title: Profound impact of Hfq on nutrient acquisition, metabolism and motility in the plant pathogen Agrobacterium tumefaciens.
abstract: 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 Agrobacterium tumefaciens. 136 of 2544 proteins identified by iTRAQ (isobaric tags for relative and absolute quantitation) were affected in the absence of Hfq. Most of them were associated with ABC transporters, general metabolism and motility. RIP-seq of chromosomally encoded Hfq3xFlag revealed 1697 mRNAs and 209 non-coding RNAs (ncRNAs) associated with Hfq. 56 ncRNAs were previously undescribed. Interestingly, 55% of the Hfq-bound ncRNAs were encoded antisense (as) to a protein-coding sequence suggesting that A. tumefaciens Hfq plays an important role in asRNA-target interactions. The exclusive enrichment of 296 mRNAs and 31 ncRNAs under virulence conditions further indicates a role for post-transcriptional regulation in A. tumefaciens-mediated plant infection. On the basis of the iTRAQ and RIP-seq data, we assembled a comprehensive model of the Hfq core regulon in A. tumefaciens.
authors.affiliation: Microbial Biology, Ruhr University Bochum, Bochum, Germany.
authors.forename: Philip
authors.initials: P
authors.lastname: Möller
authors.affiliation: Microbial Biology, Ruhr University Bochum, Bochum, Germany.
authors.forename: Aaron
authors.initials: A
authors.lastname: Overlöper
authors.affiliation: Research Center for Infectious Diseases (ZINF), Julius-Maximilian's University of Würzburg, Würzburg, Germany.
authors.forename: Konrad U
authors.initials: KU
authors.lastname: Förstner
authors.affiliation: Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.
authors.forename: Tuan-Nan
authors.initials: TN
authors.lastname: Wen
authors.affiliation: Research Center for Infectious Diseases (ZINF), Julius-Maximilian's University of Würzburg, Würzburg, Germany.
authors.forename: Cynthia M
authors.initials: CM
authors.lastname: Sharma
authors.affiliation: Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.
authors.forename: Erh-Min
authors.initials: EM
authors.lastname: Lai
authors.affiliation: Microbial Biology, Ruhr University Bochum, Bochum, Germany.
authors.forename: Franz
authors.initials: F
authors.lastname: Narberhaus
mesh_terms: D016960:Agrobacterium tumefaciens / Q000235:genetics* / Q000378:metabolism / Q000502:physiology*; D001483:Base Sequence; D015152:Blotting, Northern; D002853:Chromatography, Liquid; D004734:Energy Metabolism / Q000502:physiology*; D035001:Host Factor 1 Protein / Q000378:metabolism*; D047468:Immunoprecipitation; D008969:Molecular Sequence Data; D009068:Movement / Q000502:physiology*; D040901:Proteomics; D012333:RNA, Messenger / Q000378:metabolism; D022661:RNA, Untranslated / Q000378:metabolism; D018085:Regulon / Q000235:genetics / Q000502:physiology*; D017423:Sequence Analysis, RNA; D053719:Tandem Mass Spectrometry; D059467:Transcriptome / Q000235:genetics / Q000502:physiology*
chemical_list: D035001:Host Factor 1 Protein; D012333:RNA, Messenger; D022661:RNA, Untranslated