1
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Salgania HK, Metz J, Jeske M. ReLo is a simple and rapid colocalization assay to identify and characterize direct protein-protein interactions. Nat Commun 2024; 15:2875. [PMID: 38570497 PMCID: PMC10991417 DOI: 10.1038/s41467-024-47233-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 03/22/2024] [Indexed: 04/05/2024] Open
Abstract
The characterization of protein-protein interactions (PPIs) is fundamental to the understanding of biochemical processes. Many methods have been established to identify and study direct PPIs; however, screening and investigating PPIs involving large or poorly soluble proteins remains challenging. Here, we introduce ReLo, a simple, rapid, and versatile cell culture-based method for detecting and investigating interactions in a cellular context. Our experiments demonstrate that ReLo specifically detects direct binary PPIs. Furthermore, we show that ReLo bridging experiments can also be used to determine the binding topology of subunits within multiprotein complexes. In addition, ReLo facilitates the identification of protein domains that mediate complex formation, allows screening for interfering point mutations, and it is sensitive to drugs that mediate or disrupt an interaction. In summary, ReLo is a simple and rapid alternative for the study of PPIs, especially when studying structurally complex proteins or when established methods fail.
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Affiliation(s)
- Harpreet Kaur Salgania
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, 69120, Heidelberg, Germany
| | - Jutta Metz
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, 69120, Heidelberg, Germany
| | - Mandy Jeske
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, 69120, Heidelberg, Germany.
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2
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Feng H, Lu XJ, Maji S, Liu L, Ustianenko D, Rudnick ND, Zhang C. Structure-based prediction and characterization of photo-crosslinking in native protein-RNA complexes. Nat Commun 2024; 15:2279. [PMID: 38480694 PMCID: PMC10937933 DOI: 10.1038/s41467-024-46429-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 02/26/2024] [Indexed: 03/17/2024] Open
Abstract
UV-crosslinking of protein and RNA in direct contacts has been widely used to study protein-RNA complexes while our understanding of the photo-crosslinking mechanisms remains poor. This knowledge gap is due to the challenge of precisely mapping the crosslink sites in protein and RNA simultaneously in their native sequence and structural contexts. Here we systematically analyze protein-RNA interactions and photo-crosslinking by bridging crosslinked nucleotides and amino acids mapped using different assays with protein-RNA complex structures. We developed a computational method PxR3D-map which reliably predicts crosslink sites using structural information characterizing protein-RNA interaction interfaces. Analysis of the informative features revealed that photo-crosslinking is facilitated by base stacking with not only aromatic residues, but also dipeptide bonds that involve glycine, and distinct mechanisms are utilized by different RNA-binding domains. Our work suggests protein-RNA photo-crosslinking is highly selective in the cellular environment, which can guide data interpretation and further technology development for UV-crosslinking-based assays.
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Affiliation(s)
- Huijuan Feng
- Department of Biostatistics and Computational Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
- Center for Motor Neuron Biology and Disease, Columbia University, New York, NY, 10032, USA
| | - Xiang-Jun Lu
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
| | - Suvrajit Maji
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
- Center for Motor Neuron Biology and Disease, Columbia University, New York, NY, 10032, USA
| | - Linxi Liu
- Department of Statistics, Columbia University, New York, NY, 10027, USA
- Department of Statistics, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Dmytro Ustianenko
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
- Center for Motor Neuron Biology and Disease, Columbia University, New York, NY, 10032, USA
| | - Noam D Rudnick
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
- Wilmer Eye Institute, Johns Hopkins University, Baltimore, MD, 21287, USA
| | - Chaolin Zhang
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA.
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA.
- Center for Motor Neuron Biology and Disease, Columbia University, New York, NY, 10032, USA.
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3
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Baek M, McHugh R, Anishchenko I, Jiang H, Baker D, DiMaio F. Accurate prediction of protein-nucleic acid complexes using RoseTTAFoldNA. Nat Methods 2024; 21:117-121. [PMID: 37996753 PMCID: PMC10776382 DOI: 10.1038/s41592-023-02086-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 10/16/2023] [Indexed: 11/25/2023]
Abstract
Protein-RNA and protein-DNA complexes play critical roles in biology. Despite considerable recent advances in protein structure prediction, the prediction of the structures of protein-nucleic acid complexes without homology to known complexes is a largely unsolved problem. Here we extend the RoseTTAFold machine learning protein-structure-prediction approach to additionally predict nucleic acid and protein-nucleic acid complexes. We develop a single trained network, RoseTTAFoldNA, that rapidly produces three-dimensional structure models with confidence estimates for protein-DNA and protein-RNA complexes. Here we show that confident predictions have considerably higher accuracy than current state-of-the-art methods. RoseTTAFoldNA should be broadly useful for modeling the structure of naturally occurring protein-nucleic acid complexes, and for designing sequence-specific RNA and DNA-binding proteins.
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Affiliation(s)
- Minkyung Baek
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Ryan McHugh
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Ivan Anishchenko
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Hanlun Jiang
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Frank DiMaio
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
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4
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Scherf J, Vogel D, Gul S, Reinshagen J, Gribbon P, Rosenthal M. Limited high-throughput screening compatibility of the phenuivirus cap-binding domain. Sci Rep 2023; 13:22820. [PMID: 38129678 PMCID: PMC10739838 DOI: 10.1038/s41598-023-50158-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 12/15/2023] [Indexed: 12/23/2023] Open
Abstract
Bunyaviruses constitute a large and diverse group of viruses encompassing many emerging pathogens, such as Rift Valley fever virus (family Phenuiviridae), with public and veterinary health relevance but with very limited medical countermeasures are available. For the development of antiviral strategies, the identification and validation of virus-specific targets would be of high value. The cap-snatching mechanism is an essential process in the life cycle of bunyaviruses to produce capped mRNAs, which are then recognized and translated into viral proteins by the host cell translation machinery. Cap-snatching involves cap-binding as well as endonuclease functions and both activities have been demonstrated to be druggable in related influenza viruses. Here, we explore the suitability of the phenuivirus cap-binding function as a target in medium- and high-throughput drug discovery approaches. We developed a range of in vitro assays aiming to detect the interaction between the cap-binding domain (CBD) and the analogue of its natural cap-ligand m7GTP. However, constricted by its shallow binding pocket and low affinity for m7GTP, we conclude that the CBD has limited small molecule targeting potential using classical in vitro drug discovery approaches.
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Affiliation(s)
- Janna Scherf
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Dominik Vogel
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Sheraz Gul
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Discovery Research ScreeningPort, Hamburg, Germany
- Fraunhofer Cluster of Excellence for Immune-Mediated Diseases (CIMD), Theodor Stern Kai 7, 60590, Frankfurt, Germany
| | - Jeanette Reinshagen
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Discovery Research ScreeningPort, Hamburg, Germany
- Fraunhofer Cluster of Excellence for Immune-Mediated Diseases (CIMD), Theodor Stern Kai 7, 60590, Frankfurt, Germany
| | - Philip Gribbon
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Discovery Research ScreeningPort, Hamburg, Germany.
- Fraunhofer Cluster of Excellence for Immune-Mediated Diseases (CIMD), Theodor Stern Kai 7, 60590, Frankfurt, Germany.
| | - Maria Rosenthal
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Discovery Research ScreeningPort, Hamburg, Germany.
- Center for Structural Systems Biology, Hamburg, Germany.
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5
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Fletcher A, Clift D, de Vries E, Martinez Cuesta S, Malcolm T, Meghini F, Chaerkady R, Wang J, Chiang A, Weng SHS, Tart J, Wong E, Donohoe G, Rawlins P, Gordon E, Taylor JD, James L, Hunt J. A TRIM21-based bioPROTAC highlights the therapeutic benefit of HuR degradation. Nat Commun 2023; 14:7093. [PMID: 37925433 PMCID: PMC10625600 DOI: 10.1038/s41467-023-42546-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 10/13/2023] [Indexed: 11/06/2023] Open
Abstract
Human antigen R (HuR) is a ubiquitously expressed RNA-binding protein, which functions as an RNA regulator. Overexpression of HuR correlates with high grade tumours and poor patient prognosis, implicating it as an attractive therapeutic target. However, an effective small molecule antagonist to HuR for clinical use remains elusive. Here, a single domain antibody (VHH) that binds HuR with low nanomolar affinity was identified and shown to inhibit HuR binding to RNA. This VHH was used to engineer a TRIM21-based biological PROTAC (bioPROTAC) that could degrade endogenous HuR. Significantly, HuR degradation reverses the tumour-promoting properties of cancer cells in vivo by altering the HuR-regulated proteome, highlighting the benefit of HuR degradation and paving the way for the development of HuR-degrading therapeutics. These observations have broader implications for degrading intractable therapeutic targets, with bioPROTACs presenting a unique opportunity to explore targeted-protein degradation through a modular approach.
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Affiliation(s)
| | - Dean Clift
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, UK
| | - Emma de Vries
- Biologics Engineering, R&D, AstraZeneca, Cambridge, UK
| | - Sergio Martinez Cuesta
- Data Sciences and Quantitative Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
| | | | | | - Raghothama Chaerkady
- Centre for Genomics Research, Discovery Sciences, R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Junmin Wang
- Centre for Genomics Research, Discovery Sciences, R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Abby Chiang
- Centre for Genomics Research, Discovery Sciences, R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Shao Huan Samuel Weng
- Centre for Genomics Research, Discovery Sciences, R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Jonathan Tart
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
| | - Edmond Wong
- Biologics Engineering, R&D, AstraZeneca, Cambridge, UK
| | | | - Philip Rawlins
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
| | - Euan Gordon
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | | | - Leo James
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, UK
| | - James Hunt
- Biologics Engineering, R&D, AstraZeneca, Cambridge, UK.
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6
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Enustun E, Deep A, Gu Y, Nguyen KT, Chaikeeratisak V, Armbruster E, Ghassemian M, Villa E, Pogliano J, Corbett KD. Identification of the bacteriophage nucleus protein interaction network. Nat Struct Mol Biol 2023; 30:1653-1662. [PMID: 37667030 PMCID: PMC10643120 DOI: 10.1038/s41594-023-01094-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 08/11/2023] [Indexed: 09/06/2023]
Abstract
In the arms race between bacteria and bacteriophages (phages), some large-genome jumbo phages have evolved a protein shell that encloses their replicating genome to protect it against host immune factors. By segregating the genome from the host cytoplasm, however, the 'phage nucleus' introduces the need to specifically translocate messenger RNA and proteins through the nuclear shell and to dock capsids on the shell for genome packaging. Here, we use proximity labeling and localization mapping to systematically identify proteins associated with the major nuclear shell protein chimallin (ChmA) and other distinctive structures assembled by these phages. We identify six uncharacterized nuclear-shell-associated proteins, one of which directly interacts with self-assembled ChmA. The structure and protein-protein interaction network of this protein, which we term ChmB, suggest that it forms pores in the ChmA lattice that serve as docking sites for capsid genome packaging and may also participate in messenger RNA and/or protein translocation.
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Affiliation(s)
- Eray Enustun
- Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA
| | - Amar Deep
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Yajie Gu
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Katrina T Nguyen
- Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA
| | - Vorrapon Chaikeeratisak
- Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Emily Armbruster
- Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA
| | - Majid Ghassemian
- Biomolecular and Proteomics Mass Spectrometry Facility, University of California San Diego, La Jolla, CA, USA
| | - Elizabeth Villa
- Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA
- Howard Hughes Medical Institute, La Jolla, CA, USA
| | - Joe Pogliano
- Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA.
| | - Kevin D Corbett
- Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA.
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
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7
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Zhu H, Yang Y, Wang Y, Wang F, Huang Y, Chang Y, Wong KC, Li X. Dynamic characterization and interpretation for protein-RNA interactions across diverse cellular conditions using HDRNet. Nat Commun 2023; 14:6824. [PMID: 37884495 PMCID: PMC10603054 DOI: 10.1038/s41467-023-42547-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 10/13/2023] [Indexed: 10/28/2023] Open
Abstract
RNA-binding proteins play crucial roles in the regulation of gene expression, and understanding the interactions between RNAs and RBPs in distinct cellular conditions forms the basis for comprehending the underlying RNA function. However, current computational methods pose challenges to the cross-prediction of RNA-protein binding events across diverse cell lines and tissue contexts. Here, we develop HDRNet, an end-to-end deep learning-based framework to precisely predict dynamic RBP binding events under diverse cellular conditions. Our results demonstrate that HDRNet can accurately and efficiently identify binding sites, particularly for dynamic prediction, outperforming other state-of-the-art models on 261 linear RNA datasets from both eCLIP and CLIP-seq, supplemented with additional tissue data. Moreover, we conduct motif and interpretation analyses to provide fresh insights into the pathological mechanisms underlying RNA-RBP interactions from various perspectives. Our functional genomic analysis further explores the gene-human disease associations, uncovering previously uncharacterized observations for a broad range of genetic disorders.
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Affiliation(s)
- Haoran Zhu
- School of Artificial Intelligence, Jilin University, 130012, Changchun, China
| | - Yuning Yang
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Yunhe Wang
- School of Artificial Intelligence, Hebei University of Technology, Tianjin, China
| | - Fuzhou Wang
- Department of Computer Science, City University of Hong Kong, Hong Kong, Hong Kong SAR
| | - Yujian Huang
- College of Computer Science and Cyber Security, Chengdu University of Technology, 610059, Chengdu, China
| | - Yi Chang
- School of Artificial Intelligence, Jilin University, 130012, Changchun, China
| | - Ka-Chun Wong
- Department of Computer Science, City University of Hong Kong, Hong Kong, Hong Kong SAR.
| | - Xiangtao Li
- School of Artificial Intelligence, Jilin University, 130012, Changchun, China.
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8
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Dorn G, Gmeiner C, de Vries T, Dedic E, Novakovic M, Damberger FF, Maris C, Finol E, Sarnowski CP, Kohlbrecher J, Welsh TJ, Bolisetty S, Mezzenga R, Aebersold R, Leitner A, Yulikov M, Jeschke G, Allain FHT. Integrative solution structure of PTBP1-IRES complex reveals strong compaction and ordering with residual conformational flexibility. Nat Commun 2023; 14:6429. [PMID: 37833274 PMCID: PMC10576089 DOI: 10.1038/s41467-023-42012-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 09/27/2023] [Indexed: 10/15/2023] Open
Abstract
RNA-binding proteins (RBPs) are crucial regulators of gene expression, often composed of defined domains interspersed with flexible, intrinsically disordered regions. Determining the structure of ribonucleoprotein (RNP) complexes involving such RBPs necessitates integrative structural modeling due to their lack of a single stable state. In this study, we integrate magnetic resonance, mass spectrometry, and small-angle scattering data to determine the solution structure of the polypyrimidine-tract binding protein 1 (PTBP1/hnRNP I) bound to an RNA fragment from the internal ribosome entry site (IRES) of the encephalomyocarditis virus (EMCV). This binding, essential for enhancing the translation of viral RNA, leads to a complex structure that demonstrates RNA and protein compaction, while maintaining pronounced conformational flexibility. Acting as an RNA chaperone, PTBP1 orchestrates the IRES RNA into a few distinct conformations, exposing the RNA stems outward. This conformational diversity is likely common among RNP structures and functionally important. Our approach enables atomic-level characterization of heterogeneous RNP structures.
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Affiliation(s)
- Georg Dorn
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Christoph Gmeiner
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Zürich, Switzerland
| | - Tebbe de Vries
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Emil Dedic
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Mihajlo Novakovic
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Fred F Damberger
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Christophe Maris
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Esteban Finol
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Chris P Sarnowski
- Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Joachim Kohlbrecher
- Laboratory for Neutron Scattering and Imaging, Paul Scherrer Institut, Villigen, Switzerland
| | - Timothy J Welsh
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Zürich, Switzerland
| | - Sreenath Bolisetty
- Laboratory of Food & Soft Materials, Institute of Food, Nutrition and Health, Department for Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | - Raffaele Mezzenga
- Laboratory of Food & Soft Materials, Institute of Food, Nutrition and Health, Department for Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | - Ruedi Aebersold
- Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Alexander Leitner
- Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Maxim Yulikov
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Zürich, Switzerland.
| | - Gunnar Jeschke
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Zürich, Switzerland.
| | - Frédéric H-T Allain
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland.
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9
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Hörberg J, Reymer A. Decoding the dual recognition mechanism of the glucocorticoid receptor for DNA and RNA: sequence versus shape. Sci Rep 2023; 13:16125. [PMID: 37752333 PMCID: PMC10522765 DOI: 10.1038/s41598-023-43244-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 09/21/2023] [Indexed: 09/28/2023] Open
Abstract
Transcription factors (TFs) regulate eukaryotic transcription through selective DNA-binding, can also specifically interact with RNA, which may present another layer of transcriptional control. The mechanisms of the TFs-DNA recognition are often well-characterised, while the details of TFs-RNA complexation are less understood. Here we investigate the dual recognition mechanism of the glucocorticoid receptor (GR), which interacts with similar affinities with consensus DNA and diverse RNA hairpin motifs but discriminates against uniform dsRNA. Using atomic molecular dynamics simulations, we demonstrate that the GR binding to nucleic acids requires a wide and shallow groove pocket. The protein effectively moulds its binding site within DNA major groove, which enables base-specific interactions. Contrary, the GR binding has little effect on the grooves geometry of RNA systems, most notably in uniform dsRNA. Instead, a hairpin motif in RNA yields a wide and shallow major groove pocket, allowing the protein to anchor itself through nonspecific electrostatic contacts with RNA backbone. Addition of a bulge increases RNA hairpin flexibility, which leads to a greater number of GR-RNA contacts and, thus, higher affinity. Thus, the combination of structural motifs defines the GR-RNA selective binding: a recognition mechanism, which may be shared by other zinc finger TFs.
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Affiliation(s)
- Johanna Hörberg
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30, Göteborg, Sweden
| | - Anna Reymer
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30, Göteborg, Sweden.
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10
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Kristofich J, Nicchitta CV. Signal-noise metrics for RNA binding protein identification reveal broad spectrum protein-RNA interaction frequencies and dynamics. Nat Commun 2023; 14:5868. [PMID: 37735163 PMCID: PMC10514315 DOI: 10.1038/s41467-023-41284-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 08/30/2023] [Indexed: 09/23/2023] Open
Abstract
Recent efforts towards the comprehensive identification of RNA-bound proteomes have revealed a large, surprisingly diverse family of candidate RNA-binding proteins (RBPs). Quantitative metrics for characterization and validation of protein-RNA interactions and their dynamic interactions have, however, proven analytically challenging and prone to error. Here we report a method termed LEAP-RBP (Liquid-Emulsion-Assisted-Purification of RNA-Bound Protein) for the selective, quantitative recovery of UV-crosslinked RNA-protein complexes. By virtue of its high specificity and yield, LEAP-RBP distinguishes RNA-bound and RNA-free protein levels and reveals common sources of experimental noise in RNA-centric RBP enrichment methods. We introduce strategies for accurate RBP identification and signal-based metrics for quantifying protein-RNA complex enrichment, relative RNA occupancy, and method specificity. In this work, the utility of our approach is validated by comprehensive identification of RBPs whose association with mRNA is modulated in response to global mRNA translation state changes and through in-depth benchmark comparisons with current methodologies.
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Affiliation(s)
- JohnCarlo Kristofich
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, 27710, USA
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11
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Ray D, Laverty KU, Jolma A, Nie K, Samson R, Pour SE, Tam CL, von Krosigk N, Nabeel-Shah S, Albu M, Zheng H, Perron G, Lee H, Najafabadi H, Blencowe B, Greenblatt J, Morris Q, Hughes TR. RNA-binding proteins that lack canonical RNA-binding domains are rarely sequence-specific. Sci Rep 2023; 13:5238. [PMID: 37002329 PMCID: PMC10066285 DOI: 10.1038/s41598-023-32245-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 03/23/2023] [Indexed: 04/03/2023] Open
Abstract
Thousands of RNA-binding proteins (RBPs) crosslink to cellular mRNA. Among these are numerous unconventional RBPs (ucRBPs)-proteins that associate with RNA but lack known RNA-binding domains (RBDs). The vast majority of ucRBPs have uncharacterized RNA-binding specificities. We analyzed 492 human ucRBPs for intrinsic RNA-binding in vitro and identified 23 that bind specific RNA sequences. Most (17/23), including 8 ribosomal proteins, were previously associated with RNA-related function. We identified the RBDs responsible for sequence-specific RNA-binding for several of these 23 ucRBPs and surveyed whether corresponding domains from homologous proteins also display RNA sequence specificity. CCHC-zf domains from seven human proteins recognized specific RNA motifs, indicating that this is a major class of RBD. For Nudix, HABP4, TPR, RanBP2-zf, and L7Ae domains, however, only isolated members or closely related homologs yielded motifs, consistent with RNA-binding as a derived function. The lack of sequence specificity for most ucRBPs is striking, and we suggest that many may function analogously to chromatin factors, which often crosslink efficiently to cellular DNA, presumably via indirect recruitment. Finally, we show that ucRBPs tend to be highly abundant proteins and suggest their identification in RNA interactome capture studies could also result from weak nonspecific interactions with RNA.
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Affiliation(s)
- Debashish Ray
- Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Kaitlin U Laverty
- Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Arttu Jolma
- Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Kate Nie
- Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Reuben Samson
- Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Sara E Pour
- Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Cyrus L Tam
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Tri-Institutional Training Program in Computational Biology and Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Niklas von Krosigk
- Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Syed Nabeel-Shah
- Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Mihai Albu
- Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Hong Zheng
- Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Gabrielle Perron
- Department of Human Genetics, McGill University, Montréal, QC, H3A 0C7, Canada
- McGill Genome Centre, Montréal, QC, H3A 0G1, Canada
| | - Hyunmin Lee
- Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Hamed Najafabadi
- Department of Human Genetics, McGill University, Montréal, QC, H3A 0C7, Canada
- McGill Genome Centre, Montréal, QC, H3A 0G1, Canada
| | - Benjamin Blencowe
- Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Jack Greenblatt
- Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Quaid Morris
- Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Tri-Institutional Training Program in Computational Biology and Medicine, Weill Cornell Medicine, New York, NY, USA.
| | - Timothy R Hughes
- Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.
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12
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Yang H, Kim K, Li S, Pacheco J, Chen XS. Structural basis of sequence-specific RNA recognition by the antiviral factor APOBEC3G. Nat Commun 2022; 13:7498. [PMID: 36470880 PMCID: PMC9722718 DOI: 10.1038/s41467-022-35201-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 11/22/2022] [Indexed: 12/12/2022] Open
Abstract
An essential step in restricting HIV infectivity by the antiviral factor APOBEC3G is its incorporation into progeny virions via binding to HIV RNA. However, the mechanism of APOBEC3G capturing viral RNA is unknown. Here, we report crystal structures of a primate APOBEC3G bound to different types of RNAs, revealing that APOBEC3G specifically recognizes unpaired 5'-AA-3' dinucleotides, and to a lesser extent, 5'-GA-3' dinucleotides. APOBEC3G binds to the common 3'A in the AA/GA motifs using an aromatic/hydrophobic pocket in the non-catalytic domain. It binds to the 5'A or 5'G in the AA/GA motifs using an aromatic/hydrophobic groove conformed between the non-catalytic and catalytic domains. APOBEC3G RNA binding property is distinct from that of the HIV nucleocapsid protein recognizing unpaired guanosines. Our findings suggest that the sequence-specific RNA recognition is critical for APOBEC3G virion packaging and restricting HIV infectivity.
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Affiliation(s)
- Hanjing Yang
- Molecular and Computational Biology, Departments of Biological Sciences and Chemistry, Los Angeles, CA 90089 USA
| | - Kyumin Kim
- Molecular and Computational Biology, Departments of Biological Sciences and Chemistry, Los Angeles, CA 90089 USA
| | - Shuxing Li
- Molecular and Computational Biology, Departments of Biological Sciences and Chemistry, Los Angeles, CA 90089 USA ,grid.42505.360000 0001 2156 6853Center of Excellence in NanoBiophysics, University of Southern California, Los Angeles, CA 90089 USA
| | - Josue Pacheco
- Molecular and Computational Biology, Departments of Biological Sciences and Chemistry, Los Angeles, CA 90089 USA
| | - Xiaojiang S. Chen
- Molecular and Computational Biology, Departments of Biological Sciences and Chemistry, Los Angeles, CA 90089 USA ,grid.42505.360000 0001 2156 6853Center of Excellence in NanoBiophysics, University of Southern California, Los Angeles, CA 90089 USA ,grid.42505.360000 0001 2156 6853Genetic, Molecular and Cellular Biology Program, Keck School of Medicine, Los Angeles, CA 90033 USA ,grid.42505.360000 0001 2156 6853Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033 USA
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13
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Granik N, Katz N, Willinger O, Goldberg S, Amit R. Formation of synthetic RNA protein granules using engineered phage-coat-protein -RNA complexes. Nat Commun 2022; 13:6811. [PMID: 36357399 DOI: 10.1038/s41467-022-34644-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 11/02/2022] [Indexed: 11/12/2022] Open
Abstract
Liquid-solid transition, also known as gelation, is a specific form of phase separation in which molecules cross-link to form a highly interconnected compartment with solid - like dynamical properties. Here, we utilize RNA hairpin coat-protein binding sites to form synthetic RNA based gel-like granules via liquid-solid phase transition. We show both in-vitro and in-vivo that hairpin containing synthetic long non-coding RNA (slncRNA) molecules granulate into bright localized puncta. We further demonstrate that upon introduction of the coat-proteins, less-condensed gel-like granules form with the RNA creating an outer shell with the proteins mostly present inside the granule. Moreover, by tracking puncta fluorescence signals over time, we detected addition or shedding events of slncRNA-CP nucleoprotein complexes. Consequently, our granules constitute a genetically encoded storage compartment for protein and RNA with a programmable controlled release profile that is determined by the number of hairpins encoded into the RNA. Our findings have important implications for the potential regulatory role of naturally occurring granules and for the broader biotechnology field.
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14
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Zacco E, Kantelberg O, Milanetti E, Armaos A, Panei FP, Gregory J, Jeacock K, Clarke DJ, Chandran S, Ruocco G, Gustincich S, Horrocks MH, Pastore A, Tartaglia GG. Probing TDP-43 condensation using an in silico designed aptamer. Nat Commun 2022; 13:3306. [PMID: 35739092 PMCID: PMC9226187 DOI: 10.1038/s41467-022-30944-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 05/23/2022] [Indexed: 12/03/2022] Open
Abstract
Aptamers are artificial oligonucleotides binding to specific molecular targets. They have a promising role in therapeutics and diagnostics but are often difficult to design. Here, we exploited the catRAPID algorithm to generate aptamers targeting TAR DNA-binding protein 43 (TDP-43), whose aggregation is associated with Amyotrophic Lateral Sclerosis. On the pathway to forming insoluble inclusions, TDP-43 adopts a heterogeneous population of assemblies, many smaller than the diffraction-limit of light. We demonstrated that our aptamers bind TDP-43 and used the tightest interactor, Apt-1, as a probe to visualize TDP-43 condensates with super-resolution microscopy. At a resolution of 10 nanometers, we tracked TDP-43 oligomers undetectable by standard approaches. In cells, Apt-1 interacts with both diffuse and condensed forms of TDP-43, indicating that Apt-1 can be exploited to follow TDP-43 phase transition. The de novo generation of aptamers and their use for microscopy opens a new page to study protein condensation.
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Affiliation(s)
- Elsa Zacco
- Centre for Human Technologies (CHT), Istituto Italiano di Tecnologia (IIT), Via Enrico Melen, 83, 16152, Genova, Italy
| | - Owen Kantelberg
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, EH9 3FJ, UK
| | - Edoardo Milanetti
- Department of Physics, Sapienza University, Piazzale Aldo Moro 5, 00185, Rome, Italy.,Center for Life Nanoscience, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161, Rome, Italy
| | - Alexandros Armaos
- Centre for Human Technologies (CHT), Istituto Italiano di Tecnologia (IIT), Via Enrico Melen, 83, 16152, Genova, Italy
| | - Francesco Paolo Panei
- Department of Physics, Sapienza University, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Jenna Gregory
- UK Dementia Research Institute at University of Edinburgh, University of Edinburgh, Edinburgh bioQuarter, Chancellor's Building, 49 Little F, Edinburgh, UK.,Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK.,Euan MacDonald Centre for MND Research, University of Edinburgh, Edinburgh, UK
| | - Kiani Jeacock
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, EH9 3FJ, UK
| | - David J Clarke
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, EH9 3FJ, UK
| | - Siddharthan Chandran
- UK Dementia Research Institute at University of Edinburgh, University of Edinburgh, Edinburgh bioQuarter, Chancellor's Building, 49 Little F, Edinburgh, UK.,Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK.,Euan MacDonald Centre for MND Research, University of Edinburgh, Edinburgh, UK
| | - Giancarlo Ruocco
- Department of Physics, Sapienza University, Piazzale Aldo Moro 5, 00185, Rome, Italy.,Center for Life Nanoscience, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161, Rome, Italy
| | - Stefano Gustincich
- Centre for Human Technologies (CHT), Istituto Italiano di Tecnologia (IIT), Via Enrico Melen, 83, 16152, Genova, Italy
| | - Mathew H Horrocks
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, EH9 3FJ, UK.
| | - Annalisa Pastore
- UK Dementia Research Institute at the Maurice Wohl Institute of King's College London, London, SE5 9RT, UK.
| | - Gian Gaetano Tartaglia
- Centre for Human Technologies (CHT), Istituto Italiano di Tecnologia (IIT), Via Enrico Melen, 83, 16152, Genova, Italy. .,Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain. .,Catalan Institution for Research and Advanced Studies, ICREA, Passeig Lluís Companys 23, 08010, Barcelona, Spain. .,Department of Biology 'Charles Darwin', Sapienza University of Rome, P.le A. Moro 5, Rome, 00185, Italy.
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15
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Fraser A, Sokolova ML, Drobysheva AV, Gordeeva JV, Borukhov S, Jumper J, Severinov KV, Leiman PG. Structural basis of template strand deoxyuridine promoter recognition by a viral RNA polymerase. Nat Commun 2022; 13:3526. [PMID: 35725571 PMCID: PMC9209446 DOI: 10.1038/s41467-022-31214-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 06/07/2022] [Indexed: 11/23/2022] Open
Abstract
Recognition of promoters in bacterial RNA polymerases (RNAPs) is controlled by sigma subunits. The key sequence motif recognized by the sigma, the -10 promoter element, is located in the non-template strand of the double-stranded DNA molecule ~10 nucleotides upstream of the transcription start site. Here, we explain the mechanism by which the phage AR9 non-virion RNAP (nvRNAP), a bacterial RNAP homolog, recognizes the -10 element of its deoxyuridine-containing promoter in the template strand. The AR9 sigma-like subunit, the nvRNAP enzyme core, and the template strand together form two nucleotide base-accepting pockets whose shapes dictate the requirement for the conserved deoxyuridines. A single amino acid substitution in the AR9 sigma-like subunit allows one of these pockets to accept a thymine thus expanding the promoter consensus. Our work demonstrates the extent to which viruses can evolve host-derived multisubunit enzymes to make transcription of their own genes independent of the host.
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Affiliation(s)
- Alec Fraser
- grid.176731.50000 0001 1547 9964Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555-0647 USA
| | - Maria L. Sokolova
- grid.176731.50000 0001 1547 9964Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555-0647 USA ,grid.454320.40000 0004 0555 3608Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205 Russia
| | - Arina V. Drobysheva
- grid.454320.40000 0004 0555 3608Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205 Russia
| | - Julia V. Gordeeva
- grid.454320.40000 0004 0555 3608Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205 Russia
| | - Sergei Borukhov
- grid.262671.60000 0000 8828 4546Department of Cell Biology and Neuroscience, Rowan University School of Osteopathic Medicine at Stratford, Stratford, NJ 08084-1489 USA
| | - John Jumper
- grid.498210.60000 0004 5999 1726DeepMind Technologies Limited, London, UK
| | - Konstantin V. Severinov
- grid.454320.40000 0004 0555 3608Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205 Russia ,grid.4886.20000 0001 2192 9124Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182 Russia ,grid.430387.b0000 0004 1936 8796Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
| | - Petr G. Leiman
- grid.176731.50000 0001 1547 9964Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555-0647 USA
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16
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Wang Y, Ye W, Tian G, Zhang Y. Identification of a new RNA-binding proteins-based signature for prognostic prediction in gastric cancer. Medicine (Baltimore) 2022; 101:e28901. [PMID: 35212295 PMCID: PMC8878810 DOI: 10.1097/md.0000000000028901] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 02/01/2022] [Indexed: 01/04/2023] Open
Abstract
Gastric cancer (GC) is one of the most common cancers with high incidence and mortality worldwide. Recently, RNA-binding proteins (RBPs) have drawn more and more attention for its role in cancer pathophysiology. However, the function and clinical implication of RBPs in GC have not been fully elucidated. RNA sequencing data along with the corresponding clinical information of GC patients were downloaded from The Cancer Genome Atlas (TCGA) database. Differentially expressed RNA-binding proteins (DERBPs) between tumor and normal tissues were identified by "limma" package. Functional enrichment analysis and the protein-protein interaction (PPI) network were harnessed to explore the function and interaction of DERBPs. Next, univariate and multiple Cox regression were applied to screen prognosis-related hub RBPs and to construct a signature for GC. Meanwhile, a nomogram was built on the basis of the independent factors. A total of 296 DERBPs were found, and most of them mainly related to post-transcriptional regulation of RNA and ribonucleoprotein. A PPI network of DERBPs was constructed, consisting of 262 nodes and 2567 edges. A prognostic signature was built depending on 7 prognosis-related hub RBPs that could divide GC patients into high-risk and low-risk groups. Survival analysis showed that high-risk group had a worse prognosis compared with the low-risk group and the time-dependent receiver operating characteristic (ROC) curves suggested that signature existed moderate predictive capacities of survival for GC patients. Similar results were obtained from another independent set GSE62254, confirming the robustness of signature. Besides, the genetic variation and immune heterogeneity differences were identified between the high-risk and low-risk groups by bioinformatics methods. These findings would provide evidence of the effect of RBPs and offer a novel potential biomarker in prognostic prediction and clinical decision for GC.
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Affiliation(s)
- Yuzhi Wang
- Department of Laboratory Medicine, People's Hospital of Deyang City, Deyang, Sichuan, China
| | - Weixia Ye
- Department of Gastroenterology, Luzhou People's Hospital, Luzhou, Sichuan, China
| | - Gang Tian
- Department of Laboratory Medicine, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Yi Zhang
- Department of Blood Transfusion, People's Hospital of Deyang City, Deyang, Sichuan, China
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17
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Sakellariou D, Tiberti M, Kleiber TH, Blazquez L, López AR, Abildgaard MH, Lubas M, Bartek J, Papaleo E, Frankel LB. eIF4A3 regulates the TFEB-mediated transcriptional response via GSK3B to control autophagy. Cell Death Differ 2021; 28:3344-56. [PMID: 34158631 DOI: 10.1038/s41418-021-00822-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 06/09/2021] [Accepted: 06/10/2021] [Indexed: 02/06/2023] Open
Abstract
During autophagy, the coordinated actions of autophagosomes and lysosomes result in the controlled removal of damaged intracellular organelles and superfluous substrates. The evolutionary conservation of this process and its requirement for maintaining cellular homeostasis emphasizes the need to better dissect the pathways governing its molecular regulation. In our previously performed high-content screen, we assessed the effect of 1530 RNA-binding proteins on autophagy. Among the top regulators, we identified the eukaryotic translation initiation factor 4A-3 (eIF4A3). Here we show that depletion of eIF4A3 leads to a potent increase in autophagosome and lysosome biogenesis and an enhanced autophagic flux. This is mediated by the key autophagy transcription factor, TFEB, which becomes dephosphorylated and translocates from the cytoplasm to the nucleus where it elicits an integrated transcriptional response. We further identified an exon-skipping event in the transcript encoding for the direct TFEB kinase, GSK3B, which leads to a reduction in GSK3B expression and activity. Through analysis of TCGA data, we found a significant upregulation of eIF4A3 expression across several cancer types and confirmed the potential relevance of this newly identified signaling axis in human tumors. Hence, our data suggest a previously unrecognized role for eIF4A3 as a gatekeeper of autophagy through the control of TFEB activation, revealing a new mechanism for autophagy regulation.
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18
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Hong H, Guo Z, Sun H, Yu P, Su H, Ma X, Chen H. Two energy barriers and a transient intermediate state determine the unfolding and folding dynamics of cold shock protein. Commun Chem 2021; 4:156. [PMID: 36697724 DOI: 10.1038/s42004-021-00592-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 10/15/2021] [Indexed: 01/28/2023] Open
Abstract
Cold shock protein (Csp) is a typical two-state folding model protein which has been widely studied by biochemistry and single molecule techniques. Recently two-state property of Csp was confirmed by atomic force microscopy (AFM) through direct pulling measurement, while several long-lifetime intermediate states were found by force-clamp AFM. We systematically studied force-dependent folding and unfolding dynamics of Csp using magnetic tweezers with intrinsic constant force capability. Here we report that Csp mostly folds and unfolds with a single step over force range from 5 pN to 50 pN, and the unfolding rates show different force sensitivities at forces below and above ~8 pN, which determines a free energy landscape with two barriers and a transient intermediate state between them along one transition pathway. Our results provide a new insight on protein folding mechanism of two-state proteins.
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19
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Abstract
RNA-protein interaction can be captured by crosslinking and enrichment followed by tandem mass spectrometry, but it remains challenging to pinpoint RNA-binding sites (RBSs) or provide direct evidence for RNA-binding. To overcome these limitations, we here developed pRBS-ID, by incorporating the benefits of UVA-based photoactivatable ribonucleoside (PAR; 4-thiouridine and 6-thioguanosine) crosslinking and chemical RNA cleavage. pRBS-ID robustly detects peptides crosslinked to PAR adducts, offering direct RNA-binding evidence and identifying RBSs at single amino acid-resolution with base-specificity (U or G). Using pRBS-ID, we could profile uridine-contacting RBSs globally and discover guanosine-contacting RBSs, which allowed us to characterize the base-specific interactions. We also applied the search pipeline to analyze the datasets from UVC-based RBS-ID experiments, altogether offering a comprehensive list of human RBSs with high coverage (3,077 RBSs in 532 proteins in total). pRBS-ID is a widely applicable platform to investigate the molecular basis of posttranscriptional regulation.
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Affiliation(s)
- Jong Woo Bae
- Center for RNA Research, Institute for Basic Science, Seoul, 08826, Korea
- School of Biological Sciences, Seoul National University, Seoul, 08826, Korea
| | | | - V Narry Kim
- Center for RNA Research, Institute for Basic Science, Seoul, 08826, Korea.
- School of Biological Sciences, Seoul National University, Seoul, 08826, Korea.
| | - Jong-Seo Kim
- Center for RNA Research, Institute for Basic Science, Seoul, 08826, Korea.
- School of Biological Sciences, Seoul National University, Seoul, 08826, Korea.
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20
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Abstract
RNA-binding proteins (RBPs) have conserved domains and consensus sequences that interact with RNAs and other proteins forming ribonucleoprotein (RNP) complexes. RNPs are involved in the regulation of several cellular processes, including transcription, pre-mRNA splicing, mRNA transport, localization, degradation and storage, and ultimately control of translation. Heterogeneous nuclear ribonucleoproteins (hnRNPs) comprise a family of RBPs that mediate transcription control and nuclear processing of transcripts. Some hnRNPs are part of the spliceosome complex, a dynamic machinery formed by RNPs that regulate alternative splicing of pre-mRNAs. Here, chemical crosslinking of proteins was applied to identify specific interacting regions and protein structural features of hnRNPs: hnRNPA1, hnRNPA2/B1, hnRNPC, and RALY. The results reveal interaction of these proteins within RNA-binding domains and conserved motifs, providing evidence of a coordinated action of known regulatory sequences of RBPs. Moreover, these crosslinking data enable structural model generation for RBPs, illustrating how crosslinking mass spectrometry can complement other structural methods.
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Affiliation(s)
- Helisa H Wippel
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
| | - Mariana Fioramonte
- Department of Genome Sciences, University of Washington, Seattle, WA, USA. and University of Campinas, Campinas, SP, Brazil
| | - Juan D Chavez
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
| | - James E Bruce
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
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21
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Pipier A, Devaux A, Lavergne T, Adrait A, Couté Y, Britton S, Calsou P, Riou JF, Defrancq E, Gomez D. Constrained G4 structures unveil topology specificity of known and new G4 binding proteins. Sci Rep 2021; 11:13469. [PMID: 34188089 PMCID: PMC8241873 DOI: 10.1038/s41598-021-92806-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 06/11/2021] [Indexed: 12/20/2022] Open
Abstract
G-quadruplexes (G4) are non-canonical secondary structures consisting in stacked tetrads of hydrogen-bonded guanines bases. An essential feature of G4 is their intrinsic polymorphic nature, which is characterized by the equilibrium between several conformations (also called topologies) and the presence of different types of loops with variable lengths. In cells, G4 functions rely on protein or enzymatic factors that recognize and promote or resolve these structures. In order to characterize new G4-dependent mechanisms, extensive researches aimed at identifying new G4 binding proteins. Using G-rich single-stranded oligonucleotides that adopt non-controlled G4 conformations, a large number of G4-binding proteins have been identified in vitro, but their specificity towards G4 topology remained unknown. Constrained G4 structures are biomolecular objects based on the use of a rigid cyclic peptide scaffold as a template for directing the intramolecular assembly of the anchored oligonucleotides into a single and stabilized G4 topology. Here, using various constrained RNA or DNA G4 as baits in human cell extracts, we establish the topology preference of several well-known G4-interacting factors. Moreover, we identify new G4-interacting proteins such as the NELF complex involved in the RNA-Pol II pausing mechanism, and we show that it impacts the clastogenic effect of the G4-ligand pyridostatin.
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Affiliation(s)
- A Pipier
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
- Equipe Labellisée Ligue Contre Le Cancer 2018, Toulouse, France
| | - A Devaux
- Département de Chimie Moléculaire, UMR CNRS 5250, Université Grenoble Alpes, 38058, Grenoble, France
| | - T Lavergne
- Département de Chimie Moléculaire, UMR CNRS 5250, Université Grenoble Alpes, 38058, Grenoble, France
| | - A Adrait
- CEA, INSERM, IRIG, BGE, Université Grenoble Alpes, 38000, Grenoble, France
| | - Y Couté
- CEA, INSERM, IRIG, BGE, Université Grenoble Alpes, 38000, Grenoble, France
| | - S Britton
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
- Equipe Labellisée Ligue Contre Le Cancer 2018, Toulouse, France
| | - P Calsou
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
- Equipe Labellisée Ligue Contre Le Cancer 2018, Toulouse, France
| | - J F Riou
- Structure et Instabilité des Génomes, Muséum National d'Histoire Naturelle, CNRS, INSERM, CP 26, 75005, Paris, France
| | - E Defrancq
- Département de Chimie Moléculaire, UMR CNRS 5250, Université Grenoble Alpes, 38058, Grenoble, France
| | - D Gomez
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France.
- Equipe Labellisée Ligue Contre Le Cancer 2018, Toulouse, France.
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22
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Park S, Doherty EE, Xie Y, Padyana AK, Fang F, Zhang Y, Karki A, Lebrilla CB, Siegel JB, Beal PA. High-throughput mutagenesis reveals unique structural features of human ADAR1. Nat Commun 2020; 11:5130. [PMID: 33046702 PMCID: PMC7550611 DOI: 10.1038/s41467-020-18862-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 09/11/2020] [Indexed: 01/06/2023] Open
Abstract
Adenosine Deaminases that act on RNA (ADARs) are enzymes that catalyze adenosine to inosine conversion in dsRNA, a common form of RNA editing. Mutations in the human ADAR1 gene are known to cause disease and recent studies have identified ADAR1 as a potential therapeutic target for a subset of cancers. However, efforts to define the mechanistic effects for disease associated ADAR1 mutations and the rational design of ADAR1 inhibitors are limited by a lack of structural information. Here, we describe the combination of high throughput mutagenesis screening studies, biochemical characterization and Rosetta-based structure modeling to identify unique features of ADAR1. Importantly, these studies reveal a previously unknown zinc-binding site on the surface of the ADAR1 deaminase domain which is important for ADAR1 editing activity. Furthermore, we present structural models that explain known properties of this enzyme and make predictions about the role of specific residues in a surface loop unique to ADAR1.
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Affiliation(s)
- SeHee Park
- Department of Chemistry, University of California, Davis, Davis, CA, USA
| | - Erin E Doherty
- Department of Chemistry, University of California, Davis, Davis, CA, USA
| | - Yixuan Xie
- Department of Chemistry, University of California, Davis, Davis, CA, USA
| | | | | | - Yue Zhang
- Department of Chemistry, University of California, Davis, Davis, CA, USA
| | - Agya Karki
- Department of Chemistry, University of California, Davis, Davis, CA, USA
| | - Carlito B Lebrilla
- Department of Chemistry, University of California, Davis, Davis, CA, USA
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA, USA
| | - Justin B Siegel
- Department of Chemistry, University of California, Davis, Davis, CA, USA
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA, USA
- Genome Center, University of California Davis, Davis, CA, USA
| | - Peter A Beal
- Department of Chemistry, University of California, Davis, Davis, CA, USA.
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Bujalowski PJ, Bujalowski W, Choi KH. Identification of the viral RNA promoter stem loop A (SLA)-binding site on Zika virus polymerase NS5. Sci Rep 2020; 10:13306. [PMID: 32764551 PMCID: PMC7413259 DOI: 10.1038/s41598-020-70094-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Accepted: 07/03/2020] [Indexed: 12/17/2022] Open
Abstract
Zika virus has recently emerged as an important human pathogen that has spread to more than 60 countries. Infection of a pregnant woman with Zika virus can cause severe brain malformations in the child such as microcephaly and other birth defects. Despite the medical importance of Zika virus infection, the mechanism of viral replication, a process commonly targeted by antiviral therapeutics, is not well understood. Stem-loop A (SLA), located in the 5' untranslated region of the viral genome, acts as a promotor for viral replication and thus is critical for recognition of the viral genome by the viral polymerase NS5. However, how NS5 engages SLA is not clear. We have quantitatively examined the intrinsic affinities between Zika virus SLA and NS5, and identified the SLA-binding site on NS5. Amino acid substitutions in the thumb subdomain of the RNA-dependent RNA polymerase (RdRp) and the methyltransferase (MTase) domain reduced SLA-binding affinity, indicating that they each are part of the SLA-binding site. Furthermore, stopped-flow kinetic analysis of Zika NS5-, RdRp- and MTase-SLA interactions identified distinct intermediates during NS5 and SLA complex formation. These data suggest a model for SLA recognition and the initiation of flaviviral replication by NS5.
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Affiliation(s)
- Paul J Bujalowski
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Wlodzimierz Bujalowski
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Kyung H Choi
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch, Galveston, TX, 77555, USA.
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24
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Biswas J, Patel VL, Bhaskar V, Chao JA, Singer RH, Eliscovich C. The structural basis for RNA selectivity by the IMP family of RNA-binding proteins. Nat Commun 2019; 10:4440. [PMID: 31570709 PMCID: PMC6768852 DOI: 10.1038/s41467-019-12193-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 08/20/2019] [Indexed: 02/03/2023] Open
Abstract
The IGF2 mRNA-binding proteins (ZBP1/IMP1, IMP2, IMP3) are highly conserved post-transcriptional regulators of RNA stability, localization and translation. They play important roles in cell migration, neural development, metabolism and cancer cell survival. The knockout phenotypes of individual IMP proteins suggest that each family member regulates a unique pool of RNAs, yet evidence and an underlying mechanism for this is lacking. Here, we combine systematic evolution of ligands by exponential enrichment (SELEX) and NMR spectroscopy to demonstrate that the major RNA-binding domains of the two most distantly related IMPs (ZBP1 and IMP2) bind to different consensus sequences and regulate targets consistent with their knockout phenotypes and roles in disease. We find that the targeting specificity of each IMP is determined by few amino acids in their variable loops. As variable loops often differ amongst KH domain paralogs, we hypothesize that this is a general mechanism for evolving specificity and regulation of the transcriptome.
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Affiliation(s)
- Jeetayu Biswas
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Vivek L Patel
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Varun Bhaskar
- Friedrich Miescher Institute for Biomedical Research, CH-4058, Basel, Switzerland
| | - Jeffrey A Chao
- Friedrich Miescher Institute for Biomedical Research, CH-4058, Basel, Switzerland
| | - Robert H Singer
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA, 20147, USA.
| | - Carolina Eliscovich
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
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25
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Huang J, Lin H, Zhong M, Huang J, Sun S, Lin L, Chen Y. Role of Lin28A/let-7a/c-Myc Pathway in Growth and Malignant Behavior of Papillary Thyroid Carcinoma. Med Sci Monit 2018; 24:8899-8909. [PMID: 30531691 PMCID: PMC6296344 DOI: 10.12659/msm.908628] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Lin28 is a gene involved in many biological processes, including development, glucose metabolism, and tumorigenesis. Let-7 miRNA is a tumor-suppressor gene that is frequently inactivated in cancer cells. The role of c-Myc (a target gene of let-7) and the Lin28-let-7-c-Myc pathway in the growth and malignancy of thyroid cancer is unclear. The purpose of the present study was to evaluate the expression of Lin28A, let-7a, and c-Myc in human papillary thyroid carcinoma (PTC) and to investigate their potential mechanisms in the progression of PTC. MATERIAL AND METHODS Lin28A and c-Myc expression were assessed in PTC tissues and PTC cell lines using immunohistochemistry, Western blotting, and real-time PCR. CCK-8 and Transwell assays were performed to evaluate PTC cell proliferation, migration, and invasion in cells in which the expression of Lin28A was downregulated by RNA interference or in which let-7a was overexpressed after transfection with let-7a mimics. RESULTS The expression of Lin28A and c-Myc was upregulated in PTC tissues and cell lines, whereas the expression of let-7a was downregulated in PTC cell lines. Clinically, Lin28A was linked to a higher tumor/node/metastasis stage and the presence of lymph node metastases. Moreover, knockdown of Lin28A activated let-7a processing and inhibited the expression of the downstream gene c-Myc, suppressing cell proliferation, migration, and invasion. Similar results were obtained after let-7a overexpression. CONCLUSIONS The Lin28A/let-7a/c-Myc pathway is involved in cancer growth and malignant behavior in PTC and is a potential target for therapeutic intervention in this disease.
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Affiliation(s)
- Jiaqi Huang
- Department of Endocrinology, The First Affiliated Hospital, Shantou University Medical College, Shantou, Guangdong, P.R. China
| | - Haishan Lin
- Department of Endocrinology, The First Affiliated Hospital, Shantou University Medical College, Shantou, Guangdong, P.R. China
| | - Muxun Zhong
- Department of Endocrinology, The First Affiliated Hospital, Shantou University Medical College, Shantou, Guangdong, P.R. China
| | - Jiexiong Huang
- Department of Pathology, The First Affiliated Hospital, Shantou University Medical College, Shantou, Guangdong, P.R. China
| | - Shuming Sun
- Breast Surgery, The First Affiliated Hospital, Shantou University Medical College, Shantou, Guangdong, P.R. China
| | - Ling Lin
- Department of Rheumatology, The First Affiliated Hospital, Shantou University Medical College, Shantou, Guangdong, P.R. China
| | - Yongsong Chen
- Department of Endocrinology, The First Affiliated Hospital, Shantou University Medical College, Shantou, Guangdong, P.R. China
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Mao R, Yang R, Chen X, Harhaj EW, Wang X, Fan Y. Regnase-1, a rapid response ribonuclease regulating inflammation and stress responses. Cell Mol Immunol 2017; 14:412-422. [PMID: 28194024 PMCID: PMC5423090 DOI: 10.1038/cmi.2016.70] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Revised: 11/17/2016] [Accepted: 11/17/2016] [Indexed: 02/07/2023] Open
Abstract
RNA-binding proteins (RBPs) are central players in post-transcriptional regulation and immune homeostasis. The ribonuclease and RBP Regnase-1 exerts critical roles in both immune cells and non-immune cells. Its expression is rapidly induced under diverse conditions including microbial infections, treatment with inflammatory cytokines and chemical or mechanical stimulation. Regnase-1 activation is transient and is subject to negative feedback mechanisms including proteasome-mediated degradation or mucosa-associated lymphoid tissue 1 (MALT1) mediated cleavage. The major function of Regnase-1 is promoting mRNA decay via its ribonuclease activity by specifically targeting a subset of genes in different cell types. In monocytes, Regnase-1 downregulates IL-6 and IL-12B mRNAs, thus mitigating inflammation, whereas in T cells, it restricts T-cell activation by targeting c-Rel, Ox40 and Il-2 transcripts. In cancer cells, Regnase-1 promotes apoptosis by inhibiting anti-apoptotic genes including Bcl2L1, Bcl2A1, RelB and Bcl3. Together with up-frameshift protein-1 (UPF1), Regnase-1 specifically cleaves mRNAs that are active during translation by recognizing a stem-loop (SL) structure within the 3'UTRs of these genes in endoplasmic reticulum-bound ribosomes. Through this mechanism, Regnase-1 rapidly shapes mRNA profiles and associated protein expression, restricts inflammation and maintains immune homeostasis. Dysregulation of Regnase-1 has been described in a multitude of pathological states including autoimmune diseases, cancer and cardiovascular diseases. Here, we provide a comprehensive update on the function, regulation and molecular mechanisms of Regnase-1, and we propose that Regnase-1 may function as a master rapid response gene for cellular adaption triggered by microenvironmental changes.
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Affiliation(s)
- Renfang Mao
- Basic Medical Research Center, School of Medicine, Nantong University, Nantong, Jiangsu 226001, People's Republic of China
| | - Riyun Yang
- Basic Medical Research Center, School of Medicine, Nantong University, Nantong, Jiangsu 226001, People's Republic of China
| | - Xia Chen
- Basic Medical Research Center, School of Medicine, Nantong University, Nantong, Jiangsu 226001, People's Republic of China
| | - Edward W Harhaj
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
| | - Xiaoying Wang
- Department of Immunology, School of Medicine, Nantong University, Nantong, Jiangsu 226001, People's Republic of China
| | - Yihui Fan
- Basic Medical Research Center, School of Medicine, Nantong University, Nantong, Jiangsu 226001, People's Republic of China
- Department of Immunology, School of Medicine, Nantong University, Nantong, Jiangsu 226001, People's Republic of China
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KARAGIANNIS P, FUJITA Y, SAITO H. RNA-based gene circuits for cell regulation. Proc Jpn Acad Ser B Phys Biol Sci 2016; 92:412-422. [PMID: 27840389 PMCID: PMC5328788 DOI: 10.2183/pjab.92.412] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 08/24/2016] [Indexed: 05/20/2023]
Abstract
A major goal of synthetic biology is to control cell behavior. RNA-mediated genetic switches (RNA switches) are devices that serve this purpose, as they can control gene expressions in response to input signals. In general, RNA switches consist of two domains: an aptamer domain, which binds to an input molecule, and an actuator domain, which controls the gene expression. An input binding to the aptamer can cause the actuator to alter the RNA structure, thus changing access to translation machinery. The assembly of multiple RNA switches has led to complex gene circuits for cell therapies, including the selective killing of pathological cells and purification of cell populations. The inclusion of RNA binding proteins, such as L7Ae, increases the repertoire and precision of the circuit. In this short review, we discuss synthetic RNA switches for gene regulation and their potential therapeutic applications.
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Affiliation(s)
- Peter KARAGIANNIS
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Yoshihiko FUJITA
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Hirohide SAITO
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Sakyo-ku, Kyoto, Japan
- Correspondence should be addressed: H. Saito, Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan (e-mail: )
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Samra N, Atir-Lande A, Pnueli L, Arava Y. The elongation factor eEF3 (Yef3) interacts with mRNA in a translation independent manner. BMC Mol Biol 2015; 16:17. [PMID: 26404137 PMCID: PMC4582935 DOI: 10.1186/s12867-015-0045-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 09/17/2015] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND mRNA binding proteins (RBPs) constitute 10-15% of the eukaryotic proteome and play important part in post-transcriptional regulation of gene expression. Due to the instability of RNA and the transient nature its interaction with RBPs, identification of novel RBPs is a significant challenge. Recently, a novel methodology for RBP purification and identification (termed RaPID) was presented, which allows high affinity purification of RBPs while associated with mRNA in vivo. RESULTS We performed a RaPID screen for proteins that interact with PMP1 mRNA in order to identify novel mRNA binding proteins. PMP1 mRNA was tagged in its 3' UTR with multiple MS2 loops and co-expressed with MS2-binding protein fused to streptavidin binding protein (SBP). RNA-protein complexes were cross-linked in vivo and isolated through streptavidin beads. The eluted proteins were subjected to mass spectroscopy analysis. The screen identified many proteins, about half of them were previously shown to bind RNA. We focused on eEF3 (YEF3), an essential translation elongation factor that interacts with ribosomes. Purification of TAP-tagged Yef3 with its associated RNAs confirmed that the native PMP1 transcript is associated with it. Intriguingly, high association with Yef3-TAP was observed when purification was performed in the presence of EDTA, and with PMP1 that contains stop codons immediately downstream to the initiation codon. Furthermore, high association was observed with a transcript containing only the 3' UTR of PMP1. Complementary, RaPID isolation of MS2-tagged 3' UTRs with their associated proteins revealed that Yef3 can efficiently interact with these regions. CONCLUSIONS This study identifies many novel proteins that interact with PMP1 mRNA. Importantly, the elongation factor Yef3 was found to interact with mRNA in non-coding regions and in a translation independent manner. These results suggest an additional, non-elongation function for this factor.
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Affiliation(s)
- Nitzan Samra
- Department of Biology, Technion-Israel Institute of Technology, 32000, Haifa, Israel.
| | - Avigail Atir-Lande
- Department of Biology, Technion-Israel Institute of Technology, 32000, Haifa, Israel.
| | - Lilach Pnueli
- Department of Biology, Technion-Israel Institute of Technology, 32000, Haifa, Israel.
| | - Yoav Arava
- Department of Biology, Technion-Israel Institute of Technology, 32000, Haifa, Israel.
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29
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Tessier SN, Audas TE, Wu CW, Lee S, Storey KB. The involvement of mRNA processing factors TIA-1, TIAR, and PABP-1 during mammalian hibernation. Cell Stress Chaperones 2014; 19:813-25. [PMID: 24590458 PMCID: PMC4389841 DOI: 10.1007/s12192-014-0505-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Revised: 02/11/2014] [Accepted: 02/12/2014] [Indexed: 01/10/2023] Open
Abstract
Mammalian hibernators survive low body temperatures, ischemia-reperfusion, and restricted nutritional resources via global reductions in energy-expensive cellular processes and selective increases in stress pathways. Consequently, studies that analyze hibernation uncover mechanisms which balance metabolism and support survival by enhancing stress tolerance. We hypothesized processing factors that influence messenger ribonucleic acid (mRNA) maturation and translation may play significant roles in hibernation. We characterized the amino acid sequences of three RNA processing proteins (T cell intracellular antigen 1 (TIA-1), TIA1-related (TIAR), and poly(A)-binding proteins (PABP-1)) from thirteen-lined ground squirrels (Ictidomys tridecemlineatus), which all displayed a high degree of sequence identity with other mammals. Alternate Tia-1 and TiaR gene variants were found in the liver with higher expression of isoform b versus a in both cases. The localization of RNA-binding proteins to subnuclear structures was assessed by immunohistochemistry and confirmed by subcellular fractionation; TIA-1 was identified as a major component of subnuclear structures with up to a sevenfold increase in relative protein levels in the nucleus during hibernation. By contrast, there was no significant difference in the relative protein levels of TIARa/TIARb in the nucleus, and a decrease was observed for TIAR isoforms in cytoplasmic fractions of torpid animals. Finally, we used solubility tests to analyze the formation of reversible aggregates that are associated with TIA-1/R function during stress; a shift towards the soluble fraction (TIA-1a, TIA-1b) was observed during hibernation suggesting enhanced protein aggregation was not present during torpor. The present study identifies novel posttranscriptional regulatory mechanisms that may play a role in reducing translational rates and/or mRNA processing under unfavorable environmental conditions.
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Affiliation(s)
- Shannon N. Tessier
- />Institute of Biochemistry, Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6 Canada
| | - Timothy E. Audas
- />Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5 Canada
| | - Cheng-Wei Wu
- />Institute of Biochemistry, Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6 Canada
| | - Stephen Lee
- />Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5 Canada
| | - Kenneth B. Storey
- />Institute of Biochemistry, Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6 Canada
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Xin H, Deng K, Fu M. Post-transcriptional gene regulation by RNA-binding proteins in vascular endothelial dysfunction. Sci China Life Sci 2014; 57:836-44. [PMID: 25104457 PMCID: PMC7089175 DOI: 10.1007/s11427-014-4703-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 07/01/2014] [Indexed: 12/11/2022]
Abstract
Endothelial cell dysfunction is a term which implies the dysregulation of normal endothelial cell functions, including impairment of the barrier functions, control of vascular tone, disturbance of proliferative and migratory capacity of endothelial cells, as well as control of leukocyte trafficking. Endothelial dysfunction is an early step in vascular inflammatory diseases such as atherosclerosis, diabetic vascular complications, sepsis-induced or severe virus infection-induced organ injuries. The expressions of inflammatory cytokines and vascular adhesion molecules induced by various stimuli, such as modified lipids, smoking, advanced glycation end products and bacteria toxin, significantly contribute to the development of endothelial dysfunction. The transcriptional regulation of inflammatory cytokines and vascular adhesion molecules has been well-studied. However, the regulation of those gene expressions at post-transcriptional level is emerging. RNA-binding proteins have emerged as critical regulators of gene expression acting predominantly at the post-transcriptional level in microRNA-dependent or independent manners. This review summarizes the latest insights into the roles of RNA-binding proteins in controlling vascular endothelial cell functions and their contribution to the pathogenesis of vascular inflammatory diseases.
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Affiliation(s)
- HongBo Xin
- Institute of Translational Medicine, Nanchang University, Nanchang, 330031 China
| | - KeYu Deng
- Institute of Translational Medicine, Nanchang University, Nanchang, 330031 China
| | - MinGui Fu
- Institute of Translational Medicine, Nanchang University, Nanchang, 330031 China
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31
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Silverman IM, Li F, Gregory BD. Genomic era analyses of RNA secondary structure and RNA-binding proteins reveal their significance to post-transcriptional regulation in plants. Plant Sci 2013; 205-206:55-62. [PMID: 23498863 PMCID: PMC4079699 DOI: 10.1016/j.plantsci.2013.01.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2012] [Revised: 01/22/2013] [Accepted: 01/23/2013] [Indexed: 05/27/2023]
Abstract
The eukaryotic transcriptome is regulated both transcriptionally and post-transcriptionally. Transcriptional control was the major focus of early research efforts, while more recently post-transcriptional mechanisms have gained recognition for their significant regulatory importance. At the heart of post-transcriptional regulatory pathways are cis- and trans-acting features and factors including RNA secondary structure as well as RNA-binding proteins and their recognition sites on target RNAs. Recent advances in genomic methodologies have significantly improved our understanding of both RNA secondary structure and RNA-binding proteins and their regulatory effects within the eukaryotic transcriptome. In this review, we focus specifically on the collection of these regulatory moieties in plant transcriptomes. We describe the approaches for studying RNA secondary structure and RNA-protein interaction sites, with an emphasis on recent methodological advances that produce transcriptome-wide datasets. We discuss how these methods that include genome-wide RNA secondary structure determination and RNA-protein interaction site mapping are significantly improving our understanding of the functions of these two elements in post-transcriptional regulation. Finally, we delineate the need for additional genome-wide studies of RNA secondary structure and RNA-protein interactions in plants.
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Affiliation(s)
- Ian M. Silverman
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
- PENN Genome Frontiers Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
- Cell and Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Fan Li
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
- PENN Genome Frontiers Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
- Genomics and Computational Biology Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Brian D. Gregory
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
- PENN Genome Frontiers Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
- Cell and Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA
- Genomics and Computational Biology Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA
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32
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Liang C, Xiong K, Szulwach KE, Zhang Y, Wang Z, Peng J, Fu M, Jin P, Suzuki HI, Liu Q. Sjogren syndrome antigen B (SSB)/La promotes global microRNA expression by binding microRNA precursors through stem-loop recognition. J Biol Chem 2013; 288:723-36. [PMID: 23129761 PMCID: PMC3537071 DOI: 10.1074/jbc.m112.401323] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2012] [Revised: 10/23/2012] [Indexed: 11/06/2022] Open
Abstract
MicroRNAs (miRNA) control numerous physiological and pathological processes. Typically, the primary miRNA (pri-miRNA) transcripts are processed by nuclear Drosha complex into ~70-nucleotide stem-loop precursor miRNAs (pre-miRNA), which are further cleaved by cytoplasmic Dicer complex into ~21-nucleotide mature miRNAs. However, it is unclear how nascent pre-miRNAs are protected from ribonucleases, such as MCPIP1, that degrade pre-miRNAs to abort miRNA production. Here, we identify Sjögren syndrome antigen B (SSB)/La as a pre-miRNA-binding protein that regulates miRNA processing in vitro. All three RNA-binding motifs (LAM, RRM1, and RRM2) of La/SSB are required for efficient pre-miRNA binding. Intriguingly, La/SSB recognizes the characteristic stem-loop structure of pre-miRNAs, of which the majority lack a 3' UUU terminus. Moreover, La/SSB associates with endogenous pri-/pre-miRNAs and promotes miRNA biogenesis by stabilizing pre-miRNAs from nuclease (e.g. MCPIP1)-mediated decay in mammalian cells. Accordingly, we observed positive correlations between the expression status of La/SSB and Dicer in human cancer transcriptome and prognosis. These studies identify an important function of La/SSB as a global regulator of miRNA expression, and implicate stem-loop recognition as a major mechanism that mediates association between La/SSB and diverse RNA molecules.
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Affiliation(s)
- Chunyang Liang
- From the Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - Ke Xiong
- From the Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390
- the College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Keith E. Szulwach
- the Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Yi Zhang
- From the Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - Zhaohui Wang
- From the Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - Junmin Peng
- the Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105
| | - Mingui Fu
- the Department of Basic Medical Science, University of Missouri School of Medicine, Kansas, Missouri 64108, and
| | - Peng Jin
- the Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Hiroshi I. Suzuki
- the Department of Molecular Pathology, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan
| | - Qinghua Liu
- From the Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390
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Merret R, Martino L, Bousquet-Antonelli C, Fneich S, Descombin J, Billey É, Conte MR, Deragon JM. The association of a La module with the PABP-interacting motif PAM2 is a recurrent evolutionary process that led to the neofunctionalization of La-related proteins. RNA 2013; 19:36-50. [PMID: 23148093 PMCID: PMC3527725 DOI: 10.1261/rna.035469.112] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 10/12/2012] [Indexed: 05/27/2023]
Abstract
La-related proteins (LARPs) are largely uncharacterized factors, well conserved throughout evolution. Recent reports on the function of human LARP4 and LARP6 suggest that these proteins fulfill key functions in mRNA metabolism and/or translation. We report here a detailed evolutionary history of the LARP4 and 6 families in eukaryotes. Genes coding for LARP4 and 6 were duplicated in the common ancestor of the vertebrate lineage, but one LARP6 gene was subsequently lost in the common ancestor of the eutherian lineage. The LARP6 gene was also independently duplicated several times in the vascular plant lineage. We observed that vertebrate LARP4 and plant LARP6 duplication events were correlated with the acquisition of a PABP-interacting motif 2 (PAM2) and with a significant reorganization of their RNA-binding modules. Using isothermal titration calorimetry (ITC) and immunoprecipitation methods, we show that the two plant PAM2-containing LARP6s (LARP6b and c) can, indeed, interact with the major plant poly(A)-binding protein (PAB2), while the third plant LARP6 (LARP6a) is unable to do so. We also analyzed the RNA-binding properties and the subcellular localizations of the two types of plant LARP6 proteins and found that they display nonredundant characteristics. As a whole, our results support a model in which the acquisition by LARP4 and LARP6 of a PAM2 allowed their targeting to mRNA 3' UTRs and led to their neofunctionalization.
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Affiliation(s)
- Rémy Merret
- Université de Perpignan Via Domitia, UMR5096 LGDP, 66860 Perpignan Cedex, France
- CNRS, UMR5096 LGDP, 66860 Perpignan Cedex, France
| | - Luigi Martino
- Randall Division of Cell and Molecular Biophysics, King's College London, Guy's Campus, London SE1 1UL, United Kingdom
| | - Cécile Bousquet-Antonelli
- Université de Perpignan Via Domitia, UMR5096 LGDP, 66860 Perpignan Cedex, France
- CNRS, UMR5096 LGDP, 66860 Perpignan Cedex, France
| | - Sara Fneich
- Université de Perpignan Via Domitia, UMR5096 LGDP, 66860 Perpignan Cedex, France
- CNRS, UMR5096 LGDP, 66860 Perpignan Cedex, France
| | - Julie Descombin
- Université de Perpignan Via Domitia, UMR5096 LGDP, 66860 Perpignan Cedex, France
- CNRS, UMR5096 LGDP, 66860 Perpignan Cedex, France
| | - Élodie Billey
- Université de Perpignan Via Domitia, UMR5096 LGDP, 66860 Perpignan Cedex, France
- CNRS, UMR5096 LGDP, 66860 Perpignan Cedex, France
| | - Maria R. Conte
- Randall Division of Cell and Molecular Biophysics, King's College London, Guy's Campus, London SE1 1UL, United Kingdom
| | - Jean-Marc Deragon
- Université de Perpignan Via Domitia, UMR5096 LGDP, 66860 Perpignan Cedex, France
- CNRS, UMR5096 LGDP, 66860 Perpignan Cedex, France
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Jansen RP, Niessing D. Assembly of mRNA-protein complexes for directional mRNA transport in eukaryotes--an overview. Curr Protein Pept Sci 2012; 13:284-93. [PMID: 22708485 PMCID: PMC3474952 DOI: 10.2174/138920312801619493] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Revised: 01/10/2012] [Accepted: 01/20/2012] [Indexed: 12/11/2022]
Abstract
At all steps from transcription to translation, RNA-binding proteins play important roles in determining mRNA function. Initially it was believed that for the vast majority of transcripts the role of RNA-binding proteins is limited to general functions such as splicing and translation. However, work from recent years showed that members of this class of proteins also recognize several mRNAs via cis-acting elements for their incorporation into large motor-containing particles. These particles are transported to distant subcellular sites, where they become subsequently translated. This process, called mRNA localization, occurs along microtubules or actin filaments, and involves kinesins, dyneins, as well as myosins. Although mRNA localization has been detected in a large number of organisms from fungi to humans, the underlying molecular machineries are not well understood. In this review we will outline general principles of mRNA localization and highlight three examples, for which a comparably large body of information is available. The first example is She2p/She3p-dependent localization of ASH1 mRNA in budding yeast. It is particularly well suited to highlight the interdependence between different steps of mRNA localization. The second example is Staufen-dependent localization of oskar mRNA in the Drosophila embryo, for which the importance of nuclear events for cytoplasmic localization and translational control has been clearly demonstrated. The third example summarizes Egalitarian/Bicaudal D-dependent mRNA transport events in the oocyte and embryo of Drosophila. We will highlight general themes and differences, point to similarities in other model systems, and raise open questions that might be answered in the coming years.
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Affiliation(s)
- Ralf-Peter Jansen
- Interfaculty Institute for Biochemistry, University of Tübingen, Tübingen, Germany
| | - Dierk Niessing
- Institute of Structural Biology, Helmholtz Zentrum München–German Research Center for Environmental Health, München, Germany
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-University, München, Germany
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Baird NJ, Zhang J, Hamma T, Ferré-D'Amaré AR. YbxF and YlxQ are bacterial homologs of L7Ae and bind K-turns but not K-loops. RNA 2012; 18:759-70. [PMID: 22355167 PMCID: PMC3312563 DOI: 10.1261/rna.031518.111] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Accepted: 12/24/2011] [Indexed: 05/20/2023]
Abstract
The archaeal protein L7Ae and eukaryotic homologs such as L30e and 15.5kD comprise the best characterized family of K-turn-binding proteins. K-turns are an RNA motif comprised of a bulge flanked by canonical and noncanonical helices. They are widespread in cellular RNAs, including bacterial gene-regulatory RNAs such as the c-di-GMP-II, lysine, and SAM-I riboswitches, and the T-box. The existence in bacteria of K-turn-binding proteins of the L7Ae family has not been proven, although two hypothetical proteins, YbxF and YlxQ, have been proposed to be L7Ae homologs based on sequence conservation. Using purified, recombinant proteins, we show that Bacillus subtilis YbxF and YlxQ bind K-turns (K(d) ~270 nM and ~2300 nM, respectively). Crystallographic structure determination demonstrates that both YbxF and YlxQ adopt the same overall fold as L7Ae. Unlike the latter, neither bacterial protein recognizes K-loops, a structural motif that lacks the canonical helix of the K-turn. This property is shared between the bacterial and eukaryal family members. Comparison of our structure of YbxF in complex with the K-turn of the SAM-I riboswitch and previously determined structures of archaeal and eukaryal homologs bound to RNA indicates that L7Ae approaches the K-turn at a unique angle, which results in a considerably larger RNA-protein interface dominated by interactions with the noncanonical helix of the K-turn. Thus, the inability of the bacterial and eukaryal L7Ae homologs to bind K-loops probably results from their reliance on interactions with the canonical helix. The biological functions of YbxF and YlxQ remain to be determined.
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Affiliation(s)
- Nathan J. Baird
- Laboratory of RNA Biophysics and Cellular Physiology, National Heart, Lung and Blood Institute, Bethesda, Maryland 20892-8012, USA
| | - Jinwei Zhang
- Laboratory of RNA Biophysics and Cellular Physiology, National Heart, Lung and Blood Institute, Bethesda, Maryland 20892-8012, USA
| | - Tomoko Hamma
- Pacific Northwest University of Health Sciences, Yakima, Washington 98901, USA
| | - Adrian R. Ferré-D'Amaré
- Laboratory of RNA Biophysics and Cellular Physiology, National Heart, Lung and Blood Institute, Bethesda, Maryland 20892-8012, USA
- Corresponding author.E-mail .
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Abstract
The molecular mechanisms that govern the timing and fate of neural stem-cell differentiation toward the distinct neural lineages of the nervous system are not well defined. The contribution of post-transcriptional regulation of gene expression to neural stem-cell maintenance and differentiation, in particular, remains inadequately characterized. The RNA-binding protein Hnrpab is highly expressed in developing nervous tissue and in neurogenic regions of the adult brain, but its role in neural development and function is unknown. We raised a mouse that lacks Hnrpab expression to define what role, if any, Hnrpab plays during mouse neural development. We performed a genome-wide quantitative analysis of protein expression within the hippocampus of newborn mice to demonstrate significantly altered gene expression in mice lacking Hnrpab relative to Hnrpab-expressing littermates. The proteins affected suggested an altered pattern of neural development and also unexpectedly indicated altered glutamate signaling. We demonstrate that Hnrpab(-/-) neural stem and progenitor cells undergo altered differentiation patterns in culture, and mature Hnrpab(-/-) neurons demonstrate increased sensitivity to glutamate-induced excitotoxicity. We also demonstrate that Hnrpab nucleocytoplasmic distribution in primary neurons is regulated by developmental stage.
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Affiliation(s)
- John R. Sinnamon
- Program in Neuroscience, Stony Brook University, Stony Brook, New York 11794, USA
- Center for Nervous Systems Disorders, Centers for Molecular Medicine, Stony Brook University, Stony Brook, New York 11794, USA
| | - Catherine B. Waddell
- Center for Nervous Systems Disorders, Centers for Molecular Medicine, Stony Brook University, Stony Brook, New York 11794, USA
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York 11794, USA
| | - Sara Nik
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York 11794, USA
| | - Emily I. Chen
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York 11794, USA
- Stony Brook University Proteomics Center, Stony Brook University, Stony Brook, New York 11794, USA
| | - Kevin Czaplinski
- Center for Nervous Systems Disorders, Centers for Molecular Medicine, Stony Brook University, Stony Brook, New York 11794, USA
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York 11794, USA
- Corresponding author.E-mail .
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Naeeni AR, Conte MR, Bayfield MA. RNA chaperone activity of human La protein is mediated by variant RNA recognition motif. J Biol Chem 2012; 287:5472-82. [PMID: 22203678 PMCID: PMC3285324 DOI: 10.1074/jbc.m111.276071] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2011] [Revised: 12/23/2011] [Indexed: 02/05/2023] Open
Abstract
La proteins are conserved factors in eukaryotes that bind and protect the 3' trailers of pre-tRNAs from exonuclease digestion via sequence-specific recognition of UUU-3'OH. La has also been hypothesized to assist pre-tRNAs in attaining their native fold through RNA chaperone activity. In addition to binding polymerase III transcripts, human La has also been shown to enhance the translation of several internal ribosome entry sites and upstream ORF-containing mRNA targets, also potentially through RNA chaperone activity. Using in vitro FRET-based assays, we show that human and Schizosaccharomyces pombe La proteins harbor RNA chaperone activity by enhancing RNA strand annealing and strand dissociation. We use various RNA substrates and La mutants to show that UUU-3'OH-dependent La-RNA binding is not required for this function, and we map RNA chaperone activity to its RRM1 motif including a noncanonical α3-helix. We validate the importance of this α3-helix by appending it to the RRM of the unrelated U1A protein and show that this fusion protein acquires significant strand annealing activity. Finally, we show that residues required for La-mediated RNA chaperone activity in vitro are required for La-dependent rescue of tRNA-mediated suppression via a mutated suppressor tRNA in vivo. This work delineates the structural elements required for La-mediated RNA chaperone activity and provides a basis for understanding how La can enhance the folding of its various RNA targets.
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Affiliation(s)
- Amir R. Naeeni
- From the Department of Biology, York University, Toronto, Ontario M3J 1P3, Canada and
| | - Maria R. Conte
- the Randall Division of Cell and Molecular Biophysics, King's College London, London SE1 1UL, United Kingdom
| | - Mark A. Bayfield
- From the Department of Biology, York University, Toronto, Ontario M3J 1P3, Canada and
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MacKellar AL, Greenleaf AL. Cotranscriptional association of mRNA export factor Yra1 with C-terminal domain of RNA polymerase II. J Biol Chem 2011; 286:36385-95. [PMID: 21856751 PMCID: PMC3196081 DOI: 10.1074/jbc.m111.268144] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2011] [Revised: 07/28/2011] [Indexed: 11/06/2022] Open
Abstract
The unique C-terminal domain (CTD) of RNA polymerase II, composed of tandem heptad repeats of the consensus sequence YSPTSPS, is subject to differential phosphorylation throughout the transcription cycle. Several RNA processing factors have been shown to bind the phosphorylated CTD and use it to localize to nascent pre-mRNA during transcription. In Saccharomyces cerevisiae, the mRNA export protein Yra1 (ALY/RNA export factor in metazoa) cotranscriptionally associates with mRNA and delivers it to the nuclear pore complex for export to the cytoplasm. Here we report that Yra1 directly binds in vitro the hyperphosphorylated form of the CTD characteristic of elongating RNA polymerase II and contains a phospho-CTD-interacting domain within amino acids 18-184, which also include an "RNA recognition motif" (RRM) (residues 77-184). Using UV cross-linking, we showed that the RRM alone binds RNA, although a larger segment extending to the C terminus (amino acids 77-226) displayed stronger RNA binding activity. Although the RRM is implicated in both RNA and CTD binding, RRM point mutations separated these two functions. Both functions are important in vivo as RNA binding-defective or CTD binding-defective versions of Yra1 engendered growth and mRNA export defects. We also report the construction and characterization of a useful new temperature-sensitive YRA1 allele (R107A/F126A). Using ChIP, we demonstrated that removing the N-terminal 76 amino acids of Yra1 (all of the phospho-CTD-interacting domain up to the RRM) results in a 10-fold decrease in Yra1 recruitment to genes during elongation. These results indicate that the phospho-CTD is likely involved directly in the cotranscriptional recruitment of Yra1.
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Affiliation(s)
- April L. MacKellar
- From the Department of Biochemistry and Center for RNA Biology, Duke University Medical Center, Durham, North Carolina 27710
| | - Arno L. Greenleaf
- From the Department of Biochemistry and Center for RNA Biology, Duke University Medical Center, Durham, North Carolina 27710
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Lan P, Schmidt W. The enigma of eIF5A in the iron deficiency response of Arabidopsis. Plant Signal Behav 2011; 6:528-30. [PMID: 21383540 PMCID: PMC3142383 DOI: 10.4161/psb.6.4.14747] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2011] [Accepted: 01/06/2011] [Indexed: 05/08/2023]
Abstract
Iron (Fe) deficiency is a nutritional disorder that poses severe problems in agriculture and health due to decreased yield of crop plants and poor quality of edible plant parts. Plants respond to suboptimal Fe availability with a suite of responses, aimed at improving Fe acquisition and re-establishing cellular Fe homeostasis. In a recent study, we reported a comprehensive analysis of Fe deficiency-induced changes in the Arabidopsis root proteome using iTRAQ (Isobaric Tag for Relative and Absolute Quantification) differential LC/MS/MS. Proteins that differentially accumulate upon Fe deficiency were quantitatively identified from a total of 4,454 proteins that were detected in root cells. The abundance of several RNA-binding proteins without defined functions in the Fe deficiency response was increased by Fe deficiency. Among these were two members of the conserved eukaryotic elongation factor 5A (eIF5A) family. Due to a lack of responsiveness of the corresponding genes at the transcriptional level, these proteins have not been identified in transcriptional profiling studies. eIF5A plays an important role in regulating translation under stress conditions in eukaryotic cells and may be critical in adapting plants to prevailing environmental conditions.
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Affiliation(s)
- Ping Lan
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
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40
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Abstract
Members of the SR (serine/arginine-rich) protein gene family are key players in the regulation of alternative splicing, an important means of generating proteome diversity and regulating gene expression. In plants, marked changes in alternative splicing are induced by a wide variety of abiotic stresses, suggesting a role for this highly versatile gene regulation mechanism in the response to environmental cues. In support of this notion, the expression of plant SR proteins is stress-regulated at multiple levels, with environmental signals controlling their own alternative splicing patterns, phosphorylation status and subcellular distribution. Most importantly, functional links between these RNA-binding proteins and plant stress tolerance are beginning to emerge, including a role in the regulation of abscisic acid (ABA) signaling. Future identification of the physiological mRNA targets of plant SR proteins holds much promise for the elucidation of the molecular mechanisms underlying their role in the response to abiotic stress.
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Affiliation(s)
- Paula Duque
- Instituto Gulbenkian de Ciência, Oeiras, Portugal.
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41
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Slobodin B, Gerst JE. A novel mRNA affinity purification technique for the identification of interacting proteins and transcripts in ribonucleoprotein complexes. RNA 2010; 16:2277-90. [PMID: 20876833 PMCID: PMC2957065 DOI: 10.1261/rna.2091710] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Intracellular mRNA targeting and localized translation are potential determinants for protein localization. To facilitate targeting, mRNAs possess specific cis-acting sequence motifs that are recognized by trans-acting RNA-binding proteins (RBPs). While many mRNAs are trafficked, our knowledge of the RBPs involved and presence of additional transcripts within these ribonucleoprotein (RNP) complexes is limited. To facilitate the identification of RBPs and transcripts that bind to specific mRNAs, we developed RNA-binding protein purification and identification (RaPID), a novel technique that allows for the affinity purification of MS2 aptamer-tagged mRNAs and subsequent detection of bound RBPs and transcripts using mass-spectometry and RT-PCR, respectively. RaPID effectively isolated specific mRNAs from both yeast and mammalian cells, and identified known mRNA-RBP interactions (e.g., ASH1-She2; β-Actin-IMP1). By isolating tagged OXA1 mRNA using RaPID, we could identify a yeast COPI subunit (i.e., Sec27) as a candidate interacting protein. This finding was strengthened by the observation that a portion of OXA1 mRNA was delocalized in a sec27-1 temperature-sensitive mutant at restrictive temperatures. Finally, RaPID could also be used to show biochemically the coexistence of different RNA species within the same RNP complex (e.g., coprecipitation of the yeast SRO7, WSC2, SEC3, and IST2 mRNAs with ASH1 mRNA) for the first time.
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Affiliation(s)
- Boris Slobodin
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
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42
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Tholanikunnel BG, Joseph K, Kandasamy K, Baldys A, Raymond JR, Luttrell LM, McDermott PJ, Fernandes DJ. Novel mechanisms in the regulation of G protein-coupled receptor trafficking to the plasma membrane. J Biol Chem 2010; 285:33816-25. [PMID: 20739277 PMCID: PMC2962481 DOI: 10.1074/jbc.m110.168229] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2010] [Indexed: 11/06/2022] Open
Abstract
β(2)-adrenergic receptors (β(2)-AR) are low abundance, integral membrane proteins that mediate the effects of catecholamines at the cell surface. Whereas the processes governing desensitization of activated β(2)-ARs and their subsequent removal from the cell surface have been characterized in considerable detail, little is known about the mechanisms controlling trafficking of neo-synthesized receptors to the cell surface. Since the discovery of the signal peptide, the targeting of the integral membrane proteins to plasma membrane has been thought to be determined by structural features of the amino acid sequence alone. Here we report that localization of translationally silenced β(2)-AR mRNA to the peripheral cytoplasmic regions is critical for receptor localization to the plasma membrane. β(2)-AR mRNA is recognized by the nucleocytoplasmic shuttling RNA-binding protein HuR, which silences translational initiation while chaperoning the mRNA-protein complex to the cell periphery. When HuR expression is down-regulated, β(2)-AR mRNA translation is initiated prematurely in perinuclear polyribosomes, leading to overproduction of receptors but defective trafficking to the plasma membrane. Our results underscore the importance of the spatiotemporal relationship between β(2)-AR mRNA localization, translation, and trafficking to the plasma membrane, and establish a novel mechanism whereby G protein-coupled receptor (GPCR) responsiveness is regulated by RNA-based signals.
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Affiliation(s)
- Baby G Tholanikunnel
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina 29425, USA.
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43
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Abstract
RNA chromatography combined with mass spectrometry represents a widely used experimental approach to identify RNA-binding proteins that recognize specific RNA targets. An important drawback of most of these protocols is the high background due to direct or indirect nonspecific binding of cellular proteins to the beads. In many cases this can hamper the detection of individual proteins due to their low levels and/or comigration with contaminating proteins. Increasing the salt concentration during washing steps can reduce background, but at the cost of using less physiological salt concentrations and the likely loss of important RNA-binding proteins that are less stringently bound to a given RNA, as well as the disassembly of protein or ribonucleoprotein complexes. Here, we describe an improved RNA chromatography method that relies on the use of a cocktail of RNases in the elution step. This results in the release of proteins specifically associated with the RNA ligand and almost complete elimination of background noise, allowing a more sensitive and thorough detection of RNA-binding proteins recognizing a specific RNA transcript.
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Affiliation(s)
- Gracjan Michlewski
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh EH4 2XU, United Kingdom.
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Abstract
p21(Waf1/Cip1/Sdi1) was originally identified as an inhibitor of cyclin-dependent kinases, a mediator of p53 in growth suppression and a marker of cellular senescence. p21 is required for proper cell cycle progression and plays a role in cell death, DNA repair, senescence and aging, and induced pluripotent stem cell reprogramming. Although transcriptional regulation is considered to be the initial control point for p21 expression, there is growing evidence that post-transcriptional and post-translational regulations play a critical role in p21 expression and activity. This review will briefly discuss the activity of p21 and focus on current knowledge of the determinants that control p21 transcription, mRNA stability and translation, and protein stability and activity.
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Affiliation(s)
- Yong-Sam Jung
- Center for Comparative Oncology, University of California, Davis, California 95616, USA
| | - Yingjuan Qian
- Center for Comparative Oncology, University of California, Davis, California 95616, USA
| | - Xinbin Chen
- Center for Comparative Oncology, University of California, Davis, California 95616, USA
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45
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Abstract
Mass spectrometry (MS)-based quantitative interaction proteomics has successfully elucidated specific protein-protein, DNA-protein, and small molecule-protein interactions. Here, we developed a gel-free, sensitive, and scalable technology that addresses the important area of RNA-protein interactions. Using aptamer-tagged RNA as bait, we captured RNA-interacting proteins from stable isotope labeling by amino acids in cell culture (SILAC)-labeled mammalian cell extracts and analyzed them by high-resolution, quantitative MS. Binders specific to the RNA sequence were distinguished from background by their isotope ratios between bait and control. We demonstrated the approach by retrieving known and novel interaction partners for the HuR interaction motif, H4 stem loop, "zipcode" sequence, tRNA, and a bioinformatically-predicted RNA fold in DGCR-8/Pasha mRNA. In all experiments we unambiguously identified known interaction partners by a single affinity purification step. The 5' region of the mRNA of DGCR-8/Pasha, a component of the microprocessor complex, specifically interacts with components of the translational machinery, suggesting that it contains an internal ribosome entry site.
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Affiliation(s)
- Falk Butter
- Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany; and
| | - Marion Scheibe
- Institute for Biochemistry, University of Leipzig, Brüderstrasse 34, 04103 Leipzig, Germany
| | - Mario Mörl
- Institute for Biochemistry, University of Leipzig, Brüderstrasse 34, 04103 Leipzig, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany; and
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Abstract
The extremely well-conserved La motif (LAM), in synergy with the immediately following RNA recognition motif (RRM), allows direct binding of the (genuine) La autoantigen to RNA polymerase III primary transcripts. This motif is not only found on La homologs, but also on La-related proteins (LARPs) of unrelated function. LARPs are widely found amongst eukaryotes and, although poorly characterized, appear to be RNA-binding proteins fulfilling crucial cellular functions. We searched the fully sequenced genomes of 83 eukaryotic species scattered along the tree of life for the presence of LAM-containing proteins. We observed that these proteins are absent from archaea and present in all eukaryotes (except protists from the Plasmodium genus), strongly suggesting that the LAM is an ancestral motif that emerged early after the archaea-eukarya radiation. A complete evolutionary and structural analysis of these proteins resulted in their classification into five families: the genuine La homologs and four LARP families. Unexpectedly, in each family a conserved domain representing either a classical RRM or an RRM-like motif immediately follows the LAM of most proteins. An evolutionary analysis of the LAM-RRM/RRM-L regions shows that these motifs co-evolved and should be used as a single entity to define the functional region of interaction of LARPs with their substrates. We also found two extremely well conserved motifs, named LSA and DM15, shared by LARP6 and LARP1 family members, respectively. We suggest that members of the same family are functional homologs and/or share a common molecular mode of action on different RNA baits.
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47
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Abstract
RNA-binding proteins regulate every aspect of RNA metabolism, including pre-mRNA splicing, mRNA trafficking, stability, and translation. This review summarizes the available information on molecular mechanisms of translational repression by RNA-binding proteins. By using a specific set of well-defined examples, we also describe how regulation can be reversed.
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Affiliation(s)
- Irina Abaza
- Centre de Regulació Genòmica, Gene Regulation Programme, 08003 Barcelona, Spain
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48
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Abdelmohsen K, Kuwano Y, Kim HH, Gorospe M. Posttranscriptional gene regulation by RNA-binding proteins during oxidative stress: implications for cellular senescence. Biol Chem 2008; 389:243-255. [PMID: 18177264 PMCID: PMC8481862 DOI: 10.1515/bc.2008.022] [Citation(s) in RCA: 212] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
To respond adequately to oxidative stress, mammalian cells elicit rapid and tightly controlled changes in gene expression patterns. Besides alterations in the subsets of transcribed genes, two posttranscriptional processes prominently influence the oxidant-triggered gene expression programs: mRNA turnover and translation. Here, we review recent progress in our knowledge of the turnover and translation regulatory (TTR) mRNA-binding proteins (RBPs) that influence gene expression in response to oxidative damage. Specifically, we identify oxidant damage-regulated mRNAs that are targets of TTR-RBPs, we review the oxidant-triggered signaling pathways that govern TTR-RBP function, and we examine emerging evidence that TTR-RBP activity is altered with senescence and aging. Given the potent influence of TTR-RBPs upon oxidant-regulated gene expression profiles, we propose that the senescence-associated changes in TTR-RBPs directly contribute to the impaired responses to oxidant damage that characterize cellular senescence and advancing age.
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Newman EA, Muh SJ, Hovhannisyan RH, Warzecha CC, Jones RB, McKeehan WL, Carstens RP. Identification of RNA-binding proteins that regulate FGFR2 splicing through the use of sensitive and specific dual color fluorescence minigene assays. RNA 2006; 12:1129-41. [PMID: 16603716 PMCID: PMC1464843 DOI: 10.1261/rna.34906] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2006] [Accepted: 02/16/2006] [Indexed: 05/04/2023]
Abstract
We have developed a series of fluorescent splicing reporter minigenes for the establishment of cell-based screens to identify splicing regulatory proteins. A key technical advance in the application of these reporters was the use of two different fluorescent proteins: EGFP and monomeric Red Fluorescent Protein (mRFP). Through establishment of stable cell lines expressing such dual color fluorescent reporters, these minigenes can be used to perform enhanced screens for splicing regulatory proteins. As an example of such applications we generated fluorescent minigenes that can be used to determine the splicing of mutually exclusive FGFR2 exons IIIb and IIIc by flow cytometry. One minigene contained a coding sequence for EGFP whose translation was dependent on splicing of exon IIIb, whereas a second minigene required exon IIIc splicing for translation of an mRFP coding sequence. Stable incorporation of both minigenes into cells that express endogenous FGFR2-IIIb or FGFR2-IIIc resulted in EGFP or mRFP fluorescence, respectively. Cells stably transfected with both minigenes were used to screen a panel of cDNAs encoding known splicing regulatory proteins, and several were identified that induced a switch in splicing that could be detected specifically by an increase in green, but not red, fluorescence. We further demonstrated additional minigenes that can be used in dual color fluorescent screens for identification of splicing regulatory proteins that function through specific intronic splicing enhancer elements (ISEs). The methods and minigene designs described here should be adaptable for broader applications in identification of factors and mechanisms involved in alternative splicing of numerous other gene transcripts.
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Affiliation(s)
- Emily A Newman
- Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, 19104, USA
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Rackham O, Brown CM. Visualization of RNA-protein interactions in living cells: FMRP and IMP1 interact on mRNAs. EMBO J 2004; 23:3346-55. [PMID: 15282548 PMCID: PMC514514 DOI: 10.1038/sj.emboj.7600341] [Citation(s) in RCA: 159] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2003] [Accepted: 07/01/2004] [Indexed: 11/09/2022] Open
Abstract
Protein expression depends significantly on the stability, translation efficiency and localization of mRNA. These qualities are largely dictated by the RNA-binding proteins associated with an mRNA. Here, we report a method to visualize and localize RNA-protein interactions in living mammalian cells. Using this method, we found that the fragile X mental retardation protein (FMRP) isoform 18 and the human zipcode-binding protein 1 ortholog IMP1, an RNA transport factor, were present on common mRNAs. These interactions occurred predominantly in the cytoplasm, in granular structures. In addition, FMRP and IMP1 interacted independently of RNA. Tethering of FMRP to an mRNA caused IMP1 to be recruited to the same mRNA and resulted in granule formation. The intimate association of FMRP and IMP1 suggests a link between mRNA transport and translational repression in mammalian cells.
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Affiliation(s)
- Oliver Rackham
- Biochemistry Department, University of Otago, Dunedin, New Zealand
| | - Chris M Brown
- Biochemistry Department, University of Otago, Dunedin, New Zealand
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