title: Evidence for context-dependent complementarity of non-Shine-Dalgarno ribosome binding sites to Escherichia coli rRNA.
abstract: While the ribosome has evolved to function in complex intracellular environments, these contexts do not easily allow for the study of its inherent capabilities. We have used a synthetic, well-defined Escherichia coli (E. coli)-based translation system in conjunction with ribosome display, a powerful in vitro selection method, to identify ribosome binding sites (RBSs) that can promote the efficient translation of messenger RNAs (mRNAs) with a leader length representative of natural E. coli mRNAs. In previous work, we used a longer leader sequence and unexpectedly recovered highly efficient cytosine-rich sequences with complementarity to the 16S ribosomal RNA (rRNA) and similarity to eukaryotic RBSs. In the current study, Shine-Dalgarno (SD) sequences were prevalent, but non-SD sequences were also heavily enriched and were dominated by novel guanine- and uracil-rich motifs that showed statistically significant complementarity to the 16S rRNA. Additionally, only SD motifs exhibited position-dependent decreases in sequence entropy, indicating that non-SD motifs likely operate by increasing the local concentration of ribosomes in the vicinity of the start codon, rather than by a position-dependent mechanism. These results further support the putative generality of mRNA-rRNA complementarity in facilitating mRNA translation but also suggest that context (e.g., leader length and composition) dictates the specific subset of possible RBSs that are used for efficient translation of a given transcript.
authors: Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA.
authors: Pamela A
authors: PA
authors: Barendt
authors: Najaf A
authors: NA
authors: Shah
authors: Gregory A
authors: GA
authors: Barendt
authors: Parth A
authors: PA
authors: Kothari
authors: Casim A
authors: CA
authors: Sarkar
mesh_terms: D020121:5' Untranslated Regions; D001665:Binding Sites; D018387:Codon, Initiator; D004926:Escherichia coli / Q000235:genetics*; D006147:Guanine; D059372:Nucleotide Motifs; D012335:RNA, Ribosomal / Q000378:metabolism*; D012336:RNA, Ribosomal, 16S / Q000235:genetics / Q000378:metabolism
chemical_list: D020121:5' Untranslated Regions; D018387:Codon, Initiator; D012335:RNA, Ribosomal; D012336:RNA, Ribosomal, 16S; D006147:Guanine