Diversity of small RNAs expressed in Pseudomonas species

Mara Gomez-Lozano, Rasmus Lykke Marvig, Carlos Molina-Santiago, Paula Maria Tribelli, Juan-Luis Ramos, Søren Molin

Research output: Contribution to journalJournal articleResearchpeer-review

Abstract

RNA sequencing (RNA-seq) has revealed several hundreds of previously undetected small RNAs (sRNAs) in all bacterial species investigated, including strains of Pseudomonas aeruginosa, Pseudomonas putida and Pseudomonas syringae. Nonetheless, only little is known about the extent of conservation of expressed sRNAs across strains and species. In this study, we have used RNA-seq to identify sRNAs in P.putidaDOT-T1E and Pseudomonas extremaustralis 14-3b. This is the first strain of P.extremaustralis and the second strain of P.putida to have their transcriptomes analysed for sRNAs, and we identify the presence of around 150 novel sRNAs in each strain. Furthermore, we provide a comparison based on sequence conservation of all the sRNAs detected by RNA-seq in the Pseudomonas species investigated so far. Our results show that the extent of sRNA conservation across different species is very limited. In addition, when comparing the sRNAs expressed in different strains of the same species, we observe that numerous sRNAs exhibit a strain-specific expression pattern. These results support the idea that the evolution of most bacterial sRNAs is rapid, which limits the extent of both interspecies and intraspecies conservation.
Original languageEnglish
JournalEnvironmental Microbiology Reports
Volume7
Issue number2
Pages (from-to)227-236
Number of pages10
ISSN1758-2229
DOIs
Publication statusPublished - 2015

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