Analysis of tetra- and hepta-nucleotides motifs promoting -1 ribosomal frameshifting in Escherichia coli

• Published in: Nucleic Acids Research Vol. 42; no. 11; pp. 7210 - 7225
• Main Authors: Sharma, Virag, Prère, Marie-Françoise, Canal, Isabelle, Firth, Andrew E, Atkins, John F, Baranov, Pavel V, Fayet, Olivier
• Format: Journal Article Web Resource
• Language: English
• Published: England Oxford University Press 17.06.2014
• Subjects: Enterobacteriaceae; Escherichia coli; Escherichia coli - genetics; Frameshifting, Ribosomal; Genes, Bacterial; Life Sciences; Molecular Biology; Nucleotide Motifs; Nucleotides - analysis; RNA, Messenger - chemistry
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gku386

Programmed ribosomal -1 frameshifting is a non-standard decoding process occurring when ribosomes encounter a signal embedded in the mRNA of certain eukaryotic and prokaryotic genes. This signal has a mandatory component, the frameshift motif: it is either a Z_ZZN tetramer or a X_XXZ_ZZN heptamer (where ZZZ and XXX are three identical nucleotides) allowing cognate or near-cognate repairing to the -1 frame of the A site or A and P sites tRNAs. Depending on the signal, the frameshifting frequency can vary over a wide range, from less than 1% to more than 50%. The present study combines experimental and bioinformatics approaches to carry out (i) a systematic analysis of the frameshift propensity of all possible motifs (16 Z_ZZN tetramers and 64 X_XXZ_ZZN heptamers) in Escherichia coli and (ii) the identification of genes potentially using this mode of expression amongst 36 Enterobacteriaceae genomes. While motif efficiency varies widely, a major distinctive rule of bacterial -1 frameshifting is that the most efficient motifs are those allowing cognate re-pairing of the A site tRNA from ZZN to ZZZ. The outcome of the genomic search is a set of 69 gene clusters, 59 of which constitute new candidates for functional utilization of -1 frameshifting.