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.

CEITEC Central European Institute of Technology Masaryk University Brno Czechia

CEITEC Central European Institute of Technology Masaryk University Brno Czechia; National Centre for Biomolecular Research Faculty of Science Masaryk University Brno Czechia

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

Institute of Biophysics and Physical Biochemistry Regensburg Center for Biochemistry University of Regensburg Regensburg Germany

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