Structural basis of eukaryotic transcription termination by the Rat1 exonuclease complex

Tatsuo Yanagisawa, Yuko Murayama, Haruhiko Ehara, Mie Goto, Mari Aoki and Shun-ichi Sekine ()
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Tatsuo Yanagisawa: RIKEN Center for Biosystems Dynamics Research
Yuko Murayama: RIKEN Center for Biosystems Dynamics Research
Haruhiko Ehara: RIKEN Center for Biosystems Dynamics Research
Mie Goto: RIKEN Center for Biosystems Dynamics Research
Mari Aoki: RIKEN Center for Biosystems Dynamics Research
Shun-ichi Sekine: RIKEN Center for Biosystems Dynamics Research

Nature Communications, 2024, vol. 15, issue 1, 1-12

Abstract: Abstract The 5´–3´ exoribonuclease Rat1/Xrn2 is responsible for the termination of eukaryotic mRNA transcription by RNAPII. Rat1 forms a complex with its partner proteins, Rai1 and Rtt103, and acts as a “torpedo” to bind transcribing RNAPII and dissociate DNA/RNA from it. Here we report the cryo-electron microscopy structures of the Rat1-Rai1-Rtt103 complex and three Rat1-Rai1-associated RNAPII complexes (type-1, type-1b, and type-2) from the yeast, Komagataella phaffii. The Rat1-Rai1-Rtt103 structure revealed that Rat1 and Rai1 form a heterotetramer with a single Rtt103 bound between two Rai1 molecules. In the type-1 complex, Rat1-Rai1 forms a heterodimer and binds to the RNA exit site of RNAPII to extract RNA into the Rat1 exonuclease active site. This interaction changes the RNA path in favor of termination (the “pre-termination” state). The type-1b and type-2 complexes have no bound DNA/RNA, likely representing the “post-termination” states. These structures illustrate the termination mechanism of eukaryotic mRNA transcription.

Date: 2024
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DOI: 10.1038/s41467-024-52157-0

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