degradation pathway, which is consistent with a model in which Hfq facilitates sRNA-mRNA base pairing and the coupled degradation in Y. pestis. These results together have presented a high-quality Hfq-RNA interaction map in Y. pestis, which should be important for further deciphering the regulatory role of Hfq-sRNAs in Y. pestis.

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