Mitra Anirban, Angamuthu Kandavelmani, Jayashree Hanasoge Vasudevamurthy, Nagaraja Valakunja
Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India.
Genomics. 2009 Aug;94(2):110-6. doi: 10.1016/j.ygeno.2009.04.004. Epub 2009 Apr 23.
In Escherichia coli, the canonical intrinsic terminator of transcription includes a palindrome followed by a U-trail on the transcript. The apparent underrepresentation of such terminators in eubacterial genomes led us to develop a rapid and accurate algorithm, GeSTer, to predict putative intrinsic terminators. Now, we have analyzed 378 genome sequences with an improved version of GeSTer. Our results indicate that the canonical E. coli type terminators are not overwhelmingly abundant in eubacteria. The atypical structures, having stem-loop structures but lacking 'U' trail, occur downstream of genes in all the analyzed genomes but different phyla show conserved preference for different types of terminators. This propensity correlates with genomic GC content and presence of the factor, Rho. 60-70% of identified terminators in all the genomes show "optimized" stem-length and DeltaG. These results provide evidence that eubacteria extensively rely on the mechanism of intrinsic termination, with a considerable divergence in their structure, positioning and prevalence. The software and detailed results for individual genomes are freely available on request.
在大肠杆菌中,转录的典型固有终止子包括一个回文序列,随后是转录本上的一个U尾。真细菌基因组中此类终止子明显较少,这促使我们开发了一种快速且准确的算法GeSTer,用于预测假定的固有终止子。现在,我们使用改进版的GeSTer分析了378个基因组序列。我们的结果表明,典型的大肠杆菌型终止子在真细菌中并非大量存在。具有茎环结构但缺乏“U”尾的非典型结构出现在所有分析基因组中基因的下游,但不同门类对不同类型的终止子表现出保守偏好。这种倾向与基因组GC含量以及Rho因子的存在相关。所有基因组中60 - 70%已鉴定的终止子显示出“优化的”茎长度和ΔG。这些结果提供了证据,表明真细菌广泛依赖固有终止机制,其结构、定位和普遍性存在相当大的差异。软件以及各个基因组的详细结果可根据要求免费获取。