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PMID: 17971083 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

Identification of differentially expressed small non-coding RNAs in the legume endosymbiont Sinorhizobium meliloti by comparative genomics.

Molecular microbiology ·Vol. 66 ·No. 5 ·2007-12-00 ·Pages 1080-91

del Val C, Rivas E, Torres-Quesada O, Toro N, Jiménez-Zurdo JI

Abstract

Bacterial small non-coding RNAs (sRNAs) are being recognized as novel widespread regulators of gene expression in response to environmental signals. Here, we present the first search for sRNA-encoding genes in the nitrogen-fixing endosymbiont Sinorhizobium meliloti, performed by a genome-wide computational analysis of its intergenic regions. Comparative sequence data from eight related alpha-proteobacteria were obtained, and the interspecies pairwise alignments were scored with the programs eQRNA and RNAz as complementary predictive tools to identify conserved and stable secondary structures corresponding to putative non-coding RNAs. Northern experiments confirmed that eight of the predicted loci, selected among the original 32 candidates as most probable sRNA genes, expressed small transcripts. This result supports the combined use of eQRNA and RNAz as a robust strategy to identify novel sRNAs in bacteria. Furthermore, seven of the transcripts accumulated differentially in free-living and symbiotic conditions. Experimental mapping of the 5'-ends of the detected transcripts revealed that their encoding genes are organized in autonomous transcription units with recognizable promoter and, in most cases, termination signatures. These findings suggest novel regulatory functions for sRNAs related to the interactions of alpha-proteobacteria with their eukaryotic hosts.

MeSH Terms
Blotting, Northern Computational Biology/methods DNA, Intergenic Fabaceae/microbiology Genome, Bacterial/genetics Nucleic Acid Conformation Promoter Regions, Genetic RNA, Bacterial/biosynthesis,genetics RNA, Double-Stranded/genetics RNA, Untranslated/biosynthesis,genetics Sinorhizobium meliloti/chemistry,genetics,physiology Transcription, Genetic
Chemicals
DNA, Intergenic RNA, Bacterial RNA, Double-Stranded RNA, Untranslated
Authors & Affiliations
5 authors, click to expand affiliations / ORCID
del Val Coral
Department of Computer Science and Artificial Intelligence, E.T.S.I. Informatics, Universidad de Granada, Daniel Saucedo s/n, 18071 Granada, Spain.
Rivas Elena
Torres-Quesada Omar
Toro Nicolás
Jiménez-Zurdo José I
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Article Info
Journal
Molecular microbiology
Abbr.
Mol Microbiol
ISSN
0950-382X
DOI
10.1111/j.1365-2958.2007.05978.x
Published
2007-12-00
Epub
2007-00-25
Pages
1080-91
Language
English
Region
England
NLM ID
8712028
PMCID
PMC2780559
Subset
IM
Grants
NIGMS NIH HHS · R01 GM070538 · United States
NIGMS NIH HHS · R01GM070538-02 · United States
External Links
PubMed source DOI: 10.1111/j.1365-2958.2007.05978.x PMC Full Text View journal details
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