Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India.
Antonie Van Leeuwenhoek. 2013 Feb;103(2):331-46. doi: 10.1007/s10482-012-9813-0. Epub 2012 Sep 18.
Operons are an important feature of prokaryotic genomes. Evolution of operons is hypothesized to be adaptive and has contributed significantly towards coordinated optimization of functions. Two conflicting theories, based on (i) in situ formation to achieve co-regulation and (ii) horizontal gene transfer of functionally linked gene clusters, are generally considered to explain why and how operons have evolved. Furthermore, effects of operon evolution on genomic traits such as intergenic spacing, operon size and co-regulation are relatively less explored. Based on the conservation level in a set of diverse prokaryotes, we categorize the operonic gene pair associations and in turn the operons as ancient and recently formed. This allowed us to perform a detailed analysis of operonic structure in cyanobacteria, a morphologically and physiologically diverse group of photoautotrophs. Clustering based on operon conservation showed significant similarity with the 16S rRNA-based phylogeny, which groups the cyanobacterial strains into three clades. Clade C, dominated by strains that are believed to have undergone genome reduction, shows a larger fraction of operonic genes that are tightly packed in larger sized operons. Ancient operons are in general larger, more tightly packed, better optimized for co-regulation and part of key cellular processes. A sub-clade within Clade B, which includes Synechocystis sp. PCC 6803, shows a reverse trend in intergenic spacing. Our results suggest that while in situ formation and vertical descent may be a dominant mechanism of operon evolution in cyanobacteria, optimization of intergenic spacing and co-regulation are part of an ongoing process in the life-cycle of operons.
操纵子是原核基因组的一个重要特征。操纵子的进化被假设为是适应性的，并且对功能的协调优化有很大的贡献。两种相互冲突的理论，基于（i）原位形成以实现共调控，和（ii）功能相关基因簇的水平基因转移，通常被认为可以解释为什么以及如何进化出操纵子。此外，操纵子进化对基因组特征的影响，如基因间间距、操纵子大小和共调控，相对较少被探索。根据在一组不同的原核生物中的保守水平，我们对操纵子基因对关联进行分类，从而将操纵子分为古老的和最近形成的。这使我们能够在形态和生理上多样化的光合自养生物蓝细菌中对操纵子结构进行详细分析。基于操纵子保守性的聚类与基于 16S rRNA 的系统发育显示出显著的相似性，该系统发育将蓝细菌菌株分为三个分支。以被认为经历了基因组缩减的菌株为主的分支 C 显示出更大比例的操纵子基因紧密包装在更大的操纵子中。古老的操纵子通常更大、更紧密地包装，更有利于共调控，并且是关键细胞过程的一部分。分支 B 中的一个亚分支，包括集胞藻 PCC 6803，在基因间间距上表现出相反的趋势。我们的结果表明，虽然原位形成和垂直下降可能是蓝细菌操纵子进化的主要机制，但基因间间距和共调控的优化是操纵子生命周期中正在进行的过程的一部分。
