title: Most RNAs regulating ribosomal protein biosynthesis in Escherichia coli are narrowly distributed to Gammaproteobacteria.
abstract: In Escherichia coli, 12 distinct RNA structures within the transcripts encoding ribosomal proteins interact with specific ribosomal proteins to allow autogenous regulation of expression from large multi-gene operons, thus coordinating ribosomal protein biosynthesis across multiple operons. However, these RNA structures are typically not represented in the RNA Families Database or annotated in genomic sequences databases, and their phylogenetic distribution is largely unknown. To investigate the extent to which these RNA structures are conserved across eubacterial phyla, we created multiple sequence alignments representing 10 of these messenger RNA (mRNA) structures in E. coli. We find that while three RNA structures are widely distributed across many phyla of bacteria, seven of the RNAs are narrowly distributed to a few orders of Gammaproteobacteria. To experimentally validate our computational predictions, we biochemically confirmed dual L1-binding sites identified in many Firmicute species. This work reveals that RNA-based regulation of ribosomal protein biosynthesis is used in nearly all eubacterial phyla, but the specific RNA structures that regulate ribosomal protein biosynthesis in E. coli are narrowly distributed. These results highlight the limits of our knowledge regarding ribosomal protein biosynthesis regulation outside of E. coli, and the potential for alternative RNA structures responsible for regulating ribosomal proteins in other eubacteria.
authors: Department of Biology, Boston College, 140 Commonwealth Ave. Chestnut Hill, MA 02467, USA.
authors: Yang
authors: Y
authors: Fu
authors: Kaila
authors: K
authors: Deiorio-Haggar
authors: Jon
authors: J
authors: Anthony
authors: Michelle M
authors: MM
authors: Meyer
mesh_terms: D001665:Binding Sites; D004926:Escherichia coli / Q000235:genetics*; D029968:Escherichia coli Proteins / Q000096:biosynthesis* / Q000235:genetics / Q000378:metabolism; D020563:Gammaproteobacteria / Q000235:genetics*; D056506:Geobacillus / Q000235:genetics; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D012329:RNA, Bacterial / Q000737:chemistry* / Q000145:classification / Q000378:metabolism; D012333:RNA, Messenger / Q000737:chemistry* / Q000145:classification / Q000378:metabolism; D000080882:Ribosomal Protein L10; D012269:Ribosomal Proteins / Q000096:biosynthesis* / Q000235:genetics / Q000378:metabolism; D016415:Sequence Alignment
chemical_list: D029968:Escherichia coli Proteins; D012329:RNA, Bacterial; D012333:RNA, Messenger; D012269:Ribosomal Proteins; C028546:ribosomal protein L1; C056368:ribosomal protein L4; C544829:ribosomal protein S1, E coli; C030004:ribosomal protein S2; C029611:ribosomal protein S20; C031798:ribosomal protein S4; C488992:rplT protein, E coli
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