title: Non-canonical RNA arrangement in T4-even phages: accommodated ribosome binding site at the gene 26-25 intercistronic junction.
abstract: Translational initiation region of bacteriophage T4 gene 25 contains three potential Shine and Dalgarno sequences: SD1, SD2 and SD3. Mutational analysis has predicted that an mRNA stem-loop structure may include SD1 and SD2, bringing the most typical sequence SD3, GAGG, to the initiation codon. Here, we report physical evidence demonstrating that previously predicted mRNA stem-loop structure indeed exists in vivo during gene 25 expression in T4-infected Escherichia coli cells. The second mRNA stem-loop structure is identified 14 nucleotides upstream of the stem-loop I, while the SD3 sequence, as well as the start codon of the gene, are proved to be within an unfolded stretch of mRNA. Phylogenetic comparison of 38 T4-like phages reveals that the T-even and some pseudoT-even phages evolve a similar structural strategy for the translation initiation of 25, while pseudoT-even, schizoT-even and exoT-even phages use an alternative mRNA arrangement. Taken together, the results indicate that a specific mRNA fold forms the split ribosome binding site at the gene 26-25 intercistronic junction, which is highly competent in the translational initiation. We conclude that this ribosome binding site has evolved after T-even diverged from other T4-like phages. Additionally, we determine that the SD sequence GAGG is most widespread in T4.
authors.affiliation: Manchester Centre for Integrative Systems Biology, Faculty of Life Sciences, Manchester Interdisciplinary Biocentre, The University of Manchester, Manchester, UK. n.malys@manchester.ac.uk
authors.forename: Naglis
authors.initials: N
authors.lastname: Malys
authors.forename: Rimas
authors.initials: R
authors.lastname: Nivinskas
mesh_terms: D017122:Bacteriophage T4 / Q000235:genetics*; D020029:Base Pairing; D001665:Binding Sites; D003090:Coliphages / Q000235:genetics*; D017124:Conserved Sequence; D021901:DNA, Intergenic; D004279:DNA, Viral / Q000737:chemistry / Q000235:genetics; D004926:Escherichia coli / Q000821:virology*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012333:RNA, Messenger / Q000235:genetics*; D012367:RNA, Viral / Q000235:genetics*; D012270:Ribosomes / Q000378:metabolism*; D017422:Sequence Analysis, DNA; D012689:Sequence Homology, Nucleic Acid
chemical_list: D021901:DNA, Intergenic; D004279:DNA, Viral; D012333:RNA, Messenger; D012367:RNA, Viral