Broad-specificity mRNA-rRNA complementarity in efficient protein translation

PLoS Genet. 2012;8(3):e1002598. doi: 10.1371/journal.pgen.1002598. Epub 2012 Mar 22.

Abstract

Studies of synthetic, well-defined biomolecular systems can elucidate inherent capabilities that may be difficult to uncover in a native biological context. Here, we used a minimal, reconstituted translation system from Escherichia coli to identify efficient ribosome binding sites (RBSs) in an unbiased, high-throughput manner. We applied ribosome display, a powerful in vitro selection method, to enrich only those mRNA sequences which could direct rapid protein translation. In addition to canonical Shine-Dalgarno (SD) motifs, we unexpectedly recovered highly efficient cytosine-rich (C-rich) sequences that exhibit unmistakable complementarity to the 16S rRNA of the small subunit of the ribosome, indicating that broad-specificity base-pairing may be an inherent, general mechanism for efficient translation. Furthermore, given the conservation of ribosomal structure and function across species, the broader relevance of C-rich RBS sequences identified through our in vitro evolution approach is supported by multiple, diverse examples in nature, including C-rich RBSs in several bacteriophage and plants, a poly-C consensus before the start codon in a lower eukaryote, and Kozak-like sequences in vertebrates.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • 5' Untranslated Regions / genetics
  • Bacteriophages / genetics
  • Binding Sites* / genetics
  • Conserved Sequence
  • Cytosine / metabolism
  • Escherichia coli
  • Humans
  • Plants / genetics
  • Protein Biosynthesis / genetics*
  • RNA, Messenger / genetics*
  • RNA, Ribosomal, 16S* / genetics
  • RNA, Ribosomal, 16S* / metabolism
  • Ribosomes* / genetics

Substances

  • 5' Untranslated Regions
  • RNA, Messenger
  • RNA, Ribosomal, 16S
  • Cytosine