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Nat Commun. 2019 Jul 29;10(1):3393. doi: 10.1038/s41467-019-11339-x.

The MTR4 helicase recruits nuclear adaptors of the human RNA exosome using distinct arch-interacting motifs.

Author information

1
Department of Structural Cell Biology, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, D-82152, Martinsried, Germany.
2
Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Alle 3, 8000, Aarhus C, Denmark.
3
Center for Integrated Protein Science Munich (CIPSM) at Department of Chemistry, Technical University of Munich (TUM), 85747, Garching, Germany.
4
Institute of Structural Biology, Helmholtz-Zentrum München, 85764, Neuherberg, Germany.
5
Institute for Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ) at Johann Wolfgang Goethe-University, Frankfurt am Main, 60438, Germany.
6
Department of Structural Cell Biology, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, D-82152, Martinsried, Germany. sebastian.falk@univie.ac.at.
7
Max F. Perutz Laboratories, Department of Structural and Computational Biology, University of Vienna, Campus Vienna Biocenter 5, 1030, Vienna, Austria. sebastian.falk@univie.ac.at.
8
Department of Structural Cell Biology, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, D-82152, Martinsried, Germany. conti@biochem.mpg.de.

Abstract

The nuclear exosome and its essential co-factor, the RNA helicase MTR4, play crucial roles in several RNA degradation pathways. Besides unwinding RNA substrates for exosome-mediated degradation, MTR4 associates with RNA-binding proteins that function as adaptors in different RNA processing and decay pathways. Here, we identify and characterize the interactions of human MTR4 with a ribosome processing adaptor, NVL, and with ZCCHC8, an adaptor involved in the decay of small nuclear RNAs. We show that the unstructured regions of NVL and ZCCHC8 contain short linear motifs that bind the MTR4 arch domain in a mutually exclusive manner. These short sequences diverged from the arch-interacting motif (AIM) of yeast rRNA processing factors. Our results suggest that nuclear exosome adaptors have evolved canonical and non-canonical AIM sequences to target human MTR4 and demonstrate the versatility and specificity with which the MTR4 arch domain can recruit a repertoire of different RNA-binding proteins.

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