title: Broad-specificity mRNA-rRNA complementarity in efficient protein translation.
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.
authors.affiliation: Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America.
authors.forename: Pamela A
authors.initials: PA
authors.lastname: Barendt
authors.forename: Najaf A
authors.initials: NA
authors.lastname: Shah
authors.forename: Gregory A
authors.initials: GA
authors.lastname: Barendt
authors.forename: Casim A
authors.initials: CA
authors.lastname: Sarkar
mesh_terms: D020121:5' Untranslated Regions / Q000235:genetics; D001435:Bacteriophages / Q000235:genetics; D001665:Binding Sites / Q000235:genetics; D017124:Conserved Sequence; D003596:Cytosine / Q000378:metabolism; D004926:Escherichia coli; D006801:Humans; D010944:Plants / Q000235:genetics; D014176:Protein Biosynthesis / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics*; D012336:RNA, Ribosomal, 16S / Q000235:genetics / Q000378:metabolism; D012270:Ribosomes / Q000235:genetics
chemical_list: D020121:5' Untranslated Regions; D012333:RNA, Messenger; D012336:RNA, Ribosomal, 16S; D003596:Cytosine