title: Transcriptome profiling and functional analysis of Agrobacterium tumefaciens reveals a general conserved response to acidic conditions (pH 5.5) and a complex acid-mediated signaling involved in Agrobacterium-plant interactions.
abstract: Agrobacterium tumefaciens transferred DNA (T-DNA) transfer requires that the virulence genes (vir regulon) on the tumor-inducing (Ti) plasmid be induced by plant phenolic signals in an acidic environment. Using transcriptome analysis, we found that these acidic conditions elicit two distinct responses: (i) a general and conserved response through which Agrobacterium modulates gene expression patterns to adapt to environmental acidification and (ii) a highly specialized acid-mediated signaling response involved in Agrobacterium-plant interactions. Overall, 78 genes were induced and 74 genes were repressed significantly under acidic conditions (pH 5.5) compared to neutral conditions (pH 7.0). Microarray analysis not only confirmed previously identified acid-inducible genes but also uncovered many new acid-induced genes which may be directly involved in Agrobacterium-plant interactions. These genes include virE0, virE1, virH1, and virH2. Further, the chvG-chvI two-component system, previously shown to be critical for virulence, was also induced under acid conditions. Interestingly, acidic conditions induced a type VI secretion system and a putative nonheme catalase. We provide evidence suggesting that acid-induced gene expression was independent of the VirA-VirG two-component system. Our results, together with previous data, support the hypothesis that there is three-step sequential activation of the vir regulon. This process involves a cascade regulation and hierarchical signaling pathway featuring initial direct activation of the VirA-VirG system by the acid-activated ChvG-ChvI system. Our data strengthen the notion that Agrobacterium has evolved a mechanism to perceive and subvert the acidic conditions of the rhizosphere to an important signal that initiates and directs the early virulence program, culminating in T-DNA transfer.
authors.affiliation: Department of Microbiology, Box 357242, University of Washington, Seattle, WA 98195-7242, USA.
authors.forename: Ze-Chun
authors.initials: ZC
authors.lastname: Yuan
authors.forename: Pu
authors.initials: P
authors.lastname: Liu
authors.forename: Panatda
authors.initials: P
authors.lastname: Saenkham
authors.forename: Kathleen
authors.initials: K
authors.lastname: Kerr
authors.forename: Eugene W
authors.initials: EW
authors.lastname: Nester
mesh_terms: D016960:Agrobacterium tumefaciens / Q000235:genetics / Q000502:physiology*; D001425:Bacterial Outer Membrane Proteins / Q000096:biosynthesis; D001426:Bacterial Proteins / Q000096:biosynthesis; D002374:Catalase / Q000096:biosynthesis; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D005798:Genes, Bacterial / Q000235:genetics; D006863:Hydrogen-Ion Concentration; D026901:Membrane Transport Proteins / Q000096:biosynthesis; D018832:Molecular Chaperones / Q000096:biosynthesis; D020411:Oligonucleotide Array Sequence Analysis; D010944:Plants / Q000382:microbiology*; D011494:Protein Kinases / Q000096:biosynthesis; D015398:Signal Transduction / Q000235:genetics / Q000502:physiology*; D014157:Transcription Factors / Q000096:biosynthesis
chemical_list: D001425:Bacterial Outer Membrane Proteins; D001426:Bacterial Proteins; D026901:Membrane Transport Proteins; D018832:Molecular Chaperones; D014157:Transcription Factors; C083719:chvI protein, Bacteria; C051582:virE1 protein, Agrobacterium tumefaciens; D002374:Catalase; D011494:Protein Kinases; C083718:chvG protein, Bacteria