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Mol Plant Microbe Interact. 2015 May;28(5):580-9. doi: 10.1094/MPMI-12-14-0380-FI.

Small RNA Deep-Sequencing Analyses Reveal a New Regulator of Virulence in Agrobacterium fabrum C58.

Dequivre M1,2,3, Diel B1,2,3,4,5, Villard C1,2,3, Sismeiro O6, Durot M7,8, Coppée JY6, Nesme X1,2,4,5, Vial L1,2,4,5, Hommais F1,2,3.

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1Université de Lyon, F-69622, Lyon, France;
2Université Lyon 1, F-69622 Villeurbanne, France;
3CNRS, UMR 5240 Microbiologie Adaptation et Pathogénie, F-69622 Villeurbanne, France;
4CNRS, UMR 5557 Ecologie Microbienne, F-69622 Villeurbanne, France;
5INRA, USC 1364 Ecologie Microbienne, F-69622 Villeurbanne, France;
6Plate-forme Transcriptome et Epigénome, Département Génomes et Génétique, Institut Pasteur, 25 rue du Dr. Roux, F75015 Paris, France;
7CEA/DSV/FAR/IG/Genoscope and CNRS UMR8030 Laboratoire d'Analyses Bioinformatiques en Métabolisme et Génomique, 2 rue Gaston Crémieux 91057 Evry cedex, France;
8Total New Energies USA, 5858 Horton Street, Emeryville, CA 94608, U.S.A.


Novel ways of regulating Ti plasmid functions were investigated by studying small RNAs (sRNAs) that are known to act as posttranscriptional regulators in plant pathogenic bacteria. sRNA-seq analyses of Agrobacterium fabrum C58 allowed us to identify 1,108 small transcripts expressed in several growth conditions that could be sRNAs. A quarter of them were confirmed by bioinformatics or by biological experiments. Antisense RNAs represent 24% of the candidates and they are over-represented on the pTi (with 62% of pTi sRNAs), suggesting differences in the regulatory mechanisms between the essential and accessory replicons. Moreover, a large number of these pTi antisense RNAs are transcribed opposite to those genes involved in virulence. Others are 5'- and 3'-untranslated region RNAs and trans-encoded RNAs. We have validated, by rapid amplification of cDNA ends polymerase chain reaction, the transcription of 14 trans-encoded RNAs, among which RNA1111 is expressed from the pTiC58. Its deletion decreased the aggressiveness of A. fabrum C58 on tomatoes, tobaccos, and kalanchoe, suggesting that this sRNA activates virulence. The identification of its putative target mRNAs (6b gene, virC2, virD3, and traA) suggests that this sRNA may coordinate two of the major pTi functions, the infection of plants and its dissemination among bacteria.

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