BEAN and HABAS: Polyphyletic insertions in the DNA-directed RNA polymerase.

IF 4.5 3区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY
Protein Science Pub Date : 2024-11-01 DOI:10.1002/pro.5194
Claudia Alvarez-Carreño, Angela T Huynh, Anton S Petrov, Christine Orengo, Loren Dean Williams
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引用次数: 0

Abstract

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.

BEAN和HABAS:DNA定向RNA聚合酶中的多态插入。
RNA 聚合酶(RNAP)的 β 和 β' 亚基是大型蛋白质,具有复杂的多结构域结构,其中包括多个插入结构域。在这里,我们利用序列、实验测定的结构和 AlphaFold 结构预测分析了 RNAP-β 和 RNAP-β' 的结构域组织。我们观察到,细菌 RNAP-β 中的特异行插入结构域属于我们称之为 BEAN(广义嵌入附件)的一类。我们观察到,细菌 RNAP-β'中的行特异性插入结构域属于我们称之为 HABAS(锤头/桶状三明治混合体)的一类。BEAN 结构域具有特征性的三维结构,由两个方括号状元件组成,这两个元件相互之间是反平行的。HABAS 结构域包含一个四股开放的 β 片层,其中一条 β 链和相邻的环中有一个类似 GD 盒的图案。BEAN 结构域不仅存在于细菌的 RNAP-β'中,也存在于古生物版本的通用核糖体蛋白 L10 中。HABAS 结构域插入了多个代谢蛋白中。细菌 RNAP 的 β 和 β'亚基的特异性插入结构域的系统发育分布与生命之树一致。插入结构域的存在有助于确定蛋白质进化过程中发生事件的相对时间轴,因为插入结构域被推断为晚于基底结构域。我们讨论了在细菌和古细菌的非等同位置发现同源插入结构域的机制。
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来源期刊
Protein Science
Protein Science 生物-生化与分子生物学
CiteScore
12.40
自引率
1.20%
发文量
246
审稿时长
1 months
期刊介绍: Protein Science, the flagship journal of The Protein Society, is a publication that focuses on advancing fundamental knowledge in the field of protein molecules. The journal welcomes original reports and review articles that contribute to our understanding of protein function, structure, folding, design, and evolution. Additionally, Protein Science encourages papers that explore the applications of protein science in various areas such as therapeutics, protein-based biomaterials, bionanotechnology, synthetic biology, and bioelectronics. The journal accepts manuscript submissions in any suitable format for review, with the requirement of converting the manuscript to journal-style format only upon acceptance for publication. Protein Science is indexed and abstracted in numerous databases, including the Agricultural & Environmental Science Database (ProQuest), Biological Science Database (ProQuest), CAS: Chemical Abstracts Service (ACS), Embase (Elsevier), Health & Medical Collection (ProQuest), Health Research Premium Collection (ProQuest), Materials Science & Engineering Database (ProQuest), MEDLINE/PubMed (NLM), Natural Science Collection (ProQuest), and SciTech Premium Collection (ProQuest).
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