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Title: The small RNA transcriptome of Pseudomonas syringae pathovar tomato DC3000

item Filiatrault, Melanie
item MOLL, SIMON - Cornell University
item BAO, ZHONGMENG - Cornell University
item Maciak, Charlene
item CHEN, HANRONG - Cornell University
item MYERS, CHRISTOPHER - Cornell University
item Stodghill, Paul
item Cartinhour, Samuel

Submitted to: International Conference on Pseudomonas syringae Pathovars
Publication Type: Abstract Only
Publication Acceptance Date: 7/3/2011
Publication Date: 9/3/2011
Citation: Filiatrault, M.J., Moll, S., Bao, Z., Maciak, C.L., Chen, H., Myers, C.R., Stodghill, P., Cartinhour, S.W. 2011. The small RNA transcriptome of Pseudomonas syringae pathovar tomato DC3000. International Conference on Pseudomonas syringae Pathovars. 13:20.

Interpretive Summary:

Technical Abstract: Small non-coding RNAs (ncRNAs) are regarded as important global regulators in prokaryotes and play critical roles in a variety of metabolic and cellular processes. Pseudomonas syringae pathovar tomato strain DC3000 (DC3000) is an important plant pathogenic bacterium that causes bacterial speck of tomatoes. Little information exists concerning the number, genomic distribution and biological functions of regulatory ncRNAs in this phytopathogen. Here, RNA-Seq was performed on fractioned RNA (<200'nt) isolated from DC3000 grown in rich medium to investigate the ncRNA repertoire during mid-exponential and stationary phase growth. Over 200 putative ncRNA candidates comprised of trans-encoded, mRNA-leaders, and cis-encoded antisense transcripts were discovered, with more than 90 ncRNAs representing novel candidates that have not been previously described. The size and expression of 20 ncRNA candidates was experimentally confirmed by 5’- and 3’-RACE. Additionally, several ncRNAs exhibited differential expression during the transition from exponential to stationary phase. Furthermore, promoter-like elements were associated with a number of ncRNAs, suggesting putative mechanisms of regulation. Comparative genomic analysis established DC3000 expresses homologues of several ncRNAs candidates that are conserved among the Pseudomonads, as well as, other distantly related bacteria. Furthermore, our findings show P. syringae encodes ncRNAs that share no sequence similarity or conserved genomic context with any annotated transcripts, suggesting they are only present in strain DC3000 and possibly involved in regulatory pathways specific for DC3000. Collectively, this work represents the first comprehensive screen and analysis of ncRNAs in P. syringae and serves as a foundation for future studies investigating ncRNA-mediated regulatory networks not only in this important model phytopathogen, but in other Pseudomonas species.