National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, Room 5N50, Bethesda, MD 20894, USA.
J Struct Biol. 2012 Sep;179(3):299-319. doi: 10.1016/j.jsb.2011.12.013. Epub 2011 Dec 24.
We provide a portrait of the bacterial transcription apparatus in light of the data emerging from structural studies, sequence analysis and comparative genomics to bring out important but underappreciated features. We first describe the key structural highlights and evolutionary implications emerging from comparison of the cellular RNA polymerase subunits with the RNA-dependent RNA polymerase involved in RNAi in eukaryotes and their homologs from newly identified bacterial selfish elements. We describe some previously unnoticed domains and the possible evolutionary stages leading to the RNA polymerases of extant life forms. We then present the case for the ancient orthology of the basal transcription factors, the sigma factor and TFIIB, in the bacterial and the archaeo-eukaryotic lineages. We also present a synopsis of the structural and architectural taxonomy of specific transcription factors and their genome-scale demography. In this context, we present certain notable deviations from the otherwise invariant proteome-wide trends in transcription factor distribution and use it to predict the presence of an unusual lineage-specifically expanded signaling system in certain firmicutes like Paenibacillus. We then discuss the intersection between functional properties of transcription factors and the organization of transcriptional networks. Finally, we present some of the interesting evolutionary conundrums posed by our newly gained understanding of the bacterial transcription apparatus and potential areas for future explorations.
我们提供了一幅细菌转录装置的图谱，依据的是结构研究、序列分析和比较基因组学的数据，以突出重要但尚未被充分认识的特征。我们首先描述了细胞 RNA 聚合酶亚基与真核生物中参与 RNAi 的 RNA 依赖性 RNA 聚合酶及其从新鉴定的细菌自私元件中同源物的比较所呈现出的关键结构要点和进化意义。我们描述了一些以前未被注意到的结构域，以及可能导致现存生命形式的 RNA 聚合酶进化的阶段。然后，我们提出了细菌和古真核生物谱系中基本转录因子、σ因子和 TFIIB 的古老同源性的观点。我们还概述了特定转录因子及其基因组规模的发生情况的结构和架构分类法。在这种情况下，我们提出了某些值得注意的偏离，即在转录因子分布的否则不变的蛋白质组范围内趋势上存在显著差异，并利用它来预测某些 Firmicutes 中存在不寻常的、特定谱系扩展的信号系统，如 Paenibacillus。然后，我们讨论了转录因子的功能特性与转录网络的组织之间的交叉。最后，我们提出了一些有趣的进化难题，这些难题是我们对细菌转录装置的新认识所带来的，并提出了未来探索的潜在领域。
