The zinc-finger protein Red1 orchestrates MTREC submodules and binds the Mtl1 helicase arch domain

Tamás Fischer,Anusree Sivadas,Irmgard Sinning,Nikolay Dobrev,Komal Soni,Yasar Luqman Ahmed

doi:10.1038/s41467-021-23565-3

Tamás Fischer, Anusree Sivadas + Show 4 more

Open Access

https://doi.org/10.1038/s41467-021-23565-3

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Abstract

Cryptic unstable transcripts (CUTs) are rapidly degraded by the nuclear exosome in a process requiring the RNA helicase Mtr4 and specific adaptor complexes for RNA substrate recognition. The PAXT and MTREC complexes have recently been identified as homologous exosome adaptors in human and fission yeast, respectively. The eleven-subunit MTREC comprises the zinc-finger protein Red1 and the Mtr4 homologue Mtl1. Here, we use yeast two-hybrid and pull-down assays to derive a detailed interaction map. We show that Red1 bridges MTREC submodules and serves as the central scaffold. In the crystal structure of a minimal Mtl1/Red1 complex an unstructured region adjacent to the Red1 zinc-finger domain binds to both the Mtl1 KOW domain and stalk helices. This interaction extends the canonical interface seen in Mtr4-adaptor complexes. In vivo mutational analysis shows that this interface is essential for cell survival. Our results add to Mtr4 versatility and provide mechanistic insights into the MTREC complex.

Highlights

Cryptic unstable transcripts (CUTs) are rapidly degraded by the nuclear exosome in a process requiring the RNA helicase Mtr[4] and specific adaptor complexes for RNA substrate recognition
The nuclear exosome is a central player in this process, but the mechanism of how the exosome can selectively degrade pervasive transcripts and distinguish them from mRNAs is not well understood
The bestcharacterized adaptor complex is the TRAMP (Trf4/Air2/Mtr[4] polyadenylation) complex, which is involved in nuclear surveillance and turnover of sn/snoRNAs, pre-rRNAs, mRNAs, and ncRNAs

Summary

Introduction

Cryptic unstable transcripts (CUTs) are rapidly degraded by the nuclear exosome in a process requiring the RNA helicase Mtr[4] and specific adaptor complexes for RNA substrate recognition. In the crystal structure of a minimal Mtl1/Red[1] complex an unstructured region adjacent to the Red[1] zinc-finger domain binds to both the Mtl[1] KOW domain and stalk helices This interaction extends the canonical interface seen in Mtr4-adaptor complexes. The exosome is an evolutionarily conserved multi-subunit complex found in the cytosol and in the nucleus, and it is essential for cell viability[1,2] It comprises a catalytically inactive core composed of nine subunits, resembling a barrel-like structure[1,3].

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