1
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Qiu C, Crittenden SL, Carrick BH, Dillard LB, Costa Dos Santos SJ, Dandey VP, Dutcher RC, Viverette EG, Wine RN, Woodworth J, Campbell ZT, Wickens M, Borgnia MJ, Kimble J, Tanaka Hall TM. A higher order PUF complex is central to regulation of C. elegans germline stem cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.14.599074. [PMID: 38915480 PMCID: PMC11195197 DOI: 10.1101/2024.06.14.599074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
PUF RNA-binding proteins are broadly conserved stem cell regulators. Nematode PUF proteins maintain germline stem cells (GSCs) and, with key partner proteins, repress differentiation mRNAs, including gld-1. Here we report that PUF protein FBF-2 and its partner LST-1 form a ternary complex that represses gld-1 via a pair of adjacent FBF-2 binding elements (FBEs) in its 3ÚTR. One LST-1 molecule links two FBF-2 molecules via motifs in the LST-1 intrinsically-disordered region; the gld-1 FBE pair includes a well-established 'canonical' FBE and a newly-identified noncanonical FBE. Remarkably, this FBE pair drives both full RNA repression in GSCs and full RNA activation upon differentiation. Discovery of the LST-1-FBF-2 ternary complex, the gld-1 adjacent FBEs, and their in vivo significance predicts an expanded regulatory repertoire of different assemblies of PUF-partner complexes in nematode germline stem cells. It also suggests analogous PUF controls may await discovery in other biological contexts and organisms.
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Affiliation(s)
- Chen Qiu
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | | | - Brian H. Carrick
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
- Current address: MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Lucas B. Dillard
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
- Current address: Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Stephany J. Costa Dos Santos
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
- These authors contributed equally to the manuscript and are listed in alphabetical order
| | - Venkata P. Dandey
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
- These authors contributed equally to the manuscript and are listed in alphabetical order
| | - Robert C. Dutcher
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
- These authors contributed equally to the manuscript and are listed in alphabetical order
| | - Elizabeth G. Viverette
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
- These authors contributed equally to the manuscript and are listed in alphabetical order
- Current address: Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Robert N. Wine
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
- These authors contributed equally to the manuscript and are listed in alphabetical order
| | - Jennifer Woodworth
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
- These authors contributed equally to the manuscript and are listed in alphabetical order
| | - Zachary T. Campbell
- Department of Anesthesiology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792, USA
| | - Marvin Wickens
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Mario J. Borgnia
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Judith Kimble
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Traci M. Tanaka Hall
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
- Lead contact
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2
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Hayashi S, Iwamoto K, Yoshihisa T. A non-canonical Puf3p-binding sequence regulates CAT5/COQ7 mRNA under both fermentable and respiratory conditions in budding yeast. PLoS One 2023; 18:e0295659. [PMID: 38100455 PMCID: PMC10723686 DOI: 10.1371/journal.pone.0295659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 11/23/2023] [Indexed: 12/17/2023] Open
Abstract
The Saccharomyces cerevisiae uses a highly glycolytic metabolism, if glucose is available, through appropriately suppressing mitochondrial functions except for some of them such as Fe/S cluster biogenesis. Puf3p, a Pumillio family protein, plays a pivotal role in modulating mitochondrial activity, especially during fermentation, by destabilizing its target mRNAs and/or by repressing their translation. Puf3p preferentially binds to 8-nt conserved binding sequences in the 3'-UTR of nuclear-encoded mitochondrial (nc-mitochondrial) mRNAs, leading to broad effects on gene expression under fermentable conditions. To further explore how Puf3p post-transcriptionally regulates nc-mitochondrial mRNAs in response to cell growth conditions, we initially focused on nc-mitochondrial mRNAs known to be enriched in monosomes in a glucose-rich environment. We unexpectedly found that one of the monosome-enriched mRNAs, CAT5/COQ7 mRNA, directly interacts with Puf3p through its non-canonical Puf3p binding sequence, which is generally less considered as a Puf3p binding site. Western blot analysis showed that Puf3p represses translation of Cat5p, regardless of culture in fermentable or respiratory medium. In vitro binding assay confirmed Puf3p's direct interaction with CAT5 mRNA via this non-canonical Puf3p-binding site. Although cat5 mutants of the non-canonical Puf3p-binding site grow normally, Cat5p expression is altered, indicating that CAT5 mRNA is a bona fide Puf3p target with additional regulatory factors acting through this sequence. Unlike other yeast PUF proteins, Puf3p uniquely regulates Cat5p by destabilizing mRNA and repressing translation, shedding new light on an unknown part of the Puf3p regulatory network. Given that pathological variants of human COQ7 lead to CoQ10 deficiency and yeast cat5Δ can be complemented by hCOQ7, our findings may also offer some insights into clinical aspects of COQ7-related disorders.
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Affiliation(s)
- Sachiko Hayashi
- Graduate School of Science, University of Hyogo, Ako-gun, Hyogo, Japan
| | - Kazumi Iwamoto
- Graduate School of Life Science, University of Hyogo, Ako-gun, Hyogo, Japan
| | - Tohru Yoshihisa
- Graduate School of Science, University of Hyogo, Ako-gun, Hyogo, Japan
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3
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Feng W, Zhang H, Cao Y, Yang C, Khalid MHB, Yang Q, Li W, Wang Y, Fu F, Yu H. Comprehensive Identification of the Pum Gene Family and Its Involvement in Kernel Development in Maize. Int J Mol Sci 2023; 24:14036. [PMID: 37762337 PMCID: PMC10530998 DOI: 10.3390/ijms241814036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/07/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
The Pumilio (Pum) RNA-binding protein family regulates post-transcription and plays crucial roles in stress response and growth. However, little is known about Pum in plants. In this study, a total of 19 ZmPum genes were identified and classified into two groups in maize. Although each ZmPum contains the conserved Pum domain, the ZmPum members show diversity in the gene and protein architectures, physicochemical properties, chromosomal location, collinearity, cis-elements, and expression patterns. The typical ZmPum proteins have eight α-helices repeats, except for ZmPum2, 3, 5, 7, and 14, which have fewer α-helices. Moreover, we examined the expression profiles of ZmPum genes and found their involvement in kernel development. Except for ZmPum2, ZmPum genes are expressed in maize embryos, endosperms, or whole seeds. Notably, ZmPum4, 7, and 13 exhibited dramatically high expression levels during seed development. The study not only contributes valuable information for further validating the functions of ZmPum genes but also provides insights for improvement and enhancing maize yield.
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Affiliation(s)
- Wenqi Feng
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Hongwanjun Zhang
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Yang Cao
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Cheng Yang
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Muhammad Hayder Bin Khalid
- National Research Centre of Intercropping, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan
| | - Qingqing Yang
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Wanchen Li
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Yingge Wang
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Fengling Fu
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Haoqiang Yu
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
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4
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Ye X, Yang W, Yi S, Zhao Y, Varani G, Jankowsky E, Yang F. Two distinct binding modes provide the RNA-binding protein RbFox with extraordinary sequence specificity. Nat Commun 2023; 14:701. [PMID: 36759600 PMCID: PMC9911399 DOI: 10.1038/s41467-023-36394-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 01/30/2023] [Indexed: 02/11/2023] Open
Abstract
Specificity of RNA-binding proteins for target sequences varies considerably. Yet, it is not understood how certain few proteins achieve markedly higher sequence specificity than most others. Here we show that the RNA Recognition Motif of RbFox accomplishes extraordinary sequence specificity by employing functionally and structurally distinct binding modes. Affinity measurements of RbFox for all binding site variants reveal the existence of two distinct binding modes. The first exclusively accommodates cognate and closely related RNAs with high affinity. The second mode accommodates all other RNAs with reduced affinity by imposing large thermodynamic penalties on non-cognate sequences. NMR studies indicate marked structural differences between the two binding modes, including large conformational rearrangements distant from the RNA-binding site. Distinct binding modes by a single RNA-binding module explain extraordinary sequence selectivity and reveal an unknown layer of functional diversity, cross talk and regulation in RNA-protein interactions.
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Affiliation(s)
- Xuan Ye
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Wen Yang
- Department of Chemistry, University of Washington, Seattle, WA, USA
- Greater Bay Biomedical InnoCenter, Shenzhen Bay Laboratory, Shenzhen, 518055, China
| | - Soon Yi
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Yanan Zhao
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150080, China
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, WA, USA.
| | - Eckhard Jankowsky
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
- Case Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
- Moderna Therapeutics, 200 Technology Square, Cambridge, MA, USA.
| | - Fan Yang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150080, China.
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5
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Sadée C, Hagler LD, Becker WR, Jarmoskaite I, Vaidyanathan PP, Denny SK, Greenleaf WJ, Herschlag D. A comprehensive thermodynamic model for RNA binding by the Saccharomyces cerevisiae Pumilio protein PUF4. Nat Commun 2022; 13:4522. [PMID: 35927243 PMCID: PMC9352680 DOI: 10.1038/s41467-022-31968-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 07/07/2022] [Indexed: 11/12/2022] Open
Abstract
Genomic methods have been valuable for identifying RNA-binding proteins (RBPs) and the genes, pathways, and processes they regulate. Nevertheless, standard motif descriptions cannot be used to predict all RNA targets or test quantitative models for cellular interactions and regulation. We present a complete thermodynamic model for RNA binding to the S. cerevisiae Pumilio protein PUF4 derived from direct binding data for 6180 RNAs measured using the RNA on a massively parallel array (RNA-MaP) platform. The PUF4 model is highly similar to that of the related RBPs, human PUM2 and PUM1, with one marked exception: a single favorable site of base flipping for PUF4, such that PUF4 preferentially binds to a non-contiguous series of residues. These results are foundational for developing and testing cellular models of RNA-RBP interactions and function, for engineering RBPs, for understanding the biophysical nature of RBP binding and the evolutionary landscape of RNAs and RBPs.
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Affiliation(s)
- Christoph Sadée
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Lauren D Hagler
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Winston R Becker
- Biophysics Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Inga Jarmoskaite
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Pavanapuresan P Vaidyanathan
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Protillion Biosciences, Burlingame, CA, USA
| | - Sarah K Denny
- Biophysics Program, Stanford University School of Medicine, Stanford, CA, USA
- Scribe Therapeutics, Alameda, CA, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Applied Physics, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Daniel Herschlag
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA.
- ChEM-H Institute, Stanford University, Stanford, CA, USA.
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6
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Qiu C, Wine RN, Campbell ZT, Hall T. Bipartite interaction sites differentially modulate RNA-binding affinity of a protein complex essential for germline stem cell self-renewal. Nucleic Acids Res 2022; 50:536-548. [PMID: 34908132 PMCID: PMC8754657 DOI: 10.1093/nar/gkab1220] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/23/2021] [Accepted: 12/08/2021] [Indexed: 01/09/2023] Open
Abstract
In C. elegans, PUF proteins promote germline stem cell self-renewal. Their functions hinge on partnerships with two proteins that are redundantly required for stem cell maintenance. Here we focus on understanding how the essential partner protein, LST-1, modulates mRNA regulation by the PUF protein, FBF-2. LST-1 contains two nonidentical sites of interaction with FBF-2, LST-1 A and B. Our crystal structures of complexes of FBF-2, LST-1 A, and RNA visualize how FBF-2 associates with LST-1 A versus LST-1 B. One commonality is that FBF-2 contacts the conserved lysine and leucine side chains in the KxxL motifs in LST-1 A and B. A key difference is that FBF-2 forms unique contacts with regions N- and C-terminal to the KxxL motif. Consequently, LST-1 A does not modulate the RNA-binding affinity of FBF-2, whereas LST-1 B decreases RNA-binding affinity of FBF-2. The N-terminal region of LST-1 B, which binds near the 5' end of RNA elements, is essential to modulate FBF-2 RNA-binding affinity, while the C-terminal residues of LST-1 B contribute strong binding affinity to FBF-2. We conclude that LST-1 has the potential to impact which mRNAs are regulated depending on the precise nature of engagement through its functionally distinct FBF binding sites.
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Affiliation(s)
- Chen Qiu
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Robert N Wine
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Zachary T Campbell
- Department of Biological Sciences, University of Texas at Dallas, Richardson, TX 75025, USA
| | - Traci M Tanaka Hall
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
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7
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The Role of Pumilio RNA Binding Protein in Plants. Biomolecules 2021; 11:biom11121851. [PMID: 34944494 PMCID: PMC8699478 DOI: 10.3390/biom11121851] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 12/01/2021] [Accepted: 12/07/2021] [Indexed: 11/27/2022] Open
Abstract
Eukaryotic organisms have a posttranscriptional/translational regulation system for the control of translational efficiency. RNA binding proteins (RBPs) have been known to control target genes. One type of protein, Pumilio (Pum)/Puf family RNA binding proteins, show a specific binding of 3′ untranslational region (3′ UTR) of target mRNA and function as a post-transcriptional/translational regulator in eukaryotic cells. Plant Pum protein is involved in development and biotic/abiotic stresses. Interestingly, Arabidopsis Pum can control target genes in a sequence-specific manner and rRNA processing in a sequence-nonspecific manner. As shown in in silico Pum gene expression analysis, Arabidopsis and rice Pum genes are responsive to biotic/abiotic stresses. Plant Pum can commonly contribute to host gene regulation at the post-transcriptional/translational step, as can mammalian Pum. However, the function of plant Pum proteins is not yet fully known. In this review, we briefly summarize the function of plant Pum in defense, development, and environmental responses via recent research and bioinformatics data.
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8
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Beaudoin J, Normant V, Brault A, Henry DJ, Bachand F, Massé É, Chua G, Labbé S. Fission yeast RNA-binding proteins Puf2 and Puf4 are involved in repression of ferrireductase Frp1 expression in response to iron. Mol Microbiol 2021; 116:1361-1377. [PMID: 34614242 DOI: 10.1111/mmi.14829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 10/01/2021] [Accepted: 10/02/2021] [Indexed: 11/30/2022]
Abstract
This study identifies a post-transcriptional mechanism of iron uptake regulation by Puf2 and Puf4 of the Pumilio and FBF (Puf) family of RNA-binding proteins in Schizosaccharomyces pombe. Cells expressing Puf2 and Puf4 stimulate decay of the frp1+ mRNA encoding a key enzyme of the reductive iron uptake pathway. Results consistently showed that frp1+ mRNA is stabilized in puf2Δ puf4Δ mutant cells under iron-replete conditions. As a result, puf2Δ puf4Δ cells exhibit an increased sensitivity to iron accompanied by enhanced ferrireductase activity. A pool of GFP-frp1+ 3'UTR RNAs was generated using a reporter gene containing the 3' untranslated region (UTR) of frp1+ that was under the control of a regulatable promoter. Results showed that Puf2 and Puf4 accelerate the destabilization of mRNAs containing the frp1+ 3'UTR which harbors two Pumilio response elements (PREs). Binding studies revealed that the PUM-homology RNA-binding domain of Puf2 and Puf4 expressed in Escherichia coli specifically interacts with PREs in the frp1+ 3'UTR. Using RNA immunoprecipitation in combination with reverse transcription qPCR assays, results showed that Puf2 and Puf4 interact preferentially with frp1+ mRNA under basal and iron-replete conditions, thereby contributing to inhibit Frp1 production and protecting cells against toxic levels of iron.
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Affiliation(s)
- Jude Beaudoin
- Département de Biochimie et de Génomique Fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Vincent Normant
- Département de Biochimie et de Génomique Fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Ariane Brault
- Département de Biochimie et de Génomique Fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Darren J Henry
- Biological Sciences, Integrative Cell Biology, University of Calgary, Calgary, Alberta, Canada
| | - François Bachand
- Département de Biochimie et de Génomique Fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Éric Massé
- Département de Biochimie et de Génomique Fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Gordon Chua
- Biological Sciences, Integrative Cell Biology, University of Calgary, Calgary, Alberta, Canada
| | - Simon Labbé
- Département de Biochimie et de Génomique Fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Quebec, Canada
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9
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Zhou W, Melamed D, Banyai G, Meyer C, Tuschl T, Wickens M, Cao J, Fields S. Expanding the binding specificity for RNA recognition by a PUF domain. Nat Commun 2021; 12:5107. [PMID: 34429425 PMCID: PMC8384837 DOI: 10.1038/s41467-021-25433-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 08/10/2021] [Indexed: 02/07/2023] Open
Abstract
The ability to design a protein to bind specifically to a target RNA enables numerous applications, with the modular architecture of the PUF domain lending itself to new RNA-binding specificities. For each repeat of the Pumilio-1 PUF domain, we generate a library that contains the 8,000 possible combinations of amino acid substitutions at residues critical for RNA contact. We carry out yeast three-hybrid selections with each library against the RNA recognition sequence for Pumilio-1, with any possible base present at the position recognized by the randomized repeat. We use sequencing to score the binding of each variant, identifying many variants with highly repeat-specific interactions. From these data, we generate an RNA binding code specific to each repeat and base. We use this code to design PUF domains against 16 RNAs, and find that some of these domains recognize RNAs with two, three or four changes from the wild type sequence.
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Affiliation(s)
- Wei Zhou
- grid.34477.330000000122986657Department of Genome Sciences, University of Washington, Seattle, Washington, USA ,grid.34477.330000000122986657Molecular and Cellular Biology Program, University of Washington, Seattle, Washington, USA ,grid.134907.80000 0001 2166 1519The Rockefeller University, New York, NY USA
| | - Daniel Melamed
- grid.34477.330000000122986657Department of Genome Sciences, University of Washington, Seattle, Washington, USA ,grid.18098.380000 0004 1937 0562Department of Evolutionary and Environmental Biology, University of Haifa, Haifa, Israel ,grid.18098.380000 0004 1937 0562Institute of Evolution, University of Haifa, Haifa, Israel
| | - Gabor Banyai
- grid.134907.80000 0001 2166 1519The Rockefeller University, New York, NY USA
| | - Cindy Meyer
- grid.134907.80000 0001 2166 1519The Rockefeller University, New York, NY USA
| | - Thomas Tuschl
- grid.134907.80000 0001 2166 1519The Rockefeller University, New York, NY USA
| | - Marvin Wickens
- grid.14003.360000 0001 2167 3675Department of Biochemistry, University of Wisconsin-Madison, Madison, WI USA
| | - Junyue Cao
- grid.134907.80000 0001 2166 1519The Rockefeller University, New York, NY USA
| | - Stanley Fields
- grid.34477.330000000122986657Department of Genome Sciences, University of Washington, Seattle, Washington, USA ,grid.34477.330000000122986657Department of Medicine, University of Washington, Seattle, Washington, USA
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10
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Criscuolo S, Gatti Iou M, Merolla A, Maragliano L, Cesca F, Benfenati F. Engineering REST-Specific Synthetic PUF Proteins to Control Neuronal Gene Expression: A Combined Experimental and Computational Study. ACS Synth Biol 2020; 9:2039-2054. [PMID: 32678979 DOI: 10.1021/acssynbio.0c00119] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Regulation of gene transcription is an essential mechanism for differentiation and adaptation of organisms. A key actor in this regulation process is the repressor element 1 (RE1)-silencing transcription factor (REST), a transcriptional repressor that controls more than 2000 putative target genes, most of which are neuron-specific. With the purpose of modulating REST expression, we exploited synthetic, ad hoc designed, RNA binding proteins (RBPs) able to specifically target and dock to REST mRNA. Among the various families of RBPs, we focused on the Pumilio and FBF (PUF) proteins, present in all eukaryotic organisms and controlling a variety of cellular functions. Here, a combined experimental and computational approach was used to design and test 8- and 16-repeat PUF proteins specific for REST mRNA. We explored the conformational properties and atomic features of the PUF-RNA recognition code by Molecular Dynamics simulations. Biochemical assays revealed that the 8- and 16-repeat PUF-based variants specifically bind the endogenous REST mRNA without affecting its translational regulation. The data also indicate a key role of stacking residues in determining the binding specificity. The newly characterized REST-specific PUF-based constructs act as excellent RNA-binding modules and represent a versatile and functional platform to specifically target REST mRNA and modulate its endogenous expression.
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Affiliation(s)
- Stefania Criscuolo
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova 16132, Italy
| | - Mahad Gatti Iou
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova 16132, Italy
| | - Assunta Merolla
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova 16132, Italy
- University of Genova, Genova 16132, Italy
| | - Luca Maragliano
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova 16132, Italy
- IRCCS Ospedale Policlinico San Martino, Genova 16132, Italy
| | - Fabrizia Cesca
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova 16132, Italy
- Department of Life Sciences, University of Trieste, Trieste 34127, Italy
| | - Fabio Benfenati
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova 16132, Italy
- IRCCS Ospedale Policlinico San Martino, Genova 16132, Italy
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11
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Jarmoskaite I, AlSadhan I, Vaidyanathan PP, Herschlag D. How to measure and evaluate binding affinities. eLife 2020; 9:e57264. [PMID: 32758356 PMCID: PMC7452723 DOI: 10.7554/elife.57264] [Citation(s) in RCA: 247] [Impact Index Per Article: 61.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 08/05/2020] [Indexed: 12/23/2022] Open
Abstract
Quantitative measurements of biomolecule associations are central to biological understanding and are needed to build and test predictive and mechanistic models. Given the advances in high-throughput technologies and the projected increase in the availability of binding data, we found it especially timely to evaluate the current standards for performing and reporting binding measurements. A review of 100 studies revealed that in most cases essential controls for establishing the appropriate incubation time and concentration regime were not documented, making it impossible to determine measurement reliability. Moreover, several reported affinities could be concluded to be incorrect, thereby impacting biological interpretations. Given these challenges, we provide a framework for a broad range of researchers to evaluate, teach about, perform, and clearly document high-quality equilibrium binding measurements. We apply this framework and explain underlying fundamental concepts through experimental examples with the RNA-binding protein Puf4.
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Affiliation(s)
- Inga Jarmoskaite
- Department of Biochemistry, Stanford UniversityStanfordUnited States
| | - Ishraq AlSadhan
- Department of Biochemistry, Stanford UniversityStanfordUnited States
| | | | - Daniel Herschlag
- Department of Biochemistry, Stanford UniversityStanfordUnited States
- Department of Chemical Engineering, Stanford UniversityStanfordUnited States
- Stanford ChEM-H, Stanford UniversityStanfordUnited States
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12
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Joshna CR, Saha P, Atugala D, Chua G, Muench DG. Plant PUF RNA-binding proteins: A wealth of diversity for post-transcriptional gene regulation. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 297:110505. [PMID: 32563454 DOI: 10.1016/j.plantsci.2020.110505] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 03/30/2020] [Accepted: 04/19/2020] [Indexed: 06/11/2023]
Abstract
PUF proteins are a conserved group of sequence-specific RNA-binding proteins that typically function to negatively regulate mRNA stability and translation. PUFs are well characterized at the molecular, structural and functional levels in Drosophila, Caenorhabditis elegans, budding yeast and human systems. Although usually encoded by small gene families, PUFs are over-represented in the plant genome, with up to 36 genes identified in a single species. PUF gene expansion in plants has resulted in extensive variability in gene expression patterns, diversity in predicted RNA-binding domain structure, and novel combinations of key amino acids involved in modular nucleotide binding. Reports on the characterization of plant PUF structure and function continue to expand, and include RNA target identification, subcellular distribution, crystal structure, and molecular mechanisms. Arabidopsis PUF mutant analysis has provided insight into biological function, and has identified roles related to development and environmental stress tolerance. The diversity of plant PUFs implies an extensive role for this family of proteins in post-transcriptional gene regulation. This diversity also holds the potential for providing novel RNA-binding domains that could be engineered to produce designer PUFs to alter the metabolism of target RNAs in the cell.
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Affiliation(s)
- Chris R Joshna
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N1N4, Canada
| | - Pritha Saha
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N1N4, Canada
| | - Dilini Atugala
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N1N4, Canada
| | - Gordon Chua
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N1N4, Canada
| | - Douglas G Muench
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N1N4, Canada.
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13
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Zhang J, Teramoto T, Qiu C, Wine RN, Gonzalez LE, Baserga SJ, Tanaka Hall TM. Nop9 recognizes structured and single-stranded RNA elements of preribosomal RNA. RNA (NEW YORK, N.Y.) 2020; 26:1049-1059. [PMID: 32371454 PMCID: PMC7373996 DOI: 10.1261/rna.075416.120] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 04/29/2020] [Indexed: 05/04/2023]
Abstract
Nop9 is an essential factor in the processing of preribosomal RNA. Its absence in yeast is lethal, and defects in the human ortholog are associated with breast cancer, autoimmunity, and learning/language impairment. PUF family RNA-binding proteins are best known for sequence-specific RNA recognition, and most contain eight α-helical repeats that bind to the RNA bases of single-stranded RNA. Nop9 is an unusual member of this family in that it contains eleven repeats and recognizes both RNA structure and sequence. Here we report a crystal structure of Saccharomyces cerevisiae Nop9 in complex with its target RNA within the 20S preribosomal RNA. This structure reveals that Nop9 brings together a carboxy-terminal module recognizing the 5' single-stranded region of the RNA and a bifunctional amino-terminal module recognizing the central double-stranded stem region. We further show that the 3' single-stranded region of the 20S target RNA adds sequence-independent binding energy to the RNA-Nop9 interaction. Both the amino- and carboxy-terminal modules retain the characteristic sequence-specific recognition of PUF proteins, but the amino-terminal module has also evolved a distinct interface, which allows Nop9 to recognize either single-stranded RNA sequences or RNAs with a combination of single-stranded and structured elements.
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Affiliation(s)
- Jun Zhang
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - Takamasa Teramoto
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
| | - Chen Qiu
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
| | - Robert N Wine
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
| | - Lauren E Gonzalez
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
| | - Susan J Baserga
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06520, USA
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Traci M Tanaka Hall
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
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14
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Najdrová V, Stairs CW, Vinopalová M, Voleman L, Doležal P. The evolution of the Puf superfamily of proteins across the tree of eukaryotes. BMC Biol 2020; 18:77. [PMID: 32605621 PMCID: PMC7325665 DOI: 10.1186/s12915-020-00814-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 06/18/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Eukaryotic gene expression is controlled by a number of RNA-binding proteins (RBP), such as the proteins from the Puf (Pumilio and FBF) superfamily (PufSF). These proteins bind to RNA via multiple Puf repeat domains, each of which specifically recognizes a single RNA base. Recently, three diversified PufSF proteins have been described in model organisms, each of which is responsible for the maturation of ribosomal RNA or the translational regulation of mRNAs; however, less is known about the role of these proteins across eukaryotic diversity. RESULTS Here, we investigated the distribution and function of PufSF RBPs in the tree of eukaryotes. We determined that the following PufSF proteins are universally conserved across eukaryotes and can be broadly classified into three groups: (i) Nop9 orthologues, which participate in the nucleolar processing of immature 18S rRNA; (ii) 'classical' Pufs, which control the translation of mRNA; and (iii) PUM3 orthologues, which are involved in the maturation of 7S rRNA. In nearly all eukaryotes, the rRNA maturation proteins, Nop9 and PUM3, are retained as a single copy, while mRNA effectors ('classical' Pufs) underwent multiple lineage-specific expansions. We propose that the variation in number of 'classical' Pufs relates to the size of the transcriptome and thus the potential mRNA targets. We further distinguished full set of PufSF proteins in divergent metamonad Giardia intestinalis and initiated their cellular and biochemical characterization. CONCLUSIONS Our data suggest that the last eukaryotic common ancestor (LECA) already contained all three types of PufSF proteins and that 'classical' Pufs then underwent lineage-specific expansions.
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Affiliation(s)
- Vladimíra Najdrová
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 252 50, Vestec, Czech Republic
| | - Courtney W Stairs
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123, Uppsala, Sweden
| | - Martina Vinopalová
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 252 50, Vestec, Czech Republic
| | - Luboš Voleman
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 252 50, Vestec, Czech Republic
| | - Pavel Doležal
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 252 50, Vestec, Czech Republic.
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15
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Park SH, Kim HS, Kalita PJ, Choi SB. Structural and functional similarities and differences in nucleolar Pumilio RNA-binding proteins between Arabidopsis and the charophyte Chara corallina. BMC PLANT BIOLOGY 2020; 20:230. [PMID: 32448230 PMCID: PMC7247198 DOI: 10.1186/s12870-020-02444-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 05/13/2020] [Indexed: 05/03/2023]
Abstract
BACKGROUND Pumilio RNA-binding proteins are evolutionarily conserved throughout eukaryotes and are involved in RNA decay, transport, and translation repression in the cytoplasm. Although a majority of Pumilio proteins function in the cytoplasm, two nucleolar forms have been reported to have a function in rRNA processing in Arabidopsis. The species of the genus Chara have been known to be most closely related to land plants, as they share several characteristics with modern Embryophyta. RESULTS In this study, we identified two putative nucleolar Pumilio protein genes, namely, ChPUM2 and ChPUM3, from the transcriptome of Chara corallina. Of the two ChPUM proteins, ChPUM2 was most similar in amino acid sequence (27% identity and 45% homology) and predicted protein structure to Arabidopsis APUM23, while ChPUM3 was similar to APUM24 (35% identity and 54% homology). The transient expression of 35S:ChPUM2-RFP and 35S:ChPUM3-RFP showed nucleolar localization of fusion proteins in tobacco leaf cells, similar to the expression of 35S:APUM23-GFP and 35S:APUM24-GFP. Moreover, 35S:ChPUM2 complemented the morphological defects of the apum23 phenotypes but not those of apum24, while 35S:ChPUM3 could not complement the apum23 and apum24 mutants. Similarly, the 35S:ChPUM2/apum23 plants rescued the pre-rRNA processing defect of apum23, but 35S:ChPUM3/apum24+/- plants did not rescue that of apum24. Consistent with these complementation results, a known target RNA-binding sequence at the end of the 18S rRNA (5'-GGAAUUGACGG) for APUM23 was conserved in Arabidopsis and C. corallina, whereas a target region of ITS2 pre-rRNA for APUM24 was 156 nt longer in C. corallina than in A. thaliana. Moreover, ChPUM2 and APUM23 were predicted to have nearly identical structures, but ChPUM3 and APUM24 have different structures in the 5th C-terminal Puf RNA-binding domain, which had a longer random coil in ChPUM3 than in APUM24. CONCLUSIONS ChPUM2 of C. corallina was functional in Arabidopsis, similar to APUM23, but ChPUM3 did not substitute for APUM24 in Arabidopsis. Protein homology modeling showed high coverage between APUM23 and ChPUM2, but displayed structural differences between APUM24 and ChPUM3. Together with the protein structure of ChPUM3 itself, a short ITS2 of Arabidopsis pre-rRNA may interrupt the binding of ChPUM3 to 3'-extended 5.8S pre-rRNA.
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Affiliation(s)
- Su Hyun Park
- Division of Bioscience and Bioinformatics, Myongji University, Yongin, Kyunggi-do, 449-728, South Korea
| | - Hyung-Sae Kim
- Division of Bioscience and Bioinformatics, Myongji University, Yongin, Kyunggi-do, 449-728, South Korea
| | - Prakash Jyoti Kalita
- Division of Bioscience and Bioinformatics, Myongji University, Yongin, Kyunggi-do, 449-728, South Korea
| | - Sang-Bong Choi
- Division of Bioscience and Bioinformatics, Myongji University, Yongin, Kyunggi-do, 449-728, South Korea.
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16
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Nithin C, Mukherjee S, Bahadur RP. A structure-based model for the prediction of protein-RNA binding affinity. RNA (NEW YORK, N.Y.) 2019; 25:1628-1645. [PMID: 31395671 PMCID: PMC6859855 DOI: 10.1261/rna.071779.119] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Accepted: 08/05/2019] [Indexed: 05/28/2023]
Abstract
Protein-RNA recognition is highly affinity-driven and regulates a wide array of cellular functions. In this study, we have curated a binding affinity data set of 40 protein-RNA complexes, for which at least one unbound partner is available in the docking benchmark. The data set covers a wide affinity range of eight orders of magnitude as well as four different structural classes. On average, we find the complexes with single-stranded RNA have the highest affinity, whereas the complexes with the duplex RNA have the lowest. Nevertheless, free energy gain upon binding is the highest for the complexes with ribosomal proteins and the lowest for the complexes with tRNA with an average of -5.7 cal/mol/Å2 in the entire data set. We train regression models to predict the binding affinity from the structural and physicochemical parameters of protein-RNA interfaces. The best fit model with the lowest maximum error is provided with three interface parameters: relative hydrophobicity, conformational change upon binding and relative hydration pattern. This model has been used for predicting the binding affinity on a test data set, generated using mutated structures of yeast aspartyl-tRNA synthetase, for which experimentally determined ΔG values of 40 mutations are available. The predicted ΔGempirical values highly correlate with the experimental observations. The data set provided in this study should be useful for further development of the binding affinity prediction methods. Moreover, the model developed in this study enhances our understanding on the structural basis of protein-RNA binding affinity and provides a platform to engineer protein-RNA interfaces with desired affinity.
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Affiliation(s)
- Chandran Nithin
- Computational Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Sunandan Mukherjee
- Computational Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Ranjit Prasad Bahadur
- Computational Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
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17
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Qiu C, Dutcher RC, Porter DF, Arava Y, Wickens M, Hall TM. Distinct RNA-binding modules in a single PUF protein cooperate to determine RNA specificity. Nucleic Acids Res 2019; 47:8770-8784. [PMID: 31294800 PMCID: PMC7145691 DOI: 10.1093/nar/gkz583] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 06/19/2019] [Accepted: 06/24/2019] [Indexed: 01/07/2023] Open
Abstract
PUF proteins, named for Drosophila Pumilio (PUM) and Caenorhabditis elegans fem-3-binding factor (FBF), recognize specific sequences in the mRNAs they bind and control. RNA binding by classical PUF proteins is mediated by a characteristic PUM homology domain (PUM-HD). The Puf1 and Puf2 proteins possess a distinct architecture and comprise a highly conserved subfamily among fungal species. Puf1/Puf2 proteins contain two types of RNA-binding domain: a divergent PUM-HD and an RNA recognition motif (RRM). They recognize RNAs containing UAAU motifs, often in clusters. Here, we report a crystal structure of the PUM-HD of a fungal Puf1 in complex with a dual UAAU motif RNA. Each of the two UAAU tetranucleotides are bound by a Puf1 PUM-HD forming a 2:1 protein-to-RNA complex. We also determined crystal structures of the Puf1 RRM domain that identified a dimerization interface. The PUM-HD and RRM domains act in concert to determine RNA-binding specificity: the PUM-HD dictates binding to UAAU, and dimerization of the RRM domain favors binding to dual UAAU motifs rather than a single UAAU. Cooperative action of the RRM and PUM-HD identifies a new mechanism by which multiple RNA-binding modules in a single protein collaborate to create a unique RNA-binding specificity.
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Affiliation(s)
- Chen Qiu
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Robert C Dutcher
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Douglas F Porter
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yoav Arava
- Department of Biology, Technion—Israel Institute of Technology, Haifa 32000, Israel
| | - Marvin Wickens
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA,Correspondence may also be addressed to Marvin Wickens. Tel: +1 608 263 0858; Fax: +1 608 262 9108;
| | - Traci M Tanaka Hall
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA,To whom correspondence should be addressed. Tel: +1 984 287 3556; Fax: +1 310 480 3055;
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18
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Jarmoskaite I, Denny SK, Vaidyanathan PP, Becker WR, Andreasson JOL, Layton CJ, Kappel K, Shivashankar V, Sreenivasan R, Das R, Greenleaf WJ, Herschlag D. A Quantitative and Predictive Model for RNA Binding by Human Pumilio Proteins. Mol Cell 2019; 74:966-981.e18. [PMID: 31078383 DOI: 10.1101/403006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 01/31/2019] [Accepted: 04/05/2019] [Indexed: 05/20/2023]
Abstract
High-throughput methodologies have enabled routine generation of RNA target sets and sequence motifs for RNA-binding proteins (RBPs). Nevertheless, quantitative approaches are needed to capture the landscape of RNA-RBP interactions responsible for cellular regulation. We have used the RNA-MaP platform to directly measure equilibrium binding for thousands of designed RNAs and to construct a predictive model for RNA recognition by the human Pumilio proteins PUM1 and PUM2. Despite prior findings of linear sequence motifs, our measurements revealed widespread residue flipping and instances of positional coupling. Application of our thermodynamic model to published in vivo crosslinking data reveals quantitative agreement between predicted affinities and in vivo occupancies. Our analyses suggest a thermodynamically driven, continuous Pumilio-binding landscape that is negligibly affected by RNA structure or kinetic factors, such as displacement by ribosomes. This work provides a quantitative foundation for dissecting the cellular behavior of RBPs and cellular features that impact their occupancies.
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Affiliation(s)
- Inga Jarmoskaite
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sarah K Denny
- Biophysics Program, Stanford University School of Medicine, Stanford, CA 94305, USA; Scribe Therapeutics, Berkeley, CA, 94704, USA
| | | | - Winston R Becker
- Biophysics Program, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Johan O L Andreasson
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Curtis J Layton
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kalli Kappel
- Biophysics Program, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | - Raashi Sreenivasan
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Rhiju Das
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Applied Physics, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
| | - Daniel Herschlag
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemistry, Stanford University, Stanford, CA 94305, USA; Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA; ChEM-H Institute, Stanford University, Stanford, CA 94305, USA.
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19
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Jarmoskaite I, Denny SK, Vaidyanathan PP, Becker WR, Andreasson JOL, Layton CJ, Kappel K, Shivashankar V, Sreenivasan R, Das R, Greenleaf WJ, Herschlag D. A Quantitative and Predictive Model for RNA Binding by Human Pumilio Proteins. Mol Cell 2019; 74:966-981.e18. [PMID: 31078383 DOI: 10.1016/j.molcel.2019.04.012] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 01/31/2019] [Accepted: 04/05/2019] [Indexed: 01/09/2023]
Abstract
High-throughput methodologies have enabled routine generation of RNA target sets and sequence motifs for RNA-binding proteins (RBPs). Nevertheless, quantitative approaches are needed to capture the landscape of RNA-RBP interactions responsible for cellular regulation. We have used the RNA-MaP platform to directly measure equilibrium binding for thousands of designed RNAs and to construct a predictive model for RNA recognition by the human Pumilio proteins PUM1 and PUM2. Despite prior findings of linear sequence motifs, our measurements revealed widespread residue flipping and instances of positional coupling. Application of our thermodynamic model to published in vivo crosslinking data reveals quantitative agreement between predicted affinities and in vivo occupancies. Our analyses suggest a thermodynamically driven, continuous Pumilio-binding landscape that is negligibly affected by RNA structure or kinetic factors, such as displacement by ribosomes. This work provides a quantitative foundation for dissecting the cellular behavior of RBPs and cellular features that impact their occupancies.
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Affiliation(s)
- Inga Jarmoskaite
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sarah K Denny
- Biophysics Program, Stanford University School of Medicine, Stanford, CA 94305, USA; Scribe Therapeutics, Berkeley, CA, 94704, USA
| | | | - Winston R Becker
- Biophysics Program, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Johan O L Andreasson
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Curtis J Layton
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kalli Kappel
- Biophysics Program, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | - Raashi Sreenivasan
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Rhiju Das
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Applied Physics, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
| | - Daniel Herschlag
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemistry, Stanford University, Stanford, CA 94305, USA; Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA; ChEM-H Institute, Stanford University, Stanford, CA 94305, USA.
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20
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Schatton D, Rugarli EI. A concert of RNA-binding proteins coordinates mitochondrial function. Crit Rev Biochem Mol Biol 2019; 53:652-666. [DOI: 10.1080/10409238.2018.1553927] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Désirée Schatton
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Elena I. Rugarli
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
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21
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Bhat VD, McCann KL, Wang Y, Fonseca DR, Shukla T, Alexander JC, Qiu C, Wickens M, Lo TW, Tanaka Hall TM, Campbell ZT. Engineering a conserved RNA regulatory protein repurposes its biological function in vivo. eLife 2019; 8:43788. [PMID: 30652968 PMCID: PMC6351103 DOI: 10.7554/elife.43788] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 01/15/2019] [Indexed: 12/18/2022] Open
Abstract
PUF (PUmilio/FBF) RNA-binding proteins recognize distinct elements. In C. elegans, PUF-8 binds to an 8-nt motif and restricts proliferation in the germline. Conversely, FBF-2 recognizes a 9-nt element and promotes mitosis. To understand how motif divergence relates to biological function, we first determined a crystal structure of PUF-8. Comparison of this structure to that of FBF-2 revealed a major difference in a central repeat. We devised a modified yeast 3-hybrid screen to identify mutations that confer recognition of an 8-nt element to FBF-2. We identified several such mutants and validated structurally and biochemically their binding to 8-nt RNA elements. Using genome engineering, we generated a mutant animal with a substitution in FBF-2 that confers preferential binding to the PUF-8 element. The mutant largely rescued overproliferation in animals that spontaneously generate tumors in the absence of puf-8. This work highlights the critical role of motif length in the specification of biological function.
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Affiliation(s)
- Vandita D Bhat
- Department of Biological Sciences, University of Texas Dallas, Richardson, United States
| | - Kathleen L McCann
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, United States
| | - Yeming Wang
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, United States
| | | | - Tarjani Shukla
- Department of Biological Sciences, University of Texas Dallas, Richardson, United States
| | | | - Chen Qiu
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, United States
| | - Marv Wickens
- Department of Biochemistry, University of Wisconsin-Madison, Madison, United States
| | - Te-Wen Lo
- Department of Biology, Ithaca College, Ithaca, United States
| | - Traci M Tanaka Hall
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, United States
| | - Zachary T Campbell
- Department of Biological Sciences, University of Texas Dallas, Richardson, United States
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22
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Qiu C, Bhat VD, Rajeev S, Zhang C, Lasley AE, Wine RN, Campbell ZT, Hall TMT. A crystal structure of a collaborative RNA regulatory complex reveals mechanisms to refine target specificity. eLife 2019; 8:48968. [PMID: 31397673 PMCID: PMC6697444 DOI: 10.7554/elife.48968] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 08/09/2019] [Indexed: 01/09/2023] Open
Abstract
In the Caenorhabditis elegans germline, fem-3 Binding Factor (FBF) partners with LST-1 to maintain stem cells. A crystal structure of an FBF-2/LST-1/RNA complex revealed that FBF-2 recognizes a short RNA motif different from the characteristic 9-nt FBF binding element, and compact motif recognition coincided with curvature changes in the FBF-2 scaffold. Previously, we engineered FBF-2 to favor recognition of shorter RNA motifs without curvature change (Bhat et al., 2019). In vitro selection of RNAs bound by FBF-2 suggested sequence specificity in the central region of the compact element. This bias, reflected in the crystal structure, was validated in RNA-binding assays. FBF-2 has the intrinsic ability to bind to this shorter motif. LST-1 weakens FBF-2 binding affinity for short and long motifs, which may increase target selectivity. Our findings highlight the role of FBF scaffold flexibility in RNA recognition and suggest a new mechanism by which protein partners refine target site selection.
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Affiliation(s)
- Chen Qiu
- Epigenetics and Stem Cell Biology LaboratoryNational Institute of Environmental Health Sciences, National Institutes of HealthResearch Triangle ParkUnited States
| | - Vandita D Bhat
- Department of Biological SciencesUniversity of Texas at DallasRichardsonUnited States
| | - Sanjana Rajeev
- Department of Biological SciencesUniversity of Texas at DallasRichardsonUnited States
| | - Chi Zhang
- Department of Biological SciencesUniversity of Texas at DallasRichardsonUnited States
| | - Alexa E Lasley
- Department of Biological SciencesUniversity of Texas at DallasRichardsonUnited States
| | - Robert N Wine
- Epigenetics and Stem Cell Biology LaboratoryNational Institute of Environmental Health Sciences, National Institutes of HealthResearch Triangle ParkUnited States
| | - Zachary T Campbell
- Department of Biological SciencesUniversity of Texas at DallasRichardsonUnited States
| | - Traci M Tanaka Hall
- Epigenetics and Stem Cell Biology LaboratoryNational Institute of Environmental Health Sciences, National Institutes of HealthResearch Triangle ParkUnited States
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23
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Preparation of cooperative RNA recognition complexes for crystallographic structural studies. Methods Enzymol 2019; 623:1-22. [PMID: 31239042 PMCID: PMC6697268 DOI: 10.1016/bs.mie.2019.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
It is essential that mRNA-binding proteins recognize specific motifs in target mRNAs to control their processing, localization, and expression. Although mRNAs are typically targets of many different regulatory factors, our understanding of how they work together is limited. In some cases, RNA-binding proteins work cooperatively to regulate an mRNA target. A classic example is Drosophila melanogaster Pumilio (Pum) and Nanos (Nos). Pum is a sequence-specific RNA-binding protein. Nos also binds RNA, but interaction with some targets requires Pum to bind first. We recently determined crystal structures of complexes of Pum and Nos with two different target RNA sequences. A crystal structure in complex with the hunchback mRNA element showed how Pum and Nos together can recognize an extended RNA sequence with Nos binding to an A/U-rich sequence 5' of the Pum sequence element. Nos also enables recognition of elements that contain an A/U-rich 5' sequence, but imperfectly match the Pum sequence element. We determined a crystal structure of Pum and Nos in complex with the Cyclin B mRNA element, which demonstrated how Nos clamps the Pum-RNA complex and enables recognition of the imperfect element. Here, we describe methods for expression and purification of stable Pum-Nos-RNA complexes for crystallization, details of the crystallization and structure determination, and guidance on how to analyze protein-RNA structures and evaluate structure-driven hypotheses. We aim to provide tips and guidance that can be applied to other protein-RNA complexes. With hundreds of mRNA-binding proteins identified, combinatorial control is likely to be common, and much work remains to understand them structurally.
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24
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Kappel K, Das R. Sampling Native-like Structures of RNA-Protein Complexes through Rosetta Folding and Docking. Structure 2018; 27:140-151.e5. [PMID: 30416038 DOI: 10.1016/j.str.2018.10.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 08/27/2018] [Accepted: 10/05/2018] [Indexed: 10/27/2022]
Abstract
RNA-protein complexes underlie numerous cellular processes including translation, splicing, and posttranscriptional regulation of gene expression. The structures of these complexes are crucial to their functions but often elude high-resolution structure determination. Computational methods are needed that can integrate low-resolution data for RNA-protein complexes while modeling de novo the large conformational changes of RNA components upon complex formation. To address this challenge, we describe RNP-denovo, a Rosetta method to simultaneously fold-and-dock RNA to a protein surface. On a benchmark set of diverse RNA-protein complexes not solvable with prior strategies, RNP-denovo consistently sampled native-like structures with better than nucleotide resolution. We revisited three past blind modeling challenges involving the spliceosome, telomerase, and a methyltransferase-ribosomal RNA complex in which previous methods gave poor results. When coupled with the same sparse FRET, crosslinking, and functional data used previously, RNP-denovo gave models with significantly improved accuracy. These results open a route to modeling global folds of RNA-protein complexes from low-resolution data.
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Affiliation(s)
- Kalli Kappel
- Biophysics Program, Stanford University, Stanford, CA 94305, USA
| | - Rhiju Das
- Biophysics Program, Stanford University, Stanford, CA 94305, USA; Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Physics, Stanford University, Stanford, CA 94305, USA.
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25
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Kappel K, Liu S, Larsen KP, Skiniotis G, Puglisi EV, Puglisi JD, Zhou ZH, Zhao R, Das R. De novo computational RNA modeling into cryo-EM maps of large ribonucleoprotein complexes. Nat Methods 2018; 15:947-954. [PMID: 30377372 PMCID: PMC6636682 DOI: 10.1038/s41592-018-0172-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 07/31/2018] [Indexed: 12/19/2022]
Abstract
Increasingly, cryo-electron microscopy (cryo-EM) is used to determine the structures of RNA-protein assemblies, but nearly all maps determined with this method have biologically important regions where the local resolution does not permit RNA coordinate tracing. To address these omissions, we present de novo ribonucleoprotein modeling in real space through assembly of fragments together with experimental density in Rosetta (DRRAFTER). We show that DRRAFTER recovers near-native models for a diverse benchmark set of RNA-protein complexes including the spliceosome, mitochondrial ribosome, and CRISPR-Cas9-sgRNA complexes; rigorous blind tests include yeast U1 snRNP and spliceosomal P complex maps. Additionally, to aid in model interpretation, we present a method for reliable in situ estimation of DRRAFTER model accuracy. Finally, we apply DRRAFTER to recently determined maps of telomerase, the HIV-1 reverse transcriptase initiation complex, and the packaged MS2 genome, demonstrating the acceleration of accurate model building in challenging cases.
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Affiliation(s)
- Kalli Kappel
- Biophysics Program, Stanford University, Stanford, CA, USA
| | - Shiheng Liu
- Electron Imaging Center for Nanomachines, California NanoSystems Institute, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
- Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA, USA
| | - Kevin P Larsen
- Biophysics Program, Stanford University, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Georgios Skiniotis
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Joseph D Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Z Hong Zhou
- Electron Imaging Center for Nanomachines, California NanoSystems Institute, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
- Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA, USA
| | - Rui Zhao
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver Anschutz Medical Campus, Aurora, CO, USA
| | - Rhiju Das
- Biophysics Program, Stanford University, Stanford, CA, USA.
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Physics, Stanford University, Stanford, CA, USA.
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26
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Abstract
Cells must make careful use of the resources available to them. A key area of cellular regulation involves the biogenesis of ribosomes. Transcriptional regulation of ribosome biogenesis factor genes through alterations in histone acetylation has been well studied. This work identifies a post-transcriptional mechanism of ribosome biogenesis regulation by Puf protein control of mRNA stability. Puf proteins are eukaryotic mRNA binding proteins that play regulatory roles in mRNA degradation and translation via association with specific conserved elements in the 3' untranslated region (UTR) of target mRNAs and with degradation and translation factors. We demonstrate that several ribosome biogenesis factor mRNAs in Saccharomyces cerevisiae containing a canonical Puf4p element in their 3' UTRs are destabilized by Puf2p, Puf4, and Puf5p, yet stabilized by Puf1p and Puf3p. In the absence of all Puf proteins, these ribosome biogenesis mRNAs are destabilized by a secondary mechanism involving the same 3' UTR element. Unlike other targets of Puf4p regulation, the decay of these transcripts is not altered by carbon source. Overexpression of Puf4p results in delayed ribosomal RNA processing and altered ribosomal subunit trafficking. These results represent a novel role for Puf proteins in yeast as regulators of ribosome biogenesis transcript stability.
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Affiliation(s)
- Anthony D Fischer
- a Department of Biology , University of Missouri-St. Louis , St. Louis , MO , USA
| | - Wendy M Olivas
- a Department of Biology , University of Missouri-St. Louis , St. Louis , MO , USA
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27
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Zhao YY, Mao MW, Zhang WJ, Wang J, Li HT, Yang Y, Wang Z, Wu JW. Expanding RNA binding specificity and affinity of engineered PUF domains. Nucleic Acids Res 2018; 46:4771-4782. [PMID: 29490074 PMCID: PMC5961129 DOI: 10.1093/nar/gky134] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 02/08/2018] [Accepted: 02/16/2018] [Indexed: 12/26/2022] Open
Abstract
Specific manipulation of RNA is necessary for the research in biotechnology and medicine. The RNA-binding domains of Pumilio/fem-3 mRNA binding factors (PUF domains) are programmable RNA binding scaffolds used to engineer artificial proteins that specifically modulate RNAs. However, the native PUF domains generally recognize 8-nt RNAs, limiting their applications. Here, we modify the PUF domain of human Pumilio1 to engineer PUFs that recognize RNA targets of different length. The engineered PUFs bind to their RNA targets specifically and PUFs with more repeats have higher binding affinity than the canonical eight-repeat domains; however, the binding affinity reaches the peak at those with 9 and 10 repeats. Structural analysis on PUF with nine repeats reveals a higher degree of curvature, and the RNA binding unexpectedly and dramatically opens the curved structure. Investigation of the residues positioned in between two RNA bases demonstrates that tyrosine and arginine have favored stacking interactions. Further tests on the availability of the engineered PUFs in vitro and in splicing function assays indicate that our engineered PUFs bind RNA targets with high affinity in a programmable way.
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Affiliation(s)
- Yang-Yang Zhao
- Center for Life Sciences, Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Miao-Wei Mao
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biological Science, Shanghai 200031, China
- Synthetic Biology and Biotechnology Laboratory, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Wen-Jing Zhang
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning 116044, China
| | - Jue Wang
- Institute of Molecular Enzymology, Soochow University, Suzhou, Jiangsu 215123, China
| | - Hai-Tao Li
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yi Yang
- Synthetic Biology and Biotechnology Laboratory, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Zefeng Wang
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biological Science, Shanghai 200031, China
- Enzerna Biosciences, Inc., 125 South Road, 925B Kenan Labs, CB#3266, Chapel Hill, NC 27599, USA
| | - Jia-Wei Wu
- Center for Life Sciences, Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Institute of Molecular Enzymology, Soochow University, Suzhou, Jiangsu 215123, China
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28
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Gene Expression of Pneumocystis murina after Treatment with Anidulafungin Results in Strong Signals for Sexual Reproduction, Cell Wall Integrity, and Cell Cycle Arrest, Indicating a Requirement for Ascus Formation for Proliferation. Antimicrob Agents Chemother 2018; 62:AAC.02513-17. [PMID: 29463544 PMCID: PMC5923105 DOI: 10.1128/aac.02513-17] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 02/10/2018] [Indexed: 01/03/2023] Open
Abstract
The echinocandins are a class of antifungal agents that target β-1,3-d-glucan (BG) biosynthesis. In the ascigerous Pneumocystis species, treatment with these drugs depletes the ascus life cycle stage, which contains BG, but large numbers of forms which do not express BG remain in the infected lungs. In the present study, the gene expression profiles of Pneumocystis murina were compared between infected, untreated mice and mice treated with anidulafungin for 2 weeks to understand the metabolism of the persisting forms. Almost 80 genes were significantly up- or downregulated. Like other fungi exposed to echinocandins, genes associated with sexual replication, cell wall integrity, cell cycle arrest, and stress comprised the strongest upregulated signals in P. murina from the treated mice. The upregulation of the P. murina β-1,3-d-glucan endohydrolase and endo-1,3-glucanase was notable and may explain the disappearance of the existing asci in the lungs of treated mice since both enzymes can degrade BG. The biochemical measurement of BG in the lungs of treated mice and fluorescence microscopy with an anti-BG antibody supported the loss of BG. Downregulated signals included genes involved in cell replication, genome stability, and ribosomal biogenesis and function and the Pneumocystis-specific genes encoding the major surface glycoproteins (Msg). These studies suggest that P. murina attempted to undergo sexual replication in response to a stressed environment and was halted in any type of proliferative cycle, likely due to a lack of BG. Asci appear to be a required part of the life cycle stage of Pneumocystis, and BG may be needed to facilitate progression through the life cycle via sexual replication.
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29
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Wang M, Ogé L, Perez-Garcia MD, Hamama L, Sakr S. The PUF Protein Family: Overview on PUF RNA Targets, Biological Functions, and Post Transcriptional Regulation. Int J Mol Sci 2018; 19:ijms19020410. [PMID: 29385744 PMCID: PMC5855632 DOI: 10.3390/ijms19020410] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Revised: 01/23/2018] [Accepted: 01/25/2018] [Indexed: 12/13/2022] Open
Abstract
Post-transcriptional regulation of gene expression plays a crucial role in many processes. In cells, it is mediated by diverse RNA-binding proteins. These proteins can influence mRNA stability, translation, and localization. The PUF protein family (Pumilio and FBF) is composed of RNA-binding proteins highly conserved among most eukaryotic organisms. Previous investigations indicated that they could be involved in many processes by binding corresponding motifs in the 3′UTR or by interacting with other proteins. To date, most of the investigations on PUF proteins have been focused on Caenorhabditis elegans, Drosophila melanogaster, and Saccharomyces cerevisiae, while only a few have been conducted on Arabidopsis thaliana. The present article provides an overview of the PUF protein family. It addresses their RNA-binding motifs, biological functions, and post-transcriptional control mechanisms in Caenorhabditis elegans, Drosophila melanogaster, Saccharomyces cerevisiae, and Arabidopsis thaliana. These items of knowledge open onto new investigations into the relevance of PUF proteins in specific plant developmental processes.
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Affiliation(s)
- Ming Wang
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QUASAV, F-49045 Angers, France.
| | - Laurent Ogé
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QUASAV, F-49045 Angers, France.
| | | | - Latifa Hamama
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QUASAV, F-49045 Angers, France.
| | - Soulaiman Sakr
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QUASAV, F-49045 Angers, France.
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30
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De Franco S, O'Connell MR, Vandevenne M. Engineering RNA-Binding Proteins by Modular Assembly of RanBP2-Type Zinc Fingers. Methods Mol Biol 2018; 1867:57-74. [PMID: 30155815 DOI: 10.1007/978-1-4939-8799-3_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Deciphering the function of the nonprotein-coding portion of genomes represents one of the major challenges that molecular biology is facing today. Numerous classes of RNAs have been discovered over the last past decade and appear to play important regulatory roles in gene expression and disease. The ability to study and manipulate these RNAs relies on the development of programmable RNA-binding molecules such as RNA-binding proteins. Most RNA-binding proteins have modular architectures and combine different RNA-binding domains that provide binding affinity toward a specific RNA sequence and/or structure. Herein, we describe a general strategy to design single-stranded RNA-binding proteins using RanBP2-type zinc-finger (ZF) domains that can recognize a given RNA sequence with high affinity and specificity.
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Affiliation(s)
- Simona De Franco
- Center for Protein Engineering, University of Liège, Liège, Belgium
| | - Mitchell R O'Connell
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA
- Center for RNA Biology, University of Rochester, Rochester, NY, USA
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31
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Bao H, Wang N, Wang C, Jiang Y, Liu J, Xu L, Wu J, Shi Y. Structural basis for the specific recognition of 18S rRNA by APUM23. Nucleic Acids Res 2017; 45:12005-12014. [PMID: 29036323 PMCID: PMC5714250 DOI: 10.1093/nar/gkx872] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Accepted: 09/19/2017] [Indexed: 01/26/2023] Open
Abstract
PUF (Pumilio/fem-3 mRNA binding factor) proteins, a conserved family of RNA-binding proteins, recognize specific single-strand RNA targets in a specific modular way. Although plants have a greater number of PUF protein members than do animal and fungal systems, they have been the subject of fewer structural and functional investigations. The aim of this study was to elucidate the involvement of APUM23, a nucleolar PUF protein in the plant Arabidopsis, in pre-rRNA processing. APUM23 is distinct from classical PUF family proteins, which are located in the cytoplasm and bind to 3'UTRs of mRNA to modulate mRNA expression and localization. We found that the complete RNA target sequence of APUM23 comprises 11 nt in 18S rRNA at positions 1141-1151. The complex structure shows that APUM23 has 10 PUF repeats; it assembles into a C-shape, with an insertion located within the inner concave surface. We found several different RNA recognition features. A notable structural feature of APUM23 is an insertion in the third PUF repeat that participates in nucleotide recognition and maintains the correct conformation of the target RNA. Our findings elucidate the mechanism for APUM23's-specific recognition of 18S rRNA.
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Affiliation(s)
- Hongyu Bao
- Hefei National Laboratory for Physical Science at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Na Wang
- Hefei National Laboratory for Physical Science at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Chongyuan Wang
- Hefei National Laboratory for Physical Science at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Yiyang Jiang
- Hefei National Laboratory for Physical Science at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Jiuyang Liu
- Hefei National Laboratory for Physical Science at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Li Xu
- Hefei National Laboratory for Physical Science at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Jihui Wu
- Hefei National Laboratory for Physical Science at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Yunyu Shi
- Hefei National Laboratory for Physical Science at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China.,CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
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32
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Azizi H, Dumas C, Papadopoulou B. The Pumilio-domain protein PUF6 contributes to SIDER2 retroposon-mediated mRNA decay in Leishmania. RNA (NEW YORK, N.Y.) 2017; 23:1874-1885. [PMID: 28877997 PMCID: PMC5689007 DOI: 10.1261/rna.062950.117] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 09/05/2017] [Indexed: 06/07/2023]
Abstract
Leishmania and other trypanosomatid protozoa lack control at the level of transcription initiation and regulate gene expression exclusively post-transcriptionally. We have reported previously that Leishmania harbors a unique class of short interspersed degenerate retroposons (SIDERs) that are predominantly located within 3'UTRs and play a major role in post-transcriptional control. We have shown that members of the SIDER2 subfamily initiate mRNA decay through endonucleolytic cleavage within the second conserved 79-nt signature sequence of SIDER2 retroposons. Here, we have developed an optimized MS2 coat protein tethering system to capture trans-acting factor(s) regulating SIDER2-mediated mRNA decay. Tethering of the MS2 coat protein to a reporter RNA harboring two MS2 stem-loop aptamers and the cognate SIDER2-containing 3'UTR in combination with immunoprecipitation and mass spectrometry analysis led to the identification of RNA-binding proteins with known functions in mRNA decay. Among the candidate SIDER2-interacting proteins that were individually tethered to a SIDER2 reporter RNA, the Pumilio-domain protein PUF6 was shown to enhance degradation and reduce transcript half-life. Furthermore, we showed that PUF6 binds to SIDER2 sequences that include the regulatory 79-nt signature motif, hence contributing to the mRNA decay process. Consistent with a role of PUF6 in SIDER2-mediated decay, genetic inactivation of PUF6 resulted in increased accumulation and higher stability of endogenous SIDER2-bearing transcripts. Overall, these studies provide new insights into regulated mRNA decay pathways in Leishmania controlled by SIDER2 retroposons and propose a broader role for PUF proteins in mRNA decay within the eukaryotic kingdom.
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Affiliation(s)
- Hiva Azizi
- Research Center in Infectious Diseases, CHU de Quebec Research Center-Laval University, Quebec, QC, G1V 4G2 Canada
- Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, Laval University, Quebec, QC, G1V 0A6 Canada
| | - Carole Dumas
- Research Center in Infectious Diseases, CHU de Quebec Research Center-Laval University, Quebec, QC, G1V 4G2 Canada
- Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, Laval University, Quebec, QC, G1V 0A6 Canada
| | - Barbara Papadopoulou
- Research Center in Infectious Diseases, CHU de Quebec Research Center-Laval University, Quebec, QC, G1V 4G2 Canada
- Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, Laval University, Quebec, QC, G1V 0A6 Canada
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33
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Hotz M, Nelson WJ. Pumilio-dependent localization of mRNAs at the cell front coordinates multiple pathways required for chemotaxis. Nat Commun 2017; 8:1366. [PMID: 29118357 PMCID: PMC5678099 DOI: 10.1038/s41467-017-01536-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 09/27/2017] [Indexed: 12/26/2022] Open
Abstract
Chemotaxis is a specialized form of directed cell migration important for normal development, wound healing, and cancer metastasis. In the social amoeba Dictyostelium discoideum, four signaling pathways act synergistically to maintain directional cell migration. However, it is unknown how these pathways are coordinated in space and time to achieve persistent chemotaxis. Here, we show that the mRNAs and proteins of these four chemotaxis pathways and actin are preferentially enriched at the cell front during dynamic cell migration, which requires the Pumilio-related RNA-binding protein Puf118. Significantly, disruption of the Pumilio-binding sequence in chemotaxis pathway mRNAs, or mislocalization of Puf118 and its target mRNAs to the cell rear perturbs efficient chemotaxis in shallow cAMP gradients, without affecting the abundance of the mRNAs or encoded proteins. Thus, the polarized localization of Puf118-bound mRNAs coordinates the distribution of different chemotaxis pathway proteins in time and space, leading to cell polarization and persistent chemotaxis.
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Affiliation(s)
- Manuel Hotz
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - W James Nelson
- Department of Biology, Stanford University, Stanford, CA, 94305, USA. .,Molecular and Cellular Physiology, Stanford University, Stanford, CA, 94305, USA.
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34
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Lapointe CP, Preston MA, Wilinski D, Saunders HAJ, Campbell ZT, Wickens M. Architecture and dynamics of overlapped RNA regulatory networks. RNA (NEW YORK, N.Y.) 2017; 23:1636-1647. [PMID: 28768715 PMCID: PMC5648032 DOI: 10.1261/rna.062687.117] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 07/28/2017] [Indexed: 06/07/2023]
Abstract
A single protein can bind and regulate many mRNAs. Multiple proteins with similar specificities often bind and control overlapping sets of mRNAs. Yet little is known about the architecture or dynamics of overlapped networks. We focused on three proteins with similar structures and related RNA-binding specificities-Puf3p, Puf4p, and Puf5p of S. cerevisiae Using RNA Tagging, we identified a "super-network" comprised of four subnetworks: Puf3p, Puf4p, and Puf5p subnetworks, and one controlled by both Puf4p and Puf5p. The architecture of individual subnetworks, and thus the super-network, is determined by competition among particular PUF proteins to bind mRNAs, their affinities for binding elements, and the abundances of the proteins. The super-network responds dramatically: The remaining network can either expand or contract. These strikingly opposite outcomes are determined by an interplay between the relative abundance of the RNAs and proteins, and their affinities for one another. The diverse interplay between overlapping RNA-protein networks provides versatile opportunities for regulation and evolution.
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Affiliation(s)
- Christopher P Lapointe
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Melanie A Preston
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Daniel Wilinski
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Harriet A J Saunders
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Zachary T Campbell
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Marvin Wickens
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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35
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Wang B, Ye K. Nop9 binds the central pseudoknot region of 18S rRNA. Nucleic Acids Res 2017; 45:3559-3567. [PMID: 28053123 PMCID: PMC5389560 DOI: 10.1093/nar/gkw1323] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 12/19/2016] [Indexed: 01/21/2023] Open
Abstract
The assembly of eukaryotic ribosomes requires numerous factors that transiently associate with evolving pre-ribosomal particles. The Pumilio repeat-containing protein Nop9 briefly associates with the 90S pre-ribosome during its co-transcriptional assembly. Here, we show that Nop9 specifically binds an 11-nucleotide sequence of 18S rRNA that forms the 3΄ side of the central pseudoknot and helix 28 in the mature subunit. Crystal structures of Nop9 in the free and RNA-bound states reveal a new type of Pumilio repeat protein with a distinct structure, target sequence and RNA-binding mode. Nop9 contains 10 Pumilio repeats arranged into a U-shaped scaffold. The target RNA is recognized by two stretches of repeats in a bipartite manner, and three central bases are unrecognized as a result of the degeneracy of repeats 6 and 7. Our data suggest that Nop9 regulates the folding of 18S rRNA at early assembly stages of 90S.
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Affiliation(s)
- Bing Wang
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Beijing Normal University, Beijing 100875, China.,National Institute of Biological Sciences, Beijing 102206, China.,Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Keqiong Ye
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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PUM1 is a biphasic negative regulator of innate immunity genes by suppressing LGP2. Proc Natl Acad Sci U S A 2017; 114:E6902-E6911. [PMID: 28760986 DOI: 10.1073/pnas.1708713114] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
PUM1 is an RNA binding protein shown to regulate the stability and function of mRNAs bearing a specific sequence. We report the following: (i) A key function of PUM1 is that of a repressor of key innate immunity genes by repressing the expression of LGP2. Thus, between 12 and 48 hours after transfection of human cells with siPUM1 RNA there was an initial (phase 1) upsurge of transcripts encoding LGP2, CXCL10, IL6, and PKR. This was followed 24 hours later (phase 2) by a significant accumulation of mRNAs encoding RIG-I, SP100, MDA5, IFIT1, PML, STING, and IFNβ. The genes that were not activated encoded HDAC4 and NF-κB1. (ii) Simultaneous depletion of PUM1 and LGP2, CXCL10, or IL6 revealed that up-regulation of phase 1 and phase 2 genes was the consequence of up-regulation of LGP2. (iii) IFNβ produced 48-72 hours after transfection of siPUM1 was effective in up-regulating LGP2 and phase 2 genes and reducing the replication of HSV-1 in untreated cells. (iv) Because only half of genes up-regulated in phase 1 and 2 encode mRNAs containing PUM1 binding sites, the upsurge in gene expression could not be attributed solely to stabilization of mRNAs in the absence of PUM1. (v) Lastly, depletion of PUM2 does not result in up-regulation of phase 1 or phase 2 genes. The results of the studies presented here indicate that PUM1 is a negative regulator of LGP2, a master regulator of innate immunity genes expressed in a cascade fashion.
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37
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Mullari M, Lyon D, Jensen LJ, Nielsen ML. Specifying RNA-Binding Regions in Proteins by Peptide Cross-Linking and Affinity Purification. J Proteome Res 2017. [PMID: 28648085 DOI: 10.1021/acs.jproteome.7b00042] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
RNA-binding proteins (RBPs) allow cells to carry out pre-RNA processing and post-transcriptional regulation of gene expression, and aberrations in RBP functions have been linked to many diseases, including neurological disorders and cancer. Human cells encode thousands of RNA-binding proteins with unique RNA-binding properties. These properties are regulated through modularity of a large variety of RNA-binding domains, rendering RNA-protein interactions difficult to study. Recently, the introduction of proteomics methods has provided novel insights into RNA-binding proteins at a systems level. However, determining the exact protein sequence regions that interact with RNA remains challenging and laborious, especially considering that many RBPs lack canonical RNA-binding domains. Here we describe a streamlined proteomic workflow called peptide cross-linking and affinity purification (pCLAP) that allows rapid characterization of RNA-binding regions in proteins. pCLAP is based upon the combined use of UV cross-linking and enzymatic digestion of RNA-bound proteins followed by single-shot mass spectrometric analysis. To benchmark our method, we identified the binding regions for polyadenylated RNA-binding proteins in HEK293 cells, allowing us to map the mRNA interaction regions of more than 1000 RBPs with very high reproducibility from replicate single-shot analyses. Our results show specific enrichment of many known RNA-binding regions on many known RNA-binding proteins, confirming the specificity of our approach.
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Affiliation(s)
- Meeli Mullari
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Faculty of Health Sciences , DK-2200 Copenhagen, Denmark
| | - David Lyon
- Disease Systems Biology, The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Faculty of Health Sciences , DK-2200 Copenhagen, Denmark
| | - Lars Juhl Jensen
- Disease Systems Biology, The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Faculty of Health Sciences , DK-2200 Copenhagen, Denmark
| | - Michael L Nielsen
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Faculty of Health Sciences , DK-2200 Copenhagen, Denmark
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38
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Abstract
Alterations in regulatory networks contribute to evolutionary change. Transcriptional networks are reconfigured by changes in the binding specificity of transcription factors and their cognate sites. The evolution of RNA-protein regulatory networks is far less understood. The PUF (Pumilio and FBF) family of RNA regulatory proteins controls the translation, stability, and movements of hundreds of mRNAs in a single species. We probe the evolution of PUF-RNA networks by direct identification of the mRNAs bound to PUF proteins in budding and filamentous fungi and by computational analyses of orthologous RNAs from 62 fungal species. Our findings reveal that PUF proteins gain and lose mRNAs with related and emergent biological functions during evolution. We demonstrate at least two independent rewiring events for PUF3 orthologs, independent but convergent evolution of PUF4/5 binding specificity and the rewiring of the PUF4/5 regulons in different fungal lineages. These findings demonstrate plasticity in RNA regulatory networks and suggest ways in which their rewiring occurs.
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Kellermann SJ, Rentmeister A. A FACS-based screening strategy to assess sequence-specific RNA-binding of Pumilio protein variants in E. coli. Biol Chem 2017; 398:69-75. [DOI: 10.1515/hsz-2016-0214] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 09/15/2016] [Indexed: 12/22/2022]
Abstract
Abstract
Sequence-specific and programmable binding of proteins to RNA bears the potential to detect and manipulate target RNAs. Applications include analysis of subcellular RNA localization or post-transcriptional regulation but require sequence-specificity to be readily adjustable to any target RNA. The Pumilio homology domain binds an eight nucleotide target sequence in a predictable manner allowing for rational design of variants with new specificities. We describe a high-throughput system for screening Pumilio variants based on fluorescence-activated cell sorting of E. coli. Our approach should help optimizing variants obtained from rational design regarding folding and stability or identifying new variants with alternative binding modes.
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40
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Abstract
RNA-binding proteins play a variety of roles in cellular physiology. Some regulate mRNA processing, mRNA abundance, and translation efficiency. Some fight off invader RNA through small RNA-driven silencing pathways. Others sense foreign sequences in the form of double-stranded RNA and activate the innate immune response. Yet others, for example cytoplasmic aconitase, act as bi-functional proteins, processing metabolites in one conformation and regulating metabolic gene expression in another. Not all are involved in gene regulation. Some play structural roles, for example, connecting the translational machinery to the endoplasmic reticulum outer membrane. Despite their pervasive role and relative importance, it has remained difficult to identify new RNA-binding proteins in a systematic, unbiased way. A recent body of literature from several independent labs has defined robust, easily adaptable protocols for mRNA interactome discovery. In this review, I summarize the methods and review some of the intriguing findings from their application to a wide variety of biological systems.
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Affiliation(s)
- Sean P Ryder
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
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41
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Fei DL, Motowski H, Chatrikhi R, Prasad S, Yu J, Gao S, Kielkopf CL, Bradley RK, Varmus H. Wild-Type U2AF1 Antagonizes the Splicing Program Characteristic of U2AF1-Mutant Tumors and Is Required for Cell Survival. PLoS Genet 2016; 12:e1006384. [PMID: 27776121 PMCID: PMC5077151 DOI: 10.1371/journal.pgen.1006384] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 09/23/2016] [Indexed: 12/21/2022] Open
Abstract
We have asked how the common S34F mutation in the splicing factor U2AF1 regulates alternative splicing in lung cancer, and why wild-type U2AF1 is retained in cancers with this mutation. A human lung epithelial cell line was genetically modified so that U2AF1S34F is expressed from one of the two endogenous U2AF1 loci. By altering levels of mutant or wild-type U2AF1 in this cell line and by analyzing published data on human lung adenocarcinomas, we show that S34F-associated changes in alternative splicing are proportional to the ratio of S34F:wild-type gene products and not to absolute levels of either the mutant or wild-type factor. Preferential recognition of specific 3' splice sites in S34F-expressing cells is largely explained by differential in vitro RNA-binding affinities of mutant versus wild-type U2AF1 for those same 3' splice sites. Finally, we show that lung adenocarcinoma cell lines bearing U2AF1 mutations do not require the mutant protein for growth in vitro or in vivo. In contrast, wild-type U2AF1 is required for survival, regardless of whether cells carry the U2AF1S34F allele. Our results provide mechanistic explanations of the magnitude of splicing changes observed in U2AF1-mutant cells and why tumors harboring U2AF1 mutations always retain an expressed copy of the wild-type allele.
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Affiliation(s)
- Dennis Liang Fei
- Cancer Biology Section, Cancer Genetics Branch, National Human Genome Research Institute, Bethesda, United States Of America
- Department of Medicine, Meyer Cancer Center, Weill Cornell Medicine, New York, United States Of America
- * E-mail: (DLF); (CLK); (RKB); (HV)
| | - Hayley Motowski
- Cancer Biology Section, Cancer Genetics Branch, National Human Genome Research Institute, Bethesda, United States Of America
| | - Rakesh Chatrikhi
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester Medical Center, Rochester, United States Of America
| | - Sameer Prasad
- Cancer Biology Section, Cancer Genetics Branch, National Human Genome Research Institute, Bethesda, United States Of America
| | - Jovian Yu
- Cancer Biology Section, Cancer Genetics Branch, National Human Genome Research Institute, Bethesda, United States Of America
| | - Shaojian Gao
- Genetics Branch, National Cancer Institute, Bethesda, United States Of America
| | - Clara L. Kielkopf
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester Medical Center, Rochester, United States Of America
- * E-mail: (DLF); (CLK); (RKB); (HV)
| | - Robert K. Bradley
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States Of America
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States Of America
- * E-mail: (DLF); (CLK); (RKB); (HV)
| | - Harold Varmus
- Cancer Biology Section, Cancer Genetics Branch, National Human Genome Research Institute, Bethesda, United States Of America
- Department of Medicine, Meyer Cancer Center, Weill Cornell Medicine, New York, United States Of America
- * E-mail: (DLF); (CLK); (RKB); (HV)
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42
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Lou TF, Weidmann CA, Killingsworth J, Tanaka Hall TM, Goldstrohm AC, Campbell ZT. Integrated analysis of RNA-binding protein complexes using in vitro selection and high-throughput sequencing and sequence specificity landscapes (SEQRS). Methods 2016; 118-119:171-181. [PMID: 27729296 DOI: 10.1016/j.ymeth.2016.10.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 09/30/2016] [Accepted: 10/03/2016] [Indexed: 10/20/2022] Open
Abstract
RNA-binding proteins (RBPs) collaborate to control virtually every aspect of RNA function. Tremendous progress has been made in the area of global assessment of RBP specificity using next-generation sequencing approaches both in vivo and in vitro. Understanding how protein-protein interactions enable precise combinatorial regulation of RNA remains a significant problem. Addressing this challenge requires tools that can quantitatively determine the specificities of both individual proteins and multimeric complexes in an unbiased and comprehensive way. One approach utilizes in vitro selection, high-throughput sequencing, and sequence-specificity landscapes (SEQRS). We outline a SEQRS experiment focused on obtaining the specificity of a multi-protein complex between Drosophila RBPs Pumilio (Pum) and Nanos (Nos). We discuss the necessary controls in this type of experiment and examine how the resulting data can be complemented with structural and cell-based reporter assays. Additionally, SEQRS data can be integrated with functional genomics data to uncover biological function. Finally, we propose extensions of the technique that will enhance our understanding of multi-protein regulatory complexes assembled onto RNA.
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Affiliation(s)
- Tzu-Fang Lou
- Department of Biological Sciences, University of Texas at Dallas, Richardson, TX 75080, United States
| | - Chase A Weidmann
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, United States
| | - Jordan Killingsworth
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, United States
| | - Traci M Tanaka Hall
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, United States
| | - Aaron C Goldstrohm
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, United States; Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, United States
| | - Zachary T Campbell
- Department of Biological Sciences, University of Texas at Dallas, Richardson, TX 75080, United States.
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43
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Weidmann CA, Qiu C, Arvola RM, Lou TF, Killingsworth J, Campbell ZT, Tanaka Hall TM, Goldstrohm AC. Drosophila Nanos acts as a molecular clamp that modulates the RNA-binding and repression activities of Pumilio. eLife 2016; 5. [PMID: 27482653 PMCID: PMC4995099 DOI: 10.7554/elife.17096] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 08/01/2016] [Indexed: 01/03/2023] Open
Abstract
Collaboration among the multitude of RNA-binding proteins (RBPs) is ubiquitous, yet our understanding of these key regulatory complexes has been limited to single RBPs. We investigated combinatorial translational regulation by Drosophila Pumilio (Pum) and Nanos (Nos), which control development, fertility, and neuronal functions. Our results show how the specificity of one RBP (Pum) is modulated by cooperative RNA recognition with a second RBP (Nos) to synergistically repress mRNAs. Crystal structures of Nos-Pum-RNA complexes reveal that Nos embraces Pum and RNA, contributes sequence-specific contacts, and increases Pum RNA-binding affinity. Nos shifts the recognition sequence and promotes repression complex formation on mRNAs that are not stably bound by Pum alone, explaining the preponderance of sub-optimal Pum sites regulated in vivo. Our results illuminate the molecular mechanism of a regulatory switch controlling crucial gene expression programs, and provide a framework for understanding how the partnering of RBPs evokes changes in binding specificity that underlie regulatory network dynamics. DOI:http://dx.doi.org/10.7554/eLife.17096.001 Molecules of DNA contain the instructions needed to make proteins inside cells. Proteins perform many different roles and each needs to be produced at the right time and in the right amounts to enable the cells to survive. The DNA is first copied to make molecules of ribonucleic acid (RNA), which are then used as templates to make the proteins. One way to control protein production is to regulate the RNA molecules. A family of proteins called RNA-binding proteins can recognise and bind to specific RNA molecules and determine whether a RNA molecule is destroyed, used to produce proteins, or stored for later use. In effect, these RNA-binding proteins act as switches that turn protein production on or off. Nanos and Pumilio are two RNA-binding proteins that are found in many organisms, including humans and other animals. Genetic studies in fruit flies show that these two proteins influence development, the nervous system and the behaviour of stem cells by switching off the production of certain proteins. To investigate how Nanos and Pumilio work together to regulate protein production, Weidmann, Qiu et al. used a variety of techniques to study the activity of these proteins in cells taken from fruit fly embryos. The experiments reveal that Nanos acts like a clamp to hold Pumilio close to specific RNAs, which allows Pumilio to switch off the production of the corresponding proteins. The presence of Nanos allows Pumilio to regulate RNAs that it cannot bind to alone. Therefore, the experiments show that by working together with Nanos, Pumilio is able to regulate a wider variety of RNAs than it would otherwise be able to. These findings provide a molecular understanding for why fruit fly mutants that lack Nanos or Pumilio have severe body defects and reduced fertility. The next challenge is to identify the specific RNAs targeted by Nanos and Pumilio in stem cells, the nervous system and during development. DOI:http://dx.doi.org/10.7554/eLife.17096.002
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Affiliation(s)
- Chase A Weidmann
- Department of Biological Chemistry, University of Michigan, Ann Arbor, United States
| | - Chen Qiu
- Epigenetics and Stem Cell Biology Laboratory, National Institutes of Health, Research Triangle Park, United States.,National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, United States
| | - René M Arvola
- Department of Biological Chemistry, University of Michigan, Ann Arbor, United States
| | - Tzu-Fang Lou
- Department of Biological Sciences, University of Texas at Dallas, Richardson, United States
| | - Jordan Killingsworth
- Department of Biological Chemistry, University of Michigan, Ann Arbor, United States
| | - Zachary T Campbell
- Department of Biological Sciences, University of Texas at Dallas, Richardson, United States
| | - Traci M Tanaka Hall
- Epigenetics and Stem Cell Biology Laboratory, National Institutes of Health, Research Triangle Park, United States.,National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, United States
| | - Aaron C Goldstrohm
- Department of Biological Chemistry, University of Michigan, Ann Arbor, United States.,Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, United States
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44
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Abil Z, Zhao H. Engineering reprogrammable RNA-binding proteins for study and manipulation of the transcriptome. MOLECULAR BIOSYSTEMS 2016; 11:2658-65. [PMID: 26166256 DOI: 10.1039/c5mb00289c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
With the expanding interest in RNA biology, interest in artificial RNA-binding proteins (RBPs) is likewise increasing. RBPs can be designed in a modular fashion, whereby effector and RNA-binding domains are combined in chimeric proteins that exhibit both functions and can be applied for regulation of a broad range of biological processes. The elucidation of the RNA recognition code for Pumilio and fem-3 mRNA-binding factor (PUF) homology proteins allowed engineering of artificial RBPs for targeting endogenous mRNAs. In this review, we will focus on the recent advances in elucidating and reprogramming PUF domain specificity, update on several promising applications of PUF-based designer RBPs, and discuss some other domains that hold the potential to be used as the RNA-binding scaffolds for designer RBP engineering.
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Affiliation(s)
- Zhanar Abil
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
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45
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de Beauchene IC, de Vries SJ, Zacharias M. Fragment-based modelling of single stranded RNA bound to RNA recognition motif containing proteins. Nucleic Acids Res 2016; 44:4565-80. [PMID: 27131381 PMCID: PMC4889956 DOI: 10.1093/nar/gkw328] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 04/12/2016] [Indexed: 12/12/2022] Open
Abstract
Protein-RNA complexes are important for many biological processes. However, structural modeling of such complexes is hampered by the high flexibility of RNA. Particularly challenging is the docking of single-stranded RNA (ssRNA). We have developed a fragment-based approach to model the structure of ssRNA bound to a protein, based on only the protein structure, the RNA sequence and conserved contacts. The conformational diversity of each RNA fragment is sampled by an exhaustive library of trinucleotides extracted from all known experimental protein–RNA complexes. The method was applied to ssRNA with up to 12 nucleotides which bind to dimers of the RNA recognition motifs (RRMs), a highly abundant eukaryotic RNA-binding domain. The fragment based docking allows a precise de novo atomic modeling of protein-bound ssRNA chains. On a benchmark of seven experimental ssRNA–RRM complexes, near-native models (with a mean heavy-atom deviation of <3 Å from experiment) were generated for six out of seven bound RNA chains, and even more precise models (deviation < 2 Å) were obtained for five out of seven cases, a significant improvement compared to the state of the art. The method is not restricted to RRMs but was also successfully applied to Pumilio RNA binding proteins.
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Affiliation(s)
| | - Sjoerd J de Vries
- Physics Department T38, Technical University of Munich, James-Franck-Str. 1, 85748 Garching, Germany
| | - Martin Zacharias
- Physics Department T38, Technical University of Munich, James-Franck-Str. 1, 85748 Garching, Germany
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46
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Programmable RNA-binding protein composed of repeats of a single modular unit. Proc Natl Acad Sci U S A 2016; 113:E2579-88. [PMID: 27118836 DOI: 10.1073/pnas.1519368113] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The ability to monitor and perturb RNAs in living cells would benefit greatly from a modular protein architecture that targets unmodified RNA sequences in a programmable way. We report that the RNA-binding protein PumHD (Pumilio homology domain), which has been widely used in native and modified form for targeting RNA, can be engineered to yield a set of four canonical protein modules, each of which targets one RNA base. These modules (which we call Pumby, for Pumilio-based assembly) can be concatenated in chains of varying composition and length, to bind desired target RNAs. The specificity of such Pumby-RNA interactions was high, with undetectable binding of a Pumby chain to RNA sequences that bear three or more mismatches from the target sequence. We validate that the Pumby architecture can perform RNA-directed protein assembly and enhancement of translation of RNAs. We further demonstrate a new use of such RNA-binding proteins, measurement of RNA translation in living cells. Pumby may prove useful for many applications in the measurement, manipulation, and biotechnological utilization of unmodified RNAs in intact cells and systems.
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47
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De-coding and re-coding RNA recognition by PUF and PPR repeat proteins. Curr Opin Struct Biol 2016; 36:116-21. [PMID: 26874972 DOI: 10.1016/j.sbi.2016.01.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 01/14/2016] [Accepted: 01/15/2016] [Indexed: 11/22/2022]
Abstract
PUF and PPR proteins are two families of α-helical repeat proteins that recognize single-stranded RNA sequences. Both protein families hold promise as scaffolds for designed RNA-binding domains. A modular protein RNA recognition code was apparent from the first crystal structures of a PUF protein in complex with RNA, and recent studies continue to advance our understanding of natural PUF protein recognition (de-coding) and our ability to engineer specificity (re-coding). Degenerate recognition motifs make de-coding specificity of individual PPR proteins challenging. Nevertheless, re-coding PPR protein specificity using a consensus recognition code has been successful.
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48
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Hogan GJ, Brown PO, Herschlag D. Evolutionary Conservation and Diversification of Puf RNA Binding Proteins and Their mRNA Targets. PLoS Biol 2015; 13:e1002307. [PMID: 26587879 PMCID: PMC4654594 DOI: 10.1371/journal.pbio.1002307] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 10/23/2015] [Indexed: 12/31/2022] Open
Abstract
Reprogramming of a gene’s expression pattern by acquisition and loss of sequences recognized by specific regulatory RNA binding proteins may be a major mechanism in the evolution of biological regulatory programs. We identified that RNA targets of Puf3 orthologs have been conserved over 100–500 million years of evolution in five eukaryotic lineages. Focusing on Puf proteins and their targets across 80 fungi, we constructed a parsimonious model for their evolutionary history. This model entails extensive and coordinated changes in the Puf targets as well as changes in the number of Puf genes and alterations of RNA binding specificity including that: 1) Binding of Puf3 to more than 200 RNAs whose protein products are predominantly involved in the production and organization of mitochondrial complexes predates the origin of budding yeasts and filamentous fungi and was maintained for 500 million years, throughout the evolution of budding yeast. 2) In filamentous fungi, remarkably, more than 150 of the ancestral Puf3 targets were gained by Puf4, with one lineage maintaining both Puf3 and Puf4 as regulators and a sister lineage losing Puf3 as a regulator of these RNAs. The decrease in gene expression of these mRNAs upon deletion of Puf4 in filamentous fungi (N. crassa) in contrast to the increase upon Puf3 deletion in budding yeast (S. cerevisiae) suggests that the output of the RNA regulatory network is different with Puf4 in filamentous fungi than with Puf3 in budding yeast. 3) The coregulated Puf4 target set in filamentous fungi expanded to include mitochondrial genes involved in the tricarboxylic acid (TCA) cycle and other nuclear-encoded RNAs with mitochondrial function not bound by Puf3 in budding yeast, observations that provide additional evidence for substantial rewiring of post-transcriptional regulation. 4) Puf3 also expanded and diversified its targets in filamentous fungi, gaining interactions with the mRNAs encoding the mitochondrial electron transport chain (ETC) complex I as well as hundreds of other mRNAs with nonmitochondrial functions. The many concerted and conserved changes in the RNA targets of Puf proteins strongly support an extensive role of RNA binding proteins in coordinating gene expression, as originally proposed by Keene. Rewiring of Puf-coordinated mRNA targets and transcriptional control of the same genes occurred at different points in evolution, suggesting that there have been distinct adaptations via RNA binding proteins and transcription factors. The changes in Puf targets and in the Puf proteins indicate an integral involvement of RNA binding proteins and their RNA targets in the adaptation, reprogramming, and function of gene expression. A map of the evolutionary history of Puf proteins and their RNA targets shows that reprogramming of global gene expression programs via adaptive mutations that affect protein-RNA interactions is an important source of biological diversity. We set out to trace the evolutionary history of an RNA binding protein and how its interactions with targets change over evolution. Identifying this natural history is a step toward understanding the critical differences between organisms and how gene expression programs are rewired during evolution. Using bioinformatics and experimental approaches, we broadly surveyed the evolution of binding targets of a particular family of RNA binding proteins—the Puf proteins, whose protein sequences and target RNA sequences are relatively well-characterized—across 99 eukaryotic species. We found five groups of species in which targets have been conserved for at least 100 million years and then took advantage of genome sequences from a large number of fungal species to deeply investigate the conservation and changes in Puf proteins and their RNA targets. Our analyses identified multiple and extensive reconfigurations during the natural history of fungi and suggest that RNA binding proteins and their RNA targets are profoundly involved in evolutionary reprogramming of gene expression and help define distinct programs unique to each organism. Continuing to uncover the natural history of RNA binding proteins and their interactions will provide a unique window into the gene expression programs of present day species and point to new ways to engineer gene expression programs.
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Affiliation(s)
- Gregory J. Hogan
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, United States of America
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, United States of America
| | - Patrick O. Brown
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, United States of America
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail: (POB); (DH)
| | - Daniel Herschlag
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Chemistry, Stanford University, Stanford, California, United States of America
- Department of Chemical Engineering, Stanford University, Stanford, California, United States of America
- ChEM-H Institute, Stanford University, Stanford, California, United States of America
- * E-mail: (POB); (DH)
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49
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Zhang C, Muench DG. A Nucleolar PUF RNA-binding Protein with Specificity for a Unique RNA Sequence. J Biol Chem 2015; 290:30108-18. [PMID: 26487722 DOI: 10.1074/jbc.m115.691675] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Indexed: 12/21/2022] Open
Abstract
PUF proteins are a conserved group of sequence specific RNA-binding proteins that bind to RNA in a modular fashion. The RNA-binding domain of PUF proteins typically consists of eight clustered Puf repeats. Plant genomes code for large families of PUF proteins that show significant variability in their predicted Puf repeat number, organization, and amino acid sequence. Here we sought to determine whether the observed variability in the RNA-binding domains of four plant PUFs results in a preference for nonclassical PUF RNA target sequences. We report the identification of a novel RNA binding sequence for a nucleolar Arabidopsis PUF protein that contains an atypical RNA-binding domain. The Arabidopsis PUM23 (APUM23) binding sequence was 10 nucleotides in length, contained a centrally located UUGA core element, and had a preferred cytosine at nucleotide position 8. These RNA sequence characteristics differ from those of other PUF proteins, because all natural PUFs studied to date bind to RNAs that contain a conserved UGU sequence at their 5' end and lack specificity for cytosine. Gel mobility shift assays validated the identity of the APUM23 binding sequence and supported the location of 3 of the 10 predicted Puf repeats in APUM23, including the cytosine-binding repeat. The preferred 10-nucleotide sequence bound by APUM23 is present within the 18S rRNA sequence, supporting the known role of APUM23 in 18S rRNA maturation. This work also reveals that APUM23, an ortholog of yeast Nop9, could provide an advanced structural backbone for Puf repeat engineering and target-specific regulation of cellular RNAs.
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Affiliation(s)
- Chi Zhang
- From the Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Douglas G Muench
- From the Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
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Abstract
Pumilio is an RNA-binding protein originally identified in Drosophila, with a Puf domain made up of eight Puf repeats, three helix bundles arranged in a rainbow architecture, where each repeat recognizes a single base of the RNA-binding sequence. The eight-base recognition sequence can therefore be modified simply via mutation of the repeat that recognizes the base to be changed and this is understood in detail via high-resolution crystal structures. The binding mechanism is also altered in a variety of homologues from different species, with bases flipped out from the binding site to regenerate a consensus sequence. Thus Pumilios can be designed with bespoke RNA recognition sequences and can be fused to nucleases, split GFP, etc. as tools in vitro and in cells.
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