Transcription termination is essential for delineating the genetic information stored in DNA, as it establishes the boundaries of transcriptional units[1]. In yeast, there are two model pathways how termination of mRNA coding genes is organized: allosteric and torpedo models. The torpedo model considers that the unprotected free 5'-end of the mRNA transcript is digested by nuclease until it collides with RNA polymerase II (RNAPII), leading to dissociation from the template. Studies in the yeasts showed that exposed free 5'-end of RNA serves as an entry point for Rat1, a 5'-3' exonuclease. Stimulated by its cofactor Rai1, the Rai1/Rat1 (RR) complex greatly stimulates spontaneous termination [2]. However, the exact mechanism of how the RR complex is recruited to the site of transcription and how RNAPII is released from the DNA is unknown. Findings also suggest that the torpedo complex is recruited by Rtt103, recognizing Ser2 [3] and or Thr4 phosphorylation marks of RNAPII. This allows us to hypothesize that Rtt103 helps to recruit the 5'-3' RNA termination machinery to the site of transcription.
Due to the variations in Rai1/Rat1/Rtt103 complexes in mesophilic (yeast) and thermophilic organisms, we set out to investigate whether and how these complexes assemble in yeast Saccharomyces cerevisiae and fungi Chaetomium thermophilum. Using a combination of structure biology techniques including cryoEM, small-angle X-ray scattering (SAXS) and cross-linking mass spectrometry (XLMS) we reveal differences of how the two torpedo complexes assemble in mesophilic and thermophilic yeasts. Our observations suggest that thermophilic organisms have adapted protein-protein interfaces to favor the presence of highly structured elements, whereas mesophilic organisms prefer the utilization of unstructured elements that fold upon binding to their interaction partners.