Janga Sarath Chandra, Pérez-Rueda Ernesto
MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK.
Comput Biol Chem. 2009 Aug;33(4):261-8. doi: 10.1016/j.compbiolchem.2009.06.004. Epub 2009 Jun 26.
Escherichia coli K12 and Bacillus subtilis 168 are two of the best characterized bacterial organisms with a long history in molecular biology for understanding various mechanisms in prokaryotic species. However, at the level of transcriptional regulation little is known on a comparative scale. Here we address the question of the degree to which transcription factors (TFs) and their evolutionary families are shared between them. We found that 59 proteins and 28 families are shared between these two bacteria, whereas different subsets were lineage specific. We demonstrate that majority of the common families expand in a lineage-specific manner. More specifically, we found that AraC, ColD, Ebp, LuxR and LysR families are over-represented in E. coli, while ArsR, AsnC, MarR, MerR and TetR families have significantly expanded in B. subtilis. We introduce the notion of regulatory superfamilies based on an empirical number of functional categories regulated by them and show that these families are essentially different in the two bacteria. We further show that global regulators seem to be constrained to smaller regulatory families and generally originate from lineage-specific families. We find that although TF families may be conserved across genomes their functional roles might evolve in a lineage-specific manner and need not be conserved, indicating convergence to be an important phenomenon involved in the functional evolution of TFs of the same family. Although topologically the networks of transcriptional interactions among TF families are similar in both the genomes, we found that the players are different, suggesting different evolutionary origins for the transcriptional regulatory machinery in both bacteria. This study provides evidence from complete repertoires that not only novel families originate in different lineages but conserved TF families expand/contrast in a lineage-specific manner, and suggests that part of the global regulatory mechanisms might originate independently in different lineages.
大肠杆菌K12和枯草芽孢杆菌168是两种特征最为明确的细菌，在分子生物学领域有着悠久的历史，有助于理解原核生物的各种机制。然而，在转录调控层面，从比较的角度来看我们了解得还很少。在此，我们探讨转录因子（TFs）及其进化家族在这两种细菌之间的共享程度问题。我们发现这两种细菌共有59种蛋白质和28个家族，而不同的子集具有谱系特异性。我们证明，大多数共同家族以谱系特异性的方式扩展。更具体地说，我们发现AraC、ColD、Ebp、LuxR和LysR家族在大肠杆菌中过度富集，而ArsR、AsnC、MarR、MerR和TetR家族在枯草芽孢杆菌中显著扩展。我们基于由它们调控的功能类别的经验数量引入了调控超家族的概念，并表明这些家族在两种细菌中本质上是不同的。我们进一步表明，全局调控因子似乎局限于较小的调控家族，并且通常起源于谱系特异性家族。我们发现，尽管TF家族可能在整个基因组中保守，但其功能作用可能以谱系特异性的方式进化，不一定保守，这表明趋同是同一家族TF功能进化中涉及的一个重要现象。尽管从拓扑结构上看，两种基因组中TF家族之间的转录相互作用网络相似，但我们发现其中的参与者不同，这表明两种细菌中转录调控机制的进化起源不同。这项研究从完整的基因库中提供了证据，表明不仅新的家族起源于不同的谱系，而且保守TF家族也以谱系特异性的方式扩展/收缩，这表明部分全局调控机制可能在不同谱系中独立起源。
