Quantitative analysis of ribosome binding sites in E.coli

Doug Barrick, Keith Villanueba, John Childs, Rhonda Kalil, Thomas D. Schneider, Charles E. Lawrence, Larry Gold, Gary D. Stormo

Research output: Contribution to journalArticlepeer-review

132 Scopus citations

Abstract

185 clones with randomized ribosome binding sites, from position -11 to 0 preceding the coding region of β-galactosidase, were selected and sequenced. The translatlonal yield of each clone was determined; they varied by more than 3000-fold. Multiple linear regression analysis was used to determine the contribution to translation initiation activity of each base at each position. Features known to be important for translation initiation, such as the initiation codon, the Shlne/Dalgarno sequence, the identity of the base at position -3 and the occurrence of alternative ATGs, are all found to be important quantitatively for activity. No other features are found to be of general significance, although the effects of secondary structure can be seen as outliers. A comparison to a large number of natural E.coli translation initiation sites shows the information profile to be qualitatively similar although differing quantitatively. This is probably due to the selection for good translation initiation sites in the natural set compared to the low average activity of the randomized set.

Original languageEnglish
Pages (from-to)1287-1295
Number of pages9
JournalNucleic acids research
Volume22
Issue number7
DOIs
StatePublished - Apr 11 1994

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