title: RNA structures regulating ribosomal protein biosynthesis in bacilli.
abstract: In Bacilli, there are three experimentally validated ribosomal-protein autogenous regulatory RNAs that are not shared with E. coli. Each of these RNAs forms a unique secondary structure that interacts with a ribosomal protein encoded by a downstream gene, namely S4, S15, and L20. Only one of these RNAs that interacts with L20 is currently found in the RNA Families Database. We created, or modified, existing structural alignments for these three RNAs and used them to perform homology searches. We have determined that each structure exhibits a narrow phylogenetic distribution, mostly relegated to the Firmicute class Bacilli. This work, in conjunction with other similar work, demonstrates that there are most likely many non-homologous RNA regulatory elements regulating ribosomal protein biosynthesis that still await discovery and characterization in other bacterial species.
authors.affiliation: Boston College Department of Biology; Chestnut Hill, MA USA.
authors.forename: Kaila
authors.initials: K
authors.lastname: Deiorio-Haggar
authors.forename: Jon
authors.initials: J
authors.lastname: Anthony
authors.forename: Michelle M
authors.initials: MM
authors.lastname: Meyer
mesh_terms: D001407:Bacillus / Q000235:genetics* / Q000378:metabolism*; D001426:Bacterial Proteins / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D012329:RNA, Bacterial / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D012269:Ribosomal Proteins / Q000096:biosynthesis* / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins; C040045:L20 ribosomal protein, bacteria; D012329:RNA, Bacterial; D012269:Ribosomal Proteins; C031798:ribosomal protein S4
keywords: Bacillus subtilis; Geobacillus stearothermophilus; Infernal; Rfam; gram-positive; ribosomal leader sequence; ribosomal protein