Molecular basis for protection of ribosomal protein L4 from cellular degradation

Huber, Ferdinand M.; Hoelz, André

doi:10.1038/ncomms14354

Molecular basis for protection of ribosomal protein L4 from cellular degradation

Journal Article · Thu Feb 02 00:00:00 EST 2017 · Nature Communications

DOI:https://doi.org/10.1038/ncomms14354· OSTI ID:1623872

Huber, Ferdinand M. ^[1]; Hoelz, André ^[2]

California Institute of Technology (CalTech), Pasadena, CA (United States). Division of Chemistry and Chemical Engineering; DOE/OSTI
California Institute of Technology (CalTech), Pasadena, CA (United States). Division of Chemistry and Chemical Engineering

Eukaryotic ribosome biogenesis requires the nuclear import of B80 nascent ribosomal proteins and the elimination of excess amounts by the cellular degradation machinery. Assembly chaperones recognize nascent unassembled ribosomal proteins and transport them together with karyopherins to their nuclear destination. We report the crystal structure of ribosomal protein L4 (RpL4) bound to its dedicated assembly chaperone of L4 (Acl4), revealing extensive interactions sequestering 70 exposed residues of the extended RpL4 loop. The observed molecular recognition fundamentally differs from canonical promiscuous chaperone–substrate interactions. We demonstrate that the eukaryote-specific RpL4 extension harbours overlapping binding sites for Acl4 and the nuclear transport factor Kap104, facilitating its continuous protection from the cellular degradation machinery. Thus, Acl4 serves a dual function to facilitate nuclear import and simultaneously protect unassembled RpL4 from the cellular degradation machinery.

View Accepted Manuscript (DOE)

Research Organization:: SLAC National Accelerator Laboratory (SLAC), Menlo Park, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: AC02-76SF00515

OSTI ID:: 1623872

Journal Information:: Nature Communications, Journal Name: Nature Communications Journal Issue: 1 Vol. 8; ISSN 2041-1723

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

References (52)

A versatile toolbox for PCR-based tagging of yeast genes: new fluorescent proteins, more markers and promoter substitution cassettes Janke, Carsten; Magiera, Maria M.; Rathfelder, Nicole Yeast, Vol. 21, Issue 11 https://doi.org/10.1002/yea.1142	journal	August 2004
Crystal structure of human Karyopherin β2 bound to the PY-NLS of Saccharomyces cerevisiae Nab2 Soniat, Michael; Sampathkumar, Parthasarathy; Collett, Garen Journal of Structural and Functional Genomics, Vol. 14, Issue 2 https://doi.org/10.1007/s10969-013-9150-1	journal	March 2013
In the absence of ribosomal RNA synthesis, the ribosomal proteins of HeLa Cells are synthesized normally and degraded rapidly Warner, Jonathan R. Journal of Molecular Biology, Vol. 115, Issue 3 https://doi.org/10.1016/0022-2836(77)90157-7	journal	September 1977
Crystal Structure of the Yeast Ribosomal Protein rpS3 in Complex with Its Chaperone Yar1 Holzer, Sandro; Ban, Nenad; Klinge, Sebastian Journal of Molecular Biology, Vol. 425, Issue 22 https://doi.org/10.1016/j.jmb.2013.08.022	journal	November 2013
Coordinated Ribosomal L4 Protein Assembly into the Pre-Ribosome Is Regulated by Its Eukaryote-Specific Extension Stelter, Philipp; Huber, Ferdinand M.; Kunze, Ruth Molecular Cell, Vol. 58, Issue 5 https://doi.org/10.1016/j.molcel.2015.03.029	journal	June 2015
Ribosome assembly in eukaryotes Fromont-Racine, Micheline; Senger, Bruno; Saveanu, Cosmin Gene, Vol. 313 https://doi.org/10.1016/s0378-1119(03)00629-2	journal	August 2003
Multiple sequence alignment with Clustal X Jeanmougin, François; Thompson, Julie D.; Gouy, Manolo Trends in Biochemical Sciences, Vol. 23, Issue 10 https://doi.org/10.1016/s0968-0004(98)01285-7	journal	October 1998
Ulp1-SUMO Crystal Structure and Genetic Analysis Reveal Conserved Interactions and a Regulatory Element Essential for Cell Growth in Yeast Mossessova, Elena; Lima, Christopher D. Molecular Cell, Vol. 5, Issue 5 https://doi.org/10.1016/s1097-2765(00)80326-3	journal	May 2000
Crystal Structure of a Tetradecameric Assembly of the Association Domain of Ca2+/Calmodulin-Dependent Kinase II Hoelz, André; Nairn, Angus C.; Kuriyan, John Molecular Cell, Vol. 11, Issue 5 https://doi.org/10.1016/s1097-2765(03)00171-0	journal	May 2003
Coupled GTPase and remodelling ATPase activities form a checkpoint for ribosome export Matsuo, Yoshitaka; Granneman, Sander; Thoms, Matthias Nature, Vol. 505, Issue 7481 https://doi.org/10.1038/nature12731	journal	November 2013
Symportin 1 chaperones 5S RNP assembly during ribosome biogenesis by occupying an essential rRNA-binding site Calviño, Fabiola R.; Kharde, Satyavati; Ori, Alessandro Nature Communications, Vol. 6, Issue 1 https://doi.org/10.1038/ncomms7510	journal	April 2015
Structural basis for nuclear import of splicing factors by human Transportin 3 Maertens, G. N.; Cook, N. J.; Wang, W. Proceedings of the National Academy of Sciences, Vol. 111, Issue 7 https://doi.org/10.1073/pnas.1320755111	journal	January 2014
Electrostatics of nanosystems: Application to microtubules and the ribosome Baker, N. A.; Sept, D.; Joseph, S. Proceedings of the National Academy of Sciences, Vol. 98, Issue 18, p. 10037-10041 https://doi.org/10.1073/pnas.181342398	journal	August 2001
Two nuclear mutations that block mitochondrial protein import in yeast. Yaffe, M. P.; Schatz, G. Proceedings of the National Academy of Sciences, Vol. 81, Issue 15 https://doi.org/10.1073/pnas.81.15.4819	journal	August 1984
Yar1 Protects the Ribosomal Protein Rps3 from Aggregation Koch, Barbara; Mitterer, Valentin; Niederhauser, Johannes Journal of Biological Chemistry, Vol. 287, Issue 26 https://doi.org/10.1074/jbc.m112.365791	journal	May 2012
Interaction of Nascent Chains with the Ribosomal Tunnel Proteins Rpl4, Rpl17, and Rpl39 of Saccharomyces cerevisiae Zhang, Ying; Wölfle, Tina; Rospert, Sabine Journal of Biological Chemistry, Vol. 288, Issue 47 https://doi.org/10.1074/jbc.m113.508283	journal	September 2013
ALSCRIPT: a tool to format multiple sequence alignments Barton, Geoffrey J. "Protein Engineering, Design and Selection", Vol. 6, Issue 1 https://doi.org/10.1093/protein/6.1.37	journal	January 1993
Generation, representation and flow of phase information in structure determination: recent developments in and around SHARP 2.0 Bricogne, G.; Vonrhein, C.; Flensburg, C. Acta Crystallographica Section D Biological Crystallography, Vol. 59, Issue 11 https://doi.org/10.1107/s0907444903017694	journal	October 2003
XDS Kabsch, Wolfgang Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2 https://doi.org/10.1107/s0907444909047337	journal	January 2010
The CCP4 suite programs for protein crystallography No authors listed Acta Crystallographica Section D Biological Crystallography, Vol. 50, Issue 5, p. 760-763 https://doi.org/10.1107/s0907444994003112	journal	September 1994
Synchronizing Nuclear Import of Ribosomal Proteins with Ribosome Assembly Kressler, D.; Bange, G.; Ogawa, Y. Science, Vol. 338, Issue 6107 https://doi.org/10.1126/science.1226960	journal	November 2012
SQT1, which encodes an essential WD domain protein of Saccharomyces cerevisiae, suppresses dominant-negative mutations of the ribosomal protein gene QSR1. Eisinger, D. P.; Dick, F. A.; Denke, E. Molecular and Cellular Biology, Vol. 17, Issue 9 https://doi.org/10.1128/mcb.17.9.5146	journal	September 1997
MolProbity: all-atom contacts and structure validation for proteins and nucleic acids B., Chen, Vincent; C., Richardson, David; S., Richardson, Jane The University of North Carolina at Chapel Hill University Libraries https://doi.org/10.17615/m2an-p252	text	January 2007
A conserved quality-control pathway that mediates degradation of unassembled ribosomal proteins Sung, Min-Kyung; Porras-Yakushi, Tanya R.; Reitsma, Justin M. eLife, Vol. 5 https://doi.org/10.7554/elife.19105	journal	August 2016
Synthesis and turnover of ribosomal proteins in the absence of 60S subunit assembly in Saccharomyces cerevisiae Gorenstein, Charles; Warner, Jonathan R. Molecular and General Genetics MGG, Vol. 157, Issue 3 https://doi.org/10.1007/BF00268670	journal	January 1977
Computational studies of polyurethanases from Pseudomonas do Canto, Vanessa Petry; Thompson, Claudia Elizabeth; Netz, Paulo Augusto Journal of Molecular Modeling, Vol. 27, Issue 2 https://doi.org/10.1007/s00894-021-04671-x	journal	January 2021
Ribosome assembly in eukaryotes Fromont-Racine, Micheline; Senger, Bruno; Saveanu, Cosmin Gene, Vol. 313 https://doi.org/10.1016/S0378-1119(03)00629-2	journal	August 2003
Multiple sequence alignment with Clustal X Jeanmougin, François; Thompson, Julie D.; Gouy, Manolo Trends in Biochemical Sciences, Vol. 23, Issue 10 https://doi.org/10.1016/S0968-0004(98)01285-7	journal	October 1998
Ulp1-SUMO Crystal Structure and Genetic Analysis Reveal Conserved Interactions and a Regulatory Element Essential for Cell Growth in Yeast Mossessova, Elena; Lima, Christopher D. Molecular Cell, Vol. 5, Issue 5 https://doi.org/10.1016/S1097-2765(00)80326-3	journal	May 2000
Crystal Structure of a Tetradecameric Assembly of the Association Domain of Ca2+/Calmodulin-Dependent Kinase II Hoelz, André; Nairn, Angus C.; Kuriyan, John Molecular Cell, Vol. 11, Issue 5 https://doi.org/10.1016/S1097-2765(03)00171-0	journal	May 2003
Driving ribosome assembly Kressler, Dieter; Hurt, Ed; Baβler, Jochen Biochimica et Biophysica Acta (BBA) - Molecular Cell Research, Vol. 1803, Issue 6 https://doi.org/10.1016/j.bbamcr.2009.10.009	journal	June 2010
Rules for Nuclear Localization Sequence Recognition by Karyopherinβ2 Lee, Brittany J.; Cansizoglu, Ahmet E.; Süel, Katherine E. Cell, Vol. 126, Issue 3 https://doi.org/10.1016/j.cell.2006.05.049	journal	August 2006
Ribosomes: Lifting the Nuclear Export Ban Johnson, Arlen W. Current Biology, Vol. 24, Issue 3 https://doi.org/10.1016/j.cub.2013.12.013	journal	February 2014
A ‘garbage can’ for ribosomes: how eukaryotes degrade their ribosomes Lafontaine, Denis L. J. Trends in Biochemical Sciences, Vol. 35, Issue 5 https://doi.org/10.1016/j.tibs.2009.12.006	journal	May 2010
Co-translational capturing of nascent ribosomal proteins by their dedicated chaperones Pausch, Patrick; Singh, Ujjwala; Ahmed, Yasar Luqman Nature Communications, Vol. 6, Issue 1 https://doi.org/10.1038/ncomms8494	journal	June 2015
Noncoding RNAs in eukaryotic ribosome biogenesis and function Lafontaine, Denis L. J. Nature Structural & Molecular Biology, Vol. 22, Issue 1 https://doi.org/10.1038/nsmb.2939	journal	January 2015
Cavin1 intrinsically disordered domains are essential for fuzzy electrostatic interactions and caveola formation Tillu, Vikas A.; Rae, James; Gao, Ya Nature Communications, Vol. 12, Issue 1 https://doi.org/10.1038/s41467-021-21035-4	journal	February 2021
Yar1 Protects the Ribosomal Protein Rps3 from Aggregation Koch, Barbara; Mitterer, Valentin; Niederhauser, Johannes Journal of Biological Chemistry, Vol. 287, Issue 26 https://doi.org/10.1074/jbc.M112.365791	journal	May 2012
Interaction of Nascent Chains with the Ribosomal Tunnel Proteins Rpl4, Rpl17, and Rpl39 of Saccharomyces cerevisiae Zhang, Ying; Wölfle, Tina; Rospert, Sabine Journal of Biological Chemistry, Vol. 288, Issue 47 https://doi.org/10.1074/jbc.M113.508283	journal	September 2013
Piecemeal Microautophagy of Nucleus in Saccharomyces cerevisiae Roberts, Paul; Moshitch-Moshkovitz, Sharon; Kvam, Erik Molecular Biology of the Cell, Vol. 14, Issue 1 https://doi.org/10.1091/mbc.e02-08-0483	journal	January 2003
MolProbity: all-atom contacts and structure validation for proteins and nucleic acids Davis, I. W.; Leaver-Fay, A.; Chen, V. B. Nucleic Acids Research, Vol. 35, Issue Web Server https://doi.org/10.1093/nar/gkm216	journal	May 2007
A short history of SHELX Sheldrick, George M. Acta Crystallographica Section A Foundations of Crystallography, Vol. 64, Issue 1, p. 112-122 https://doi.org/10.1107/S0108767307043930	journal	December 2007
Generation, representation and flow of phase information in structure determination: recent developments in and around SHARP 2.0 Bricogne, G.; Vonrhein, C.; Flensburg, C. Acta Crystallographica Section D Biological Crystallography, Vol. 59, Issue 11 https://doi.org/10.1107/S0907444903017694	journal	October 2003
Coot model-building tools for molecular graphics Emsley, Paul; Cowtan, Kevin Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12, p. 2126-2132 https://doi.org/10.1107/S0907444904019158	journal	November 2004
XDS Kabsch, Wolfgang Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2 https://doi.org/10.1107/S0907444909047337	journal	January 2010
PHENIX: a comprehensive Python-based system for macromolecular structure solution Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221 https://doi.org/10.1107/S0907444909052925	journal	January 2010
Structure of trypanothione reductase from Crithidia fasciculata at 2.6 Å resolution; enzyme–NADP interactions at 2.8 Å resolution Bailey, S.; Fairlamb, A. H.; Hunter, W. N. Acta Crystallographica Section D Biological Crystallography, Vol. 50, Issue 2 https://doi.org/10.1107/S0907444993011898	journal	March 1994
The Structure of the Eukaryotic Ribosome at 3.0 A Resolution Ben-Shem, A.; Garreau de Loubresse, N.; Melnikov, S. Science, Vol. 334, Issue 6062 https://doi.org/10.1126/science.1212642	journal	November 2011
SQT1, which encodes an essential WD domain protein of Saccharomyces cerevisiae, suppresses dominant-negative mutations of the ribosomal protein gene QSR1. Eisinger, D. P.; Dick, F. A.; Denke, E. Molecular and Cellular Biology, Vol. 17, Issue 9 https://doi.org/10.1128/MCB.17.9.5146	journal	September 1997
The Dedicated Chaperone Acl4 Escorts Ribosomal Protein Rpl4 to Its Nuclear Pre-60S Assembly Site Pillet, Benjamin; García-Gómez, Juan J.; Pausch, Patrick PLOS Genetics, Vol. 11, Issue 10 https://doi.org/10.1371/journal.pgen.1005565	journal	October 2015
PHENIX: a comprehensive Python-based system for macromolecular structure solution. Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.45787	text	January 2010
A conserved quality-control pathway that mediates degradation of unassembled ribosomal proteins Sung, Min-Kyung; Porras-Yakushi, Tanya R.; Reitsma, Justin M. eLife, Vol. 5 https://doi.org/10.7554/eLife.19105	journal	August 2016

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Eukaryotic ribosome assembly, transport and quality control Peña, Cohue; Hurt, Ed; Panse, Vikram Govind Nature Structural & Molecular Biology, Vol. 24, Issue 9 https://doi.org/10.1038/nsmb.3454	journal	September 2017
Molecular basis for disassembly of an importin:ribosomal protein complex by the escortin Tsr2 Schütz, Sabina; Michel, Erich; Damberger, Fred F. Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-06160-x	journal	September 2018
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Dimerization of human Rio2 kinase/ATPase locks its ATP-binding site in an apo state Maurice, Frédérique; Pérébaskine, Natacha; Fribourg, Sébastien RNA Biology https://doi.org/10.1101/553800	journal	August 2019
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