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 <i>Escherichia coli </i>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 <i>E. coli </i>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 <i>E. coli</i> 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.<br><br>

若要在特定宿主生物中大规模合成目标分子，需对异源基因实现可调节、可控的表达。完成这一目标需要两步关键过程：一是异源基因的转录，二是将信使RNA（messenger RNA, mRNA）翻译为蛋白质——该蛋白质既可以作为最终产物，也可作为酶催化底物发生生物转化，生成所需目标产物。其作用原理与招募σ因子（sigma factor）以启动转录的启动子（promoter）相似，核糖体结合位点（ribosome binding site, RBS）可促进核糖体小亚基（small subunit, SSU）与mRNA结合，从而启动翻译过程。核糖体结合位点的序列差异（通常被注释为起始密码子上游25个核苷酸的区域），决定了其与核糖体小亚基之间的相对结合亲和力，进而影响翻译起始的效率与最终获得的蛋白质产物产量。因此，相关研究致力于开发能够显著增强核糖体与mRNA结合、进而启动翻译的高效RBS，但这类研究需要预先掌握特定基因的RBS序列信息。

本研究构建了一份RBS数据库，收录了大肠杆菌（Escherichia coli）K-12菌株MG1655（GenBank登录号：NC_000913.3）所有基因的RBS序列。该数据库将RBS序列定义为基因起始密码子上游25个核苷酸组成的DNA片段，并通过自研MATLAB脚本从大肠杆菌K-12菌株MG1655的注释基因组序列中自动提取得到。数据库以Excel文件形式存储，包含两列数据：基因标识符与RBS序列。综上，大肠杆菌K-12菌株MG1655的RBS数据库可作为参考工具，用于探究RBS序列对翻译效率的影响，同时也可应用于质粒构建过程中需要明确定义RBS序列的分子克隆实验。

搜集汇总

背景与挑战

背景概述

该数据集提供了大肠杆菌K-12 MG1655菌株中所有基因的核糖体结合位点（RBS）序列，用于研究RBS序列对翻译效率的影响及分子克隆中的质粒构建。数据以Excel文件形式存储，包含基因身份和RBS序列两列信息。