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

被引:84
作者
del Val, Coral
Rivas, Elena
Torres-Quesada, Omar
Toro, Nicolas
Jimenez-Zurdo, Jose I.
机构
[1] CSIC, Estac Expt Zaidin, Grp Ecol Genet Rizosfera, E-18008 Granada, Spain
[2] Univ Granada, ETSI Informat, Dept Comp Sci & Artificial Intelligence, E-18071 Granada, Spain
[3] Howard Hughes Med Inst, Ashburn, VA 20147 USA
关键词
ESCHERICHIA-COLI; ENCODING GENES; COMPUTATIONAL APPROACH; GLOBAL ANALYSIS; SOLUBLE-RNAS; PREDICTION; DISCOVERY; BACTERIA; PROTEIN; HFQ;
D O I
10.1111/j.1365-2958.2007.05978.x
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
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.
引用
收藏
页码:1080 / 1091
页数:12
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