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Identification of Hfq bound RNA by co-immunoprecipitation and RNA-sequencing

ABSTRACT: Co-immunoprecipitation with endogenous Hfq3xFlag in exponential, stationary, non-induced and virulence induced conditions, followed by RNA-sequencing, revealed 1697 mRNAs and 208 ncRNAs associated with Hfq. We identified 56 new ncRNAs and validated 3 Hfq-dependent trans sRNAs on by Northern blot analysis. Interestingly, 55% of the ncRNAs were encoded antisense to a protein coding sequence. Abundance of 4 asRNAs and their corresponding target mRNAs was altered upon hfq, indicating a substantial influence of Hfq on asRNA-target interactions. 8 cDNA libraries were sequenced. A. tumefaciens hfq3xFlag and hfqWT (control) strains were grown to stationary and exponential growth phase and under non-induced and virulence induced conditions.

ORGANISM(S): Agrobacterium tumefaciens

SUBMITTER: Konrad FM-CM-6rstner

PROVIDER: E-GEOD-59123 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Profound impact of Hfq on nutrient acquisition, metabolism and motility in the plant pathogen Agrobacterium tumefaciens.

Möller Philip P Overlöper Aaron A Förstner Konrad U KU Wen Tuan-Nan TN Sharma Cynthia M CM Lai Erh-Min EM Narberhaus Franz F

PloS one 20141017 10

As matchmaker between mRNA and sRNA interactions, the RNA chaperone Hfq plays a key role in riboregulation of many bacteria. Often, the global influence of Hfq on the transcriptome is reflected by substantially altered proteomes and pleiotropic phenotypes in hfq mutants. Using quantitative proteomics and co-immunoprecipitation combined with RNA-sequencing (RIP-seq) of Hfq-bound RNAs, we demonstrate the pervasive role of Hfq in nutrient acquisition, metabolism and motility of the plant pathogen A ...[more]

PMID: 25330313

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