title: A Search for Ribonucleic Antiterminator Sites in Bacterial Genomes: Not Only Antitermination?
abstract: BglG/LicT-like proteins are transcriptional antiterminators that prevent termination of transcription at intrinsic terminators by binding to ribonucleic antiterminator (RAT) sites and stabilizing an RNA conformation which is mutually exclusive with the terminator structure. The known RAT sites, which are located in intergenic regions of sugar utilization operons, show low sequence conservation but significant structural analogy. To assess the prevalence of RATs in bacterial genomes, we employed bioinformatic tools that describe RNA motifs based on both sequence and structural constraints. Using descriptors with different stringency, we searched the genomes of Escherichiacoli K12, uropathogenic E. coli and Bacillus subtilis for putative RATs. Our search identified all known RATs and additional putative RAT elements. Surprisingly, most putative RATs do not overlap an intrinsic terminator and many reside within open reading frames (ORFs). The ability of one of the putative RATs, which is located within an antiterminator-encoding ORF and does not overlap a terminator, to bind to its cognate antiterminator protein in vitro and in vivo was confirmed experimentally. Our results suggest that the capacity of RAT elements has been exploited during evolution to mediate activities other than antitermination, for example control of transcription elongation or of RNA stability.
authors.affiliation: Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, Jerusalem, Israel.
authors.forename: Noa
authors.initials: N
authors.lastname: Gordon
authors.forename: Ronen
authors.initials: R
authors.lastname: Rosenblum
authors.forename: Anat
authors.initials: A
authors.lastname: Nussbaum-Shochat
authors.forename: Elad
authors.initials: E
authors.lastname: Eliahoo
authors.forename: Orna
authors.initials: O
authors.lastname: Amster-Choder
mesh_terms: D000818:Animals; D001412:Bacillus subtilis / Q000235:genetics*; D001426:Bacterial Proteins / Q000235:genetics; D001483:Base Sequence; D017124:Conserved Sequence; D004926:Escherichia coli / Q000235:genetics*; D015964:Gene Expression Regulation, Bacterial; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D009690:Nucleic Acid Conformation; D009876:Operon; D012329:RNA, Bacterial / Q000737:chemistry / Q000235:genetics*; D016601:RNA-Binding Proteins / Q000235:genetics; D016415:Sequence Alignment; D013728:Terminator Regions, Genetic; D014158:Transcription, Genetic
chemical_list: D001426:Bacterial Proteins; D012329:RNA, Bacterial; D016601:RNA-Binding Proteins; C064872:antiterminator proteins, Bacteria