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Mahale S, Setia M, Prajapati B, Subhash S, Yadav MP, Thankaswamy Kosalai S, Deshpande A, Kuchlyan J, Di Marco M, Westerlund F, Wilhelmsson LM, Kanduri C, Kanduri M. HnRNPK maintains single strand RNA through controlling double-strand RNA in mammalian cells. Nat Commun 2022; 13:4865. [PMID: 36038571 PMCID: PMC9424213 DOI: 10.1038/s41467-022-32537-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 08/04/2022] [Indexed: 11/09/2022] Open
Abstract
Although antisense transcription is a widespread event in the mammalian genome, double-stranded RNA (dsRNA) formation between sense and antisense transcripts is very rare and mechanisms that control dsRNA remain unknown. By characterizing the FGF-2 regulated transcriptome in normal and cancer cells, we identified sense and antisense transcripts IER3 and IER3-AS1 that play a critical role in FGF-2 controlled oncogenic pathways. We show that IER3 and IER3-AS1 regulate each other's transcription through HnRNPK-mediated post-transcriptional regulation. HnRNPK controls the mRNA stability and colocalization of IER3 and IER3-AS1. HnRNPK interaction with IER3 and IER3-AS1 determines their oncogenic functions by maintaining them in a single-stranded form. hnRNPK depletion neutralizes their oncogenic functions through promoting dsRNA formation and cytoplasmic accumulation. Intriguingly, hnRNPK loss-of-function and gain-of-function experiments reveal its role in maintaining global single- and double-stranded RNA. Thus, our data unveil the critical role of HnRNPK in maintaining single-stranded RNAs and their physiological functions by blocking RNA-RNA interactions.
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Affiliation(s)
- Sagar Mahale
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 40530, Gothenburg, Sweden
| | - Meenakshi Setia
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 40530, Gothenburg, Sweden
| | - Bharat Prajapati
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 40530, Gothenburg, Sweden
| | - Santhilal Subhash
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 40530, Gothenburg, Sweden
| | - Mukesh Pratap Yadav
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 40530, Gothenburg, Sweden
| | - Subazini Thankaswamy Kosalai
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 40530, Gothenburg, Sweden
| | - Ananya Deshpande
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 40530, Gothenburg, Sweden
| | - Jagannath Kuchlyan
- Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Mirco Di Marco
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 40530, Gothenburg, Sweden
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chemical Biology, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - L Marcus Wilhelmsson
- Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Chandrasekhar Kanduri
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 40530, Gothenburg, Sweden.
| | - Meena Kanduri
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 40530, Gothenburg, Sweden.
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2
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D’Souza MH, Mrozowich T, Badmalia MD, Geeraert M, Frederickson A, Henrickson A, Demeler B, Wolfinger M, Patel T. Biophysical characterisation of human LincRNA-p21 sense and antisense Alu inverted repeats. Nucleic Acids Res 2022; 50:5881-5898. [PMID: 35639511 PMCID: PMC9177966 DOI: 10.1093/nar/gkac414] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 04/26/2022] [Accepted: 05/09/2022] [Indexed: 12/05/2022] Open
Abstract
Human Long Intergenic Noncoding RNA-p21 (LincRNA-p21) is a regulatory noncoding RNA that plays an important role in promoting apoptosis. LincRNA-p21 is also critical in down-regulating many p53 target genes through its interaction with a p53 repressive complex. The interaction between LincRNA-p21 and the repressive complex is likely dependent on the RNA tertiary structure. Previous studies have determined the two-dimensional secondary structures of the sense and antisense human LincRNA-p21 AluSx1 IRs using SHAPE. However, there were no insights into its three-dimensional structure. Therefore, we in vitro transcribed the sense and antisense regions of LincRNA-p21 AluSx1 Inverted Repeats (IRs) and performed analytical ultracentrifugation, size exclusion chromatography, light scattering, and small angle X-ray scattering (SAXS) studies. Based on these studies, we determined low-resolution, three-dimensional structures of sense and antisense LincRNA-p21. By adapting previously known two-dimensional information, we calculated their sense and antisense high-resolution models and determined that they agree with the low-resolution structures determined using SAXS. Thus, our integrated approach provides insights into the structure of LincRNA-p21 Alu IRs. Our study also offers a viable pipeline for combining the secondary structure information with biophysical and computational studies to obtain high-resolution atomistic models for long noncoding RNAs.
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Affiliation(s)
- Michael H D’Souza
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
| | - Tyler Mrozowich
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
| | - Maulik D Badmalia
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
| | - Mitchell Geeraert
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
| | - Angela Frederickson
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
| | - Amy Henrickson
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
| | - Borries Demeler
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
- Department of Chemistry and Biochemistry, University of Montana, Missoula, MT 59812, USA
- NorthWest Biophysics Consortium, University of Lethbridge, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
| | - Michael T Wolfinger
- Bioinformatics and Computational Biology, Faculty of Computer Science, Währingerstrasse 29, 1090 Vienna, Austria
- Department of Theoretical Chemistry, University of Vienna, Währingerstrasse 17, 1090 Vienna, Austria
| | - Trushar R Patel
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
- Department of Microbiology, Immunology and Infectious Disease, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
- Li Ka Shing Institute of Virology and Discovery Lab, University of Alberta, Edmonton, AB T6G 2E1, Canada
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3
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Janecki DM, Swiatkowska A, Szpotkowska J, Urbanowicz A, Kabacińska M, Szpotkowski K, Ciesiołka J. Poly(C)-binding Protein 2 Regulates the p53 Expression via Interactions with the 5'-Terminal Region of p53 mRNA. Int J Mol Sci 2021; 22:ijms222413306. [PMID: 34948101 PMCID: PMC8708005 DOI: 10.3390/ijms222413306] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/03/2021] [Accepted: 12/07/2021] [Indexed: 11/16/2022] Open
Abstract
The p53 protein is one of the major transcriptional factors which guards cell homeostasis. Here, we showed that poly(C)-binding protein 2 (PCBP2) can bind directly to the 5′ terminus of p53 mRNA by means of electrophoretic mobility shift assay. Binding sites of PCBP2 within this region of p53 mRNA were mapped using Pb2+-induced cleavage and SAXS methods. Strikingly, the downregulation of PCBP2 in HCT116 cells resulted in a lower level of p53 protein under normal and stress conditions. Quantitative analysis of p53 mRNA in PCBP2-downregulated cells revealed a lower level of p53 mRNA under normal conditions suggesting the involvement of PCBP2 in p53 mRNA stabilisation. However, no significant change in p53 mRNA level was observed upon PCBP2 depletion under genotoxic stress. Moreover, a higher level of p53 protein in the presence of rapamycin or doxorubicin and the combination of both antibiotics was noticed in PCBP2-overexpressed cells compared to control cells. These observations indicate the potential involvement of PCBP2 in cap-independent translation of p53 mRNA especially occurring under stress conditions. It has been postulated that the PCBP2 protein is engaged in the enhancement of p53 mRNA stability, probably via interacting with its 3′ end. Our data show that under stress conditions PCBP2 also modulates p53 translation through binding to the 5′ terminus of p53 mRNA. Thus PCBP2 emerges as a double-function factor in the p53 expression.
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4
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HnRNP K mislocalisation is a novel protein pathology of frontotemporal lobar degeneration and ageing and leads to cryptic splicing. Acta Neuropathol 2021; 142:609-627. [PMID: 34274995 PMCID: PMC8423707 DOI: 10.1007/s00401-021-02340-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 06/28/2021] [Accepted: 06/29/2021] [Indexed: 02/08/2023]
Abstract
Heterogeneous nuclear ribonucleoproteins (HnRNPs) are a group of ubiquitously expressed RNA-binding proteins implicated in the regulation of all aspects of nucleic acid metabolism. HnRNP K is a member of this highly versatile hnRNP family. Pathological redistribution of hnRNP K to the cytoplasm has been linked to the pathogenesis of several malignancies but, until now, has been underexplored in the context of neurodegenerative disease. Here we show hnRNP K mislocalisation in pyramidal neurons of the frontal cortex to be a novel neuropathological feature that is associated with both frontotemporal lobar degeneration and ageing. HnRNP K mislocalisation is mutually exclusive to TDP-43 and tau pathological inclusions in neurons and was not observed to colocalise with mitochondrial, autophagosomal or stress granule markers. De-repression of cryptic exons in RNA targets following TDP-43 nuclear depletion is an emerging mechanism of potential neurotoxicity in frontotemporal lobar degeneration and the mechanistically overlapping disorder amyotrophic lateral sclerosis. We silenced hnRNP K in neuronal cells to identify the transcriptomic consequences of hnRNP K nuclear depletion. Intriguingly, by performing RNA-seq analysis we find that depletion of hnRNP K induces 101 novel cryptic exon events. We validated cryptic exon inclusion in an SH-SY5Y hnRNP K knockdown and in FTLD brain exhibiting hnRNP K nuclear depletion. We, therefore, present evidence for hnRNP K mislocalisation to be associated with FTLD and for this to induce widespread changes in splicing.
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5
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Korn SM, Ulshöfer CJ, Schneider T, Schlundt A. Structures and target RNA preferences of the RNA-binding protein family of IGF2BPs: An overview. Structure 2021; 29:787-803. [PMID: 34022128 DOI: 10.1016/j.str.2021.05.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 03/12/2021] [Accepted: 04/30/2021] [Indexed: 02/08/2023]
Abstract
Insulin-like growth factor 2 mRNA-binding proteins (IMPs, IGF2BPs) act in mRNA transport and translational control but are oncofetal tumor marker proteins. The IMP protein family represents a number of bona fide multi-domain RNA-binding proteins with up to six RNA-binding domains, resulting in a high complexity of possible modes of interactions with target mRNAs. Their exact mechanism in stability control of oncogenic mRNAs is only partially understood. Our and other laboratories' recent work has significantly pushed the understanding of IMP protein specificities both toward RNA engagement and between each other from NMR and crystal structures serving the basis for systematic biochemical and functional investigations. We here summarize the known structural and biochemical information about IMP RNA-binding domains and their RNA preferences. The article also touches on the respective roles of RNA secondary and protein tertiary structures for specific RNA-protein complexes, including the limited knowledge about IMPs' protein-protein interactions, which are often RNA mediated.
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Affiliation(s)
- Sophie Marianne Korn
- Institute for Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Corinna Jessica Ulshöfer
- Institute of Biochemistry, Justus-Liebig-University of Giessen, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Tim Schneider
- Institute of Biochemistry, Justus-Liebig-University of Giessen, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Andreas Schlundt
- Institute for Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany.
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6
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Malaney P, Velasco-Estevez M, Aguilar-Garrido P, Aitken MJL, Chan LE, Zhang X, Post SM, Gallardo M. The Eµ-hnRNP K Murine Model of Lymphoma: Novel Insights into the Role of hnRNP K in B-Cell Malignancies. Front Immunol 2021; 12:634584. [PMID: 33912162 PMCID: PMC8072109 DOI: 10.3389/fimmu.2021.634584] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 03/23/2021] [Indexed: 01/18/2023] Open
Abstract
B-cell lymphomas are one of the most biologically and molecularly heterogeneous group of malignancies. The inherent complexity of this cancer subtype necessitates the development of appropriate animal model systems to characterize the disease with the ultimate objective of identifying effective therapies. In this article, we discuss a new driver of B-cell lymphomas - hnRNP K (heterogenous nuclear ribonucleoprotein K)-an RNA-binding protein. We introduce the Eµ-Hnrnpk mouse model, a murine model characterized by hnRNP K overexpression in B cells, which develops B-cell lymphomas with high penetrance. Molecular analysis of the disease developed in this model reveals an upregulation of the c-Myc oncogene via post-transcriptional and translational mechanisms underscoring the impact of non-genomic MYC activation in B-cell lymphomas. Finally, the transplantability of the disease developed in Eµ-Hnrnpk mice makes it a valuable pre-clinical platform for the assessment of novel therapeutics.
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MESH Headings
- Animals
- Animals, Genetically Modified
- B-Lymphocytes/immunology
- B-Lymphocytes/metabolism
- B-Lymphocytes/pathology
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/immunology
- Cell Transformation, Neoplastic/metabolism
- Cell Transformation, Neoplastic/pathology
- Disease Models, Animal
- Gene Expression Regulation, Neoplastic
- Genetic Predisposition to Disease
- Heterogeneous-Nuclear Ribonucleoprotein K/genetics
- Heterogeneous-Nuclear Ribonucleoprotein K/metabolism
- Lymphoma, B-Cell/genetics
- Lymphoma, B-Cell/immunology
- Lymphoma, B-Cell/metabolism
- Lymphoma, B-Cell/pathology
- Phenotype
- Proto-Oncogene Proteins c-myc/genetics
- Proto-Oncogene Proteins c-myc/metabolism
- Up-Regulation
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Affiliation(s)
- Prerna Malaney
- Department of Leukemia, MD Anderson Cancer Center, Houston, TX, United States
| | | | | | - Marisa J. L. Aitken
- Department of Leukemia, MD Anderson Cancer Center, Houston, TX, United States
| | - Lauren E. Chan
- Department of Leukemia, MD Anderson Cancer Center, Houston, TX, United States
| | - Xiaorui Zhang
- Department of Leukemia, MD Anderson Cancer Center, Houston, TX, United States
| | - Sean M. Post
- Department of Leukemia, MD Anderson Cancer Center, Houston, TX, United States
| | - Miguel Gallardo
- H12O–CNIO Haematological Malignancies Clinical Research Unit, CNIO, Madrid, Spain
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7
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Nakamoto MY, Lammer NC, Batey RT, Wuttke DS. hnRNPK recognition of the B motif of Xist and other biological RNAs. Nucleic Acids Res 2020; 48:9320-9335. [PMID: 32813011 PMCID: PMC7498318 DOI: 10.1093/nar/gkaa677] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 07/29/2020] [Accepted: 08/06/2020] [Indexed: 12/26/2022] Open
Abstract
Heterogeneous nuclear ribonuclear protein K (hnRNPK) is an abundant RNA-binding protein crucial for a wide variety of biological processes. While its binding preference for multi-cytosine-patch (C-patch) containing RNA is well documented, examination of binding to known cellular targets that contain C-patches reveals an unexpected breadth of binding affinities. Analysis of in-cell crosslinking data reinforces the notion that simple C-patch preference is not fully predictive of hnRNPK localization within transcripts. The individual RNA-binding domains of hnRNPK work together to interact with RNA tightly, with the KH3 domain being neither necessary nor sufficient for binding. Rather, the RG/RGG domain is implicated in providing essential contributions to RNA-binding, but not DNA-binding, affinity. hnRNPK is essential for X chromosome inactivation, where it interacts with Xist RNA specifically through the Xist B-repeat region. We use this interaction with an RNA motif derived from this B-repeat region to determine the RNA-structure dependence of C-patch recognition. While the location preferences of hnRNPK for C-patches are conformationally restricted within the hairpin, these structural constraints are relieved in the absence of RNA secondary structure. Together, these results illustrate how this multi-domain protein's ability to accommodate and yet discriminate between diverse cellular RNAs allows for its broad cellular functions.
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Affiliation(s)
- Meagan Y Nakamoto
- Department of Biochemistry, University of Colorado, Boulder, CO 80309-0596, USA
| | - Nickolaus C Lammer
- Department of Biochemistry, University of Colorado, Boulder, CO 80309-0596, USA
| | - Robert T Batey
- Department of Biochemistry, University of Colorado, Boulder, CO 80309-0596, USA
| | - Deborah S Wuttke
- Department of Biochemistry, University of Colorado, Boulder, CO 80309-0596, USA
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8
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Chetverina DA, Lomaev DV, Erokhin MM. Polycomb and Trithorax Group Proteins: The Long Road from Mutations in Drosophila to Use in Medicine. Acta Naturae 2020; 12:66-85. [PMID: 33456979 PMCID: PMC7800605 DOI: 10.32607/actanaturae.11090] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 09/30/2020] [Indexed: 12/12/2022] Open
Abstract
Polycomb group (PcG) and Trithorax group (TrxG) proteins are evolutionarily conserved factors responsible for the repression and activation of the transcription of multiple genes in Drosophila and mammals. Disruption of the PcG/TrxG expression is associated with many pathological conditions, including cancer, which makes them suitable targets for diagnosis and therapy in medicine. In this review, we focus on the major PcG and TrxG complexes, the mechanisms of PcG/TrxG action, and their recruitment to chromatin. We discuss the alterations associated with the dysfunction of a number of factors of these groups in oncology and the current strategies used to develop drugs based on small-molecule inhibitors.
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Affiliation(s)
- D. A. Chetverina
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russia
| | - D. V. Lomaev
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russia
| | - M. M. Erokhin
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russia
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9
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Beckham SA, Matak MY, Belousoff MJ, Venugopal H, Shah N, Vankadari N, Elmlund H, Nguyen JHC, Semler BL, Wilce MCJ, Wilce JA. Structure of the PCBP2/stem-loop IV complex underlying translation initiation mediated by the poliovirus type I IRES. Nucleic Acids Res 2020; 48:8006-8021. [PMID: 32556302 PMCID: PMC7641305 DOI: 10.1093/nar/gkaa519] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 05/15/2020] [Accepted: 06/06/2020] [Indexed: 02/02/2023] Open
Abstract
The poliovirus type I IRES is able to recruit ribosomal machinery only in the presence of host factor PCBP2 that binds to stem-loop IV of the IRES. When PCBP2 is cleaved in its linker region by viral proteinase 3CD, translation initiation ceases allowing the next stage of replication to commence. Here, we investigate the interaction of PCBP2 with the apical region of stem-loop IV (SLIVm) of poliovirus RNA in its full-length and truncated form. CryoEM structure reconstruction of the full-length PCBP2 in complex with SLIVm solved to 6.1 Å resolution reveals a compact globular complex of PCBP2 interacting with the cruciform RNA via KH domains and featuring a prominent GNRA tetraloop. SEC-SAXS, SHAPE and hydroxyl-radical cleavage establish that PCBP2 stabilizes the SLIVm structure, but upon cleavage in the linker domain the complex becomes more flexible and base accessible. Limited proteolysis and REMSA demonstrate the accessibility of the linker region in the PCBP2/SLIVm complex and consequent loss of affinity of PCBP2 for the SLIVm upon cleavage. Together this study sheds light on the structural features of the PCBP2/SLIV complex vital for ribosomal docking, and the way in which this key functional interaction is regulated following translation of the poliovirus genome.
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Affiliation(s)
- Simone A Beckham
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia
| | - Mehdi Y Matak
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia
| | - Matthew J Belousoff
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia
| | - Hariprasad Venugopal
- The Ramaciotti Centre for Cryo-Electron Microscopy, Monash University, Victoria 3800, Australia
| | - Neelam Shah
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia
| | - Naveen Vankadari
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia
| | - Hans Elmlund
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia
| | - Joseph H C Nguyen
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, CA 92697-4025, USA
| | - Bert L Semler
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, CA 92697-4025, USA
| | - Matthew C J Wilce
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia
| | - Jacqueline A Wilce
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia
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10
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Escobar-Hoyos LF, Penson A, Kannan R, Cho H, Pan CH, Singh RK, Apken LH, Hobbs GA, Luo R, Lecomte N, Babu S, Pan FC, Alonso-Curbelo D, Morris JP, Askan G, Grbovic-Huezo O, Ogrodowski P, Bermeo J, Saglimbeni J, Cruz CD, Ho YJ, Lawrence SA, Melchor JP, Goda GA, Bai K, Pastore A, Hogg SJ, Raghavan S, Bailey P, Chang DK, Biankin A, Shroyer KR, Wolpin BM, Aguirre AJ, Ventura A, Taylor B, Der CJ, Dominguez D, Kümmel D, Oeckinghaus A, Lowe SW, Bradley RK, Abdel-Wahab O, Leach SD. Altered RNA Splicing by Mutant p53 Activates Oncogenic RAS Signaling in Pancreatic Cancer. Cancer Cell 2020; 38:198-211.e8. [PMID: 32559497 PMCID: PMC8028848 DOI: 10.1016/j.ccell.2020.05.010] [Citation(s) in RCA: 94] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 01/17/2020] [Accepted: 05/11/2020] [Indexed: 12/13/2022]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is driven by co-existing mutations in KRAS and TP53. However, how these mutations collaborate to promote this cancer is unknown. Here, we uncover sequence-specific changes in RNA splicing enforced by mutant p53 which enhance KRAS activity. Mutant p53 increases expression of splicing regulator hnRNPK to promote inclusion of cytosine-rich exons within GTPase-activating proteins (GAPs), negative regulators of RAS family members. Mutant p53-enforced GAP isoforms lose cell membrane association, leading to heightened KRAS activity. Preventing cytosine-rich exon inclusion in mutant KRAS/p53 PDACs decreases tumor growth. Moreover, mutant p53 PDACs are sensitized to inhibition of splicing via spliceosome inhibitors. These data provide insight into co-enrichment of KRAS and p53 mutations and therapeutics targeting this mechanism in PDAC.
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Affiliation(s)
- Luisa F Escobar-Hoyos
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Therapeutic Radiology, Yale University, School of Medicine, New Haven, CT 06520, USA; Department of Biology, Research Group Genetic Toxicology and Cytogenetics, School of Natural Sciences and Education, Universidad del Cauca, Popayán, Colombia; Department of Pathology, Renaissance School of Medicine, Stony Brook University, New York, NY 11794, USA.
| | - Alex Penson
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Marie-José and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ram Kannan
- Howard Hughes Medical Institute, Cancer Biology & Genetics Program, Sloan-Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Hana Cho
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Chun-Hao Pan
- Department of Pathology, Renaissance School of Medicine, Stony Brook University, New York, NY 11794, USA
| | - Rohit K Singh
- Institute of Biochemistry, University of Münster, Münster, Germany
| | - Lisa H Apken
- Institute of Molecular Tumor Biology, University of Münster, Münster, Germany
| | - G Aaron Hobbs
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Renhe Luo
- Gerstner Sloan Kettering Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Nicolas Lecomte
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Sruthi Babu
- Department of Pathology, Renaissance School of Medicine, Stony Brook University, New York, NY 11794, USA
| | - Fong Cheng Pan
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Direna Alonso-Curbelo
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Marie-José and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - John P Morris
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Marie-José and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Gokce Askan
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Olivera Grbovic-Huezo
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Marie-José and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Paul Ogrodowski
- Howard Hughes Medical Institute, Cancer Biology & Genetics Program, Sloan-Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jonathan Bermeo
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Joseph Saglimbeni
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Cristian D Cruz
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Yu-Jui Ho
- Howard Hughes Medical Institute, Cancer Biology & Genetics Program, Sloan-Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Sharon A Lawrence
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jerry P Melchor
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Grant A Goda
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Karen Bai
- Department of Pathology, Renaissance School of Medicine, Stony Brook University, New York, NY 11794, USA
| | - Alessandro Pastore
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Simon J Hogg
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Srivatsan Raghavan
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Peter Bailey
- Department of General Surgery, University of Heidelberg, Im Neuenheimer Feld 110, Heidelberg, Baden-Württemberg 69120, Germany; Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, G61 1Q, Glasgow, UK
| | - David K Chang
- The Kinghorn Cancer Centre, and the Cancer Research Program, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, Australia; Department of Surgery, Bankstown Hospital, Eldridge Road, Bankstown, Sydney, NSW, Australia; South Western Sydney Clinical School, Faculty of Medicine, University of New South Wales, Liverpool, NSW, Australia
| | - Andrew Biankin
- Department of General Surgery, University of Heidelberg, Im Neuenheimer Feld 110, Heidelberg, Baden-Württemberg 69120, Germany; Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, G61 1Q, Glasgow, UK; The Kinghorn Cancer Centre, and the Cancer Research Program, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, Australia; Department of Surgery, Bankstown Hospital, Eldridge Road, Bankstown, Sydney, NSW, Australia
| | - Kenneth R Shroyer
- Department of Pathology, Renaissance School of Medicine, Stony Brook University, New York, NY 11794, USA
| | - Brian M Wolpin
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA 02215, USA
| | - Andrew J Aguirre
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Andrea Ventura
- Howard Hughes Medical Institute, Cancer Biology & Genetics Program, Sloan-Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Barry Taylor
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Marie-José and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Departments of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Channing J Der
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Daniel Dominguez
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Daniel Kümmel
- Institute of Biochemistry, University of Münster, Münster, Germany
| | - Andrea Oeckinghaus
- Institute of Molecular Tumor Biology, University of Münster, Münster, Germany
| | - Scott W Lowe
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Howard Hughes Medical Institute, Cancer Biology & Genetics Program, Sloan-Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Robert K Bradley
- Fred Hutchinson Cancer Research Center Seattle, Seattle, WA 98109-1024, USA
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Steven D Leach
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Dartmouth Norris Cotton Cancer Center, Lebanon, NH 03766, USA.
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11
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Souza WC, Dias LD, de Queiroz JE, Vidal HD, da Silva VB, Leopoldino AM, de Paula da Silva CH, Verde GM, Aquino GL. Synthesis and In silico Studies of N-acylhydrazone Derivatives as hnRNP K Ligands with Potential Anti-cancer Activity. ACTA ACUST UNITED AC 2020. [DOI: 10.2174/1573407215666190131121059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Background:
A green and efficient synthetic methodology for a wide family of Nacylhydrazones
(yields: 42-76%) using microwave irradiation is described, as well as their full characterization.
Their potential antineoplastic activity was evaluated in vitro via EMSA by testing protein-
DNA interactions. Among the 11 compounds tested, N-acylhydrazone derivative 5 bearing a hydroxyl
group, showed the highest affinity to bind and inhibit the hnRNP K KH3 domain. Docking simulations
of compound 5 showed three possible modes of interaction between the KH3 domain of hnRNP K protein
and compound predict.
:
The N-acylhydrazones are knows as powerful chemical entities for Medicinal Chemistry, since it has
been identified in a huge number of hit and lead compounds that act on various types of molecular targets,
including in tumorigenesis processes.
Objective:
We evaluated their potential ability to inhibit the KH3 domain of the hnRNP K protein binding
to single stranded DNA (ssDNA). Furthermore, a docking simulation was performed for the newly
synthetized compounds to evaluate their interactions between proteins and N-acylhydrazine derivative.
Methods:
The N-acylhydrazone derivatives were synthetized through three reaction steps, from a simple
and commercial substrate, using microwave irradiation as a green energy source. The N-acylhydrazone
derivatives ability to bind with the hnRNP K protein was evaluated via EMSA by testing protein-DNA
interactions. The docking simulations were performed in a Gold 5.2.2 software using 100 conformers,
10.000 operations, 95 mutations and 95 crossovers.
Results:
Eleven new N-acylhydrazone derivatives were synthetized using microwave showing yields
between 42% and 76%. Among the eleven compounds tested, compound 5 was shown to be most
capable to prevent the natural binding of hnRNP K protein to the oligonucleotide. Regarding the docking
simulation, compound 5 can bind to the main binding residues of KH3 domain and compete with the
natural ligand ssDNA of this protein.
Conclusion:
A green and efficient synthetic methodology for a wide family of N-acylhydrazones
(yields: 42-76%) using microwave irradiation is described, as well as their full characterization. Their
potential antineoplastic activity was evaluated in vitro via EMSA by testing protein-DNA interactions.
Among the 11 compounds tested, N-acylhydrazone derivative 5 bearing a hydroxyl group, showed the
highest affinity to bind and inhibit the hnRNP K KH3 domain. Docking simulations of compound 5
showed three possible modes of interaction between the KH3 domain of hnRNP K protein and compound
predict.
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Affiliation(s)
- Wanderson C. Souza
- Faculty of Pharmacy, Unit of Exact and Technological Sciences, State University of Goias, Br 153, 75132400, Anapolis, Goias, Brazil
| | - Lucas D. Dias
- Coimbra Chemistry Center (CQC), Department of Chemistry, University of Coimbra, Rua Larga, 3004-535 Coimbra, Portugal
| | - Jaqueline E. de Queiroz
- Laboratory on Bioproducts and Synthesis Research (LPbioS), Universidade State of Goias, Br 153, 75132400, Anápolis, Goias, Brazil
| | - Hérika D.A. Vidal
- Laboratory on Bioproducts and Synthesis Research (LPbioS), Universidade State of Goias, Br 153, 75132400, Anápolis, Goias, Brazil
| | - Vinícius B. da Silva
- School of Medical, Pharmaceutical Sciences and Biomedical at PUC, Rua 232, Setor Leste Universitario, 74605140, Goiania, Goias, Brazil
| | - Andréia M. Leopoldino
- Science Department Pharmacists of the Faculty of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, Ribeirao Black, Sao Paulo, Brazil
| | - Carlos H.T. de Paula da Silva
- Science Department Pharmacists of the Faculty of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, Ribeirao Black, Sao Paulo, Brazil
| | - Giuliana M.V. Verde
- Laboratory on Bioproducts and Synthesis Research (LPbioS), Universidade State of Goias, Br 153, 75132400, Anápolis, Goias, Brazil
| | - Gilberto L.B. Aquino
- Laboratory on Bioproducts and Synthesis Research (LPbioS), Universidade State of Goias, Br 153, 75132400, Anápolis, Goias, Brazil
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12
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Abstract
The X inactive-specific transcript (Xist) gene is the master regulator of X chromosome inactivation in mammals. Xist produces a long noncoding (lnc)RNA that accumulates over the entire length of the chromosome from which it is transcribed, recruiting factors to modify underlying chromatin and silence X-linked genes in cis Recent years have seen significant progress in identifying important functional elements in Xist RNA, their associated RNA-binding proteins (RBPs), and the downstream pathways for chromatin modification and gene silencing. In this review, we summarize progress in understanding both how these pathways function in Xist-mediated silencing and the complex interplay between them.
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Affiliation(s)
- Neil Brockdorff
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Joseph S Bowness
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Guifeng Wei
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
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13
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Almeida M, Bowness JS, Brockdorff N. The many faces of Polycomb regulation by RNA. Curr Opin Genet Dev 2020; 61:53-61. [PMID: 32403014 PMCID: PMC7653676 DOI: 10.1016/j.gde.2020.02.023] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/12/2020] [Accepted: 02/22/2020] [Indexed: 02/06/2023]
Abstract
Many intricate pathways contribute to the timely control of gene expression during development. Polycomb repressive complexes (PRC1 and PRC2) and long non-coding RNAs (lncRNAs) are players associated with gene repression in various developmental processes such as X chromosome inactivation (XCI) and genomic imprinting. Historically, lncRNAs were proposed to directly recruit PRC2. However, recent evidence suggests that promiscuous interactions between PRC2 and RNA fine-tune the function of the complex through a multiplicity of mechanisms. A PRC2-recruitment model was definitively overturned in the paradigm of XCI by Xist RNA, being replaced by a novel mechanism which puts PRC1 in the spotlight. This review focuses on these recent advances in understanding the interplay between RNA and Polycomb complexes for gene expression control.
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Affiliation(s)
- Mafalda Almeida
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Joseph S Bowness
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Neil Brockdorff
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom.
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14
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Cohen-Zontag O, Baez C, Lim LQJ, Olender T, Schirman D, Dahary D, Pilpel Y, Gerst JE. A secretion-enhancing cis regulatory targeting element (SECReTE) involved in mRNA localization and protein synthesis. PLoS Genet 2019; 15:e1008248. [PMID: 31260446 PMCID: PMC6625729 DOI: 10.1371/journal.pgen.1008248] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 07/12/2019] [Accepted: 06/13/2019] [Indexed: 12/19/2022] Open
Abstract
The localization of mRNAs encoding secreted/membrane proteins (mSMPs) to the endoplasmic reticulum (ER) likely facilitates the co-translational translocation of secreted proteins. However, studies have shown that mSMP recruitment to the ER in eukaryotes can occur in a manner that is independent of the ribosome, translational control, and the signal recognition particle, although the mechanism remains largely unknown. Here, we identify a cis-acting RNA sequence motif that enhances mSMP localization to the ER and appears to increase mRNA stability, and both the synthesis and secretion of secretome proteins. Termed SECReTE, for secretion-enhancing cis regulatory targeting element, this motif is enriched in mRNAs encoding secretome proteins translated on the ER in eukaryotes and on the inner membrane of prokaryotes. SECReTE consists of ≥10 nucleotide triplet repeats enriched with pyrimidine (C/U) every third base (i.e. NNY, where N = any nucleotide, Y = pyrimidine) and can be present in the untranslated as well as the coding regions of the mRNA. Synonymous mutations that elevate the SECReTE count in a given mRNA (e.g. SUC2, HSP150, and CCW12) lead to an increase in protein secretion in yeast, while a reduction in count led to less secretion and physiological defects. Moreover, the addition of SECReTE to the 3'UTR of an mRNA for an exogenously expressed protein (e.g. GFP) led to its increased secretion from yeast cells. Thus, SECReTE constitutes a novel RNA motif that facilitates ER-localized mRNA translation and protein secretion.
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Affiliation(s)
- Osnat Cohen-Zontag
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Camila Baez
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Lisha Qiu Jin Lim
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Tsviya Olender
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Dvir Schirman
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Dvir Dahary
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Yitzhak Pilpel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Jeffrey E. Gerst
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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15
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Liu XH, Ma J, Feng JX, Feng Y, Zhang YF, Liu LX. Regulation and related mechanism of GSN mRNA level by hnRNPK in lung adenocarcinoma cells. Biol Chem 2019; 400:951-963. [PMID: 30771276 DOI: 10.1515/hsz-2018-0417] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 02/11/2019] [Indexed: 01/20/2023]
Abstract
Gelsolin (GSN) is an actin filament-capping protein that plays a key role in cell migration. Here we show that heterogeneous nuclear ribonucleoprotein K (hnRNPK) regulates GSN expression level by binding to the 3'-untranslated region (3'UTR) of GSN mRNA in non-small cell lung cancers (NSCLC) H1299 cells which are highly metastatic and express high level of GSN. We found that hnRNPK overexpression increased the mRNA and protein level of GSN, whereas hnRNPK knockdown by siRNA decreased the mRNA and protein level of GSN in both H1299 and A549 cells, indicating a positive role of hnRNPK in the regulation of GSN expression. Furthermore, hnRNPK knockdown affected the migration ability of H1299 and A549 cells which could be rescued by ectopic expression of GSN in those cells. Conversely, GSN knockdown in hnRNPK-overexpressing cells could abort the stimulatory effect of hnRNPK on the cell migration. These results suggest that hnRNPK function in the regulation of cell migration is GSN-dependent. Taken together, these data unveiled a new mechanism of regulation of the GSN expression by hnRNPK and provides new clues for the discovery of new anti-metastatic therapy.
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Affiliation(s)
- Xiao-Hui Liu
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Jie Ma
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Jun-Xia Feng
- Department of Nephrology, Huadu District People's Hospital of Guangzhou, Southern Medical University, Guangzhou 510800, China
| | - Yuan Feng
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Yun-Fang Zhang
- Department of Nephrology, Huadu District People's Hospital of Guangzhou, Southern Medical University, Guangzhou 510800, China
| | - Lang-Xia Liu
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
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16
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Bioinformatics Approaches to Gain Insights into cis-Regulatory Motifs Involved in mRNA Localization. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1203:165-194. [PMID: 31811635 DOI: 10.1007/978-3-030-31434-7_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Messenger RNA (mRNA) is a fundamental intermediate in the expression of proteins. As an integral part of this important process, protein production can be localized by the targeting of mRNA to a specific subcellular compartment. The subcellular destination of mRNA is suggested to be governed by a region of its primary sequence or secondary structure, which consequently dictates the recruitment of trans-acting factors, such as RNA-binding proteins or regulatory RNAs, to form a messenger ribonucleoprotein particle. This molecular ensemble is requisite for precise and spatiotemporal control of gene expression. In the context of RNA localization, the description of the binding preferences of an RNA-binding protein defines a motif, and one, or more, instance of a given motif is defined as a localization element (zip code). In this chapter, we first discuss the cis-regulatory motifs previously identified as mRNA localization elements. We then describe motif representation in terms of entropy and information content and offer an overview of motif databases and search algorithms. Finally, we provide an outline of the motif topology of asymmetrically localized mRNA molecules.
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17
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Shin CH, Kim HH. Functional roles of heterogeneous nuclear ribonucleoprotein K in post-transcriptional gene regulation. PRECISION AND FUTURE MEDICINE 2018. [DOI: 10.23838/pfm.2018.00107] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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18
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Local Tandem Repeat Expansion in Xist RNA as a Model for the Functionalisation of ncRNA. Noncoding RNA 2018; 4:ncrna4040028. [PMID: 30347781 PMCID: PMC6316617 DOI: 10.3390/ncrna4040028] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 10/15/2018] [Accepted: 10/16/2018] [Indexed: 01/08/2023] Open
Abstract
Xist, the master regulator of the X chromosome inactivation in mammals, is a 17 kb lncRNA that acts in cis to silence the majority of genes along the chromosome from which it is transcribed. The two key processes required for Xist RNA function, localisation in cis and recruitment of silencing factors, are genetically separable, at least in part. Recent studies have identified Xist RNA sequences and associated RNA-binding proteins (RBPs) that are important for these processes. Notably, several of the key Xist RNA elements correspond to local tandem repeats. In this review, I use examples to illustrate different modes whereby tandem repeat amplification has been exploited to allow orthodox RBPs to confer new functions for Xist-mediated chromosome inactivation. I further discuss the potential generality of tandem repeat expansion in the evolution of functional long non-coding RNAs (lncRNAs).
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19
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Mackedenski S, Wang C, Li WM, Lee CH. Characterizing the interaction between insulin-like growth factor 2 mRNA-binding protein 1 (IMP1) and KRAS expression. Biochem J 2018; 475:2749-2767. [PMID: 30104206 DOI: 10.1042/bcj20180575] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Revised: 08/08/2018] [Accepted: 08/10/2018] [Indexed: 12/15/2022]
Abstract
Insulin-like growth factor 2 mRNA-binding protein-1 (IMP1) has high affinity for KRAS mRNA, and it can regulate KRAS expression in cells. We first characterized the molecular interaction between IMP1 and KRAS mRNA. Using IMP1 variants with a point mutation in the GXXG motif at each KH domain, we showed that all KH domains play a critical role in the binding of KRAS RNA. We mapped the IMP1-binding sites on KRAS mRNA and show that IMP1 has the highest affinity for nts 1-185. Although it has lower affinity, IMP1 does bind to other coding regions and the 3'-UTR of KRAS mRNA. Eight antisense oligonucleotides (AONs) were designed against KRAS RNA in the nts 1-185 region, but only two, SM6 and SM7, show potent inhibition of the IMP1-KRAS RNA interaction in vitro To test the activity of these two AONs in SW480 human colon cancer cells, we used 2'-O-methyl-modified versions of SM6 and SM7 in an attempt to down-regulate KRAS expression. To our surprise, both SM6 and SM7 had no effect on KRAS mRNA and protein expression, but significantly inhibited IMP1 protein expression without altering IMP1 mRNA level. On the other hand, knockdown of IMP1 using siRNA lowered the expression of KRAS. Using Renilla luciferase as a reporter, we found that IMP1 translation is significantly reduced in SM7-treated cells with no change in let-7a levels. The present study shows that the regulation of KRAS expression by IMP1 is complex and may involve both the IMP1 protein and its mRNA transcript.
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Affiliation(s)
- Sebastian Mackedenski
- Chemistry Program, University of Northern British Columbia, Prince George, British Columbia, Canada V2N 4Z9
| | - Chuyi Wang
- Chemistry Program, University of Northern British Columbia, Prince George, British Columbia, Canada V2N 4Z9
| | - Wai-Ming Li
- Chemistry Program, University of Northern British Columbia, Prince George, British Columbia, Canada V2N 4Z9
| | - Chow H Lee
- Chemistry Program, University of Northern British Columbia, Prince George, British Columbia, Canada V2N 4Z9
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20
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Identification and Characterization of Sindbis Virus RNA-Host Protein Interactions. J Virol 2018; 92:JVI.02171-17. [PMID: 29321325 DOI: 10.1128/jvi.02171-17] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 12/21/2017] [Indexed: 12/11/2022] Open
Abstract
Arthropod-borne viruses, such as the members of the genus Alphavirus, are a significant concern to global public health. As obligate intracellular pathogens, RNA viruses must interact with the host cell machinery to establish and complete their life cycles. Despite considerable efforts to define the host-pathogen interactions essential for alphaviral replication, an unbiased and inclusive assessment of alphaviral RNA-protein interactions has not been undertaken. Moreover, the biological and molecular importance of these interactions, in the full context of their molecular function as RNA-binding proteins, has not been fully realized. The data presented here introduce a robust viral RNA-protein discovery method to elucidate the Sindbis virus (SINV) RNA-protein host interface. Cross-link-assisted mRNP purification (CLAMP) assessment revealed an extensive array of host-pathogen interactions centered on the viral RNAs (vRNAs). After prioritization of the host proteins associated with the vRNAs, we identified the site of protein-vRNA interaction by a UV cross-linking and immunoprecipitation sequencing (CLIP-seq) approach and assessed the consequences of the RNA-protein binding event of hnRNP K, hnRNP I, and hnRNP M in regard to viral infection. Here, we demonstrate that mutation of the prioritized hnRNP-vRNA interaction sites effectively disrupts hnRNP-vRNA interaction. Correlating with disrupted hnRNP-vRNA binding, SINV growth kinetics were reduced relative to wild-type parental viral infections in vertebrate and invertebrate tissue culture models of infection. The molecular mechanism leading to reduced viral growth kinetics was found to be dysregulated structural-gene expression. Collectively, this study further defines the scope and importance of the alphavirus host-pathogen vRNA-protein interactions.IMPORTANCE Members of the genus Alphavirus are widely recognized for their potential to cause severe disease. Despite this recognition, there are no antiviral therapeutics, or safe and effective vaccines, currently available to treat alphaviral infection. Alphaviruses utilize the host cell machinery to efficiently establish and complete their life cycle. However, the extent and importance of host-pathogen RNA-protein interactions are woefully undercharacterized. The efforts detailed in this study fill this critical gap, and the significance of this research is 3-fold. First, the data presented here fundamentally expand the scope and understanding of alphavirus host-pathogen interactions. Second, this study identifies the sites of interaction for several prioritized interactions and defines the contribution of the RNA-protein interaction at the molecular level. Finally, these studies build a strategy by which the importance of the given host-pathogen interactions may be assessed in the future, using a mouse model of infection.
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21
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Lubelsky Y, Ulitsky I. Sequences enriched in Alu repeats drive nuclear localization of long RNAs in human cells. Nature 2018; 555:107-111. [PMID: 29466324 PMCID: PMC6047738 DOI: 10.1038/nature25757] [Citation(s) in RCA: 226] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Accepted: 12/29/2017] [Indexed: 12/12/2022]
Abstract
Long noncoding RNAs (lncRNAs) are emerging as key parts of multiple cellular pathways, but their modes of action and how these are dictated by sequence remain unclear. lncRNAs tend to be enriched in the nuclear fraction, whereas most mRNAs are overtly cytoplasmic, although several studies have found that hundreds of mRNAs in various cell types are retained in the nucleus. It is thus conceivable that some mechanisms that promote nuclear enrichment are shared between lncRNAs and mRNAs. Here, to identify elements in lncRNAs and mRNAs that can force nuclear localization, we screened libraries of short fragments tiled across nuclear RNAs, which were cloned into the untranslated regions of an efficiently exported mRNA. The screen identified a short sequence derived from Alu elements and bound by HNRNPK that increased nuclear accumulation. Binding of HNRNPK to C-rich motifs outside Alu elements is also associated with nuclear enrichment in both lncRNAs and mRNAs, and this mechanism is conserved across species. Our results thus identify a pathway for regulation of RNA accumulation and subcellular localization that has been co-opted to regulate the fate of transcripts with integrated Alu elements.
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Affiliation(s)
- Yoav Lubelsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
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22
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Pintacuda G, Wei G, Roustan C, Kirmizitas BA, Solcan N, Cerase A, Castello A, Mohammed S, Moindrot B, Nesterova TB, Brockdorff N. hnRNPK Recruits PCGF3/5-PRC1 to the Xist RNA B-Repeat to Establish Polycomb-Mediated Chromosomal Silencing. Mol Cell 2017; 68:955-969.e10. [PMID: 29220657 PMCID: PMC5735038 DOI: 10.1016/j.molcel.2017.11.013] [Citation(s) in RCA: 208] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 09/15/2017] [Accepted: 11/10/2017] [Indexed: 01/01/2023]
Abstract
The Polycomb-repressive complexes PRC1 and PRC2 play a key role in chromosome silencing induced by the non-coding RNA Xist. Polycomb recruitment is initiated by the PCGF3/5-PRC1 complex, which catalyzes chromosome-wide H2A lysine 119 ubiquitylation, signaling recruitment of other PRC1 complexes, and PRC2. However, the molecular mechanism for PCGF3/5-PRC1 recruitment by Xist RNA is not understood. Here we define the Xist RNA Polycomb Interaction Domain (XR-PID), a 600 nt sequence encompassing the Xist B-repeat element. Deletion of XR-PID abolishes Xist-dependent Polycomb recruitment, in turn abrogating Xist-mediated gene silencing and reversing Xist-induced chromatin inaccessibility. We identify the RNA-binding protein hnRNPK as the principal XR-PID binding factor required to recruit PCGF3/5-PRC1. Accordingly, synthetically tethering hnRNPK to Xist RNA lacking XR-PID is sufficient for Xist-dependent Polycomb recruitment. Our findings define a key pathway for Polycomb recruitment by Xist RNA, providing important insights into mechanisms of chromatin modification by non-coding RNA. A 600 nt element in Xist RNA, XR-PID, is required for Polycomb recruitment Deletion of XR-PID abrogates Xist-mediated chromosome silencing hnRNPK binds XR-PID to recruit the Polycomb-initiating complex PCGF3/5-PRC1 Tethering hnRNPK to Xist RNA bypasses the requirement for XR-PID
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Affiliation(s)
- Greta Pintacuda
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Guifeng Wei
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Chloë Roustan
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Burcu Anil Kirmizitas
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Nicolae Solcan
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Andrea Cerase
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Alfredo Castello
- Posttranscriptional Networks in Infection and Cell Cycle Progression, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Shabaz Mohammed
- Proteomics Technology Development and Application, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Benoît Moindrot
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Tatyana B Nesterova
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Neil Brockdorff
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
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23
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Feigerlová E, Battaglia-Hsu SF. Role of post-transcriptional regulation of mRNA stability in renal pathophysiology: focus on chronic kidney disease. FASEB J 2016; 31:457-468. [PMID: 27849555 DOI: 10.1096/fj.201601087rr] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 11/07/2016] [Indexed: 11/11/2022]
Abstract
Chronic kidney disease (CKD) represents an important public health problem. Its progression to end-stage renal disease is associated with increased morbidity and mortality. The determinants of renal function decline are not fully understood. Recent progress in the understanding of post-transcriptional regulation of mRNA stability has helped the identification of both the trans- and cis-acting elements of mRNA as potential markers and therapeutic targets for difficult-to-diagnose and -treat diseases, including CKDs such as diabetic nephropathy. Human antigen R (HuR), a trans-acting element of mRNA, is an RNA binding factor (RBF) best known for its ability to stabilize AU-rich-element-containing mRNAs. Deregulated HuR subcellular localization or expression occurs in a wide range of renal diseases, such as metabolic acidosis, ischemia, and fibrosis. Besides RBFs, recent evidence revealed that noncoding RNA, such as microRNA and long noncoding RNA, participates in regulating mRNA stability and that aberrant noncoding RNA expression accounts for many pathologic renal conditions. The goal of this review is to provide an overview of our current understanding of the post-transcriptional regulation of mRNA stability in renal pathophysiology and to offer perspectives for this class of diseases. We use examples of diverse renal diseases to illustrate different mRNA stability pathways in specific cellular compartments and discuss the roles and impacts of both the cis- and trans-activating factors on the regulation of mRNA stability in these diseases.-Feigerlová, E., Battaglia-Hsu, S.-F. Role of post-transcriptional regulation of mRNA stability in renal pathophysiology: focus on chronic kidney disease.
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Affiliation(s)
- Eva Feigerlová
- Service d'Endocrinologie, Centre Hospitalier Universitaire de Poitiers, Pôle DUNE, Poitiers, France; .,Université de Poitiers, Unité de Formation et de Recherche Médecine Pharmacie, Poitiers, France.,Clinical Investigation Centre 1402, Unité 1082, INSERM, Poitiers, France; and
| | - Shyue-Fang Battaglia-Hsu
- Nutrition Génétique et Exposition aux Risques Environnementaux, INSERM Unité 954, Université de Lorraine et Centre Hospitalier Regional Universitaire de Nancy, Vandœuvre les Nancy, France
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24
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Hutchins EJ, Belrose JL, Szaro BG. A novel role for the nuclear localization signal in regulating hnRNP K protein stability in vivo. Biochem Biophys Res Commun 2016; 478:772-6. [DOI: 10.1016/j.bbrc.2016.08.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 08/04/2016] [Indexed: 01/12/2023]
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25
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Asnani M, Pestova TV, Hellen CUT. PCBP2 enables the cadicivirus IRES to exploit the function of a conserved GRNA tetraloop to enhance ribosomal initiation complex formation. Nucleic Acids Res 2016; 44:9902-9917. [PMID: 27387282 PMCID: PMC5175331 DOI: 10.1093/nar/gkw609] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 06/24/2016] [Accepted: 06/24/2016] [Indexed: 12/22/2022] Open
Abstract
The cadicivirus IRES diverges structurally from canonical Type 1 IRESs (e.g. poliovirus) but nevertheless also contains an essential GNRA tetraloop in a subdomain (d10c) that is homologous to poliovirus dIVc. In addition to canonical initiation factors, the canonical Type 1 and divergent cadicivirus IRESs require the same IRES trans-acting factor, poly(C)-binding protein 2 (PCBP2). PCBP2 has three KH domains and binds poliovirus IRES domain dIV in the vicinity of the tetraloop. How PCBP2 binds the cadicivirus IRES, and the roles of PCBP2 and the tetraloop in Type 1 IRES function are unknown. Here, directed hydroxyl radical probing showed that KH1 also binds near the cadicivirus tetraloop. KH2 and KH3 bind adjacently to an IRES subdomain (d10b) that is unrelated to dIV, with KH3 in an inverted orientation. KH3 is critical for PCBP2's binding to this IRES whereas KH1 is essential for PCBP2's function in promoting initiation. PCBP2 enforced the wild-type structure of d10c when it contained minor destabilizing substitutions, exposing the tetraloop. Strikingly, PCBP2 enhanced initiation on mutant IRESs that retained consensus GNRA tetraloops, whereas mutants with divergent sequences did not respond to PCBP2. These studies show that PCBP2 enables the IRES to exploit the GNRA tetraloop to enhance initiation.
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Affiliation(s)
- Mukta Asnani
- Department of Cell Biology, SUNY Downstate Medical Center, 450 Clarkson Avenue, MSC 44, Brooklyn, NY 11203, USA
| | - Tatyana V Pestova
- Department of Cell Biology, SUNY Downstate Medical Center, 450 Clarkson Avenue, MSC 44, Brooklyn, NY 11203, USA
| | - Christopher U T Hellen
- Department of Cell Biology, SUNY Downstate Medical Center, 450 Clarkson Avenue, MSC 44, Brooklyn, NY 11203, USA
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26
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Barnes M, van Rensburg G, Li WM, Mehmood K, Mackedenski S, Chan CM, King DT, Miller AL, Lee CH. Molecular insights into the coding region determinant-binding protein-RNA interaction through site-directed mutagenesis in the heterogeneous nuclear ribonucleoprotein-K-homology domains. J Biol Chem 2014; 290:625-39. [PMID: 25389298 DOI: 10.1074/jbc.m114.614735] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The ability of its four heterogeneous nuclear RNP-K-homology (KH) domains to physically associate with oncogenic mRNAs is a major criterion for the function of the coding region determinant-binding protein (CRD-BP). However, the particular RNA-binding role of each of the KH domains remains largely unresolved. Here, we mutated the first glycine to an aspartate in the universally conserved GXXG motif of the KH domain as an approach to investigate their role. Our results show that mutation of a single GXXG motif generally had no effect on binding, but the mutation in any two KH domains, with the exception of the combination of KH3 and KH4 domains, completely abrogated RNA binding in vitro and significantly retarded granule formation in zebrafish embryos, suggesting that any combination of at least two KH domains cooperate in tandem to bind RNA efficiently. Interestingly, we found that any single point mutation in one of the four KH domains significantly impacted CRD-BP binding to mRNAs in HeLa cells, suggesting that the dynamics of the CRD-BP-mRNA interaction vary over time in vivo. Furthermore, our results suggest that different mRNAs bind preferentially to distinct CRD-BP KH domains. The novel insights revealed in this study have important implications on the understanding of the oncogenic mechanism of CRD-BP as well as in the future design of inhibitors against CRD-BP function.
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Affiliation(s)
- Mark Barnes
- From the Chemistry Program, University of Northern British Columbia, Prince George, British Columbia V2N 4Z9, Canada
| | - Gerrit van Rensburg
- From the Chemistry Program, University of Northern British Columbia, Prince George, British Columbia V2N 4Z9, Canada
| | - Wai-Ming Li
- From the Chemistry Program, University of Northern British Columbia, Prince George, British Columbia V2N 4Z9, Canada
| | - Kashif Mehmood
- From the Chemistry Program, University of Northern British Columbia, Prince George, British Columbia V2N 4Z9, Canada
| | - Sebastian Mackedenski
- From the Chemistry Program, University of Northern British Columbia, Prince George, British Columbia V2N 4Z9, Canada
| | - Ching-Man Chan
- the Division of Life Science and The Key State Laboratory for Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, and
| | - Dustin T King
- From the Chemistry Program, University of Northern British Columbia, Prince George, British Columbia V2N 4Z9, Canada
| | - Andrew L Miller
- the Division of Life Science and The Key State Laboratory for Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, and the Marine Biological Laboratory, Woods Hole, Massachusetts 02543
| | - Chow H Lee
- From the Chemistry Program, University of Northern British Columbia, Prince George, British Columbia V2N 4Z9, Canada,
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27
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Anxiety-associated alternative polyadenylation of the serotonin transporter mRNA confers translational regulation by hnRNPK. Proc Natl Acad Sci U S A 2013; 110:11624-9. [PMID: 23798440 DOI: 10.1073/pnas.1301485110] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The serotonin transporter (SERT) is a major regulator of serotonergic neurotransmission and anxiety-related behaviors. SERT is expressed in two alternative polyadenylation forms that differ by an evolutionarily conserved element in the 3' untranslated region of its mRNA. Expression of SERT mRNA containing the distal polyadenylation element is associated with decreased anxiety-related behaviors in mice and humans, suggesting that this element has behaviorally relevant modulatory effects on SERT expression. We have identified heterogeneous nuclear ribonucleoprotein K (hnRNPK), a protein known to integrate multiple signal transduction pathways with gene expression, as a SERT distal polyadenylation element binding protein. This interaction is functionally meaningful because genetic manipulation of hnRNPK alters expression of the SERT protein. Furthermore, the trophic factor S100β induces Src-family kinase-mediated tyrosine phosphorylation of hnRNPK and increased SERT expression. These results identify a previously unknown mechanism of regulated SERT expression and provide a putative mechanism by which the SERT distal polyadenylation element modulates anxiety-related behaviors.
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28
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van Domselaar R, de Poot SAH, Remmerswaal EBM, Lai KW, ten Berge IJM, Bovenschen N. Granzyme M targets host cell hnRNP K that is essential for human cytomegalovirus replication. Cell Death Differ 2013; 20:419-29. [PMID: 23099853 PMCID: PMC3569982 DOI: 10.1038/cdd.2012.132] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Revised: 09/03/2012] [Accepted: 09/14/2012] [Indexed: 11/08/2022] Open
Abstract
Human cytomegalovirus (HCMV) is the most frequent viral cause of congenital defects and HCMV infection in immunocompromised patients may trigger devastating disease. Cytotoxic lymphocytes control HCMV by releasing granzymes towards virus-infected cells. In mice, granzyme M (GrM) has a physiological role in controlling murine CMV infection. However, the underlying mechanism remains poorly understood. In this study, we showed that human GrM was expressed by HCMV-specific CD8(+) T cells both in latently infected healthy individuals and in transplant patients during primary HCMV infection. We identified host cell heterogeneous nuclear ribonucleoprotein K (hnRNP K) as a physiological GrM substrate. GrM most efficiently cleaved hnRNP K in the presence of RNA at multiple sites, thereby likely destroying hnRNP K function. Host cell hnRNP K was essential for HCMV replication not only by promoting viability of HCMV-infected cells but predominantly by regulating viral immediate-early 2 (IE2) protein levels. Furthermore, hnRNP K interacted with IE2 mRNA. Finally, GrM decreased IE2 protein expression in HCMV-infected cells. Our data suggest that targeting of hnRNP K by GrM contributes to the mechanism by which cytotoxic lymphocytes inhibit HCMV replication. This is the first evidence that cytotoxic lymphocytes target host cell proteins to control HCMV infections.
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Affiliation(s)
- R van Domselaar
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - S A H de Poot
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - E B M Remmerswaal
- Department of Experimental Immunology, Academic Medical Center, Amsterdam, The Netherlands
- Renal Transplant Unit, Department of Internal Medicine, Academic Medical Center, Amsterdam, The Netherlands
| | - K W Lai
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - I J M ten Berge
- Renal Transplant Unit, Department of Internal Medicine, Academic Medical Center, Amsterdam, The Netherlands
| | - N Bovenschen
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
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29
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Wen J, Chen Z, Cai X. A biophysical model for identifying splicing regulatory elements and their interactions. PLoS One 2013; 8:e54885. [PMID: 23382993 PMCID: PMC3559881 DOI: 10.1371/journal.pone.0054885] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Accepted: 12/17/2012] [Indexed: 11/18/2022] Open
Abstract
Alternative splicing (AS) of precursor mRNA (pre-mRNA) is a crucial step in the expression of most eukaryotic genes. Splicing factors (SFs) play an important role in AS regulation by binding to the cis-regulatory elements on the pre-mRNA. Although many splicing factors (SFs) and their binding sites have been identified, their combinatorial regulatory effects remain to be elucidated. In this paper, we derive a biophysical model for AS regulation that integrates combinatorial signals of cis-acting splicing regulatory elements (SREs) and their interactions. We also develop a systematic framework for model inference. Applying the biophysical model to a human RNA-Seq data set, we demonstrate that our model can explain 49.1%–66.5% variance of the data, which is comparable to the best result achieved by biophysical models for transcription. In total, we identified 119 SRE pairs between different regions of cassette exons that may regulate exon or intron definition in splicing, and 77 SRE pairs from the same region that may arise from a long motif or two different SREs bound by different SFs. Particularly, putative binding sites of polypyrimidine tract-binding protein (PTB), heterogeneous nuclear ribonucleoprotein (hnRNP) F/H and E/K are identified as interacting SRE pairs, and have been shown to be consistent with the interaction models proposed in previous experimental results. These results show that our biophysical model and inference method provide a means of quantitative modeling of splicing regulation and is a useful tool for identifying SREs and their interactions. The software package for model inference is available under an open source license.
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Affiliation(s)
- Ji Wen
- Department of Electrical and Computer Engineering, University of Miami, Coral Gables, Florida, United States of America
| | - Zhibin Chen
- Department of Microbiology and Immunology, University of Miami, Miami, Florida, United States of America
| | - Xiaodong Cai
- Department of Electrical and Computer Engineering, University of Miami, Coral Gables, Florida, United States of America
- * E-mail:
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30
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Löscher M, Schosserer M, Dausse E, Lee K, Ajuh P, Grillari-Voglauer R, Lamond AI, Toulmé JJ, Grillari J. Inhibition of pre-mRNA splicing by a synthetic Blom7α-interacting small RNA. PLoS One 2012; 7:e47497. [PMID: 23144703 PMCID: PMC3483155 DOI: 10.1371/journal.pone.0047497] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Accepted: 09/17/2012] [Indexed: 12/02/2022] Open
Abstract
Originally the novel protein Blom7α was identified as novel pre-mRNA splicing factor that interacts with SNEVPrp19/Pso4, an essential protein involved in extension of human endothelial cell life span, DNA damage repair, the ubiquitin-proteasome system, and pre-mRNA splicing. Blom7α belongs to the heteronuclear ribonucleoprotein K homology (KH) protein family, displaying 2 KH domains, a well conserved and widespread RNA-binding motif. In order to identify specific sequence binding motifs, we here used Systematic Evolution of Ligands by Exponential Enrichment (SELEX) with a synthetic RNA library. Besides sequence motifs like (U/A)1–4 C2–6 (U/A)1–5, we identified an AC-rich RNA-aptamer that we termed AK48 (Aptamer KH-binding 48), binding to Blom7α with high affinity. Addition of AK48 to pre-mRNA splicing reactions in vitro inhibited the formation of mature spliced mRNA and led to a slight accumulation of the H complex of the spliceosome. These results suggest that the RNA binding activity of Blom7α might be required for pre-mRNA splicing catalysis. The inhibition of in-vitro splicing by the small RNA AK48 indicates the potential use of small RNA molecules in targeting the spliceosome complex as a novel target for drug development.
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Affiliation(s)
- Marlies Löscher
- Department of Biotechnology, BOKU - University of Natural Resources and Life Sciences, Vienna, Austria
| | - Markus Schosserer
- Department of Biotechnology, BOKU - University of Natural Resources and Life Sciences, Vienna, Austria
| | - Eric Dausse
- INSERM U869, European Institute of Chemistry and Biology, Pessac, France
- University of Bordeaux, Bordeaux, France
| | - Kiseok Lee
- Department of Biotechnology, BOKU - University of Natural Resources and Life Sciences, Vienna, Austria
| | - Paul Ajuh
- School of Life Sciences, Welcome Trust Biocentre, University of Dundee, Dundee, United Kingdom
| | - Regina Grillari-Voglauer
- Department of Biotechnology, BOKU - University of Natural Resources and Life Sciences, Vienna, Austria
- ACIB, Vienna, Austria
- Evercyte GmbH, Vienna, Austria
| | - Angus I. Lamond
- School of Life Sciences, Welcome Trust Biocentre, University of Dundee, Dundee, United Kingdom
| | - Jean-Jacques Toulmé
- INSERM U869, European Institute of Chemistry and Biology, Pessac, France
- University of Bordeaux, Bordeaux, France
| | - Johannes Grillari
- Department of Biotechnology, BOKU - University of Natural Resources and Life Sciences, Vienna, Austria
- Evercyte GmbH, Vienna, Austria
- * E-mail:
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31
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Martin F. Fifteen years of the yeast three-hybrid system: RNA-protein interactions under investigation. Methods 2012; 58:367-75. [PMID: 22841566 DOI: 10.1016/j.ymeth.2012.07.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2011] [Revised: 05/04/2012] [Accepted: 07/13/2012] [Indexed: 01/14/2023] Open
Abstract
In 1996, the Wickens and the Kuhl labs developed the yeast three-hybrid system independently. By expressing two chimeric proteins and one chimeric RNA molecule in Saccharomyces cerevisiae, this method allows in vivo monitoring of RNA-protein interactions by measuring the expression levels of HIS3 and LacZ reporter genes. Specific RNA targets have been used to characterize unknown RNA binding proteins. Previously described RNA binding proteins have also been used as bait to select new RNA targets. Finally, this method has been widely used to investigate or confirm previously suspected RNA-protein interactions. However, this method falls short in some aspects, such as RNA display and selection of false positive molecules. This review will summarize the results obtained with this method from the past 15years, as well as on recent efforts to improve its specificity.
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Affiliation(s)
- Franck Martin
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, Institut de Biologie Moléculaire et Cellulaire, Strasbourg CEDEX, France.
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32
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van Domselaar R, Quadir R, van der Made AM, Broekhuizen R, Bovenschen N. All human granzymes target hnRNP K that is essential for tumor cell viability. J Biol Chem 2012; 287:22854-64. [PMID: 22582387 PMCID: PMC3391115 DOI: 10.1074/jbc.m112.365692] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Revised: 05/11/2012] [Indexed: 11/06/2022] Open
Abstract
Granule exocytosis by cytotoxic lymphocytes is the key mechanism to eliminate virus-infected cells and tumor cells. These lytic granules contain the pore-forming protein perforin and a set of five serine proteases called granzymes. All human granzymes display distinct substrate specificities and induce cell death by cleaving critical intracellular death substrates. In the present study, we show that all human granzymes directly cleaved the DNA/RNA-binding protein heterogeneous nuclear ribonucleoprotein K (hnRNP K), designating hnRNP K as the first known pan-granzyme substrate. Cleavage of hnRNP K was more efficient in the presence of RNA and occurred in two apparent proteolysis-sensitive amino acid regions, thereby dissecting the functional DNA/RNA-binding hnRNP K domains. HnRNP K was cleaved under physiological conditions when purified granzymes were delivered into living tumor cells and during lymphokine-activated killer cell-mediated attack. HnRNP K is essential for tumor cell viability, since knockdown of hnRNP K resulted in spontaneous tumor cell apoptosis with caspase activation and reactive oxygen species production. This apoptosis was more pronounced at low tumor cell density where hnRNP K knockdown also triggered a caspase-independent apoptotic pathway. This suggests that hnRNP K promotes tumor cell survival in the absence of cell-cell contact. Silencing of hnRNP K protein expression rendered tumor cells more susceptible to cellular cytotoxicity. We conclude that hnRNP K is indispensable for tumor cell viability and our data suggest that targeting of hnRNP K by granzymes contributes to or reinforces the cell death mechanisms by which cytotoxic lymphocytes eliminate tumor cells.
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Affiliation(s)
- Robert van Domselaar
- From the Department of Pathology, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
| | - Razi Quadir
- From the Department of Pathology, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
| | - Astrid M. van der Made
- From the Department of Pathology, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
| | - Roel Broekhuizen
- From the Department of Pathology, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
| | - Niels Bovenschen
- From the Department of Pathology, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
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33
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Abstract
RNA-binding proteins (RBPs) exert many roles in the post-transcriptional regulation of gene expression in eukaryotic cells. However, our understanding of how they recognize their target RNAs in vivo remains limited. In the January 1, 2012, issue of Genes & Development, Patel and colleagues (p. 43-53) provide detailed mechanistic insights into how one of the best-studied RBPs, zipcode-binding protein 1 (ZBP1), recognizes a bipartite RNA sequence element within the β-actin mRNA.
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Affiliation(s)
- Michael Doyle
- Center for Brain Research, Medical University of Vienna, 1090 Vienna, Austria
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34
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Liu Y, Szaro BG. hnRNP K post-transcriptionally co-regulates multiple cytoskeletal genes needed for axonogenesis. Development 2011; 138:3079-90. [PMID: 21693523 DOI: 10.1242/dev.066993] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The RNA-binding protein, hnRNP K, is essential for axonogenesis. Suppressing its expression in Xenopus embryos yields terminally specified neurons with severely disorganized microtubules, microfilaments and neurofilaments, raising the hypothesis that hnRNP K post-transcriptionally regulates multiple transcripts of proteins that organize the axonal cytoskeleton. To identify downstream candidates for this regulation, RNAs that co-immunoprecipitated from juvenile brain with hnRNP K were identified on microarrays. A substantial number of these transcripts were linked to the cytoskeleton and to intracellular localization, trafficking and transport. Injection into embryos of a non-coding RNA bearing multiple copies of an hnRNP K RNA-binding consensus sequence found within these transcripts largely phenocopied hnRNP K knockdown, further supporting the idea that it regulates axonogenesis through its binding to downstream target RNAs. For further study of regulation by hnRNP K of the cytoskeleton during axon outgrowth, we focused on three validated RNAs representing elements associated with all three polymers - Arp2, tau and an α-internexin-like neurofilament. All three were co-regulated post-transcriptionally by hnRNP K, as hnRNP K knockdown yielded comparable defects in their nuclear export and translation but not transcription. Directly knocking down expression of all three together, but not each one individually, substantially reproduced the axonless phenotype, providing further evidence that regulation of axonogenesis by hnRNP K occurs largely through pleiotropic effects on cytoskeletal-associated targets. These experiments provide evidence that hnRNP K is the nexus of a novel post-transcriptional regulatory module controlling the synthesis of proteins that integrate all three cytoskeletal polymers to form the axon.
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Affiliation(s)
- Yuanyuan Liu
- Department of Biological Sciences and the Center for Neuroscience Research, University at Albany, State University of New York, Albany, NY 12222, USA
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Li H, Liu J. Identification of heterogeneous nuclear ribonucleoprotein K as a transactivator for human low density lipoprotein receptor gene transcription. J Biol Chem 2010; 285:17789-97. [PMID: 20371611 PMCID: PMC2878543 DOI: 10.1074/jbc.m109.082057] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2009] [Revised: 03/05/2010] [Indexed: 01/09/2023] Open
Abstract
hnRNP K, a member of the family of heterogeneous ribonucleoproteins, is known to exert various functional roles in the nucleus, cytoplasm, and mitochondria to affect different cellular processes including chromatin remodeling, transcription, splicing, and translation. Here we report, for the first time, that hnRNP K is specifically involved in human LDL receptor (LDLR) gene transcription in HepG2 cells. We show that depletion of hnRNP K by siRNA transfection reduces the expression of LDLR mRNA and protein by more than 50% as measured by quantitative real-time PCR and Western blot analysis. Importantly, we show that the decay rate of LDLR mRNA is not affected by hnRNP K siRNA transfection, whereas the LDLR promoter activity is significantly decreased. Furthermore, overexpression of hnRNP K increased the LDLR promoter activity by the luciferase reporter assay. By utilizing a series of mutational and deletional constructs of LDLR promoter luciferase reporters, we mapped the K-responsive element to the repeat 3 (R3) sequence of the LDLR promoter. Electrophoretic mobility shift assays show that the K protein binds to a single-stranded DNA probe containing the CT-rich element of R3, which is in contrast to the requirement of double-stranded DNA for Sp1 to bind to R3. Finally, chromatin immunoprecipitation assays reveal a direct interaction of hnRNP K with the LDLR promoter in intact HepG2 cells. These new findings provide strong evidence demonstrating that hnRNP K is an important transactivator for human LDLR gene transcription. This work sheds new light on our current understanding of how LDLR gene expression is controlled at the transcriptional level.
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Affiliation(s)
- Hai Li
- From the Department of Veterans Affairs Palo Alto Health Care System, Palo Alto, California 94304
| | - Jingwen Liu
- From the Department of Veterans Affairs Palo Alto Health Care System, Palo Alto, California 94304
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Revil T, Pelletier J, Toutant J, Cloutier A, Chabot B. Heterogeneous nuclear ribonucleoprotein K represses the production of pro-apoptotic Bcl-xS splice isoform. J Biol Chem 2009; 284:21458-67. [PMID: 19520842 DOI: 10.1074/jbc.m109.019711] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The Bcl-x pre-mRNA is alternatively spliced to produce the anti-apoptotic Bcl-x(L) and the pro-apoptotic Bcl-x(S) isoforms. By performing deletion mutagenesis on a human Bcl-x minigene, we have identified a novel exonic element that controls the use of the 5' splice site of Bcl-x(S). The proximal portion of this element acts as a repressor and is located downstream of an enhancer. Further mutational analysis provided a detailed topological map of the regulatory activities revealing a sharp transition between enhancer and repressor sequences. Portions of the enhancer can function when transplanted in another alternative splicing unit. Chromatography and immunoprecipitation assays indicate that the silencer element interacts with heterogeneous ribonucleoprotein particle (hnRNP) K, consistent with the presence of putative high affinity sites for this protein. Finally, down-regulation of hnRNP K by RNA interference enhanced splicing to Bcl-x(S), an effect seen only when the sequences bound by hnRNP K are present. Our results therefore document a clear role for hnRNP K in preventing the production of the pro-apoptotic Bcl-x(S) splice isoform.
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Affiliation(s)
- Timothée Revil
- RNA/RNP Group, Département de Microbiologie et d'Infectiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Québec J1H 5N4, Canada
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The interactome: predicting the protein-protein interactions in cells. Cell Mol Biol Lett 2008; 14:1-22. [PMID: 18839074 PMCID: PMC6275871 DOI: 10.2478/s11658-008-0024-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2008] [Accepted: 04/03/2008] [Indexed: 12/03/2022] Open
Abstract
The term Interactome describes the set of all molecular interactions in cells, especially in the context of protein-protein interactions. These interactions are crucial for most cellular processes, so the full representation of the interaction repertoire is needed to understand the cell molecular machinery at the system biology level. In this short review, we compare various methods for predicting protein-protein interactions using sequence and structure information. The ultimate goal of those approaches is to present the complete methodology for the automatic selection of interaction partners using their amino acid sequences and/or three dimensional structures, if known. Apart from a description of each method, details of the software or web interface needed for high throughput prediction on the whole genome scale are also provided. The proposed validation of the theoretical methods using experimental data would be a better assessment of their accuracy.
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Friedman BA, Stadler MB, Shomron N, Ding Y, Burge CB. Ab initio identification of functionally interacting pairs of cis-regulatory elements. Genome Res 2008; 18:1643-51. [PMID: 18799692 DOI: 10.1101/gr.080085.108] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cooperatively acting pairs of cis-regulatory elements play important roles in many biological processes. Here, we describe a statistical approach, compositionally orthogonalized co-occurrence analysis (coCOA) that detects pairs of oligonucleotides that preferentially co-occur in pairs of sequence regions, controlling for correlations between the compositions of the analyzed regions. coCOA identified three clusters of oligonucleotide pairs that frequently co-occur at 5' and 3' ends of human and mouse introns. The largest cluster involved GC-rich sequences at the 5' ends of introns that co-occur and are co-conserved with specific AU-rich sequences near intron 3' ends. These motifs are preferentially conserved when they occur together, as measured by a new co-conservation measure, supporting common in vivo function. These motif pairs are also enriched in introns flanking alternative "cassette" exons, suggesting a role in silencing of intervening exons, and we showed that these motifs can cooperatively silence splicing of an intervening exon in a splicing reporter assay. This approach can be easily generalized to problems beyond RNA splicing.
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Affiliation(s)
- Brad A Friedman
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
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Bouvrette DJ, Price SJ, Bryda EC. K homology domains of the mouse polycystic kidney disease-related protein, Bicaudal-C (Bicc1), mediate RNA binding in vitro. Nephron Clin Pract 2008; 108:e27-34. [PMID: 18182784 DOI: 10.1159/000112913] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2007] [Accepted: 10/08/2007] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND/AIMS The mouse Bicc1(mBicc1) gene is the orthologue of the DrosophilaBicaudal-C(Bic-C) gene. While the role of Bicc1 in the mouse is unknown, mutations in the mouse Bicc1 gene are associated with polycystic kidney disease (PKD). The mBicc1 protein contains three K homology (KH) domains. Evidence from other KH domain-containing proteins as well as studies involving both Drosophila and Xenopus Bic-C, suggest that this motif is important in interactions with RNA. METHODS RNA-binding assays were used to test whether mouse Bicc1 binds homoribopolymers in vitro. A series of constructs coding for different regions of the mBicc1 protein were used to determine which regions of the mBicc1 protein were important for in vitro RNA binding. RESULTS Mouse Bicc1 binds homoribopolymers in vitro and the third KH domain is necessary and sufficient for in vitro RNA binding. The mutation responsible for PKD in the jcpk mouse model results in a protein that is incapable of binding RNA in vitro. CONCLUSIONS This study demonstrates that mouse Bicc1, a protein associated with PKD, has the ability to bind RNA in vitro. Disruption of this binding capability may be responsible for cyst formation in animals carrying mutations in the mBicc1 gene.
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Affiliation(s)
- Denise J Bouvrette
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, Mo., USA
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Iwasaki T, Koretomo Y, Fukuda T, Paronetto MP, Sette C, Fukami Y, Sato KI. Expression, phosphorylation, and mRNA-binding of heterogeneous nuclear ribonucleoprotein K in Xenopus oocytes, eggs, and early embryos. Dev Growth Differ 2007; 50:23-40. [DOI: 10.1111/j.1440-169x.2007.00974.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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41
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Feliers D, Lee MJ, Ghosh-Choudhury G, Bomsztyk K, Kasinath BS. Heterogeneous nuclear ribonucleoprotein K contributes to angiotensin II stimulation of vascular endothelial growth factor mRNA translation. Am J Physiol Renal Physiol 2007; 293:F607-15. [PMID: 17581920 DOI: 10.1152/ajprenal.00497.2006] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
ANG II rapidly increases VEGF synthesis in proximal tubular epithelial cells through mRNA translation. The role of heterogeneous nuclear ribonucleoprotein K (hnRNP K) in ANG II regulation of VEGF mRNA translation initiation was examined. ANG II activated hnRNP K as judged by binding to poly(C)- and poly(U)-agarose. ANG II increased hnRNP K binding to VEGF mRNA at the same time as it stimulated its translation, suggesting that hnRNP K contributes to VEGF mRNA translation. Inhibition of hnRNP K expression by RNA interference significantly reduced ANG II stimulation of VEGF synthesis. ANG II increased hnRNP K phosphorylation on both tyrosine and serine residues with distinct time courses; only Ser302 phosphorylation paralleled binding to VEGF mRNA. Src inhibition using PP2 or RNA interference inhibited PKCδ activity and prevented hnRNP K phosphorylation on both tyrosine and serine residues and its binding to VEGF mRNA. Under these conditions, ANG II-induced VEGF synthesis was inhibited. ANG II treatment induced redistribution of both VEGF mRNA and hnRNP K protein from light to heavy polysomal fractions, suggesting increased binding of hnRNP K to VEGF mRNA that is targeted for increased translation. This study shows that hnRNP K augments efficiency of VEGF mRNA translation stimulated by ANG II.
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Affiliation(s)
- Denis Feliers
- Dept. of Medicine/Nephrology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Dr., San Antonio, TX, USA.
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Local dipole interactions induce helicity of (S)-2-butyl-N-(1,8-naphthaloyl)-2-aminobenzoate molecules containing 1,8-naphthalimide rings utilized as a column building blocks: X-ray and quantum mechanical studies. Struct Chem 2007. [DOI: 10.1007/s11224-007-9182-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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43
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Abe Y, Jo T, Matsuda Y, Matsunaga C, Katayama T, Ueda T. Structure and function of DnaA N-terminal domains: specific sites and mechanisms in inter-DnaA interaction and in DnaB helicase loading on oriC. J Biol Chem 2007; 282:17816-27. [PMID: 17420252 DOI: 10.1074/jbc.m701841200] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
DnaA forms a homomultimeric complex with the origin of chromosomal replication (oriC) to unwind duplex DNA. The interaction of the DnaA N terminus with the DnaB helicase is crucial for the loading of DnaB onto the unwound region. Here, we determined the DnaA N terminus structure using NMR. This region (residues 1-108) consists of a rigid region (domain I) and a flexible region (domain II). Domain I has an alpha-alpha-beta-beta-alpha-beta motif, similar to that of the K homology (KH) domain, and has weak affinity for oriC single-stranded DNA, consistent with KH domain function. A hydrophobic surface carrying Trp-6 most likely forms the interface for domain I dimerization. Glu-21 is located on the opposite surface of domain I from the Trp-6 site and is crucial for DnaB helicase loading. These findings suggest a model for DnaA homomultimer formation and DnaB helicase loading on oriC.
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Affiliation(s)
- Yoshito Abe
- Department of Immunology, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
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Brykailo MA, Corbett AH, Fridovich-Keil JL. Functional overlap between conserved and diverged KH domains in Saccharomyces cerevisiae SCP160. Nucleic Acids Res 2007; 35:1108-18. [PMID: 17264125 PMCID: PMC1994781 DOI: 10.1093/nar/gkl1160] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2006] [Revised: 12/20/2006] [Accepted: 12/20/2006] [Indexed: 01/26/2023] Open
Abstract
The K homology (KH) domain is a remarkably versatile and highly conserved RNA-binding motif. Classical KH domains include a characteristic pattern of hydrophobic residues, a Gly-X-X-Gly (GXXG) segment, and a variable loop. KH domains typically occur in clusters, with some retaining their GXXG sequence (conserved), while others do not (diverged). As a first step towards addressing whether GXXG is essential for KH-domain function, we explored the roles of conserved and diverged KH domains in Scp160p, a multiple-KH-domain-containing protein in Saccharomyces cerevisiae. We specifically wanted to know (1) whether diverged KH domains were essential for Scp160p function, and (2) whether diverged KH domains could functionally replace conserved KH domains. To address these questions, we deleted and/or interchanged conserved and diverged KH domains of Scp160p and expressed the mutated alleles in yeast. Our results demonstrated that the answer to each question was yes. Both conserved and diverged KH domains are essential for Scp160p function, and diverged KH domains can function in place of conserved KH domains. These findings challenge the prevailing notions about the requisite features of a KH domain and raise the possibility that there may be more functional KH domains in the proteome than previously appreciated.
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Affiliation(s)
- Melissa A. Brykailo
- Graduate Program in Genetics and Molecular Biology, Emory University Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322 and Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Anita H. Corbett
- Graduate Program in Genetics and Molecular Biology, Emory University Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322 and Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Judith L. Fridovich-Keil
- Graduate Program in Genetics and Molecular Biology, Emory University Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322 and Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
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Rogne M, Landsverk HB, Van Eynde A, Beullens M, Bollen M, Collas P, Küntziger T. The KH-Tudor Domain of A-Kinase Anchoring Protein 149 Mediates RNA-Dependent Self-Association. Biochemistry 2006; 45:14980-9. [PMID: 17154535 DOI: 10.1021/bi061418y] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
A-Kinase anchoring proteins (AKAPs) control the subcellular localization and temporal specificity of protein phosphorylation mediated by cAMP-dependent protein kinase. AKAP149 (AKAP1) is found in mitochondria and in the endoplasmic reticulum-nuclear envelope network where it anchors protein kinases, phosphatases, and a phosphodiesterase. AKAP149 harbors in its COOH-terminal part one KH and one Tudor domain, both known to be involved in RNA binding. We investigated the properties of the COOH-terminal domain of AKAP149. We show here that AKAP149 is a self-associating protein with RNA binding features. The KH domain of AKAP149 is sufficient for self-association in a RNA-dependent manner. The Tudor domain is not necessary for self-association, but it is required together with the KH domain for targeting to well-defined nuclear foci. These foci are spatially closely related to nucleolar subcompartments. We also show that the KH-Tudor-containing domain of AKAP149 binds RNA in vitro and in RNA coprecipitation experiments. AKAP149 emerges as a scaffolding protein involved in the integration of intracellular signals and possibly in RNA metabolism.
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Affiliation(s)
- Marie Rogne
- Institute of Basic Medical Sciences, Department of Biochemistry, Faculty of Medicine, University of Oslo, P.O. Box 1112 Blindern, 0317 Oslo, Norway
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Malik AK, Flock KE, Godavarthi CL, Loh HH, Ko JL. Molecular basis underlying the poly C binding protein 1 as a regulator of the proximal promoter of mouse mu-opioid receptor gene. Brain Res 2006; 1112:33-45. [PMID: 16904079 DOI: 10.1016/j.brainres.2006.07.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2005] [Revised: 06/07/2006] [Accepted: 07/05/2006] [Indexed: 11/19/2022]
Abstract
Previous studies showed poly C binding protein 1 (PCBP) participating in the mu-opioid receptor (MOR) gene regulation via binding to a single-stranded (ss) DNA element. In this report, we therefore investigate the molecular basis of PCBP regulating the MOR gene expression. Various truncated PCBPs, including one domain (KH1, KH2, variable or KH3), two- (K12, K2v or Kv3) or three-sequential domains (K12v or K2v3), were constructed. The MOR ssDNA binding abilities of these truncated PCBPs were examined using electrophoretic mobility shift assay (EMSA). KH1 domain possessed a strong MOR ssDNA binding activity. Variable domain displayed no binding, and KH2 or KH3 domain possessed a weak MOR ssDNA binding activity. Binding of two-domain PCBPs indicated an additive effect of two-domain combinations. Interestingly, K2v3, a three-domain PCBP, displayed as strong ssDNA binding as that of K12v, suggesting synergism of KH2, KH3 and variable domains for the binding activity. Functional analysis demonstrated one-domain PCBPs exhibiting no transactivation on the MOR proximal promoter. Two-domain PCBPs displayed approximately 20% activity, while three-domain PCBPs displayed 70%-85% of full-length PCBP activity. Taken together, these results suggested that no single domain possessed sufficient functional activity to serve as an independent transactivation domain, and the combination of three sequential domains was necessary for its optimal activity to activate the MOR proximal promoter. In summary, our data suggested that cooperativity of three sequential domains is essential for PCBP functioning as a MOR gene regulator. Various ways in which this cooperativity could occur are discussed.
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MESH Headings
- Animals
- Base Sequence
- Carrier Proteins/physiology
- Cell Line, Tumor
- DNA-Binding Proteins
- Electrophoretic Mobility Shift Assay/methods
- Gene Expression Regulation/physiology
- Methionine/metabolism
- Mice
- Neuroblastoma
- Phosphorus Isotopes/metabolism
- Promoter Regions, Genetic/physiology
- Protein Binding/drug effects
- Protein Binding/physiology
- Protein Structure, Tertiary/physiology
- RNA, Messenger/metabolism
- RNA-Binding Proteins
- Receptors, Opioid, mu/genetics
- Receptors, Opioid, mu/metabolism
- Regulatory Sequences, Nucleic Acid
- Reverse Transcriptase Polymerase Chain Reaction/methods
- Transcription, Genetic
- Transfection/methods
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Affiliation(s)
- Adnan K Malik
- Department of Biology, Seton Hall University, 208 McNulty Hall, 400 South Orange Ave. South Orange, NJ 07079, USA
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47
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Messias AC, Harnisch C, Ostareck-Lederer A, Sattler M, Ostareck DH. The DICE-binding activity of KH domain 3 of hnRNP K is affected by c-Src-mediated tyrosine phosphorylation. J Mol Biol 2006; 361:470-81. [PMID: 16854432 DOI: 10.1016/j.jmb.2006.06.025] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2006] [Revised: 05/09/2006] [Accepted: 06/12/2006] [Indexed: 10/24/2022]
Abstract
hnRNP K and hnRNP E1/E2 are RNA-binding proteins comprised of three hnRNP K-homology (KH) domains. These proteins are involved in the translational control and stabilization of mRNAs in erythroid cells. hnRNP E1 and hnRNP K regulate the translation of reticulocyte 15-lipoxygenase (r15-LOX) mRNA. Both proteins bind specifically to the differentiation control element (DICE) in the 3' untranslated region (3'UTR) of the r15-LOX mRNA. It has been shown that hnRNP K is a substrate of the tyrosine kinase c-Src and that tyrosine phosphorylation by c-Src inhibits the binding of hnRNP K to the DICE. Here, we investigate which of the three KH domains of hnRNP E1 and hnRNP K mediate the DICE interaction. Using RNA-binding assays, we demonstrate DICE-binding of the KH domains 1 and 3 of hnRNP E1, and KH domain 3 of hnRNP K. Furthermore, with RNA-binding assays, NMR experiments and in vitro translation studies, we show that tyrosine 458 in KH domain 3 of hnRNP K is important for the DICE interaction and we provide evidence that it is a target of c-Src.
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Affiliation(s)
- Ana C Messias
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstr. 1, 69117 Heidelberg, Germany
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48
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Nagano K, Bornhauser BC, Warnasuriya G, Entwistle A, Cramer R, Lindholm D, Naaby-Hansen S. PDGF regulates the actin cytoskeleton through hnRNP-K-mediated activation of the ubiquitin E3-ligase MIR. EMBO J 2006; 25:1871-82. [PMID: 16619033 PMCID: PMC1456933 DOI: 10.1038/sj.emboj.7601059] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2005] [Accepted: 03/01/2006] [Indexed: 11/08/2022] Open
Abstract
PDGF is a potent chemotactic mitogen and a strong inductor of fibroblast motility. In Swiss 3T3 fibroblasts, exposure to PDGF but not EGF or IGF-1 causes a rapid loss of actin stress fibers (SFs) and focal adhesions (FAs), which is followed by the development of retractile dendritic protrusions and induction of motility. The PDGF-specific actin reorganization was blocked by inhibition of Src-kinase and the 26S proteasome. PDGF induced Src-dependent association between the multifunctional transcription/translation regulator hnRNP-K and the mRNA-encoding myosin regulatory light-chain (MRLC)-interacting protein (MIR), a E(3)-ubiquitin ligase that is MRLC specific. This in turn rapidly increased MIR expression, and led to ubiquitination and proteasome-mediated degradation of MRLC. Downregulation of MIR by RNA muting prevented the reorganization of actin structures and severely reduced the migratory and wound-healing potential of PDGF-treated cells. The results show that activation of MIR and the resulting removal of diphosphorylated MRLC are essential for PDGF to instigate and maintain control over the actin-myosin-based contractile system in Swiss 3T3 fibroblasts. The PDGF induced protein destabilization through the regulation of hnRNP-K controlled ubiquitin -ligase translation identifies a novel pathway by which external stimuli can regulate phenotypic development through rapid, organelle-specific changes in the activity and stability of cytoskeletal regulators.
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Affiliation(s)
- Kohji Nagano
- Ludwig Institute for Cancer Research, Royal Free and University College London, Medical School, London, UK
| | | | - Gayathri Warnasuriya
- Ludwig Institute for Cancer Research, Royal Free and University College London, Medical School, London, UK
| | - Alan Entwistle
- Ludwig Institute for Cancer Research, Royal Free and University College London, Medical School, London, UK
| | - Rainer Cramer
- Ludwig Institute for Cancer Research, Royal Free and University College London, Medical School, London, UK
- Department of Biochemistry and Molecular Biology, University College London, London, UK
| | - Dan Lindholm
- Department of Neuroscience, University of Uppsala, Uppsala, Sweden
- Minerva Research Institute, Biomedicum Helsinki, Helsinki, Finland
| | - Soren Naaby-Hansen
- Ludwig Institute for Cancer Research, Royal Free and University College London, Medical School, London, UK
- Department of Biochemistry and Molecular Biology, University College London, London, UK
- Ludwig Institute for Cancer Research, Royal Free and University College London Medical School, Courtauld Building, 91 Riding House Street, London W1W 7BS, UK. Tel.: +44 208 346 4948; Fax: +44 207 878 4040; E-mail:
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49
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Klimek-Tomczak K, Mikula M, Dzwonek A, Paziewska A, Karczmarski J, Hennig E, Bujnicki JM, Brągoszewski P, Denisenko O, Bomsztyk K, Ostrowski J. Editing of hnRNP K protein mRNA in colorectal adenocarcinoma and surrounding mucosa. Br J Cancer 2006; 94:586-92. [PMID: 16404425 PMCID: PMC2361188 DOI: 10.1038/sj.bjc.6602938] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The heterogeneous nuclear ribonucleoprotein K (hnRNP K) protein is an RNA-binding protein involved in many processes that compose gene expression. K protein is upregulated in the malignant processes and has been shown to modulate the expression of genes involved in mitogenic responses and tumorigenesis. To explore the possibility that there are alternative isoforms of K protein expressed in colon cancer, we amplified and sequenced K protein mRNA that was isolated from colorectal cancers as well as from normal tissues surrounding the tumours. Sequencing revealed a single G-to-A base substitution at position 274 that was found in tumours and surrounding mucosa, but not in individuals that had no colorectal tumour. This substitution most likely reflects an RNA editing event because it was not found in the corresponding genomic DNAs. Sequencing of RNA from normal colonic mucosa of patients with prior resection of colorectal cancer revealed only the wild-type K protein transcript, indicating that G274A isoform is tumour related. To our knowledge, this is the first example of an RNA editing event in cancer and its surrounding tissue, a finding that may offer a new diagnostic and treatment marker.
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Affiliation(s)
- K Klimek-Tomczak
- Department of Gastroenterology, Medical Center for Postgraduate Education and Maria Skłodowska-Curie Memorial Cancer Center and Institute of Oncology, ul. Roentgena 5, Warsaw 02-781, Poland
| | - M Mikula
- Department of Gastroenterology, Medical Center for Postgraduate Education and Maria Skłodowska-Curie Memorial Cancer Center and Institute of Oncology, ul. Roentgena 5, Warsaw 02-781, Poland
| | - A Dzwonek
- Department of Gastroenterology, Medical Center for Postgraduate Education and Maria Skłodowska-Curie Memorial Cancer Center and Institute of Oncology, ul. Roentgena 5, Warsaw 02-781, Poland
| | - A Paziewska
- Department of Gastroenterology, Medical Center for Postgraduate Education and Maria Skłodowska-Curie Memorial Cancer Center and Institute of Oncology, ul. Roentgena 5, Warsaw 02-781, Poland
| | - J Karczmarski
- Department of Gastroenterology, Medical Center for Postgraduate Education and Maria Skłodowska-Curie Memorial Cancer Center and Institute of Oncology, ul. Roentgena 5, Warsaw 02-781, Poland
| | - E Hennig
- Department of Gastroenterology, Medical Center for Postgraduate Education and Maria Skłodowska-Curie Memorial Cancer Center and Institute of Oncology, ul. Roentgena 5, Warsaw 02-781, Poland
| | - J M Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Warsaw 02-109, Poland
| | - P Brągoszewski
- Department of Gastroenterology, Medical Center for Postgraduate Education and Maria Skłodowska-Curie Memorial Cancer Center and Institute of Oncology, ul. Roentgena 5, Warsaw 02-781, Poland
| | - O Denisenko
- Department of Medicine, UW Medicine Lake Union, University of Washington, Seattle, WA 98109, USA
| | - K Bomsztyk
- Department of Medicine, UW Medicine Lake Union, University of Washington, Seattle, WA 98109, USA
| | - J Ostrowski
- Department of Gastroenterology, Medical Center for Postgraduate Education and Maria Skłodowska-Curie Memorial Cancer Center and Institute of Oncology, ul. Roentgena 5, Warsaw 02-781, Poland
- Department of Gastroenterology, Medical Center for Postgraduate Education and Maria Skłodowska-Curie Memorial Cancer Center and Institute of Oncology, ul. Roentgena 5, Warsaw 02-781, Poland. E-mail:
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Yiu CPB, Beavil RL, Chan HYE. Biophysical characterisation reveals structural disorder in the nucleolar protein, Dribble. Biochem Biophys Res Commun 2006; 343:311-8. [PMID: 16542639 DOI: 10.1016/j.bbrc.2006.02.153] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2006] [Accepted: 02/24/2006] [Indexed: 10/24/2022]
Abstract
Dribble (DBE) is an essential protein in Drosophila that belongs to the evolutionarily conserved Krr1p protein family. Proteins in this family are localised in the cell nucleolus and are important for the processing of ribosomal RNAs. However, little is known about their structural and biophysical properties. We have expressed and purified full-length DBE protein from Escherichia coli. Consistent with the native role of DBE in RNA processing, recombinant DBE was shown to bind RNA homo-polymers in vitro. By bioinformatics, size-exclusion chromatography, equilibrium sedimentation analysis, controlled proteolysis, and a variety of spectroscopic techniques, we have found that DBE is a monomeric protein in solution containing both alpha- and beta-structures. Moreover, the structure of DBE is expanded and significantly disordered (approximately 45% disordered). Natively disordered proteins are thought to provide a disproportionately large surface area and structural plasticity for nucleic acid binding. We therefore propose that the presence of structural disorder is an important feature of DBE that facilitates the protein to interact with RNAs in the nucleolus.
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Affiliation(s)
- C-P Benny Yiu
- Laboratory of Drosophila Research, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China
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