Alvarez-Carreno, Claudia;
Huynh, Angela T;
Petrov, Anton S;
Orengo, Christine;
Williams, Loren Dean;
(2024)
BEAN and HABAS: Polyphyletic insertions in the DNA-directed RNA polymerase.
Protein Science
, 33
(11)
, Article e5194. 10.1002/pro.5194.
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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.
| Type: | Article |
|---|---|
| Title: | BEAN and HABAS: Polyphyletic insertions in the DNA-directed RNA polymerase |
| Location: | United States |
| Open access status: | An open access version is available from UCL Discovery |
| DOI: | 10.1002/pro.5194 |
| Publisher version: | https://doi.org/10.1002/pro.5194 |
| Language: | English |
| Additional information: | This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. © 2024 The Author(s). Protein Science published by Wiley Periodicals LLC on behalf of The Protein Society |
| Keywords: | Science & Technology, Life Sciences & Biomedicine, Biochemistry & Molecular Biology, bacteria, insertional domains, protein evolution, transcription, BETA-SUBUNIT, PROTEIN, EVOLUTION, ORIGIN, DOMAIN, CLASSIFICATION, PERFORMANCE, SUGGESTS |
| UCL classification: | UCL UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Structural and Molecular Biology |
| URI: | https://discovery.ucl.ac.uk/id/eprint/10207739 |
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