title: Computational prediction and transcriptional analysis of sRNAs in Nitrosomonas europaea.
abstract: Bacterial small noncoding RNAs (sRNAs) have been discovered in many genetically well-studied microorganisms and have been shown to regulate critical cellular processes at the post-transcriptional level. In this study, we used comparative genomics and microarray data to analyze the genome of the ammonia-oxidizing bacterium Nitrosomonas europaea for the presence and expression of sRNAs. Fifteen genes encoding putative sRNAs (psRNAs) were identified. Most of these genes showed altered expression in a variety of experimental conditions. The transcripts of two psRNAs were further characterized by mapping their 5'- and 3'-ends and by real-time PCR. The results of these analyses suggested that one of them, psRNA11, is involved in iron homeostasis in N. europaea.
authors.affiliation: Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA.
authors.forename: Barbara O
authors.initials: BO
authors.lastname: Gvakharia
authors.forename: Brian
authors.initials: B
authors.lastname: Tjaden
authors.forename: Neeraja
authors.initials: N
authors.lastname: Vajrala
authors.forename: Luis A
authors.initials: LA
authors.lastname: Sayavedra-Soto
authors.forename: Daniel J
authors.initials: DJ
authors.lastname: Arp
mesh_terms: D001483:Base Sequence; D019295:Computational Biology; D015964:Gene Expression Regulation, Bacterial; D016680:Genome, Bacterial; D043370:Nitrosomonas europaea / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D009690:Nucleic Acid Conformation; D020411:Oligonucleotide Array Sequence Analysis; D012329:RNA, Bacterial / Q000235:genetics* / Q000378:metabolism; D058727:RNA, Small Untranslated / Q000235:genetics* / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D012329:RNA, Bacterial; D058727:RNA, Small Untranslated