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Title: RNA regulatory networks diversified through curvature of the PUF protein scaffold

Abstract

Proteins bind and control mRNAs, directing their localization, translation and stability. Members of the PUF family of RNA-binding proteins control multiple mRNAs in a single cell, and play key roles in development, stem cell maintenance and memory formation. Here we identified the mRNA targets of a S. cerevisiae PUF protein, Puf5p, by ultraviolet-crosslinking-affinity purification and high-throughput sequencing (HITS-CLIP). The binding sites recognized by Puf5p are diverse, with variable spacer lengths between two specific sequences. Each length of site correlates with a distinct biological function. Crystal structures of Puf5p–RNA complexes reveal that the protein scaffold presents an exceptionally flat and extended interaction surface relative to other PUF proteins. In complexes with RNAs of different lengths, the protein is unchanged. A single PUF protein repeat is sufficient to induce broadening of specificity. Changes in protein architecture, such as alterations in curvature, may lead to evolution of mRNA regulatory networks.

Authors:
 [1];  [2];  [1];  [1];  [1];  [2];  [1]
  1. Univ. of Wisconsin, Madison, WI (United States). Dept. of Biochemistry
  2. National Institutes of Health, Research Triangle Park, NC (United States). Epigenetics and Stem Cell Biology Lab.
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES)
OSTI Identifier:
1214654
Grant/Contract Number:  
AC02-06CH11357; W-31-109-ENG-38
Resource Type:
Accepted Manuscript
Journal Name:
Nature Communications
Additional Journal Information:
Journal Volume: 6; Journal ID: ISSN 2041-1723
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Wilinski, Daniel, Qiu, Chen, Lapointe, Christopher P., Nevil, Markus, Campbell, Zachary T., Tanaka Hall, Traci M., and Wickens, Marvin. RNA regulatory networks diversified through curvature of the PUF protein scaffold. United States: N. p., 2015. Web. doi:10.1038/ncomms9213.
Wilinski, Daniel, Qiu, Chen, Lapointe, Christopher P., Nevil, Markus, Campbell, Zachary T., Tanaka Hall, Traci M., & Wickens, Marvin. RNA regulatory networks diversified through curvature of the PUF protein scaffold. United States. doi:https://doi.org/10.1038/ncomms9213
Wilinski, Daniel, Qiu, Chen, Lapointe, Christopher P., Nevil, Markus, Campbell, Zachary T., Tanaka Hall, Traci M., and Wickens, Marvin. Mon . "RNA regulatory networks diversified through curvature of the PUF protein scaffold". United States. doi:https://doi.org/10.1038/ncomms9213. https://www.osti.gov/servlets/purl/1214654.
@article{osti_1214654,
title = {RNA regulatory networks diversified through curvature of the PUF protein scaffold},
author = {Wilinski, Daniel and Qiu, Chen and Lapointe, Christopher P. and Nevil, Markus and Campbell, Zachary T. and Tanaka Hall, Traci M. and Wickens, Marvin},
abstractNote = {Proteins bind and control mRNAs, directing their localization, translation and stability. Members of the PUF family of RNA-binding proteins control multiple mRNAs in a single cell, and play key roles in development, stem cell maintenance and memory formation. Here we identified the mRNA targets of a S. cerevisiae PUF protein, Puf5p, by ultraviolet-crosslinking-affinity purification and high-throughput sequencing (HITS-CLIP). The binding sites recognized by Puf5p are diverse, with variable spacer lengths between two specific sequences. Each length of site correlates with a distinct biological function. Crystal structures of Puf5p–RNA complexes reveal that the protein scaffold presents an exceptionally flat and extended interaction surface relative to other PUF proteins. In complexes with RNAs of different lengths, the protein is unchanged. A single PUF protein repeat is sufficient to induce broadening of specificity. Changes in protein architecture, such as alterations in curvature, may lead to evolution of mRNA regulatory networks.},
doi = {10.1038/ncomms9213},
journal = {Nature Communications},
number = ,
volume = 6,
place = {United States},
year = {2015},
month = {9}
}

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Free Publicly Available Full Text
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Cited by: 19 works
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Works referenced in this record:

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    Works referencing / citing this record:

    A crystal structure of a collaborative RNA regulatory complex reveals mechanisms to refine target specificity
    journal, August 2019


    Toward Identifying Subnetworks from FBF Binding Landscapes in Caenorhabditis Spermatogenic or Oogenic Germlines
    journal, November 2018

    • Porter, Douglas F.; Prasad, Aman; Carrick, Brian H.
    • G3: Genes|Genomes|Genetics, Vol. 9, Issue 1
    • DOI: 10.1534/g3.118.200300

    Transcriptome-wide Identification of RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIP
    journal, April 2010


    Cell-free Formation of RNA Granules: Low Complexity Sequence Domains Form Dynamic Fibers within Hydrogels
    journal, May 2012


    Cooperativity in RNA-Protein Interactions: Global Analysis of RNA Binding Specificity
    journal, May 2012


    Modular peptide binding: From a comparison of natural binders to designed armadillo repeat proteins
    journal, February 2014

    • Reichen, Christian; Hansen, Simon; Plückthun, Andreas
    • Journal of Structural Biology, Vol. 185, Issue 2
    • DOI: 10.1016/j.jsb.2013.07.012

    PUF proteins: repression, activation and mRNA localization
    journal, February 2011


    CPEB: a life in translation
    journal, June 2007


    [20] Processing of X-ray diffraction data collected in oscillation mode
    book, January 1997


    Natural history and evolutionary principles of gene duplication in fungi
    journal, September 2007

    • Wapinski, Ilan; Pfeffer, Avi; Friedman, Nir
    • Nature, Vol. 449, Issue 7158
    • DOI: 10.1038/nature06107

    HITS-CLIP yields genome-wide insights into brain alternative RNA processing
    journal, November 2008

    • Licatalosi, Donny D.; Mele, Aldo; Fak, John J.
    • Nature, Vol. 456, Issue 7221
    • DOI: 10.1038/nature07488

    Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data
    journal, June 2011

    • Zhang, Chaolin; Darnell, Robert B.
    • Nature Biotechnology, Vol. 29, Issue 7
    • DOI: 10.1038/nbt.1873

    Fast gapped-read alignment with Bowtie 2
    journal, March 2012

    • Langmead, Ben; Salzberg, Steven L.
    • Nature Methods, Vol. 9, Issue 4
    • DOI: 10.1038/nmeth.1923

    RNA regulons: coordination of post-transcriptional events
    journal, July 2007

    • Keene, Jack D.
    • Nature Reviews Genetics, Vol. 8, Issue 7
    • DOI: 10.1038/nrg2111

    A protein-RNA specificity code enables targeted activation of an endogenous human transcript
    journal, June 2014

    • Campbell, Zachary T.; Valley, Cary T.; Wickens, Marvin
    • Nature Structural & Molecular Biology, Vol. 21, Issue 8
    • DOI: 10.1038/nsmb.2847

    Expanding the RNA-recognition code of PUF proteins
    journal, August 2014

    • Hall, Traci M. Tanaka
    • Nature Structural & Molecular Biology, Vol. 21, Issue 8
    • DOI: 10.1038/nsmb.2863

    Engineering RNA sequence specificity of Pumilio repeats
    journal, September 2006

    • Cheong, C. -G.; Hall, T. M. T.
    • Proceedings of the National Academy of Sciences, Vol. 103, Issue 37
    • DOI: 10.1073/pnas.0606294103

    A 5' cytosine binding pocket in Puf3p specifies regulation of mitochondrial mRNAs
    journal, November 2009

    • Zhu, D.; Stumpf, C. R.; Krahn, J. M.
    • Proceedings of the National Academy of Sciences, Vol. 106, Issue 48
    • DOI: 10.1073/pnas.0812079106

    Genome-wide analysis of mRNA targets for Caenorhabditis elegans FBF, a conserved stem cell regulator
    journal, February 2010

    • Kershner, Aaron M.; Kimble, Judith
    • Proceedings of the National Academy of Sciences, Vol. 107, Issue 8
    • DOI: 10.1073/pnas.1000495107

    Patterns and plasticity in RNA-protein interactions enable recruitment of multiple proteins through a single site
    journal, March 2012

    • Valley, C. T.; Porter, D. F.; Qiu, C.
    • Proceedings of the National Academy of Sciences, Vol. 109, Issue 16
    • DOI: 10.1073/pnas.1200521109

    Recurrent rewiring and emergence of RNA regulatory networks
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    • Wilinski, Daniel; Buter, Natascha; Klocko, Andrew D.
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    • DOI: 10.1073/pnas.1617777114

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    journal, August 1996

    • SenGupta, D. J.; Zhang, B.; Kraemer, B.
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    • DOI: 10.1073/pnas.93.16.8496

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    • DOI: 10.1073/pnas.97.26.14085

    Manipulation of FASTQ data with Galaxy
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    Pyicos: a versatile toolkit for the analysis of high-throughput sequencing data
    journal, October 2011


    YeastMine—an integrated data warehouse for Saccharomyces cerevisiae data as a multipurpose tool-kit
    journal, January 2012


    Post-transcriptional regulation through the HO 3'-UTR by Mpt5, a yeast homolog of Pumilio and FBF
    journal, February 2001


    MolProbity: all-atom contacts and structure validation for proteins and nucleic acids
    journal, May 2007

    • Davis, I. W.; Leaver-Fay, A.; Chen, V. B.
    • Nucleic Acids Research, Vol. 35, Issue Web Server
    • DOI: 10.1093/nar/gkm216

    Saccharomyces Genome Database: the genomics resource of budding yeast
    journal, November 2011

    • Cherry, J. M.; Hong, E. L.; Amundsen, C.
    • Nucleic Acids Research, Vol. 40, Issue D1
    • DOI: 10.1093/nar/gkr1029

    Nop9 binds the central pseudoknot region of 18S rRNA
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    Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
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    Coot model-building tools for molecular graphics
    journal, November 2004

    • Emsley, Paul; Cowtan, Kevin
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    • DOI: 10.1107/s0907444904019158

    PHENIX: a comprehensive Python-based system for macromolecular structure solution
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    • DOI: 10.1107/s0907444909052925

    CLIP Identifies Nova-Regulated RNA Networks in the Brain
    journal, November 2003


    RNA Protein Interaction in Neurons
    journal, July 2013


    Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
    journal, January 2010


    Pervasive and dynamic protein binding sites of the mRNA transcriptome in Saccharomyces cerevisiae
    journal, January 2013


    The PUF binding landscape in metazoan germ cells
    journal, May 2016


    Translational repression by PUF proteins in vitro
    journal, April 2010


    Puf1p acts in combination with other yeast Puf proteins to control mRNA stability
    journal, December 2007


    Extensive Association of Functionally and Cytotopically Related mRNAs with Puf Family RNA-Binding Proteins in Yeast
    journal, March 2004


    Control of Signaling in a MAP-kinase Pathway by an RNA-Binding Protein
    journal, February 2007


    Yeast Mitochondrial Biogenesis: A Role for the PUF RNA-Binding Protein Puf3p in mRNA Localization
    journal, June 2008


    Recurrent rewiring and emergence of RNA regulatory networks
    journal, March 2017

    • Wilinski, Daniel; Buter, Natascha; Klocko, Andrew D.
    • Proceedings of the National Academy of Sciences, Vol. 114, Issue 14
    • DOI: 10.1073/pnas.1617777114

    Nop9 binds the central pseudoknot region of 18S rRNA
    journal, January 2017


    The PUF binding landscape in metazoan germ cells
    journal, May 2016


    Toward Identifying Subnetworks from FBF Binding Landscapes in Caenorhabditis Spermatogenic or Oogenic Germlines
    journal, November 2018

    • Porter, Douglas F.; Prasad, Aman; Carrick, Brian H.
    • G3: Genes|Genomes|Genetics, Vol. 9, Issue 1
    • DOI: 10.1534/g3.118.200300

    A crystal structure of a collaborative RNA regulatory complex reveals mechanisms to refine target specificity
    journal, August 2019


    Protein-RNA networks revealed through covalent RNA marks
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    • Lapointe, Christopher P.; Wilinski, Daniel; Saunders, Harriet A. J.
    • Nature Methods, Vol. 12, Issue 12
    • DOI: 10.1038/nmeth.3651

    Multiple Puf proteins regulate the stability of ribosome biogenesis transcripts
    journal, September 2018


    Expanding RNA binding specificity and affinity of engineered PUF domains
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    • Zhao, Yang-Yang; Mao, Miao-Wei; Zhang, Wen-Jing
    • Nucleic Acids Research, Vol. 46, Issue 9
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    Distinct RNA-binding modules in a single PUF protein cooperate to determine RNA specificity
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    Regulation of LRG1 expression by RNA‐binding protein Puf5 in the budding yeast cell wall integrity pathway
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