title: Genome-wide identification and characterization of small RNAs in Rhodobacter capsulatus and identification of small RNAs affected by loss of the response regulator CtrA.
abstract: Small non-coding RNAs (sRNAs) are involved in the control of numerous cellular processes through various regulatory mechanisms, and in the past decade many studies have identified sRNAs in a multitude of bacterial species using RNA sequencing (RNA-seq). Here, we present the first genome-wide analysis of sRNA sequencing data in Rhodobacter capsulatus, a purple nonsulfur photosynthetic alphaproteobacterium. Using a recently developed bioinformatics approach, sRNA-Detect, we detected 422 putative sRNAs from R. capsulatus RNA-seq data. Based on their sequence similarity to sRNAs in a sRNA collection, consisting of published putative sRNAs from 23 additional bacterial species, and RNA databases, the sequences of 124 putative sRNAs were conserved in at least one other bacterial species; and, 19 putative sRNAs were assigned a predicted function. We bioinformatically characterized all putative sRNAs and applied machine learning approaches to calculate the probability of a nucleotide sequence to be a bona fide sRNA. The resulting quantitative model was able to correctly classify 95.2% of sequences in a validation set. We found that putative cis-targets for antisense and partially overlapping sRNAs were enriched with protein-coding genes involved in primary metabolic processes, photosynthesis, compound binding, and with genes forming part of macromolecular complexes. We performed differential expression analysis to compare the wild type strain to a mutant lacking the response regulator CtrA, an important regulator of gene expression in R. capsulatus, and identified 18 putative sRNAs with differing levels in the two strains. Finally, we validated the existence and expression patterns of four novel sRNAs by Northern blot analysis.
authors.affiliation: a Department of Biology , Memorial University of Newfoundland , St. John's , NL , Canada.
authors.forename: Marc P
authors.initials: MP
authors.lastname: Grüll
authors.affiliation: a Department of Biology , Memorial University of Newfoundland , St. John's , NL , Canada.|b Department of Computer Science , Memorial University of Newfoundland , St. John's , NL , Canada.
authors.forename: Lourdes
authors.identifier: 0000-0002-0643-2547
authors.initials: L
authors.lastname: Peña-Castillo
authors.affiliation: c Department of Biochemistry , Memorial University of Newfoundland , St. John's , NL , Canada.
authors.forename: Martin E
authors.initials: ME
authors.lastname: Mulligan
authors.affiliation: a Department of Biology , Memorial University of Newfoundland , St. John's , NL , Canada.
authors.forename: Andrew S
authors.identifier: 0000-0002-4510-7683
authors.initials: AS
authors.lastname: Lang
mesh_terms: D001426:Bacterial Proteins / Q000378:metabolism*; D001483:Base Sequence; D019295:Computational Biology; D015964:Gene Expression Regulation, Bacterial; D056426:Genetic Loci; D016680:Genome, Bacterial; D058977:Molecular Sequence Annotation; D011401:Promoter Regions, Genetic / Q000235:genetics; D011485:Protein Binding; D016372:RNA, Antisense / Q000378:metabolism; D012329:RNA, Bacterial / Q000378:metabolism*; D012343:RNA, Transfer / Q000235:genetics; D015203:Reproducibility of Results; D016354:Rhodobacter capsulatus / Q000235:genetics*; D017423:Sequence Analysis, RNA
chemical_list: D001426:Bacterial Proteins; D016372:RNA, Antisense; D012329:RNA, Bacterial; D012343:RNA, Transfer
keywords: CtrA; RNA-seq; Rhodobacter capsulatus; logistic regression; sRNA-Detect; small non-coding RNAs