Database of ribosome binding site of all genes in Escherichia coli K-12 MG1655

Desire of synthesizing target molecules in large quantities in specific host organism requires the tunable and controllable expression of heterologous genes. Doing so necessitates the transcription of the heterologous genes as well as translation of the mRNA into a protein which may be the end product or serves as an enzyme catalyzing the biotransformation of a substrate into desired product. Similar in concept to promoters that recruit sigma factor for initiating transcription, ribosome binding sites (RBS) facilitate the binding of the small subunit (SSU) of the ribosome to mRNA to initiate translation. Differences in sequence of the ribosome binding site, which is generally annotated as 25 nucleotides upstream of the start codon, determines the relative binding affinity between it and the SSU of ribosome. This, in turn, influences the extent in which translation can be initiated and the quantity of protein product obtained. Hence, research effort has been directed to obtaining strong RBS that would significantly enhance the binding of the ribosome to the mRNA molecule for initiating translation. However, such efforts require prior knowledge of the RBS of particular genes. In this contribution, a database was created that catalogued the RBS sequence of all genes in Escherichia coli K-12 strain MG1655 (Genbank reference number, NC_000913.3). RBS sequence was defined as the stretch of DNA comprising 25 nucleotides upstream of the start codon of the gene, and was automatically parsed from the annotated genome sequence of E. coli K-12 strain MG1655 using an in-house MATLAB function. The database was created as an Excel file with two columns: gene identity and RBS sequence. Collectively, the RBS database of E. coli K-12 strain MG1655 should be useful as reference in understanding the influence of RBS sequence on translation efficiency as well as for molecular cloning work requiring the definition of the RBS sequence during plasmid construction.