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Bioinformatics and Translation Initiation

  • Xuhua Xia
Chapter

Abstract

Translation consists of three subprocesses: initiation, elongation, and termination, all involving signal motifs and their decoders. Shine-Dalgarno (SD) sequences in prokaryotic mRNA are decoded by anti-SD (aSD) sequences at the 3’ end of the small subunit rRNA (3’TAIL). Sense codons are decoded by tRNAs and stop codons by release factors. The signal motifs are stronger in highly expressed genes than lowly expressed genes. This chapter focuses on translation initiation and presents several new bioinformatics methods for characterizing evolution and co-evolution of signal motifs and their decoders. These methods are amply illustrated with real prokaryotic and eukaryotic data. The main factors determining translation initiation efficiency is the strength of the signal motif (e.g., location and pairing strength of SD and the nature of start codon), abundance of their decoder (e.g., number of ribosomes), and secondary structure that may embed SD and start codon rendering them inaccessible by their decoders. Mutations that result in SD/aSD incompatibility between a bacteriophage and a subset of its hosts leads to a more restricted host range.

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