title: Deep sequencing uncovers numerous small RNAs on all four replicons of the plant pathogen Agrobacterium tumefaciens.
abstract: Agrobacterium species are capable of interkingdom gene transfer between bacteria and plants. The genome of Agrobacterium tumefaciens consists of a circular and a linear chromosome, the At-plasmid and the Ti-plasmid, which harbors bacterial virulence genes required for tumor formation in plants. Little is known about promoter sequences and the small RNA (sRNA) repertoire of this and other α-proteobacteria. We used a differential RNA sequencing (dRNA-seq) approach to map transcriptional start sites of 388 annotated genes and operons. In addition, a total number of 228 sRNAs was revealed from all four Agrobacterium replicons. Twenty-two of these were confirmed by independent RNA gel blot analysis and several sRNAs were differentially expressed in response to growth media, growth phase, temperature or pH. One sRNA from the Ti-plasmid was massively induced under virulence conditions. The presence of 76 cis-antisense sRNAs, two of them on the reverse strand of virulence genes, suggests considerable antisense transcription in Agrobacterium. The information gained from this study provides a valuable reservoir for an in-depth understanding of sRNA-mediated regulation of the complex physiology and infection process of Agrobacterium.
authors.affiliation: Lehrstuhl für Biologie der Mikroorganismen, Ruhr-Universität Bochum, Bochum, Germany.
authors.forename: Ina
authors.initials: I
authors.lastname: Wilms
authors.forename: Aaron
authors.initials: A
authors.lastname: Overlöper
authors.forename: Minou
authors.initials: M
authors.lastname: Nowrousian
authors.forename: Cynthia M
authors.initials: CM
authors.lastname: Sharma
authors.forename: Franz
authors.initials: F
authors.lastname: Narberhaus
mesh_terms: D020121:5' Untranslated Regions; D016960:Agrobacterium tumefaciens / Q000235:genetics* / Q000378:metabolism; D001483:Base Sequence; D016384:Consensus Sequence; D015964:Gene Expression Regulation, Bacterial; D005798:Genes, Bacterial; D059014:High-Throughput Nucleotide Sequencing; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D009876:Operon; D012329:RNA, Bacterial / Q000235:genetics* / Q000378:metabolism; D058727:RNA, Small Untranslated / Q000235:genetics* / Q000378:metabolism; D012093:Replicon; D017423:Sequence Analysis, RNA; D059467:Transcriptome; D037521:Virulence Factors / Q000235:genetics
chemical_list: D020121:5' Untranslated Regions; D012329:RNA, Bacterial; D058727:RNA, Small Untranslated; D037521:Virulence Factors