Structural basis of 3;#8242;-end poly(A) RNA recognition by LARP1

Kozlov, Guennadi; Mattijssen, Sandy; Jiang, Jianning; Nyandwi, Samuel; Sprules, Tara; Iben, James R.; Coon, Steven L.; Gaidamakov, Sergei; Noronha, Anne M.; Wilds, Christopher J.; Maraia, Richard J.; Gehring, Kalle

doi:10.1093/nar/gkac696

Structural basis of 3;#8242;-end poly(A) RNA recognition by LARP1

Journal Article · 01 September 2022 · Nucleic Acids Res.

DOI:https://doi.org/10.1093/nar/gkac696· OSTI ID:1901100

Kozlov, Guennadi; Mattijssen, Sandy; Jiang, Jianning; Nyandwi, Samuel; Sprules, Tara; Iben, James R.; Coon, Steven L.; Gaidamakov, Sergei; Noronha, Anne M.; Wilds, Christopher J.; Maraia, Richard J.; Gehring, Kalle

Research Organization:: Advanced Photon Source (APS), Argonne National Laboratory (ANL), Argonne, IL (US)

Sponsoring Organization:: DOE - Office Of Science; NIH

OSTI ID:: 1901100

Journal Information:: Nucleic Acids Res., Journal Name: Nucleic Acids Res. Journal Issue: (16) Vol. 50

Country of Publication:: United States

Language:: ENGLISH

References (58)

LARP1 post-transcriptionally regulates mTOR and contributes to cancer progression Mura, M.; Hopkins, T. G.; Michael, T. Oncogene, Vol. 34, Issue 39 https://doi.org/10.1038/onc.2014.428	journal	December 2014
Macromolecular TLS Refinement in REFMAC at Moderate Resolutions Winn, Martyn D.; Murshudov, Garib N.; Papiz, Miroslav Z. Methods in Enzymology https://doi.org/10.1016/S0076-6879(03)74014-2	book	January 2003
Structural dynamics in the La-module of La-related proteins Lizarrondo, Javier; Dock-Bregeon, Anne-Catherine; Martino, Luigi RNA Biology, Vol. 18, Issue 2 https://doi.org/10.1080/15476286.2020.1733799	journal	March 2020
Single-Molecule Imaging of mRNA Localization and Regulation during the Integrated Stress Response Wilbertz, Johannes H.; Voigt, Franka; Horvathova, Ivana Molecular Cell, Vol. 73, Issue 5 https://doi.org/10.1016/j.molcel.2018.12.006	journal	March 2019
[20] Processing of X-ray diffraction data collected in oscillation mode Otwinowski, Zbyszek; Minor, Wladek Macromolecular Crystallography Part A, 307-326 https://doi.org/10.1016/S0076-6879(97)76066-X	book	January 1997
Synergic interplay of the La motif, RRM1 and the interdomain linker of LARP6 in the recognition of collagen mRNA expands the RNA binding repertoire of the La module Martino, Luigi; Pennell, Simon; Kelly, Geoff Nucleic Acids Research, Vol. 43, Issue 1 https://doi.org/10.1093/nar/gku1287	journal	December 2014
The association of a La module with the PABP-interacting motif PAM2 is a recurrent evolutionary process that led to the neofunctionalization of La-related proteins Merret, Rémy; Martino, Luigi; Bousquet-Antonelli, Cécile RNA, Vol. 19, Issue 1 https://doi.org/10.1261/rna.035469.112	journal	November 2012
Controversies around the function of LARP1 Berman, Andrea J.; Thoreen, Carson C.; Dedeic, Zinaida RNA Biology, Vol. 18, Issue 2 https://doi.org/10.1080/15476286.2020.1733787	journal	April 2020
C. elegans La-related protein, LARP-1, localizes to germline P bodies and attenuates Ras-MAPK signaling during oogenesis Nykamp, K.; Lee, M. -H.; Kimble, J. RNA, Vol. 14, Issue 7 https://doi.org/10.1261/rna.1066008	journal	May 2008
Structural Basis for Recognition and Sequestration of UUUOH 3′ Temini of Nascent RNA Polymerase III Transcripts by La, a Rheumatic Disease Autoantigen Teplova, Marianna; Yuan, Yu-Ren; Phan, Anh Tuân Molecular Cell, Vol. 21, Issue 1 https://doi.org/10.1016/j.molcel.2005.10.027	journal	January 2006
La-Related Protein 4 Binds Poly(A), Interacts with the Poly(A)-Binding Protein MLLE Domain via a Variant PAM2w Motif, and Can Promote mRNA Stability Yang, Ruiqing; Gaidamakov, Sergei A.; Xie, Jingwei Molecular and Cellular Biology, Vol. 31, Issue 3 https://doi.org/10.1128/MCB.01162-10	journal	February 2011
AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models Varadi, Mihaly; Anyango, Stephen; Deshpande, Mandar Nucleic Acids Research, Vol. 50, Issue D1 https://doi.org/10.1093/nar/gkab1061	journal	November 2021
LARP1 functions as a molecular switch for mTORC1-mediated translation of an essential class of mRNAs Hong, Sungki; Freeberg, Mallory A.; Han, Ting eLife, Vol. 6 https://doi.org/10.7554/eLife.25237	journal	June 2017
The Yeast La Protein Is Required for the 3′ Endonucleolytic Cleavage That Matures tRNA Precursors Yoo, Christopher J.; Wolin, Sandra L. Cell, Vol. 89, Issue 3 https://doi.org/10.1016/S0092-8674(00)80220-2	journal	May 1997
Phaser crystallographic software McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D. Journal of Applied Crystallography, Vol. 40, Issue 4 https://doi.org/10.1107/S0021889807021206	journal	July 2007
Structural basis for recognition of human 7SK long noncoding RNA by the La-related protein Larp7 Eichhorn, Catherine D.; Yang, Yuan; Repeta, Lucas Proceedings of the National Academy of Sciences, Vol. 115, Issue 28 https://doi.org/10.1073/pnas.1806276115	journal	June 2018
The mTOR regulated RNA-binding protein LARP1 requires PABPC1 for guided mRNA interaction Smith, Ewan M.; Benbahouche, Nour El Houda; Morris, Katherine Nucleic Acids Research, Vol. 49, Issue 1 https://doi.org/10.1093/nar/gkaa1189	journal	December 2020
The LARP1 La-Module recognizes both ends of TOP mRNAs Al-Ashtal, Hiba A.; Rubottom, Courtney M.; Leeper, Thomas C. RNA Biology https://doi.org/10.1080/15476286.2019.1669404	journal	October 2019
A La protein requirement for efficient pre-tRNA folding Chakshusmathi, G. The EMBO Journal, Vol. 22, Issue 24 https://doi.org/10.1093/emboj/cdg625	journal	December 2003
JPred4: a protein secondary structure prediction server Drozdetskiy, Alexey; Cole, Christian; Procter, James Nucleic Acids Research, Vol. 43, Issue W1 https://doi.org/10.1093/nar/gkv332	journal	April 2015
Translational coregulation of 5′TOP mRNAs by TIA-1 and TIAR Damgaard, Christian Kroun; Lykke-Andersen, Jens Genes & Development, Vol. 25, Issue 19 https://doi.org/10.1101/gad.17355911	journal	October 2011
The isolated La-module of LARP1 mediates 3’ poly(A) protection and mRNA stabilization, dependent on its intrinsic PAM2 binding to PABPC1 Mattijssen, Sandy; Kozlov, Guennadi; Gaidamakov, Sergei RNA Biology, Vol. 18, Issue 2 https://doi.org/10.1080/15476286.2020.1860376	journal	December 2020
LARP1 specifically recognizes the 3′ terminus of poly(A) mRNA Aoki, Kazuma; Adachi, Shungo; Homoto, Masae FEBS Letters, Vol. 587, Issue 14 https://doi.org/10.1016/j.febslet.2013.05.035	journal	May 2013
CDK1 couples proliferation with protein synthesis Haneke, Katharina; Schott, Johanna; Lindner, Doris Journal of Cell Biology, Vol. 219, Issue 3 https://doi.org/10.1083/jcb.201906147	journal	February 2020
The La and related RNA-binding proteins (LARPs): structures, functions, and evolving perspectives: The LARPs, La, and related RNA-binding proteins Maraia, Richard J.; Mattijssen, Sandy; Cruz-Gallardo, Isabel Wiley Interdisciplinary Reviews: RNA, Vol. 8, Issue 6 https://doi.org/10.1002/wrna.1430	journal	August 2017
The RNA-binding protein LARP1 is a post-transcriptional regulator of survival and tumorigenesis in ovarian cancer Hopkins, Thomas G.; Mura, Manuela; Al-Ashtal, Hiba A. Nucleic Acids Research, Vol. 44, Issue 3 https://doi.org/10.1093/nar/gkv1515	journal	December 2015
LARP1 and LARP4: up close with PABP for mRNA 3’ poly(A) protection and stabilization Mattijssen, Sandy; Kozlov, Guennadi; Fonseca, Bruno D. RNA Biology, Vol. 18, Issue 2 https://doi.org/10.1080/15476286.2020.1868753	journal	January 2021
Getting to the end of RNA: Structural analysis of protein recognition of 5′ and 3′ termini Curry, Stephen; Kotik-Kogan, Olga; Conte, Maria R. Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, Vol. 1789, Issue 9-10 https://doi.org/10.1016/j.bbagrm.2009.07.003	journal	September 2009
LARP4A recognizes polyA RNA via a novel binding mechanism mediated by disordered regions and involving the PAM2w motif, revealing interplay between PABP, LARP4A and mRNA Cruz-Gallardo, Isabel; Martino, Luigi; Kelly, Geoff Nucleic Acids Research, Vol. 47, Issue 8 https://doi.org/10.1093/nar/gkz144	journal	March 2019
LARP4 mRNA codon-tRNA match contributes to LARP4 activity for ribosomal protein mRNA poly(A) tail length protection Mattijssen, Sandy; Arimbasseri, Aneeshkumar G.; Iben, James R. eLife, Vol. 6 https://doi.org/10.7554/eLife.28889	journal	September 2017
The Phenix software for automated determination of macromolecular structures Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor Methods, Vol. 55, Issue 1 https://doi.org/10.1016/j.ymeth.2011.07.005	journal	September 2011
Mammalian stress granules and P bodies at a glance Riggs, Claire L.; Kedersha, Nancy; Ivanov, Pavel Journal of Cell Science, Vol. 133, Issue 16 https://doi.org/10.1242/jcs.242487	journal	August 2020
La-related Protein 1 (LARP1) Represses Terminal Oligopyrimidine (TOP) mRNA Translation Downstream of mTOR Complex 1 (mTORC1) Fonseca, Bruno D.; Zakaria, Chadi; Jia, Jian-Jun Journal of Biological Chemistry, Vol. 290, Issue 26 https://doi.org/10.1074/jbc.M114.621730	journal	May 2015
Structural Analysis Reveals Conformational Plasticity in the Recognition of RNA 3′ Ends by the Human La Protein Kotik-Kogan, Olga; Valentine, Elizabeth R.; Sanfelice, Domenico Structure, Vol. 16, Issue 6 https://doi.org/10.1016/j.str.2008.02.021	journal	June 2008
The La-related proteins: structures and interactions of a versatile superfamily of RNA-binding proteins Dock-Bregeon, Anne-Catherine; Lewis, Karen A.; Conte, Maria R. RNA Biology https://doi.org/10.1080/15476286.2019.1695712	journal	December 2019
Conserved and divergent features of the structure and function of La and La-related proteins (LARPs) Bayfield, Mark A.; Yang, Ruiqing; Maraia, Richard J. Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, Vol. 1799, Issue 5-6 https://doi.org/10.1016/j.bbagrm.2010.01.011	journal	May 2010
NMRPipe: A multidimensional spectral processing system based on UNIX pipes Delaglio, Frank; Grzesiek, Stephan; Vuister, GeertenW. Journal of Biomolecular NMR, Vol. 6, Issue 3 https://doi.org/10.1007/BF00197809	journal	November 1995
La-related protein 1 (LARP1) repression of TOP mRNA translation is mediated through its cap-binding domain and controlled by an adjacent regulatory region Philippe, Lucas; Vasseur, Jean-Jacques; Debart, Françoise Nucleic Acids Research, Vol. 46, Issue 3 https://doi.org/10.1093/nar/gkx1237	journal	December 2017
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
Influence of nucleotide modifications at the C2’ position on the Hoogsteen base-paired parallel-stranded duplex of poly(A) RNA Copp, William; Denisov, Alexey Y.; Xie, Jingwei Nucleic Acids Research, Vol. 45, Issue 17 https://doi.org/10.1093/nar/gkx713	journal	August 2017
Structural analysis of cooperative RNA binding by the La motif and central RRM domain of human La protein Alfano, Caterina; Sanfelice, Domenico; Babon, Jeff Nature Structural & Molecular Biology, Vol. 11, Issue 4 https://doi.org/10.1038/nsmb747	journal	March 2004
PABP Cooperates with the CCR4-NOT Complex to Promote mRNA Deadenylation and Block Precocious Decay Yi, Hyerim; Park, Joha; Ha, Minju Molecular Cell, Vol. 70, Issue 6 https://doi.org/10.1016/j.molcel.2018.05.009	journal	June 2018
Global analysis of LARP1 translation targets reveals tunable and dynamic features of 5′ TOP motifs Philippe, Lucas; van den Elzen, Antonia M. G.; Watson, Maegan J. Proceedings of the National Academy of Sciences, Vol. 117, Issue 10 https://doi.org/10.1073/pnas.1912864117	journal	February 2020
XRN4 and LARP1 Are Required for a Heat-Triggered mRNA Decay Pathway Involved in Plant Acclimation and Survival during Thermal Stress Merret, Rémy; Descombin, Julie; Juan, Yu-ting Cell Reports, Vol. 5, Issue 5 https://doi.org/10.1016/j.celrep.2013.11.019	journal	December 2013
LARP4 Is Regulated by Tumor Necrosis Factor Alpha in a Tristetraprolin-Dependent Manner Mattijssen, Sandy; Maraia, Richard J. Molecular and Cellular Biology, Vol. 36, Issue 4 https://doi.org/10.1128/MCB.00804-15	journal	February 2016
The tandem zinc finger RNA binding domain of members of the tristetraprolin protein family Lai, Wi S.; Wells, Melissa L.; Perera, Lalith WIREs RNA, Vol. 10, Issue 4 https://doi.org/10.1002/wrna.1531	journal	March 2019
ATPase-Modulated Stress Granules Contain a Diverse Proteome and Substructure Jain, Saumya; Wheeler, Joshua R.; Walters, Robert W. Cell, Vol. 164, Issue 3 https://doi.org/10.1016/j.cell.2015.12.038	journal	January 2016
Structural basis for the recruitment of the human CCR4–NOT deadenylase complex by tristetraprolin Fabian, Marc R.; Frank, Filipp; Rouya, Christopher Nature Structural & Molecular Biology, Vol. 20, Issue 6 https://doi.org/10.1038/nsmb.2572	journal	May 2013
Structural insight into the mechanism of stabilization of the 7SK small nuclear RNA by LARP7 Uchikawa, Emiko; Natchiar, Kundhavai S.; Han, Xiao Nucleic Acids Research, Vol. 43, Issue 6 https://doi.org/10.1093/nar/gkv173	journal	March 2015
Structural basis of RNA conformational switching in the transcriptional regulator 7SK RNP Yang, Yuan; Liu, Shiheng; Egloff, Sylvain Molecular Cell, Vol. 82, Issue 9 https://doi.org/10.1016/j.molcel.2022.03.001	journal	May 2022
Single molecule poly(A) tail-seq shows LARP4 opposes deadenylation throughout mRNA lifespan with most impact on short tails Mattijssen, Sandy; Iben, James R.; Li, Tianwei eLife, Vol. 9 https://doi.org/10.7554/eLife.59186	journal	August 2020
Concerted action of poly(A) nucleases and decapping enzyme in mammalian mRNA turnover Yamashita, Akio; Chang, Tsung-Cheng; Yamashita, Yukiko Nature Structural & Molecular Biology, Vol. 12, Issue 12 https://doi.org/10.1038/nsmb1016	journal	November 2005
A Compendium of Genetic Modifiers of Mitochondrial Dysfunction Reveals Intra-organelle Buffering To, Tsz-Leung; Cuadros, Alejandro M.; Shah, Hardik Cell, Vol. 179, Issue 5 https://doi.org/10.1016/j.cell.2019.10.032	journal	November 2019
Structure of the La motif: a winged helix domain mediates RNA binding via a conserved aromatic patch Dong, Gang; Chakshusmathi, Ghadiyaram; Wolin, Sandra L. The EMBO Journal, Vol. 23, Issue 5 https://doi.org/10.1038/sj.emboj.7600115	journal	February 2004
Dali: a network tool for protein structure comparison Holm, Liisa; Sander, Chris Trends in Biochemical Sciences, Vol. 20, Issue 11 https://doi.org/10.1016/S0968-0004(00)89105-7	journal	November 1995
La-related protein 1 (LARP1) binds the mRNA cap, blocking eIF4F assembly on TOP mRNAs Lahr, Roni M.; Fonseca, Bruno D.; Ciotti, Gabrielle E. eLife, Vol. 6 https://doi.org/10.7554/eLife.24146	journal	April 2017
Antagonistic actions of two human Pan3 isoforms on global mRNA turnover Chen, Chyi-Ying A.; Zhang, Yueqiang; Xiang, Yu RNA, Vol. 23, Issue 9 https://doi.org/10.1261/rna.061556.117	journal	May 2017
A comprehensive analysis of the La-motif protein superfamily Bousquet-Antonelli, C.; Deragon, J. -M. RNA, Vol. 15, Issue 5 https://doi.org/10.1261/rna.1478709	journal	March 2009

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