title: Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline.
abstract: We applied a computational pipeline based on comparative genomics to bacteria, and identified 22 novel candidate RNA motifs. We predicted six to be riboswitches, which are mRNA elements that regulate gene expression on binding a specific metabolite. In separate studies, we confirmed that two of these are novel riboswitches. Three other riboswitch candidates are upstream of either a putative transporter gene in the order Lactobacillales, citric acid cycle genes in Burkholderiales or molybdenum cofactor biosynthesis genes in several phyla. The remaining riboswitch candidate, the widespread Genes for the Environment, for Membranes and for Motility (GEMM) motif, is associated with genes important for natural competence in Vibrio cholerae and the use of metal ions as electron acceptors in Geobacter sulfurreducens. Among the other motifs, one has a genetic distribution similar to a previously published candidate riboswitch, ykkC/yxkD, but has a different structure. We identified possible non-coding RNAs in five phyla, and several additional cis-regulatory RNAs, including one in epsilon-proteobacteria (upstream of purD, involved in purine biosynthesis), and one in Cyanobacteria (within an ATP synthase operon). These candidate RNAs add to the growing list of RNA motifs involved in multiple cellular processes, and suggest that many additional RNAs remain to be discovered.
authors.affiliation: Department of Molecular, Cellular and Developmental Biology, Yale University, Box 208103, New Haven, CT 06520-8103, USA. zasha.weinberg@yale.edu
authors.forename: Zasha
authors.initials: Z
authors.lastname: Weinberg
authors.forename: Jeffrey E
authors.initials: JE
authors.lastname: Barrick
authors.forename: Zizhen
authors.initials: Z
authors.lastname: Yao
authors.forename: Adam
authors.initials: A
authors.lastname: Roth
authors.forename: Jane N
authors.initials: JN
authors.lastname: Kim
authors.forename: Jeremy
authors.initials: J
authors.lastname: Gore
authors.forename: Joy Xin
authors.initials: JX
authors.lastname: Wang
authors.forename: Elaine R
authors.initials: ER
authors.lastname: Lee
authors.forename: Kirsten F
authors.initials: KF
authors.lastname: Block
authors.forename: Narasimhan
authors.initials: N
authors.lastname: Sudarsan
authors.forename: Shane
authors.initials: S
authors.lastname: Neph
authors.forename: Martin
authors.initials: M
authors.lastname: Tompa
authors.forename: Walter L
authors.initials: WL
authors.lastname: Ruzzo
authors.forename: Ronald R
authors.initials: RR
authors.lastname: Breaker
mesh_terms: D001483:Base Sequence; D019295:Computational Biology; D016384:Consensus Sequence; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods*; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012329:RNA, Bacterial / Q000737:chemistry*; D012333:RNA, Messenger / Q000737:chemistry; D022661:RNA, Untranslated / Q000737:chemistry; D038621:Regulatory Sequences, Ribonucleic Acid; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: D012329:RNA, Bacterial; D012333:RNA, Messenger; D022661:RNA, Untranslated; D038621:Regulatory Sequences, Ribonucleic Acid