Kalia Vipin Chandra, Kumar Prasun
Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, Delhi, 110007 India.
Indian J Microbiol. 2015 Dec;55(4):366-74. doi: 10.1007/s12088-015-0552-6. Epub 2015 Sep 9.
Bacterial identification on the basis of the highly conserved 16S rRNA (rrs) gene is limited by its presence in multiple copies and a very high level of similarity among them. The need is to look for other genes with unique characteristics to be used as biomarkers. Fifty-one sequenced genomes belonging to 10 different Yersinia species were used for searching genes common to all the genomes. Out of 304 common genes, 34 genes of sizes varying from 0.11 to 4.42 kb, were selected and subjected to in silico digestion with 10 different Restriction endonucleases (RE) (4-6 base cutters). Yersinia species have 6-7 copies of rrs per genome, which are difficult to distinguish by multiple sequence alignments or their RE digestion patterns. However, certain unique combinations of other common gene sequences-carB, fadJ, gluM, gltX, ileS, malE, nusA, ribD, and rlmL and their RE digestion patterns can be used as markers for identifying 21 strains belonging to 10 Yersinia species: Y. aldovae, Y. enterocolitica, Y. frederiksenii, Y. intermedia, Y. kristensenii, Y. pestis, Y. pseudotuberculosis, Y. rohdei, Y. ruckeri, and Y. similis. This approach can be applied for rapid diagnostic applications.
基于高度保守的16S rRNA（rrs）基因进行细菌鉴定存在局限性，因为该基因有多个拷贝且它们之间相似度非常高。需要寻找具有独特特征的其他基因用作生物标志物。使用属于10种不同耶尔森菌属物种的51个测序基因组来搜索所有基因组共有的基因。在304个共有基因中，选择了34个大小从0.11到4.42 kb不等的基因，并用10种不同的限制性内切酶（RE）（4 - 6碱基切割酶）进行电子消化。耶尔森菌属物种每个基因组有6 - 7个rrs拷贝，通过多序列比对或其RE消化模式很难区分。然而，其他共有基因序列（carB、fadJ、gluM、gltX、ileS、malE、nusA、ribD和rlmL）的某些独特组合及其RE消化模式可作为鉴定属于10种耶尔森菌属物种（阿尔多瓦耶尔森菌、小肠结肠炎耶尔森菌、费氏耶尔森菌、中间耶尔森菌、克里斯滕森耶尔森菌、鼠疫耶尔森菌、假结核耶尔森菌、罗德耶尔森菌、鲁氏耶尔森菌和似耶尔森菌）的21个菌株的标志物。这种方法可应用于快速诊断。
