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Small non‐coding RNAs in Caulobacter crescentus
Author(s) -
Landt Stephen G.,
Abeliuk Eduardo,
McGrath Patrick T.,
Lesley Joseph A.,
McAdams Harley H.,
Shapiro Lucy
Publication year - 2008
Publication title -
molecular microbiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.857
H-Index - 247
eISSN - 1365-2958
pISSN - 0950-382X
DOI - 10.1111/j.1365-2958.2008.06172.x
Subject(s) - caulobacter crescentus , biology , genetics , gene , regulon , rna , non coding rna , regulation of gene expression , antisense rna , gene expression , transfer rna , long non coding rna , computational biology , cell cycle
Summary Small non‐coding RNAs (sRNAs) are active in many bacterial cell functions, including regulation of the cell's response to environmental challenges. We describe the identification of 27 novel Caulobacter crescentus sRNAs by analysis of RNA expression levels assayed using a tiled Caulobacter microarray and a protocol optimized for detection of sRNAs. The principal analysis method involved identification of sets of adjacent probes with unusually high correlation between the individual intergenic probes within the set, suggesting presence of a sRNA. Among the validated sRNAs, two are candidate transposase gene antisense RNAs. The expression of 10 of the sRNAs is regulated by either entry into stationary phase, carbon starvation, or rich versus minimal media. The expression of four of the novel sRNAs changes as the cell cycle progresses. One of these shares a promoter motif with several genes expressed at the swarmer‐to‐stalked cell transition; while another appears to be controlled by the CtrA global transcriptional regulator. The probe correlation analysis approach reported here is of general use for large‐scale sRNA identification for any sequenced microbial genome.