Assembly of the Xrn2/Rat1-Rai1-Rtt103 termination complexes in mesophilic and thermophilic organisms

Alzbeta Dikunova; Nikola Noskova; Jan H Overbeck; Martin Polak; David Stelzig; David Zapletal; Karel Kubicek; Jiri Novacek; Remco Sprangers; Richard Stefl

doi:10.1016/j.str.2024.11.010

Assembly of the Xrn2/Rat1-Rai1-Rtt103 termination complexes in mesophilic and thermophilic organisms

Structure. 2024 Nov 29:S0969-2126(24)00500-8. doi: 10.1016/j.str.2024.11.010. Online ahead of print.

Authors

Affiliations

¹ CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czechia; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia.
² Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany.
³ CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czechia.
⁴ CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czechia; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia; Department of Condensed Matter Physics, Faculty of Science, Masaryk University, Brno, Czechia; Institute of Molecular Genetics of the Czech Academy of Sciences, v.v.i., Prague, Czechia.
⁵ CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czechia; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia. Electronic address: [email protected].

PMID: 39657659
DOI: 10.1016/j.str.2024.11.010

Abstract

The 5'-3' exoribonuclease Xrn2, known as Rat1 in yeasts, terminates mRNA transcription by RNA polymerase II (RNAPII). In the torpedo model of termination, the activity of Xrn2/Rat1 is enhanced by Rai1, which is recruited to the termination site by Rtt103, an adaptor protein binding to the RNAPII C-terminal domain (CTD). The overall architecture of the Xrn2/Rat1-Rai1-Rtt103 complex remains unknown. We combined structural biology methods to characterize the torpedo complex from Saccharomyces cerevisiae and Chaetomium thermophilum. Comparison of the structures from these organisms revealed a conserved protein core fold of the subunits, but significant variability in their interaction interfaces. We found that in the mesophile, Rtt103 utilizes an unstructured region to augment a Rai1 β-sheet, while in the thermophile Rtt103 binds to a C-terminal helix of Rai1 via its CTD-interacting domain with an α-helical fold. These different torpedo complex assemblies reflect adaptations to the environment and impact complex recruitment to RNAPII.

Keywords: NMR; RNAPII; cryo-EM; exonuclease; structure; termination; thermophiles; torpedo complex.