1
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Zhao S, Li F, Li W, Wang M, Wang Y, Zhang Y, Xia P, Chen J. Mass Spectrometry-Based Proteomic Analysis of Potential Host Proteins Interacting with N in PRRSV-Infected PAMs. Int J Mol Sci 2024; 25:7219. [PMID: 39000325 PMCID: PMC11241482 DOI: 10.3390/ijms25137219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 06/23/2024] [Accepted: 06/25/2024] [Indexed: 07/16/2024] Open
Abstract
One of the most significant diseases in the swine business, porcine reproductive and respiratory syndrome virus (PRRSV) causes respiratory problems in piglets and reproductive failure in sows. The PRRSV nucleocapsid (N) protein is essential for the virus' assembly, replication, and immune evasion. Stages in the viral replication cycle can be impacted by interactions between the PRRSV nucleocapsid protein and the host protein components. Therefore, it is of great significance to explore the interaction between the PRRSV nucleocapsid protein and the host. Nevertheless, no information has been published on the network of interactions between the nucleocapsid protein and the host proteins in primary porcine alveolar macrophages (PAMs). In this study, 349 host proteins interacting with nucleocapsid protein were screened in the PRRSV-infected PAMs through a liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based proteomics approach. Bioinformatics analysis, which included gene ontology annotation, Kyoto Encyclopedia of Genes and Genomes database enrichment, and a protein-protein interaction (PPI) network, revealed that the host proteins interacting with PRRSV-N may be involved in protein binding, DNA transcription, metabolism, and innate immune responses. This study confirmed the interaction between the nucleocapsid protein and the natural immune-related proteins. Ultimately, our findings suggest that the nucleocapsid protein plays a pivotal role in facilitating immune evasion during a PRRSV infection. This study contributes to enhancing our understanding of the role played by the nucleocapsid protein in viral pathogenesis and virus-host interaction, thereby offering novel insights for the prevention and control of PRRS as well as the development of vaccines.
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Affiliation(s)
- Shijie Zhao
- College of Veterinary Medicine, Henan Agricultural University, Longzi Lake 15#, Zhengzhou 450046, China; (S.Z.); (F.L.); (W.L.); (M.W.); (Y.W.); (Y.Z.)
| | - Fahao Li
- College of Veterinary Medicine, Henan Agricultural University, Longzi Lake 15#, Zhengzhou 450046, China; (S.Z.); (F.L.); (W.L.); (M.W.); (Y.W.); (Y.Z.)
| | - Wen Li
- College of Veterinary Medicine, Henan Agricultural University, Longzi Lake 15#, Zhengzhou 450046, China; (S.Z.); (F.L.); (W.L.); (M.W.); (Y.W.); (Y.Z.)
| | - Mengxiang Wang
- College of Veterinary Medicine, Henan Agricultural University, Longzi Lake 15#, Zhengzhou 450046, China; (S.Z.); (F.L.); (W.L.); (M.W.); (Y.W.); (Y.Z.)
| | - Yueshuai Wang
- College of Veterinary Medicine, Henan Agricultural University, Longzi Lake 15#, Zhengzhou 450046, China; (S.Z.); (F.L.); (W.L.); (M.W.); (Y.W.); (Y.Z.)
| | - Yina Zhang
- College of Veterinary Medicine, Henan Agricultural University, Longzi Lake 15#, Zhengzhou 450046, China; (S.Z.); (F.L.); (W.L.); (M.W.); (Y.W.); (Y.Z.)
| | - Pingan Xia
- College of Veterinary Medicine, Henan Agricultural University, Longzi Lake 15#, Zhengzhou 450046, China; (S.Z.); (F.L.); (W.L.); (M.W.); (Y.W.); (Y.Z.)
| | - Jing Chen
- College of Life Science, Henan Agricultural University, Longzi Lake 15#, Zhengzhou 450046, China
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2
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Feng H, Lu XJ, Maji S, Liu L, Ustianenko D, Rudnick ND, Zhang C. Structure-based prediction and characterization of photo-crosslinking in native protein-RNA complexes. Nat Commun 2024; 15:2279. [PMID: 38480694 PMCID: PMC10937933 DOI: 10.1038/s41467-024-46429-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 02/26/2024] [Indexed: 03/17/2024] Open
Abstract
UV-crosslinking of protein and RNA in direct contacts has been widely used to study protein-RNA complexes while our understanding of the photo-crosslinking mechanisms remains poor. This knowledge gap is due to the challenge of precisely mapping the crosslink sites in protein and RNA simultaneously in their native sequence and structural contexts. Here we systematically analyze protein-RNA interactions and photo-crosslinking by bridging crosslinked nucleotides and amino acids mapped using different assays with protein-RNA complex structures. We developed a computational method PxR3D-map which reliably predicts crosslink sites using structural information characterizing protein-RNA interaction interfaces. Analysis of the informative features revealed that photo-crosslinking is facilitated by base stacking with not only aromatic residues, but also dipeptide bonds that involve glycine, and distinct mechanisms are utilized by different RNA-binding domains. Our work suggests protein-RNA photo-crosslinking is highly selective in the cellular environment, which can guide data interpretation and further technology development for UV-crosslinking-based assays.
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Affiliation(s)
- Huijuan Feng
- Department of Biostatistics and Computational Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
- Center for Motor Neuron Biology and Disease, Columbia University, New York, NY, 10032, USA
| | - Xiang-Jun Lu
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
| | - Suvrajit Maji
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
- Center for Motor Neuron Biology and Disease, Columbia University, New York, NY, 10032, USA
| | - Linxi Liu
- Department of Statistics, Columbia University, New York, NY, 10027, USA
- Department of Statistics, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Dmytro Ustianenko
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
- Center for Motor Neuron Biology and Disease, Columbia University, New York, NY, 10032, USA
| | - Noam D Rudnick
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
- Wilmer Eye Institute, Johns Hopkins University, Baltimore, MD, 21287, USA
| | - Chaolin Zhang
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA.
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA.
- Center for Motor Neuron Biology and Disease, Columbia University, New York, NY, 10032, USA.
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3
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Gu H, Yang J, Zhang J, Song Y, Zhang Y, Xu P, Zhu Y, Wang L, Zhang P, Li L, Chen D, Sun Q. PCBP2 maintains antiviral signaling homeostasis by regulating cGAS enzymatic activity via antagonizing its condensation. Nat Commun 2022; 13:1564. [PMID: 35322803 PMCID: PMC8943206 DOI: 10.1038/s41467-022-29266-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 03/07/2022] [Indexed: 02/07/2023] Open
Abstract
Cyclic GMP-AMP synthase (cGAS) plays a major role in detecting pathogenic DNA. It produces cyclic dinucleotide cGAMP, which subsequently binds to the adaptor protein STING and further triggers antiviral innate immune responses. However, the molecular mechanisms regulating cGAS enzyme activity remain largely unknown. Here, we characterize the cGAS-interacting protein Poly(rC)-binding protein 2 (PCBP2), which plays an important role in controlling cGAS enzyme activity, thereby mediating appropriate cGAS-STING signaling transduction. We find that PCBP2 overexpression reduces cGAS-STING antiviral signaling, whereas loss of PCBP2 significantly increases cGAS activity. Mechanistically, we show that PCBP2 negatively regulates anti-DNA viral signaling by specifically interacting with cGAS but not other components. Moreover, PCBP2 decreases cGAS enzyme activity by antagonizing cGAS condensation, thus ensuring the appropriate production of cGAMP and balancing cGAS-STING signal transduction. Collectively, our findings provide insight into how the cGAS-mediated antiviral signaling is regulated.
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Affiliation(s)
- Haiyan Gu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Datun Road, Chaoyang District, Beijing, 100101, China.,Institute of Biomedical Research, Yunnan University, Kunming, 650500, China.,Institute of Stem Cells and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.,School of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jing Yang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Datun Road, Chaoyang District, Beijing, 100101, China
| | - Jiayu Zhang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Datun Road, Chaoyang District, Beijing, 100101, China.,Institute of Stem Cells and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.,School of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ying Song
- Institute of Biomedical Research, Yunnan University, Kunming, 650500, China
| | - Yao Zhang
- Institute of Biomedical Research, Yunnan University, Kunming, 650500, China
| | - Pengfei Xu
- Institute of Biomedical Research, Yunnan University, Kunming, 650500, China
| | - Yuanxiang Zhu
- Institute of Biomedical Research, Yunnan University, Kunming, 650500, China
| | - Liangliang Wang
- Institute of Biomedical Research, Yunnan University, Kunming, 650500, China
| | - Pengfei Zhang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Datun Road, Chaoyang District, Beijing, 100101, China
| | - Lin Li
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Datun Road, Chaoyang District, Beijing, 100101, China.,Institute of Stem Cells and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
| | - Dahua Chen
- Institute of Biomedical Research, Yunnan University, Kunming, 650500, China.
| | - Qinmiao Sun
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Datun Road, Chaoyang District, Beijing, 100101, China. .,Institute of Stem Cells and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China. .,School of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
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4
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Zhao H, Wei Z, Shen G, Chen Y, Hao X, Li S, Wang R. Poly(rC)-binding proteins as pleiotropic regulators in hematopoiesis and hematological malignancy. Front Oncol 2022; 12:1045797. [PMID: 36452487 PMCID: PMC9701828 DOI: 10.3389/fonc.2022.1045797] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 10/26/2022] [Indexed: 11/16/2022] Open
Abstract
Poly(rC)-binding proteins (PCBPs), a defined subfamily of RNA binding proteins, are characterized by their high affinity and sequence-specific interaction with poly-cytosine (poly-C). The PCBP family comprises five members, including hnRNP K and PCBP1-4. These proteins share a relatively similar structure motif, with triple hnRNP K homology (KH) domains responsible for recognizing and combining C-rich regions of mRNA and single- and double-stranded DNA. Numerous studies have indicated that PCBPs play a prominent role in hematopoietic cell growth, differentiation, and tumorigenesis at multiple levels of regulation. Herein, we summarized the currently available literature regarding the structural and functional divergence of various PCBP family members. Furthermore, we focused on their roles in normal hematopoiesis, particularly in erythropoiesis. More importantly, we also discussed and highlighted their involvement in carcinogenesis, including leukemia and lymphoma, aiming to clarify the pleiotropic roles and molecular mechanisms in the hematopoietic compartment.
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Affiliation(s)
- Huijuan Zhao
- Henan International Joint Laboratory of Thrombosis and Hemostasis, Henan University of Science and Technology, Luoyang, China.,Basic Medical College, Henan University of Science and Technology, Luoyang, China
| | - Ziqing Wei
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Guomin Shen
- Henan International Joint Laboratory of Thrombosis and Hemostasis, Henan University of Science and Technology, Luoyang, China.,Basic Medical College, Henan University of Science and Technology, Luoyang, China
| | - Yixiang Chen
- Henan International Joint Laboratory of Thrombosis and Hemostasis, Henan University of Science and Technology, Luoyang, China.,Basic Medical College, Henan University of Science and Technology, Luoyang, China
| | - Xueqin Hao
- Basic Medical College, Henan University of Science and Technology, Luoyang, China
| | - Sanqiang Li
- Basic Medical College, Henan University of Science and Technology, Luoyang, China
| | - Rong Wang
- Department of Clinical Laboratory, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, China
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5
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Yuan C, Chen M, Cai X. Advances in poly(rC)-binding protein 2: Structure, molecular function, and roles in cancer. Biomed Pharmacother 2021; 139:111719. [PMID: 34233389 DOI: 10.1016/j.biopha.2021.111719] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 04/29/2021] [Accepted: 05/07/2021] [Indexed: 02/08/2023] Open
Abstract
Poly(rC)-binding protein 2 (PCBP2) is an RNA-binding protein that is characterized by its ability to interact with poly(C) with high affinity in a sequence-specific manner. PCBP2 contains three K homology domains, which are consensus RNA-binding domains that play a role in recognizing and combining with RNA and DNA. The specific structure and localization of PCBP2 lay the foundation for its multiple roles in transcriptional, posttranscriptional, and translational processes, even in iron metabolism. Numerous studies have indicated that PCBP2 expression is increased in many cancer types. PCBP2 is considered as an oncogene that promotes tumorigenesis, development of cancer cells, and metastasis. Here, we summarized the current evidence regarding PCBP2 in the proliferation, migration, invasion of cancer cells, and drug resistance, aiming to clarify the molecular mechanisms of PCBP2 in cancer. Results from this review suggest that an in-depth study of PCBP2 in cancer may provide novel biomarkers for prognostic or therapeutic purposes.
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Affiliation(s)
- Chendong Yuan
- Department of Vascular Surgery, Zhuji Affiliated Hospital of Shaoxing University, Zhuji, Zhejiang 311800, China.
| | - Mingxiang Chen
- Department of Cardiovascular surgery, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, Yubei 401120, China.
| | - Xiaolu Cai
- Department of Oncological Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China.
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6
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Patel A, Treffers EE, Meier M, Patel TR, Stetefeld J, Snijder EJ, Mark BL. Molecular characterization of the RNA-protein complex directing -2/-1 programmed ribosomal frameshifting during arterivirus replicase expression. J Biol Chem 2020; 295:17904-17921. [PMID: 33127640 PMCID: PMC7939443 DOI: 10.1074/jbc.ra120.016105] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/22/2020] [Indexed: 12/12/2022] Open
Abstract
Programmed ribosomal frameshifting (PRF) is a mechanism used by arteriviruses like porcine reproductive and respiratory syndrome virus (PRRSV) to generate multiple proteins from overlapping reading frames within its RNA genome. PRRSV employs -1 PRF directed by RNA secondary and tertiary structures within its viral genome (canonical PRF), as well as a noncanonical -1 and -2 PRF that are stimulated by the interactions of PRRSV nonstructural protein 1β (nsp1β) and host protein poly(C)-binding protein (PCBP) 1 or 2 with the viral genome. Together, nsp1β and one of the PCBPs act as transactivators that bind a C-rich motif near the shift site to stimulate -1 and -2 PRF, thereby enabling the ribosome to generate two frameshift products that are implicated in viral immune evasion. How nsp1β and PCBP associate with the viral RNA genome remains unclear. Here, we describe the purification of the nsp1β:PCBP2:viral RNA complex on a scale sufficient for structural analysis using small-angle X-ray scattering and stochiometric analysis by analytical ultracentrifugation. The proteins associate with the RNA C-rich motif as a 1:1:1 complex. The monomeric form of nsp1β within the complex differs from previously reported homodimer identified by X-ray crystallography. Functional analysis of the complex via mutational analysis combined with RNA-binding assays and cell-based frameshifting reporter assays reveal a number of key residues within nsp1β and PCBP2 that are involved in complex formation and function. Our results suggest that nsp1β and PCBP2 both interact directly with viral RNA during formation of the complex to coordinate this unusual PRF mechanism.
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Affiliation(s)
- Ankoor Patel
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Emmely E Treffers
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Markus Meier
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Trushar R Patel
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Jörg Stetefeld
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Eric J Snijder
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Brian L Mark
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada.
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7
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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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8
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Comparative structural analyses and nucleotide-binding characterization of the four KH domains of FUBP1. Sci Rep 2020; 10:13459. [PMID: 32778776 PMCID: PMC7417555 DOI: 10.1038/s41598-020-69832-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 07/13/2020] [Indexed: 12/18/2022] Open
Abstract
The FUBP1-FUSE complex is an essential component of a transcription molecular machinery that is necessary for tight regulation of expression of many key genes including c-Myc and p21. FUBP1 utilizes its four articulated KH modules, which function cooperatively, for FUSE nucleotide binding. To understand molecular mechanisms fundamental to the intermolecular interaction, we present a set of crystal structures, as well ssDNA-binding characterization of FUBP1 KH domains. All KH1-4 motifs were highly topologically conserved, and were able to interact with FUSE individually and independently. Nevertheless, differences in nucleotide binding properties among the four KH domains were evident, including higher nucleotide-binding potency for KH3 as well as diverse nucleotide sequence preferences. Variations in amino acid compositions at one side of the binding cleft responsible for nucleobase resulted in diverse shapes and electrostatic charge interaction, which might feasibly be a contributing factor for different nucleotide-binding propensities among KH1-4. Nonetheless, conservation of structure and nucleotide-binding property in all four KH motifs is essential for the cooperativity of multi KH modules present in FUBP1 towards nanomolar affinity for FUSE interaction. Comprehensive structural comparison and ssDNA binding characteristics of all four KH domains presented here provide molecular insights at a fundamental level that might be beneficial for elucidating the mechanisms of the FUBP1-FUSE interaction.
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9
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Shishkin SS, Kovalev LI, Pashintseva NV, Kovaleva MA, Lisitskaya K. Heterogeneous Nuclear Ribonucleoproteins Involved in the Functioning of Telomeres in Malignant Cells. Int J Mol Sci 2019; 20:E745. [PMID: 30744200 PMCID: PMC6387250 DOI: 10.3390/ijms20030745] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 01/31/2019] [Accepted: 02/04/2019] [Indexed: 12/12/2022] Open
Abstract
Heterogeneous nuclear ribonucleoproteins (hnRNPs) are structurally and functionally distinct proteins containing specific domains and motifs that enable the proteins to bind certain nucleotide sequences, particularly those found in human telomeres. In human malignant cells (HMCs), hnRNP-A1-the most studied hnRNP-is an abundant multifunctional protein that interacts with telomeric DNA and affects telomerase function. In addition, it is believed that other hnRNPs in HMCs may also be involved in the maintenance of telomere length. Accordingly, these proteins are considered possible participants in the processes associated with HMC immortalization. In our review, we discuss the results of studies on different hnRNPs that may be crucial to solving molecular oncological problems and relevant to further investigations of these proteins in HMCs.
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Affiliation(s)
- Sergey S Shishkin
- Laboratory of Biomedical Research, Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospekt, 33, bld. 2, 119071 Moscow, Russia.
| | - Leonid I Kovalev
- Laboratory of Biomedical Research, Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospekt, 33, bld. 2, 119071 Moscow, Russia.
| | - Natalya V Pashintseva
- Laboratory of Biomedical Research, Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospekt, 33, bld. 2, 119071 Moscow, Russia.
| | - Marina A Kovaleva
- Laboratory of Biomedical Research, Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospekt, 33, bld. 2, 119071 Moscow, Russia.
| | - Ksenia Lisitskaya
- Laboratory of Biomedical Research, Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospekt, 33, bld. 2, 119071 Moscow, Russia.
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10
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High expression of PCBP2 is associated with progression and poor prognosis in patients with glioblastoma. Biomed Pharmacother 2017; 94:659-665. [PMID: 28787701 DOI: 10.1016/j.biopha.2017.07.103] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 07/20/2017] [Accepted: 07/20/2017] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Poly(C)-binding protein 2 (PCBP2) has been found to have ambiguous functions in a variety of cancers. However, the specific biological function of PCBP2 and its mechanism in glioblastoma remain unclear. We investigated the expression of PCBP2 in 143 glioblastoma specimens to explore the linkage between PCBP2 expression and clinicopathological parameters as well as clinical significance. Furthermore, the underlying mechanisms of PCBP2 on glioblastoma progression were discussed in vitro. METHODS The transcriptional and translational levels of PCBP2 in 143 glioblastoma patients were detected by quantitative Real-time PCR (qRT-PCR) and western blot. The association of prognostic outcomes and PCBP2 expression was evaluated using Kaplan-Meier analysis. RESULTS PCBP2 expression was markedly increased in higher stages of glioblastoma compared with those in lower stages (P<0.001). High expression of PCBP2 was associated with higher clinical stage and histological grade (P<0.001). Further research suggested that PCBP2 upregulation was connected with poorer prognosis in patients with glioblastoma (P<0.001). Moreover, PCBP2 knockdown could significantly decreased the colony formation and invasion capability of glioblastoma cells (P<0.01). Conversely, PCBP2 overexpression could increase the colony formation and invasion capability (P<0.01). CONCLUSION These findings indicated that PCBP2 might be a novel prognostic biomarker and a potential therapeutic target of glioblastoma.
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11
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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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12
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Alba JJ, Sadurní A, Gargallo R. Nucleic Acid i-Motif Structures in Analytical Chemistry. Crit Rev Anal Chem 2016; 46:443-54. [DOI: 10.1080/10408347.2016.1143347] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Joan Josep Alba
- Department of Analytical Chemistry, University of Barcelona, Barcelona, Spain
| | - Anna Sadurní
- Department of Analytical Chemistry, University of Barcelona, Barcelona, Spain
| | - Raimundo Gargallo
- Department of Analytical Chemistry, University of Barcelona, Barcelona, Spain
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13
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Wagener R, Aukema SM, Schlesner M, Haake A, Burkhardt B, Claviez A, Drexler HG, Hummel M, Kreuz M, Loeffler M, Rosolowski M, López C, Möller P, Richter J, Rohde M, Betts MJ, Russell RB, Bernhart SH, Hoffmann S, Rosenstiel P, Schilhabel M, Szczepanowski M, Trümper L, Klapper W, Siebert R. ThePCBP1gene encoding poly(rc) binding protein i is recurrently mutated in Burkitt lymphoma. Genes Chromosomes Cancer 2015; 54:555-64. [DOI: 10.1002/gcc.22268] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 05/11/2015] [Indexed: 12/19/2022] Open
Affiliation(s)
- Rabea Wagener
- Institute of Human Genetics, Christian-Albrechts-University Kiel and University Hospital Schleswig-Holstein; Campus Kiel Kiel Germany
| | - Sietse M. Aukema
- Institute of Human Genetics, Christian-Albrechts-University Kiel and University Hospital Schleswig-Holstein; Campus Kiel Kiel Germany
| | - Matthias Schlesner
- Deutsches Krebsforschungszentrum Heidelberg (DKFZ), Division Theoretical Bioinformatics; Heidelberg Germany
| | - Andrea Haake
- Institute of Human Genetics, Christian-Albrechts-University Kiel and University Hospital Schleswig-Holstein; Campus Kiel Kiel Germany
| | - Birgit Burkhardt
- Non-Hodgkin Lymphoma Berlin-Frankfurt-Münster Group Study Center, Department of Pediatric Hematology and Oncology, University Children's Hospital; Münster Germany
| | - Alexander Claviez
- Department of Pediatrics; University Hospital Schleswig-Holstein Campus Kiel/Christian-Albrechts University; Kiel Germany
| | - Hans G. Drexler
- Leibniz-Institute DSMZ- German Collection of Microorganisms and Cell Cultures GmbH; Braunschweig Germany
| | - Michael Hummel
- Institute of Pathology, Campus Benjamin Franklin, Charité-Universitätsmedizin; Berlin Germany
| | - Markus Kreuz
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig; Germany
| | - Markus Loeffler
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig; Germany
| | - Maciej Rosolowski
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig; Germany
| | - Cristina López
- Institute of Human Genetics, Christian-Albrechts-University Kiel and University Hospital Schleswig-Holstein; Campus Kiel Kiel Germany
| | - Peter Möller
- Institute of Pathology, Universitätsklinikum Ulm; Ulm Germany
| | - Julia Richter
- Institute of Human Genetics, Christian-Albrechts-University Kiel and University Hospital Schleswig-Holstein; Campus Kiel Kiel Germany
| | - Marius Rohde
- Department of Pediatric Hematology and Oncology; Justus Liebig University; Giessen Germany
| | - Matthew J. Betts
- Cell Networks, Bioquant, University of Heidelberg; Heidelberg Germany
| | - Robert B. Russell
- Cell Networks, Bioquant, University of Heidelberg; Heidelberg Germany
| | - Stephan H. Bernhart
- Transcriptome Bioinformatics, LIFE Research Center for Civilization Diseases, University of Leipzig; Leipzig Germany
| | - Steve Hoffmann
- Transcriptome Bioinformatics, LIFE Research Center for Civilization Diseases, University of Leipzig; Leipzig Germany
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, University Hospital Schleswig-Holstein Campus Kiel/Christian-Albrechts University Kiel; Kiel Germany
| | - Markus Schilhabel
- Institute of Clinical Molecular Biology, University Hospital Schleswig-Holstein Campus Kiel/Christian-Albrechts University Kiel; Kiel Germany
| | - Monika Szczepanowski
- Institute of Hematopathology, University Hospital Schleswig-Holstein Campus Kiel/Christian-Albrechts University Kiel; Germany
| | - Lorenz Trümper
- Department of Hematology and Oncology; Georg-August University of Göttingen; Germany
| | - Wolfram Klapper
- Institute of Hematopathology, University Hospital Schleswig-Holstein Campus Kiel/Christian-Albrechts University Kiel; Germany
| | - Reiner Siebert
- Institute of Human Genetics, Christian-Albrechts-University Kiel and University Hospital Schleswig-Holstein; Campus Kiel Kiel Germany
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14
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Školáková P, Foldynová-Trantírková S, Bednářová K, Fiala R, Vorlíčková M, Trantírek L. Unique C. elegans telomeric overhang structures reveal the evolutionarily conserved properties of telomeric DNA. Nucleic Acids Res 2015; 43:4733-45. [PMID: 25855805 PMCID: PMC4482068 DOI: 10.1093/nar/gkv296] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2015] [Accepted: 03/25/2015] [Indexed: 11/16/2022] Open
Abstract
There are two basic mechanisms that are associated with the maintenance of the telomere length, which endows cancer cells with unlimited proliferative potential. One mechanism, referred to as alternative lengthening of telomeres (ALT), accounts for approximately 10–15% of all human cancers. Tumours engaged in the ALT pathway are characterised by the presence of the single stranded 5′-C-rich telomeric overhang (C-overhang). This recently identified hallmark of ALT cancers distinguishes them from healthy tissues and renders the C-overhang as a clear target for anticancer therapy. We analysed structures of the 5′-C-rich and 3′-G-rich telomeric overhangs from human and Caenorhabditis elegans, the recently established multicellular in vivo model of ALT tumours. We show that the telomeric DNA from C. elegans and humans forms fundamentally different secondary structures. The unique structural characteristics of C. elegans telomeric DNA that are distinct not only from those of humans but also from those of other multicellular eukaryotes allowed us to identify evolutionarily conserved properties of telomeric DNA. Differences in structural organisation of the telomeric DNA between the C. elegans and human impose limitations on the use of the C. elegans as an ALT tumour model.
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Affiliation(s)
- Petra Školáková
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska, 135, 612 65 Brno, Czech Republic
| | - Silvie Foldynová-Trantírková
- Central European Institute of Technology, Masaryk University, Kamenice 735/5, 625 00 Brno, Czech Republic Institute of Parasitology, Academy of Sciences of the Czech Republic, Branisovska, 31, 375 05 Ceske Budejovice, Czech Republic
| | - Klára Bednářová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska, 135, 612 65 Brno, Czech Republic Central European Institute of Technology, Masaryk University, Kamenice 735/5, 625 00 Brno, Czech Republic
| | - Radovan Fiala
- Central European Institute of Technology, Masaryk University, Kamenice 735/5, 625 00 Brno, Czech Republic
| | - Michaela Vorlíčková
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska, 135, 612 65 Brno, Czech Republic Central European Institute of Technology, Masaryk University, Kamenice 735/5, 625 00 Brno, Czech Republic
| | - Lukáš Trantírek
- Central European Institute of Technology, Masaryk University, Kamenice 735/5, 625 00 Brno, Czech Republic
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15
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Dickey TH, Altschuler SE, Wuttke DS. Single-stranded DNA-binding proteins: multiple domains for multiple functions. Structure 2014; 21:1074-84. [PMID: 23823326 DOI: 10.1016/j.str.2013.05.013] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 05/15/2013] [Accepted: 05/20/2013] [Indexed: 10/26/2022]
Abstract
The recognition of single-stranded DNA (ssDNA) is integral to myriad cellular functions. In eukaryotes, ssDNA is present stably at the ends of chromosomes and at some promoter elements. Furthermore, it is formed transiently by several cellular processes including telomere synthesis, transcription, and DNA replication, recombination, and repair. To coordinate these diverse activities, a variety of proteins have evolved to bind ssDNA in a manner specific to their function. Here, we review the recognition of ssDNA through the analysis of high-resolution structures of proteins in complex with ssDNA. This functionally diverse set of proteins arises from a limited set of structural motifs that can be modified and arranged to achieve distinct activities, including a range of ligand specificities. We also investigate the ways in which these domains interact in the context of large multidomain proteins/complexes. These comparisons reveal the structural features that define the range of functions exhibited by these proteins.
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Affiliation(s)
- Thayne H Dickey
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
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16
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Benabou S, Aviñó A, Eritja R, González C, Gargallo R. Fundamental aspects of the nucleic acid i-motif structures. RSC Adv 2014. [DOI: 10.1039/c4ra02129k] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The latest research on fundamental aspects of i-motif structures is reviewed with special attention to their hypothetical rolein vivo.
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Affiliation(s)
- S. Benabou
- Department of Analytical Chemistry
- University of Barcelona
- E-08028 Barcelona, Spain
| | - A. Aviñó
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC)
- CIBER-BBN Networking Centre on Bioengineering
- Biomaterials and Nanomedicine
- E-08034 Barcelona, Spain
| | - R. Eritja
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC)
- CIBER-BBN Networking Centre on Bioengineering
- Biomaterials and Nanomedicine
- E-08034 Barcelona, Spain
| | - C. González
- Institute of Physical Chemistry “Rocasolano”
- CSIC
- E-28006 Madrid, Spain
| | - R. Gargallo
- Department of Analytical Chemistry
- University of Barcelona
- E-08028 Barcelona, Spain
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17
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Insights into the biomedical effects of carboxylated single-wall carbon nanotubes on telomerase and telomeres. Nat Commun 2012; 3:1074. [DOI: 10.1038/ncomms2091] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Accepted: 08/24/2012] [Indexed: 02/06/2023] Open
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18
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Hollingworth D, Candel AM, Nicastro G, Martin SR, Briata P, Gherzi R, Ramos A. KH domains with impaired nucleic acid binding as a tool for functional analysis. Nucleic Acids Res 2012; 40:6873-86. [PMID: 22547390 PMCID: PMC3413153 DOI: 10.1093/nar/gks368] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Revised: 04/05/2012] [Accepted: 04/11/2012] [Indexed: 02/07/2023] Open
Abstract
In eukaryotes, RNA-binding proteins that contain multiple K homology (KH) domains play a key role in coordinating the different steps of RNA synthesis, metabolism and localization. Understanding how the different KH modules participate in the recognition of the RNA targets is necessary to dissect the way these proteins operate. We have designed a KH mutant with impaired RNA-binding capability for general use in exploring the role of individual KH domains in the combinatorial functional recognition of RNA targets. A double mutation in the hallmark GxxG loop (GxxG-to-GDDG) impairs nucleic acid binding without compromising the stability of the domain. We analysed the impact of the GDDG mutations in individual KH domains on the functional properties of KSRP as a prototype of multiple KH domain-containing proteins. We show how the GDDG mutant can be used to directly link biophysical information on the sequence specificity of the different KH domains of KSRP and their role in mRNA recognition and decay. This work defines a general molecular biology tool for the investigation of the function of individual KH domains in nucleic acid binding proteins.
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Affiliation(s)
- David Hollingworth
- Molecular Structure Division, Physical Biochemistry Division, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK and Gene Expression Regulation Laboratory, IRCCS AOU San Martino – IST, Largo R. Benzi 10, Genova, Italy
| | - Adela M. Candel
- Molecular Structure Division, Physical Biochemistry Division, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK and Gene Expression Regulation Laboratory, IRCCS AOU San Martino – IST, Largo R. Benzi 10, Genova, Italy
| | - Giuseppe Nicastro
- Molecular Structure Division, Physical Biochemistry Division, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK and Gene Expression Regulation Laboratory, IRCCS AOU San Martino – IST, Largo R. Benzi 10, Genova, Italy
| | - Stephen R. Martin
- Molecular Structure Division, Physical Biochemistry Division, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK and Gene Expression Regulation Laboratory, IRCCS AOU San Martino – IST, Largo R. Benzi 10, Genova, Italy
| | - Paola Briata
- Molecular Structure Division, Physical Biochemistry Division, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK and Gene Expression Regulation Laboratory, IRCCS AOU San Martino – IST, Largo R. Benzi 10, Genova, Italy
| | - Roberto Gherzi
- Molecular Structure Division, Physical Biochemistry Division, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK and Gene Expression Regulation Laboratory, IRCCS AOU San Martino – IST, Largo R. Benzi 10, Genova, Italy
| | - Andres Ramos
- Molecular Structure Division, Physical Biochemistry Division, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK and Gene Expression Regulation Laboratory, IRCCS AOU San Martino – IST, Largo R. Benzi 10, Genova, Italy
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19
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Palusa S, Ndaluka C, Bowen RA, Wilusz CJ, Wilusz J. The 3' untranslated region of the rabies virus glycoprotein mRNA specifically interacts with cellular PCBP2 protein and promotes transcript stability. PLoS One 2012; 7:e33561. [PMID: 22438951 PMCID: PMC3306424 DOI: 10.1371/journal.pone.0033561] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2011] [Accepted: 02/14/2012] [Indexed: 12/25/2022] Open
Abstract
Viral polymerase entry and pausing at intergenic junctions is predicted to lead to a defined polarity in the levels of rhabdovirus gene expression. Interestingly, we observed that the rabies virus glycoprotein mRNA is differentially over-expressed based on this model relative to other transcripts during infection of 293T cells. During infection, the rabies virus glycoprotein mRNA also selectively interacts with the cellular poly(rC)-binding protein 2 (PCBP2), a factor known to influence mRNA stability. Reporter assays performed both in electroporated cells and in a cell-free RNA decay system indicate that the conserved portion of the 3' UTR of the rabies virus glycoprotein mRNA contains an RNA stability element. PCBP2 specifically interacts with reporter transcripts containing this 72 base 3' UTR sequence. Furthermore, the PCBP2 interaction is directly associated with the stability of reporter transcripts. Therefore, we conclude that PCBP2 specifically and selectively interacts with the rabies virus glycoprotein mRNA and that this interaction may contribute to the post-transcriptional regulation of glycoprotein expression.
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Affiliation(s)
- Saiprasad Palusa
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Christina Ndaluka
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
- Department of Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - Richard A. Bowen
- Department of Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - Carol J. Wilusz
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Jeffrey Wilusz
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
- * E-mail:
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20
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Yoga YMK, Traore DAK, Sidiqi M, Szeto C, Pendini NR, Barker A, Leedman PJ, Wilce JA, Wilce MCJ. Contribution of the first K-homology domain of poly(C)-binding protein 1 to its affinity and specificity for C-rich oligonucleotides. Nucleic Acids Res 2012; 40:5101-14. [PMID: 22344691 PMCID: PMC3367169 DOI: 10.1093/nar/gks058] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Poly-C-binding proteins are triple KH (hnRNP K homology) domain proteins with specificity for single stranded C-rich RNA and DNA. They play diverse roles in the regulation of protein expression at both transcriptional and translational levels. Here, we analyse the contributions of individual αCP1 KH domains to binding C-rich oligonucleotides using biophysical and structural methods. Using surface plasmon resonance (SPR), we demonstrate that KH1 makes the most stable interactions with both RNA and DNA, KH3 binds with intermediate affinity and KH2 only interacts detectibly with DNA. The crystal structure of KH1 bound to a 5′-CCCTCCCT-3′ DNA sequence shows a 2:1 protein:DNA stoichiometry and demonstrates a molecular arrangement of KH domains bound to immediately adjacent oligonucleotide target sites. SPR experiments, with a series of poly-C-sequences reveals that cytosine is preferred at all four positions in the oligonucleotide binding cleft and that a C-tetrad binds KH1 with 10 times higher affinity than a C-triplet. The basis for this high affinity interaction is finally detailed with the structure determination of a KH1.W.C54S mutant bound to 5′-ACCCCA-3′ DNA sequence. Together, these data establish the lead role of KH1 in oligonucleotide binding by αCP1 and reveal the molecular basis of its specificity for a C-rich tetrad.
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Affiliation(s)
- Yano M K Yoga
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC Australia
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21
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Proepper C, Steinestel K, Schmeisser MJ, Heinrich J, Steinestel J, Bockmann J, Liebau S, Boeckers TM. Heterogeneous nuclear ribonucleoprotein k interacts with Abi-1 at postsynaptic sites and modulates dendritic spine morphology. PLoS One 2011; 6:e27045. [PMID: 22102872 PMCID: PMC3216941 DOI: 10.1371/journal.pone.0027045] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2011] [Accepted: 10/09/2011] [Indexed: 12/31/2022] Open
Abstract
Background Abelson-interacting protein 1 (Abi-1) plays an important role for dendritic branching and synapse formation in the central nervous system. It is localized at the postsynaptic density (PSD) and rapidly translocates to the nucleus upon synaptic stimulation. At PSDs Abi-1 is in a complex with several other proteins including WASP/WAVE or cortactin thereby regulating the actin cytoskeleton via the Arp 2/3 complex. Principal Findings We identified heterogeneous nuclear ribonucleoprotein K (hnRNPK), a 65 kDa ssDNA/RNA-binding-protein that is involved in multiple intracellular signaling cascades, as a binding partner of Abi-1 at postsynaptic sites. The interaction with the Abi-1 SH3 domain is mediated by the hnRNPK-interaction (KI) domain. We further show that during brain development, hnRNPK expression becomes more and more restricted to granule cells of the cerebellum and hippocampal neurons where it localizes in the cell nucleus as well as in the spine/dendritic compartment. The downregulation of hnRNPK in cultured hippocampal neurons by RNAi results in an enlarged dendritic tree and a significant increase in filopodia formation. This is accompanied by a decrease in the number of mature synapses. Both effects therefore mimic the neuronal morphology after downregulation of Abi-1 mRNA in neurons. Conclusions Our findings demonstrate a novel interplay between hnRNPK and Abi-1 in the nucleus and at synaptic sites and show obvious similarities regarding both protein knockdown phenotypes. This indicates that hnRNPK and Abi-1 act synergistic in a multiprotein complex that regulates the crucial balance between filopodia formation and synaptic maturation in neurons.
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Affiliation(s)
| | - Konrad Steinestel
- Institute for Anatomy and Cell Biology, Ulm University, Ulm, Germany
- Department of Pathology, BWK Hospital Ulm, Ulm, Germany
| | | | - Jutta Heinrich
- Institute for Anatomy and Cell Biology, Ulm University, Ulm, Germany
| | - Julie Steinestel
- Institute for Anatomy and Cell Biology, Ulm University, Ulm, Germany
| | - Juergen Bockmann
- Institute for Anatomy and Cell Biology, Ulm University, Ulm, Germany
| | - Stefan Liebau
- Institute for Anatomy and Cell Biology, Ulm University, Ulm, Germany
- * E-mail: (TMB); (SL)
| | - Tobias M. Boeckers
- Institute for Anatomy and Cell Biology, Ulm University, Ulm, Germany
- * E-mail: (TMB); (SL)
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22
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Yoga YMK, Traore DAK, Wilce JA, Wilce MCJ. Mutation and crystallization of the first KH domain of human polycytosine-binding protein 1 (PCBP1) in complex with DNA. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:1257-61. [PMID: 22102042 PMCID: PMC3212377 DOI: 10.1107/s1744309111028004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2011] [Accepted: 07/12/2011] [Indexed: 11/11/2022]
Abstract
Polycytosine-binding proteins (PCBPs) are triple KH-domain proteins that play an important role in the regulation of translation of eukaryotic mRNA. They are also utilized by viral RNA and have been shown to interact with ssDNA. Underlying their function is the specific recognition of C-rich nucleotides by their KH domains. However, the structural basis of this recognition is only partially understood. Here, the preparation of a His-tagged KH domain is described, representing the first domain of PCBP1 that incorporates a C54S mutation as well as the addition of a C-terminal tryptophan. This construct has facilitated the preparation of highly diffracting crystals in complex with C-rich DNA (sequence ACCCCA). Crystals of the KH1-DNA complex were grown using the hanging-drop vapour-diffusion method in 0.1 M phosphate-citrate pH 4.2, 40%(v/v) PEG 300. X-ray diffraction data were collected to 1.77 Å resolution and the diffraction was consistent with space group P2(1), with unit-cell parameters a = 38.59, b = 111.88, c = 43.42 Å, α = γ = 90.0, β = 93.37°. The structure of the KH1-DNA complex will further our insight into the basis of cytosine specificity by PCBPs.
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Affiliation(s)
- Yano M. K. Yoga
- Department of Biochemistry and Molecular Biology, Monash University, VIC 3800, Australia
| | - Daouda A. K. Traore
- Department of Biochemistry and Molecular Biology, Monash University, VIC 3800, Australia
| | - Jacqueline A. Wilce
- Department of Biochemistry and Molecular Biology, Monash University, VIC 3800, Australia
| | - Matthew C. J. Wilce
- Department of Biochemistry and Molecular Biology, Monash University, VIC 3800, Australia
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23
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Uribe DJ, Guo K, Shin YJ, Sun D. Heterogeneous nuclear ribonucleoprotein K and nucleolin as transcriptional activators of the vascular endothelial growth factor promoter through interaction with secondary DNA structures. Biochemistry 2011; 50:3796-806. [PMID: 21466159 PMCID: PMC3119528 DOI: 10.1021/bi101633b] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The human vascular endothelial growth factor (VEGF) promoter contains a polypurine/polypyrimidine (pPu/pPy) tract that is known to play a critical role in its transcriptional regulation. This pPu/pPy tract undergoes a conformational transition between B-DNA, single-stranded DNA, and atypical secondary DNA structures such as G-quadruplexes and i-motifs. We studied the interaction of the cytosine-rich (C-rich) and guanine-rich (G-rich) strands of this tract with transcription factors heterogeneous nuclear ribonucleoprotein (hnRNP) K and nucleolin, respectively, both in vitro and in vivo and their potential role in the transcriptional control of VEGF. Using chromatin immunoprecipitation (ChIP) assay for our in vivo studies and electrophoretic mobility shift assay (EMSA) for our in vitro studies, we demonstrated that both nucleolin and hnRNP K bind selectively to the G- and C-rich sequences, respectively, in the pPu/pPy tract of the VEGF promoter. The small interfering RNA (siRNA)-mediated silencing of either nucleolin or hnRNP K resulted in the down-regulation of basal VEGF gene, suggesting that they act as activators of VEGF transcription. Taken together, the identification of transcription factors that can recognize and bind to atypical DNA structures within the pPu/pPy tract will provide new insight into mechanisms of transcriptional regulation of the VEGF gene.
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Affiliation(s)
- Diana J. Uribe
- Cancer Biology Graduate Interdisciplinary Program, University of Arizona, Tucson, AZ, 85721
| | - Kexiao Guo
- Pharmacology and Toxicology Department, University of Arizona, Tucson, AZ, 85721
| | - Yoon-Joo Shin
- Pharmacology and Toxicology Department, University of Arizona, Tucson, AZ, 85721
| | - Daekyu Sun
- Pharmacology and Toxicology Department, University of Arizona, Tucson, AZ, 85721
- Cancer Biology Graduate Interdisciplinary Program, University of Arizona, Tucson, AZ, 85721
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Iron chaperones for mitochondrial Fe-S cluster biosynthesis and ferritin iron storage. Curr Opin Chem Biol 2011; 15:312-8. [PMID: 21288761 DOI: 10.1016/j.cbpa.2011.01.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2010] [Revised: 12/17/2010] [Accepted: 01/03/2011] [Indexed: 10/18/2022]
Abstract
Protein controlled iron homeostasis is essential for maintaining appropriate levels and availability of metal within cells. Recently, two iron chaperones have been discovered that direct metal within two unique pathways: (1) mitochondrial iron-sulfur (Fe-S) cluster assembly and (2) within the ferritin iron storage system. Although structural and functional details describing how these iron chaperones operate are emerging, both share similar iron binding affinities and metal-ligand site structures that enable them to bind and release Fe2+ to specific protein partners. Molecular details related to iron binding and delivery by these chaperones will be explored within this review.
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25
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Qiu ZR, Schwer B, Shuman S. Determinants of Nam8-dependent splicing of meiotic pre-mRNAs. Nucleic Acids Res 2011; 39:3427-45. [PMID: 21208980 PMCID: PMC3082912 DOI: 10.1093/nar/gkq1328] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Nam8, a component of yeast U1 snRNP, is optional for mitotic growth but required during meiosis, because Nam8 collaborates with Mer1 to promote splicing of essential meiotic mRNAs AMA1, MER2 and MER3. Here, we identify SPO22 and PCH2 as novel targets of Nam8-dependent meiotic splicing. Whereas SPO22 splicing is co-dependent on Mer1, PCH2 is not. The SPO22 intron has a non-consensus 5′ splice site (5′SS) that dictates its Nam8/Mer1-dependence. SPO22 splicing relies on Mer1 recognition, via its KH domain, of an intronic enhancer 5′-AYACCCUY. Mutagenesis of KH and the enhancer highlights Arg214 and Gln243 and the CCC triplet as essential for Mer1 activity. The Nam8-dependent PCH2 pre-mRNA has a consensus 5′SS and lacks a Mer1 enhancer. For PCH2, a long 5′ exon and a non-consensus intron branchpoint dictate Nam8-dependence. Our results implicate Nam8 in two distinct meiotic splicing regulons. Nam8 is composed of three RRM domains, flanked by N-terminal leader and C-terminal tail segments. The leader, tail and RRM1 are dispensable for splicing meiotic targets and unnecessary for vegetative Nam8 function in multiple synthetic lethal genetic backgrounds. Nam8 activity is enfeebled by alanine mutations in the putative RNA binding sites of the RRM2 and RRM3 domains.
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Affiliation(s)
- Zhicheng R Qiu
- Sloan-Kettering Institute, Weill Cornell Medical College, New York, NY 10065, USA
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26
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Du Z, Fenn S, Tjhen R, James TL. Structure of a construct of a human poly(C)-binding protein containing the first and second KH domains reveals insights into its regulatory mechanisms. J Biol Chem 2008; 283:28757-66. [PMID: 18701464 PMCID: PMC2568903 DOI: 10.1074/jbc.m803046200] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2008] [Revised: 08/01/2008] [Indexed: 11/06/2022] Open
Abstract
Poly(C)-binding proteins (PCBPs) are important regulatory proteins that contain three KH (hnRNP K homology) domains. Binding poly(C) D/RNA sequences via KH domains is essential for multiple PCBP functions. To reveal the basis for PCBP-D/RNA interactions and function, we determined the structure of a construct containing the first two domains (KH1-KH2) of human PCBP2 by NMR. KH1 and KH2 form an intramolecular pseudodimer. The large hydrophobic dimerization surface of each KH domain is on the side opposite the D/RNA binding interface. Chemical shift mapping indicates both domains bind poly(C) DNA motifs without disrupting the KH1-KH2 interaction. Spectral comparison of KH1-KH2, KH3, and full-length PCBP2 constructs suggests that the KH1-KH2 pseudodimer forms, but KH3 does not interact with other parts of the protein. From NMR studies and modeling, we propose possible modes of cooperative binding tandem poly(C) motifs by the KH domains. D/RNA binding may induce pseudodimer dissociation or stabilize dissociated KH1 and KH2, making protein interaction surfaces available to PCBP-binding partners. This conformational change may represent a regulatory mechanism linking D/RNA binding to PCBP functions.
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Affiliation(s)
- Zhihua Du
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, USA
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27
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Zell R, Ihle Y, Effenberger M, Seitz S, Wutzler P, Görlach M. Interaction of poly(rC)-binding protein 2 domains KH1 and KH3 with coxsackievirus RNA. Biochem Biophys Res Commun 2008; 377:500-503. [PMID: 18929541 DOI: 10.1016/j.bbrc.2008.09.156] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2008] [Accepted: 09/30/2008] [Indexed: 11/19/2022]
Abstract
Recombinant hnRNP K-homology (KH) domains 1 and 3 of the poly(rC)-binding protein (PCBP) 2 were purified and assayed for interaction with coxsackievirus B3 RNA in electrophoretic mobility shift assays using in vitro transcribed RNAs which represent signal structures of the 5'-nontranslated region. KH domains 1 and 3 interact with the extended cloverleaf RNA and domain IV RNA of the internal ribosome entry site (IRES). KH1 but not KH3 interacts with subdomain IV/C RNA, whereas KH3 interacts with subdomain IV/B. All in vitro results are consistent with yeast three-hybrid experiments performed in parallel. The data demonstrate interaction of isolated PCBP2 KH1 and KH3 domains to four distinct target sites within the 5'-nontranslated region of the CVB3 genomic RNA.
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Affiliation(s)
- Roland Zell
- Institute for Virology and Antiviral Therapy, Friedrich Schiller University, Hans-Knöll-Str. 2, D-07745 Jena, Germany.
| | - Yvonne Ihle
- Biomolecular NMR Spectroscopy, Leibniz Institute for Age Research, Fritz Lipmann Institute, Beutenbergstr. 11, D-07745 Jena, Germany
| | - Madlen Effenberger
- Institute for Virology and Antiviral Therapy, Friedrich Schiller University, Hans-Knöll-Str. 2, D-07745 Jena, Germany
| | - Simone Seitz
- Institute for Virology and Antiviral Therapy, Friedrich Schiller University, Hans-Knöll-Str. 2, D-07745 Jena, Germany
| | - Peter Wutzler
- Institute for Virology and Antiviral Therapy, Friedrich Schiller University, Hans-Knöll-Str. 2, D-07745 Jena, Germany
| | - Matthias Görlach
- Biomolecular NMR Spectroscopy, Leibniz Institute for Age Research, Fritz Lipmann Institute, Beutenbergstr. 11, D-07745 Jena, Germany
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28
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Sean P, Nguyen JHC, Semler BL. The linker domain of poly(rC) binding protein 2 is a major determinant in poliovirus cap-independent translation. Virology 2008; 378:243-53. [PMID: 18656221 DOI: 10.1016/j.virol.2008.05.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2008] [Revised: 02/11/2008] [Accepted: 05/10/2008] [Indexed: 11/19/2022]
Abstract
Poliovirus, a member of the enterovirus genus in the family Picornaviridae, is the causative agent of poliomyelitis. Translation of the viral genome is mediated through an internal ribosomal entry site (IRES) encoded within the 5' noncoding region (5' NCR). IRES elements are highly structured RNA sequences that facilitate the recruitment of ribosomes for translation. Previous studies have shown that binding of a cellular protein, poly(rC) binding protein 2 (PCBP2), to a major stem-loop structure in the genomic 5' NCR is necessary for the translation of picornaviruses containing type I IRES elements, including poliovirus, coxsackievirus, and human rhinovirus. PCBP1, an isoform that shares approximately 90% amino acid identity to PCBP2, cannot efficiently stimulate poliovirus IRES-mediated translation, most likely due to its reduced binding affinity to stem-loop IV within the poliovirus IRES. The primary differences between PCBP1 and PCBP2 are found in the so-called linker domain between the second and third K-homology (KH) domains of these proteins. We hypothesize that the linker region of PCBP2 augments binding to poliovirus stem-loop IV RNA. To test this hypothesis, we generated six PCBP1/PCBP2 chimeric proteins. The recombinant PCBP1/PCBP2 chimeric proteins were able to interact with poliovirus stem-loop I RNA and participate in protein-protein interactions. We demonstrated that the PCBP1/PCBP2 chimeric proteins with the PCBP2 linker, but not with the PCBP1 linker, were able to interact with poliovirus stem-loop IV RNA, and could subsequently stimulate poliovirus IRES-mediated translation. In addition, using a monoclonal anti-PCBP2 antibody (directed against the PCBP2 linker domain) in mobility shift assays, we showed that the PCBP2 linker domain modulates binding to poliovirus stem-loop IV RNA via a mechanism that is not inhibited by the antibody.
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Affiliation(s)
- Polen Sean
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, CA 92697, USA
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29
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Abstract
The hnRNP K homology (KH) domain was first identified in the protein human heterogeneous nuclear ribonucleoprotein K (hnRNP K) 14 years ago. Since then, KH domains have been identified as nucleic acid recognition motifs in proteins that perform a wide range of cellular functions. KH domains bind RNA or ssDNA, and are found in proteins associated with transcriptional and translational regulation, along with other cellular processes. Several diseases, e.g. fragile X mental retardation syndrome and paraneoplastic disease, are associated with the loss of function of a particular KH domain. Here we discuss the progress made towards understanding both general and specific features of the molecular recognition of nucleic acids by KH domains. The typical binding surface of KH domains is a cleft that is versatile but that can typically accommodate only four unpaired bases. Van der Waals forces and hydrophobic interactions and, to a lesser extent, electrostatic interactions, contribute to the nucleic acid binding affinity. 'Augmented' KH domains or multiple copies of KH domains within a protein are two strategies that are used to achieve greater affinity and specificity of nucleic acid binding. Isolated KH domains have been seen to crystallize as monomers, dimers and tetramers, but no published data support the formation of noncovalent higher-order oligomers by KH domains in solution. Much attention has been given in the literature to a conserved hydrophobic residue (typically Ile or Leu) that is present in most KH domains. The interest derives from the observation that an individual with this Ile mutated to Asn, in the KH2 domain of fragile X mental retardation protein, exhibits a particularly severe form of the syndrome. The structural effects of this mutation in the fragile X mental retardation protein KH2 domain have recently been reported. We discuss the use of analogous point mutations at this position in other KH domains to dissect both structure and function.
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Affiliation(s)
- Roberto Valverde
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520, USA
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30
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Ulyanov NB, Shefer K, James TL, Tzfati Y. Pseudoknot structures with conserved base triples in telomerase RNAs of ciliates. Nucleic Acids Res 2007; 35:6150-60. [PMID: 17827211 PMCID: PMC2094054 DOI: 10.1093/nar/gkm660] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Telomerase maintains the integrity of telomeres, the ends of linear chromosomes, by adding G-rich repeats to their 3′-ends. Telomerase RNA is an integral component of telomerase. It contains a template for the synthesis of the telomeric repeats by the telomerase reverse transcriptase. Although telomerase RNAs of different organisms are very diverse in their sequences, a functional non-template element, a pseudoknot, was predicted in all of them. Pseudoknot elements in human and the budding yeast Kluyveromyces lactis telomerase RNAs contain unusual triple-helical segments with AUU base triples, which are critical for telomerase function. Such base triples in ciliates have not been previously reported. We analyzed the pseudoknot sequences in 28 ciliate species and classified them in six different groups based on the lengths of the stems and loops composing the pseudoknot. Using miniCarlo, a helical parameter-based modeling program, we calculated 3D models for a representative of each morphological group. In all cases, the predicted structure contains at least one AUU base triple in stem 2, except for that of Colpidium colpoda, which contains unconventional GCG and AUA triples. These results suggest that base triples in a pseudoknot element are a conserved feature of all telomerases.
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Affiliation(s)
- Nikolai B. Ulyanov
- Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA 94158-2517, USA and Department of Genetics, The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat Ram, 91904 Jerusalem, Israel
- *To whom correspondence should be addressed. +1 415 476 0707+1 415 502 8298 Correspondence may also be addressed to Yehuda Tzfati. +972 2 6584902+972 2 6586975
| | - Kinneret Shefer
- Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA 94158-2517, USA and Department of Genetics, The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat Ram, 91904 Jerusalem, Israel
| | - Thomas L. James
- Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA 94158-2517, USA and Department of Genetics, The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat Ram, 91904 Jerusalem, Israel
| | - Yehuda Tzfati
- Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA 94158-2517, USA and Department of Genetics, The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat Ram, 91904 Jerusalem, Israel
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31
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Du Z, Lee JK, Fenn S, Tjhen R, Stroud RM, James TL. X-ray crystallographic and NMR studies of protein-protein and protein-nucleic acid interactions involving the KH domains from human poly(C)-binding protein-2. RNA (NEW YORK, N.Y.) 2007; 13:1043-51. [PMID: 17526645 PMCID: PMC1894928 DOI: 10.1261/rna.410107] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Poly(C)-binding proteins (PCBPs) are KH (hnRNP K homology) domain-containing proteins that recognize poly(C) DNA and RNA sequences in mammalian cells. Binding poly(C) sequences via the KH domains is critical for PCBP functions. To reveal the mechanisms of KH domain-D/RNA recognition and its functional importance, we have determined the crystal structures of PCBP2 KH1 domain in complex with a 12-nucleotide DNA corresponding to two repeats of the human C-rich strand telomeric DNA and its RNA equivalent. The crystal structures reveal molecular details for not only KH1-DNA/RNA interaction but also protein-protein interaction between two KH1 domains. NMR studies on a protein construct containing two KH domains (KH1 + KH2) of PCBP2 indicate that KH1 interacts with KH2 in a way similar to the KH1-KH1 interaction. The crystal structures and NMR data suggest possible ways by which binding certain nucleic acid targets containing tandem poly(C) motifs may induce structural rearrangement of the KH domains in PCBPs; such structural rearrangement may be crucial for some PCBP functions.
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Affiliation(s)
- Zhihua Du
- Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA 94158-2517, USA
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