title: Prediction of candidate small non-coding RNAs in Agrobacterium by computational analysis.
abstract: Small non-coding RNAs with important regulatory roles are not confined to eukaryotes. Recent work has uncovered a growing number of bacterial small RNAs (sRNAs), some of which have been shown to regulate critical cellular processes. Computational approaches, in combination with molecular experiments, have played an important role in the identification of these sRNAs. At present, there is no information on the presence of small non-coding RNAs and their genes in the Agrobacterium tumefaciens genome. To identify potential sRNAs in this important bacterium, deep sequencing of the short RNA populations isolated from Agrobacterium tumefaciens C58 was carried out. From a data set of more than 10,000 short sequences, 16 candidate sRNAs have been tentatively identified based on computational analysis. All of these candidates can form stem-loop structures by RNA folding predictions and the majority of the secondary structures are rich in GC base pairs. Some are followed by a short stretch of U residues, indicative of a rho-independent transcription terminator, whereas some of the short RNAs are found in the stem region of the hairpin, indicative of eukaryotic-like sRNAs. Experimental strategies will need to be used to verify these candidates. The study of an expanded list of candidate sRNAs in Agrobacterium will allow a more complete understanding of the range of roles played by regulatory RNAs in prokaryotes.
authors.affiliation: The Laboratory Center for Basic Medical Sciences, Nanjing Medical University, Nanjing 210029, Jiangsu Province, China.
authors.forename: Tingting
authors.initials: T
authors.lastname: Zhao
authors.forename: Ren
authors.initials: R
authors.lastname: Zhang
authors.forename: Mingbo
authors.initials: M
authors.lastname: Wang
keywords: Agrobacterium tumefaciens genome; small RNAs; small non-coding RNAs; solexa sequencing technology
references.citation: Curr Opin Microbiol. 2007 Apr;10(2):96-101
references.pmid: 17383222
references.citation: Trends Genet. 2005 Jul;21(7):399-404
references.pmid: 15913835
references.citation: Mol Microbiol. 1995 Feb;15(3):411-4
references.pmid: 7540245
references.citation: Curr Opin Microbiol. 2007 Jun;10(3):257-61
references.pmid: 17553733
references.citation: Nature. 1989 Jul 20;340(6230):190-1
references.pmid: 2666855
references.citation: Curr Biol. 2001 Jun 26;11(12):941-50
references.pmid: 11448770
references.citation: Curr Opin Microbiol. 2007 Jun;10(3):262-70
references.pmid: 17574901
references.citation: Genes Dev. 2003 Oct 1;17(19):2374-83
references.pmid: 12975324
references.citation: Annu Rev Microbiol. 1994;48:713-42
references.pmid: 7826024
references.citation: Methods. 2008 Jan;44(1):13-21
references.pmid: 18158128
references.citation: Curr Opin Microbiol. 2003 Apr;6(2):120-4
references.pmid: 12732300
references.citation: Curr Biol. 2001 Sep 4;11(17):1369-73
references.pmid: 11553332
references.citation: Methods. 2007 Oct;43(2):131-9
references.pmid: 17889800
references.citation: Nucleic Acids Res. 2005 Jan 1;33(Database issue):D121-4
references.pmid: 15608160
references.citation: Annu Rev Microbiol. 2004;58:303-28
references.pmid: 15487940
references.citation: Nucleic Acids Res. 2005 Feb 17;33(3):1040-50
references.pmid: 15718303
references.citation: Nucleic Acids Res. 2005 Jul 26;33(13):4096-105
references.pmid: 16049021
references.citation: Science. 2001 Oct 26;294(5543):853-8
references.pmid: 11679670
references.citation: Nucleic Acids Res. 2003 Apr 1;31(7):1813-20
references.pmid: 12654996
references.citation: Biol Chem. 2005 Dec;386(12):1219-38
references.pmid: 16336117
references.citation: Genes Dev. 2001 Jul 1;15(13):1637-51
references.pmid: 11445539
references.citation: Biosystems. 2002 Mar-May;65(2-3):157-77
references.pmid: 12069726