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

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.

Structural analysis of Red1 as a conserved scaffold of the RNA-targeting MTREC/PAXT complex

“…Our Y2H assays also show that Iss10 interacts with Mmi1, known to directly bind to meiotic transcripts 21 , indicating that Iss10 links Red1 to Mmi1 and hence to target transcripts. The same Y2H interaction was recently reported in 14 . In iss10Δ cells, the interaction between Red1 and Mmi1 is severely compromised but not completely lost 7, 26 .…”

“…In addition, we report a coiled-coil mediated homo-dimerization of Red1. Together with the recently reported crystal structure of the complex between Red1 and Mtl1 14 , these results provide molecular insights into the Red1 function as a scaffold of the MTREC complex, linking together individual sub-complexes. We also show that these MTREC features are conserved in the human analogue PAXT complex.…”

“…In iss10Δ cells, the interaction between Red1 and Mmi1 is severely compromised but not completely lost 7, 26 . It is thus possible that while Iss10-mediated interaction of Mmi1 with Red1 is important for MTREC activity, particularly in sub-optimal conditions, Mmi1 might also be recruited into MTREC by alternative interactions as proposed in 14 . The fact that the impact of the Iss10-Red1 interaction varies according to the environmental growth conditions might be linked to the Iss10 regulation by TORC1 27 .…”

“…Red1 consists of 711 residues (compared to the 1989 residues of its ZFC3H1 counterpart in human PAXT) and is predicted to be mostly disordered. Red1 interacts with the Mtl1 Arch domain via its zinc-finger containing domain at its C-terminus 14 . In human and S. cerevisiae , Mtl1 counterpart MTR4 has been structurally characterised 15 revealing molecular details of its interactions with its partners including the NEXT subunit ZCCHC8 16 and the RNA exosome to whom MTR4 presents the targeted RNA for degradation 17, 18 .…”

“…The subunit composition of the S. pombe MTREC and human PAXT complexes has been characterized by proteomics [6][7][8][9]11 . In MTREC, the Red1 protein was suggested to form a scaffold of the complex, interacting with multiple subunits and linking individual sub-modules together 6,7,14 . Red1 consists of 711 residues (compared to the 1989 residues of its ZFC3H1 counterpart in human PAXT) and is predicted to be mostly disordered.…”