Institute of Structural and Molecular Biology, University College London, London, UK.
School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA.
Protein Sci. 2024 Nov;33(11):e5194. doi: 10.1002/pro.5194.
The β and β' subunits of the RNA polymerase (RNAP) are large proteins with complex multi-domain architectures that include several insertional domains. Here, we analyze the domain organizations of RNAP-β and RNAP-β' using sequence, experimentally determined structures and AlphaFold structure predictions. We observe that lineage-specific insertional domains in bacterial RNAP-β belong to a group that we call BEAN (broadly embedded annex). We observe that lineage-specific insertional domains in bacterial RNAP-β' belong to a group that we call HABAS (hammerhead/barrel-sandwich hybrid). The BEAN domain has a characteristic three-dimensional structure composed of two square bracket-like elements that are antiparallel relative to each other. The HABAS domain contains a four-stranded open β-sheet with a GD-box-like motif in one of the β-strands and the adjoining loop. The BEAN domain is inserted not only in the bacterial RNAP-β', but also in the archaeal version of universal ribosomal protein L10. The HABAS domain is inserted in several metabolic proteins. The phylogenetic distributions of bacterial lineage-specific insertional domains of β and β' subunits of RNAP follow the Tree of Life. The presence of insertional domains can help establish a relative timeline of events in the evolution of a protein because insertion is inferred to post-date the base domain. We discuss mechanisms that might account for the discovery of homologous insertional domains in non-equivalent locations in bacteria and archaea.
RNA 聚合酶（RNAP）的β和β'亚基是具有复杂多结构域架构的大型蛋白质，其中包括几个插入结构域。在这里，我们使用序列、实验确定的结构和 AlphaFold 结构预测来分析 RNAP-β 和 RNAP-β'的结构域组织。我们观察到细菌 RNAP-β 中的谱系特异性插入结构域属于我们称之为 BEAN（广泛嵌入附件）的一组。我们观察到细菌 RNAP-β'中的谱系特异性插入结构域属于我们称之为 HABAS（锤头/桶-三明治杂交）的一组。BEAN 结构域具有特征性的三维结构，由两个相对的正方形括号样元素组成。HABAS 结构域包含一个四股开放的β-片层，其中一个β-链和相邻的环中含有 GD 盒样基序。BEAN 结构域不仅插入细菌 RNAP-β'中，也插入到普遍核糖体蛋白 L10 的古菌版本中。HABAS 结构域插入到几个代谢蛋白中。RNAP 的β和β'亚基的细菌谱系特异性插入结构域的系统发育分布遵循生命之树。插入结构域的存在可以帮助确定蛋白质进化过程中事件的相对时间线，因为插入被推断发生在基本结构域之后。我们讨论了可能解释在细菌和古菌中在非等效位置发现同源插入结构域的机制。
