BEAN and HABAS: Polyphyletic insertions in RNAP that point to deep evolutionary divergence of bacteria

Abstract

The {beta} and {beta} subunits of the RNA polymerase (RNAP) are large proteins with complex multi-domain architectures that include several insertional domains. Here, we analyze the multi-domain organizations of bacterial RNAP-{beta} and RNAP-{beta} using sequence, experimentally determined structures and AlphaFold structure predictions. We observe that bacterial lineage-specific domains in RNAP-{beta} belong to a group of domains that we call BEAN (Broadly Embedded ANnex) and that in RNAP-{beta}, bacterial lineage-specific domains are HAmmerhead/BArrel-Sandwich Hybrid (HABAS) domains. 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 {beta}-sheet with a GD-box-like motif in one of the {beta}-strands and the adjoining loop. The BEAN domain is identified not only in the bacterial RNAP-{beta}, but also in the archaeal version of universal ribosomal protein L10. The HABAS domain is observed as an insertional domain in several metabolic proteins. The phylogenetic distributions of bacterial lineage-specific insertional domains of {beta} and {beta} 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.