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Title: Construction of an rsmX co-variance model and identification of five rsmX-like ncRNAs in Pseudomonas syringae pv. tomato DC3000

Author
item MOLL, SIMON - Cornell University
item Schneider, David
item Stodghill, Paul
item MYERS, CHRISTOPHER - Cornell University
item Cartinhour, Samuel
item Filiatrault, Melanie

Submitted to: RNA Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/11/2010
Publication Date: 9/1/2010
Citation: Moll, S., Schneider, D.J., Stodghill, P., Myers, C.R., Cartinhour, S.W., Filiatrault, M.J. 2010. Construction of an rsmX co-variance model and identification of five rsmX-like ncRNAs in Pseudomonas syringae pv. tomato DC3000. RNA Biology. 7(5):1-10.

Interpretive Summary: Genes can be thought of as templates used to direct the synthesis of a special kind of secondary template known as RNA that have many roles in the cell. Most of these RNAs, so called messenger RNAs, are used as secondary templates for coding proteins responsible for most essential cellular functions. However, some special classes of genes are used as templates that produce RNAs that have other roles in the cell. One of these alternative roles for so-called non-coding RNAs is to regulate the expression of other genes and proteins. Non-coding RNAs are known to be intimately involved in the regulation of critical functions related to virulence and biocontrol in many species of agricultural relevance in the genus Pseudomonas. In this publication we show how computational methods can be used to find additional members of a class of non-coding RNAs in Pseudomonas species that are structurally related to those involved in biocontrol functions in various strains of Pseudomonas fluorescens. These computational results were experimentally validated in an important model plant pathogen, Pseudomonas syringae pv. tomato DC3000. Taken together, these results reveal the existence of a very complex genetic network and suggest new experiments to elucidate the specific details of this network in a variety of organisms.

Technical Abstract: Non-coding RNAs (ncRNAs) are important components of many regulatory pathways in many Pseudomonad species. In particular, the GacA/S two-component system directly regulates to at least two ncRNAs that act by sequestration of translation repressor proteins to control expression of exproducts. The core set of two ncRNAs, rsmY and rsmZ, are augmented in some species such as Pseudomonas fluorescens CHA0 that possesses a third ncRNA, rsmX. In this study we confirmed expression of five RsmX-like products in Pseudomonas syringae pv. tomato DC3000 and determined the distribution of the members of the rsmX ncRNA family by screening available genomic sequences of the Pseudomonads. Variable numbers of the rsmX family exist in Pseudomonas genomes, with up to five copies in Pseudomonas syringae strains. The RsmX-like transcripts are 112 to 120 nucleotides in length with multiple exposed GGA motifs predicted in short hairpin loops, consistent with known structure of RsmY and RsmZ. We also found that in P. syringae pv. tomato DC3000, the rsmX-like ncRNAs share a conserved upstream region suggesting that their expression is dependent on GacA.