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

PLoS One. 2014 Oct 17;9(10):e110427. doi: 10.1371/journal.pone.0110427. eCollection 2014.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Agrobacterium tumefaciens / genetics*
  • Agrobacterium tumefaciens / metabolism
  • Agrobacterium tumefaciens / physiology*
  • Base Sequence
  • Blotting, Northern
  • Chromatography, Liquid
  • Energy Metabolism / physiology*
  • Host Factor 1 Protein / metabolism*
  • Immunoprecipitation
  • Molecular Sequence Data
  • Movement / physiology*
  • Proteomics
  • RNA, Messenger / metabolism
  • RNA, Untranslated / metabolism
  • Regulon / genetics
  • Regulon / physiology*
  • Sequence Analysis, RNA
  • Tandem Mass Spectrometry
  • Transcriptome / genetics
  • Transcriptome / physiology*


  • Host Factor 1 Protein
  • RNA, Messenger
  • RNA, Untranslated

Grant support

This study was supported by a grant from the German Research Foundation (DFG priority program SPP 1258; NA 240/8-1) to FN, a grant from Academia Sinica to EML, and a joint grant from the German Academic Exchange Service (DAAD) and the Taiwan National Science Council (100-2911-I-001-053) to FN and EML. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.