title: Prediction, microarray and northern blot analyses identify new intergenic small RNAs in Aliivibrio salmonicida.
abstract: Bacterial small RNAs (sRNAs) are trans-encoded regulatory RNAs that typically bind mRNAs by short-sequence complementarities and change the expression of the corresponding proteins. Some of the well-characterized sRNAs serve critical steps in the regulation of important cellular processes, such as quorum sensing (Qrr), iron homeostasis (RyhB), oxidative stress (OxyS), and carbon metabolism (Spot 42). However, many sRNAs remain to be identified, and the functional roles of sRNAs are known for only a small fraction. For example, of the hundreds of candidate sRNAs from members of the bacterial family Vibrionaceae, the function is known for only 9. We have in this study significantly contributed to the discovery and verification of new sRNAs in a representative of Vibrionaceae, i.e. the Aliivibrio salmonicida, which causes severe disease in farmed Atlantic salmon and other fishes. A computational search for intergenic non-coding (nc) RNAs in the 4.6-Mb genome identified a total of 252 potential ncRNAs (including 233 putative sRNAs). Depending on the set threshold value for fluorescence signal in our microarray approach, we identified 50-80 putative ncRNAs, 12 of which were verified by Northern blot analysis. In total, we identified 9 new sRNAs.
authors.affiliation: The Norwegian Structural Biology Centre and Department of Chemistry, Faculty of Science and Technology, University of Tromsø, Tromsø, Norway.
authors.forename: Rafi
authors.initials: R
authors.lastname: Ahmad
authors.forename: Geir Åsmund
authors.initials: GÅ
authors.lastname: Hansen
authors.forename: Hilde
authors.initials: H
authors.lastname: Hansen
authors.forename: Erik
authors.initials: E
authors.lastname: Hjerde
authors.forename: Hege Lynum
authors.initials: HL
authors.lastname: Pedersen
authors.forename: Steinar M
authors.initials: SM
authors.lastname: Paulsen
authors.forename: May Liss Julianne
authors.initials: ML
authors.lastname: Nyrud
authors.forename: Anja
authors.initials: A
authors.lastname: Strauss
authors.forename: Nils-Peder
authors.initials: NP
authors.lastname: Willassen
authors.forename: Peik
authors.initials: P
authors.lastname: Haugen
mesh_terms: D044165:Aliivibrio salmonicida / Q000235:genetics*; D015152:Blotting, Northern; D019295:Computational Biology; D021901:DNA, Intergenic; D015964:Gene Expression Regulation, Bacterial; D046228:Microarray Analysis; D058727:RNA, Small Untranslated / Q000235:genetics*
chemical_list: D021901:DNA, Intergenic; D058727:RNA, Small Untranslated