title: How Changes in Anti-SD Sequences Would Affect SD Sequences inEscherichia coliandBacillus subtilis.
abstract: The 3' end of the small ribosomal RNAs (ssu rRNA) in bacteria is directly involved in the selection and binding of mRNA transcripts during translation initiation via well-documented interactions between a Shine-Dalgarno (SD) sequence located upstream of the initiation codon and an anti-SD (aSD) sequence at the 3' end of the ssu rRNA. Consequently, the 3' end of ssu rRNA (3'TAIL) is strongly conserved among bacterial species because a change in the region may impact the translation of many protein-coding genes.Escherichia coliandBacillus subtilisdiffer in their 3' ends of ssu rRNA, being GAUCACCUCCUUA3' inE. coliand GAUCACCUCCUUUCU3' or GAUCACCUCCUUUCUA3' inB. subtilisSuch differences in 3'TAIL lead to species-specific SDs (designated SDEcforE. coliand SDBsforB. subtilis) that can form strong and well-positioned SD/aSD pairing in one species but not in the other. Selection mediated by the species-specific 3'TAIL is expected to favor SDBsagainst SDEcinB. subtilis, but favor SDEcagainst SDBsinE. coliAmong well-positioned SDs, SDEcis used more inE. colithan inB. subtilis, and SDBsmore inB. subtilisthan inE. coliHighly expressed genes and genes of high translation efficiency tend to have longer SDs than lowly expressed genes and genes with low translation efficiency in both species, but more so inB. subtilisthan inE. coliBoth species overuse SDs matching the bolded part of the 3'TAIL shown above. The 3'TAIL difference contributes to the host specificity of phages.
authors.affiliation: Department of Biology, University of Ottawa, Ontario K1N 6N5, Canada.
authors.forename: Akram
authors.initials: A
authors.lastname: Abolbaghaei
authors.affiliation: Ottawa Institute of Systems Biology, Ontario K1H 8M5, Canada.
authors.forename: Jordan R
authors.initials: JR
authors.lastname: Silke
authors.affiliation: Department of Biology, University of Ottawa, Ontario K1N 6N5, Canada xxia@uottawa.ca.|Ottawa Institute of Systems Biology, Ontario K1H 8M5, Canada.
authors.forename: Xuhua
authors.identifier: 0000-0002-3092-7566
authors.initials: X
authors.lastname: Xia
mesh_terms: D001412:Bacillus subtilis / Q000235:genetics*; D020029:Base Pairing; D017124:Conserved Sequence; D004926:Escherichia coli / Q000235:genetics*; D015964:Gene Expression Regulation, Bacterial; D010442:Peptide Chain Initiation, Translational; D016372:RNA, Antisense / Q000737:chemistry / Q000235:genetics; D012329:RNA, Bacterial / Q000737:chemistry / Q000235:genetics; D012335:RNA, Ribosomal / Q000737:chemistry / Q000235:genetics*; D038621:Regulatory Sequences, Ribonucleic Acid
chemical_list: D016372:RNA, Antisense; D012329:RNA, Bacterial; D012335:RNA, Ribosomal; D038621:Regulatory Sequences, Ribonucleic Acid
keywords: Bacillus subtilis; Escherichia coli; Shine-Dalgarno; anti-SD-sequence; ssu rRNA; translation efficiency