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Juniku B, Mignon J, Carême R, Genco A, Obeid AM, Mottet D, Monari A, Michaux C. Intrinsic disorder and salt-dependent conformational changes of the N-terminal region of TFIP11 splicing factor. Int J Biol Macromol 2024; 277:134291. [PMID: 39089542 DOI: 10.1016/j.ijbiomac.2024.134291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 07/21/2024] [Accepted: 07/28/2024] [Indexed: 08/04/2024]
Abstract
Tuftelin Interacting Protein 11 (TFIP11) was identified as a critical human spliceosome assembly regulator, interacting with multiple proteins and localising in membrane-less organelles. However, a lack of structural information on TFIP11 limits the rationalisation of its biological role. TFIP11 is predicted as an intrinsically disordered protein (IDP), and more specifically concerning its N-terminal (N-TER) region. IDPs lack a defined tertiary structure, existing as a dynamic conformational ensemble, favouring protein-protein and protein-RNA interactions. IDPs are involved in liquid-liquid phase separation (LLPS), driving the formation of subnuclear compartments. Combining disorder prediction, molecular dynamics, and spectroscopy methods, this contribution shows the first evidence TFIP11 N-TER is a polyampholytic IDP, exhibiting a structural duality with the coexistence of ordered and disordered assemblies, depending on the ionic strength. Increasing the salt concentration enhances the protein conformational flexibility, presenting a more globule-like shape, and a fuzzier unstructured arrangement that could favour LLPS and protein-RNA interaction. The most charged and hydrophilic regions are the most impacted, including the G-Patch domain essential to TFIP11 function. This study gives a better understanding of the salt-dependent conformational behaviour of the N-TER TFIP11, supporting the hypothesis of the formation of different types of protein assembly, in line with its multiple biological roles.
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Affiliation(s)
- Blinera Juniku
- Laboratory of Physical Chemistry of Biomolecules, UCPTS, University of Namur, Rue de Bruxelles 61, B-5000 Namur, Belgium; Namur Research Institute for Life Sciences (NARILIS), University of Namur, Namur, Belgium; Namur Institute of Structured Matter (NISM), University of Namur, Namur, Belgium; GIGA-Molecular Biology of Diseases, Molecular Analysis of Gene Expression (MAGE) Laboratory, University of Liege, B34, Avenue de l'Hôpital, B-4000 Liège, Belgium
| | - Julien Mignon
- Laboratory of Physical Chemistry of Biomolecules, UCPTS, University of Namur, Rue de Bruxelles 61, B-5000 Namur, Belgium; Namur Research Institute for Life Sciences (NARILIS), University of Namur, Namur, Belgium; Namur Institute of Structured Matter (NISM), University of Namur, Namur, Belgium
| | - Rachel Carême
- Laboratory of Physical Chemistry of Biomolecules, UCPTS, University of Namur, Rue de Bruxelles 61, B-5000 Namur, Belgium
| | - Alexia Genco
- GIGA-Molecular Biology of Diseases, Molecular Analysis of Gene Expression (MAGE) Laboratory, University of Liege, B34, Avenue de l'Hôpital, B-4000 Liège, Belgium
| | - Anna Maria Obeid
- GIGA-Molecular Biology of Diseases, Molecular Analysis of Gene Expression (MAGE) Laboratory, University of Liege, B34, Avenue de l'Hôpital, B-4000 Liège, Belgium
| | - Denis Mottet
- GIGA-Molecular Biology of Diseases, Molecular Analysis of Gene Expression (MAGE) Laboratory, University of Liege, B34, Avenue de l'Hôpital, B-4000 Liège, Belgium.
| | - Antonio Monari
- Université Paris Cité and CNRS, ITODYS, F-75006, Paris, France
| | - Catherine Michaux
- Laboratory of Physical Chemistry of Biomolecules, UCPTS, University of Namur, Rue de Bruxelles 61, B-5000 Namur, Belgium; Namur Research Institute for Life Sciences (NARILIS), University of Namur, Namur, Belgium; Namur Institute of Structured Matter (NISM), University of Namur, Namur, Belgium.
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Chen J, Wu M, Yang Y, Ruan C, Luo Y, Song L, Wu T, Huang J, Yang B, Liu T. TFIP11 promotes replication fork reversal to preserve genome stability. Nat Commun 2024; 15:1262. [PMID: 38341452 PMCID: PMC10858868 DOI: 10.1038/s41467-024-45684-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 01/31/2024] [Indexed: 02/12/2024] Open
Abstract
Replication fork reversal, a critical protective mechanism against replication stress in higher eukaryotic cells, is orchestrated via a series of coordinated enzymatic reactions. The Bloom syndrome gene product, BLM, a member of the highly conserved RecQ helicase family, is implicated in this process, yet its precise regulation and role remain poorly understood. In this study, we demonstrate that the GCFC domain-containing protein TFIP11 forms a complex with the BLM helicase. TFIP11 exhibits a preference for binding to DNA substrates that mimic the structure generated at stalled replication forks. Loss of either TFIP11 or BLM leads to the accumulation of the other protein at stalled forks. This abnormal accumulation, in turn, impairs RAD51-mediated fork reversal and slowing, sensitizes cells to replication stress-inducing agents, and enhances chromosomal instability. These findings reveal a previously unidentified regulatory mechanism that modulates the activities of BLM and RAD51 at stalled forks, thereby impacting genome integrity.
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Affiliation(s)
- Junliang Chen
- Zhejiang Provincial Key Laboratory of Geriatrics and Geriatrics Institute of Zhejiang Province, Affiliated Zhejiang Hospital, Zhejiang University School of Medicine, 310058, Hangzhou, China
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, 310058, Hangzhou, China
- Center for Life Sciences, Shaoxing Institute, Zhejiang University, 321000, Shaoxing, China
| | - Mingjie Wu
- The Trauma Center, The First Affiliated Hospital, Zhejiang University School of Medicine, 310058, Hangzhou, China
| | - Yulan Yang
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, 310058, Hangzhou, China
| | - Chunyan Ruan
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, 310058, Hangzhou, China
| | - Yi Luo
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, 310058, Hangzhou, China
| | - Lizhi Song
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, 310058, Hangzhou, China
| | - Ting Wu
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, 310058, Hangzhou, China
| | - Jun Huang
- Zhejiang Provincial Key Laboratory of Geriatrics and Geriatrics Institute of Zhejiang Province, Affiliated Zhejiang Hospital, Zhejiang University School of Medicine, 310058, Hangzhou, China
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, 310058, Hangzhou, China
| | - Bing Yang
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, 310058, Hangzhou, China
| | - Ting Liu
- Zhejiang Provincial Key Laboratory of Geriatrics and Geriatrics Institute of Zhejiang Province, Affiliated Zhejiang Hospital, Zhejiang University School of Medicine, 310058, Hangzhou, China.
- Department of Cell Biology, Zhejiang University School of Medicine, 310058, Hangzhou, China.
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3
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Kim H, Kim J, Choi G. Epidermal phyB requires RRC1 to promote light responses by activating the circadian rhythm. THE NEW PHYTOLOGIST 2023; 238:705-723. [PMID: 36651061 DOI: 10.1111/nph.18746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 12/30/2022] [Indexed: 06/17/2023]
Abstract
Phytochrome B (phyB) expressed in the epidermis is sufficient to promote red light responses, including the inhibition of hypocotyl elongation and hypocotyl negative gravitropism. Nonetheless, the downstream mechanism of epidermal phyB in promoting light responses had been elusive. Here, we mutagenized the epidermis-specific phyB-expressing line (MLB) using ethyl methanesulfonate (EMS) and characterized a novel mutant allele of RRC1 (rrc1-689), which causes reduced epidermal phyB-mediated red light responses. The rrc1-689 mutation increases the alternative splicing of major clock gene transcripts, including PRR7 and TOC1, disrupting the rhythmic expression of the entire clock and clock-controlled genes. Combined with the result that MLB/prr7 exhibits the same red-hyposensitive phenotypes as MLB/rrc1-689, our data support that the circadian clock is required for the ability of epidermal phyB to promote light responses. We also found that, unlike phyB, RRC1 preferentially acts in the endodermis to maintain the circadian rhythm by suppressing the alternative splicing of core clock genes. Together, our results suggest that epidermal phyB requires RRC1 to promote light responses by activating the circadian rhythm in Arabidopsis thaliana.
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Affiliation(s)
- Hanim Kim
- Department of Biological Sciences, KAIST, Daejeon, 34141, Korea
| | - Jaewook Kim
- Department of Biological Sciences, KAIST, Daejeon, 34141, Korea
| | - Giltsu Choi
- Department of Biological Sciences, KAIST, Daejeon, 34141, Korea
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Bohnsack KE, Kanwal N, Bohnsack MT. Prp43/DHX15 exemplify RNA helicase multifunctionality in the gene expression network. Nucleic Acids Res 2022; 50:9012-9022. [PMID: 35993807 PMCID: PMC9458436 DOI: 10.1093/nar/gkac687] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 07/10/2022] [Accepted: 08/01/2022] [Indexed: 12/24/2022] Open
Abstract
Dynamic regulation of RNA folding and structure is critical for the biogenesis and function of RNAs and ribonucleoprotein (RNP) complexes. Through their nucleotide triphosphate-dependent remodelling functions, RNA helicases are key modulators of RNA/RNP structure. While some RNA helicases are dedicated to a specific target RNA, others are multifunctional and engage numerous substrate RNAs in different aspects of RNA metabolism. The discovery of such multitasking RNA helicases raises the intriguing question of how these enzymes can act on diverse RNAs but also maintain specificity for their particular targets within the RNA-dense cellular environment. Furthermore, the identification of RNA helicases that sit at the nexus between different aspects of RNA metabolism raises the possibility that they mediate cross-regulation of different cellular processes. Prominent and extensively characterized multifunctional DEAH/RHA-box RNA helicases are DHX15 and its Saccharomyces cerevisiae (yeast) homologue Prp43. Due to their central roles in key cellular processes, these enzymes have also served as prototypes for mechanistic studies elucidating the mode of action of this type of enzyme. Here, we summarize the current knowledge on the structure, regulation and cellular functions of Prp43/DHX15, and discuss the general concept and implications of RNA helicase multifunctionality.
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Affiliation(s)
- Katherine E Bohnsack
- Correspondence may also be addressed to Katherine E. Bohnsack. Tel: +49 551 3969305; Fax: +49 551 395960;
| | - Nidhi Kanwal
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Markus T Bohnsack
- To whom correspondence should be addressed. Tel: +49 551 395968; Fax: +49 551 395960;
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5
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DHX15-independent roles for TFIP11 in U6 snRNA modification, U4/U6.U5 tri-snRNP assembly and pre-mRNA splicing fidelity. Nat Commun 2021; 12:6648. [PMID: 34789764 PMCID: PMC8599867 DOI: 10.1038/s41467-021-26932-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 10/22/2021] [Indexed: 11/29/2022] Open
Abstract
The U6 snRNA, the core catalytic component of the spliceosome, is extensively modified post-transcriptionally, with 2'-O-methylation being most common. However, how U6 2'-O-methylation is regulated remains largely unknown. Here we report that TFIP11, the human homolog of the yeast spliceosome disassembly factor Ntr1, localizes to nucleoli and Cajal Bodies and is essential for the 2'-O-methylation of U6. Mechanistically, we demonstrate that TFIP11 knockdown reduces the association of U6 snRNA with fibrillarin and associated snoRNAs, therefore altering U6 2'-O-methylation. We show U6 snRNA hypomethylation is associated with changes in assembly of the U4/U6.U5 tri-snRNP leading to defects in spliceosome assembly and alterations in splicing fidelity. Strikingly, this function of TFIP11 is independent of the RNA helicase DHX15, its known partner in yeast. In sum, our study demonstrates an unrecognized function for TFIP11 in U6 snRNP modification and U4/U6.U5 tri-snRNP assembly, identifying TFIP11 as a critical spliceosome assembly regulator.
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Lou F, Zhang Y, Song N, Ji D, Gao T. Comprehensive Transcriptome Analysis Reveals Insights into Phylogeny and Positively Selected Genes of Sillago Species. Animals (Basel) 2020; 10:ani10040633. [PMID: 32272562 PMCID: PMC7222750 DOI: 10.3390/ani10040633] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 03/31/2020] [Accepted: 04/01/2020] [Indexed: 01/09/2023] Open
Abstract
Sillago species lives in the demersal environments and face multiple stressors, such as localized oxygen depletion, sulfide accumulation, and high turbidity. In this study, we performed transcriptome analyses of seven Sillago species to provide insights into the phylogeny and positively selected genes of this species. After de novo assembly, 82,024, 58,102, 63,807, 85,990, 102,185, 69,748, and 102,903 unigenes were generated from S. japonica, S. aeolus, S. sp.1, S. sihama, S. sp.2, S. parvisquamis, and S. sinica, respectively. Furthermore, 140 shared orthologous exon markers were identified and then applied to reconstruct the phylogenetic relationships of the seven Sillago species. The reconstructed phylogenetic structure was significantly congruent with the prevailing morphological and molecular biological view of Sillago species relationships. In addition, a total of 44 genes were identified to be positively selected, and these genes were potential participants in the stress response, material (carbohydrate, amino acid and lipid) and energy metabolism, growth and differentiation, embryogenesis, visual sense, and other biological processes. We suspected that these genes possibly allowed Sillago species to increase their ecological adaptation to multiple environmental stressors.
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Affiliation(s)
- Fangrui Lou
- Fishery College, Zhejiang Ocean University, Zhoushan 316022, Zhejiang, China;
| | - Yuan Zhang
- Fishery College, Ocean University of China, Qingdao 266003, Shandong, China; (Y.Z.); (N.S.)
| | - Na Song
- Fishery College, Ocean University of China, Qingdao 266003, Shandong, China; (Y.Z.); (N.S.)
| | - Dongping Ji
- Agricultural Machinery Service Center, Fangchenggang 538000, Guangxi, China;
| | - Tianxiang Gao
- Fishery College, Zhejiang Ocean University, Zhoushan 316022, Zhejiang, China;
- Correspondence: ; Tel.: +86-580-2089-333
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Pattabhi S, Knoll ML, Gale M, Loo YM. DHX15 Is a Coreceptor for RLR Signaling That Promotes Antiviral Defense Against RNA Virus Infection. J Interferon Cytokine Res 2019; 39:331-346. [PMID: 31090472 PMCID: PMC6590726 DOI: 10.1089/jir.2018.0163] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 03/01/2019] [Indexed: 12/23/2022] Open
Abstract
RNA helicases play an important role in the response to microbial infection. Retinoic acid inducible gene-I (RIG-I) and members of the RIG-I-like receptor (RLR) family of helicases function as cytoplasmic pattern recognition receptors (PRRs) whose actions are essential for recognition of RNA viruses. RIG-I association with pathogen-associated molecular patterns (PAMPs) within viral RNA leads to its activation and signaling via the mitochondrial antiviral signaling (MAVS) adapter protein. This interaction mediates downstream signaling events that drive the innate immune response to virus infection. Here we identify the DEAH-box RNA helicase DHX15 as a RLR binding partner and signaling cofactor. In human cells, DHX15 is required for virus-induced RLR signaling of innate immune gene expression. Knockdown of DHX15 increased susceptibility to infection by RNA viruses of diverse genera, including Paramyxoviridae, Rhabdoviridae, and Picornaviridae. DHX15 associates with RIG-I caspase activation and recruitment domains (CARDs) through its amino terminus, in which the complex is recruited to MAVS on virus infection. Importantly, although DHX15 cannot substitute for RIG-I in innate immune signaling, DHX15 selectively binds PAMP RNA to promote RIG-I ATP hydrolysis and signaling activation in response to viral RNA. Our results define DHX15 as a coreceptor required for RLR innate immune responses to control RNA virus infection.
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Affiliation(s)
- Sowmya Pattabhi
- Department of Global Health, University of Washington, Seattle, Washington
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington, Seattle, Washington
| | - Megan L. Knoll
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington, Seattle, Washington
- Department of Immunology, University of Washington, Seattle, Washington
| | - Michael Gale
- Department of Global Health, University of Washington, Seattle, Washington
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington, Seattle, Washington
- Department of Immunology, University of Washington, Seattle, Washington
| | - Yueh-Ming Loo
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington, Seattle, Washington
- Department of Immunology, University of Washington, Seattle, Washington
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8
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Perčulija V, Ouyang S. Diverse Roles of DEAD/DEAH-Box Helicases in Innate Immunity and Diseases. HELICASES FROM ALL DOMAINS OF LIFE 2019. [PMCID: PMC7158350 DOI: 10.1016/b978-0-12-814685-9.00009-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
DEAD/DEAH-box helicases are enzymes that belong to the DEAD/H-box family of SF2 helicase superfamily. These enzymes are essential in RNA metabolism, where they are involved in a number of processes that require manipulation of RNA structure. Recent studies have found that some DEAD/DEAH-box helicases play important roles in innate immunity, where they act as sensors of cytosolic DNA/RNA, as adaptor proteins, or as regulators of signaling and gene expression. In spite of their function in immunity, DEAD/DEAH-box helicases can also be hijacked and exploited by viruses to circumvent detection and aid in viral replication. These findings not only imply that DEAD/DEAH-box helicases have a broader function than previously thought, but also give us a much better understanding of immune mechanisms and diseases that arise due to the dysregulation or evasion thereof. In this chapter, we demonstrate the known scope of activities of human DEAD/DEAH-box helicases in innate immunity and interaction with viruses or other pathogens. Additionally, we give an outline of diseases in which they are, or may be, involved in the context of immunity.
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9
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Inesta-Vaquera F, Chaugule VK, Galloway A, Chandler L, Rojas-Fernandez A, Weidlich S, Peggie M, Cowling VH. DHX15 regulates CMTR1-dependent gene expression and cell proliferation. Life Sci Alliance 2018; 1:e201800092. [PMID: 30079402 PMCID: PMC6071836 DOI: 10.26508/lsa.201800092] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
DHX15 helicase regulates CMTR1-dependent first transcribed nucleotide ribose O-2 methylation. CMTR1 contributes to mRNA cap formation by methylating the first transcribed nucleotide ribose at the O-2 position. mRNA cap O-2 methylation has roles in mRNA stabilisation and translation, and self-RNA tolerance in innate immunity. We report that CMTR1 is recruited to serine-5–phosphorylated RNA Pol II C-terminal domain, early in transcription. We isolated CMTR1 in a complex with DHX15, an RNA helicase functioning in splicing and ribosome biogenesis, and characterised it as a regulator of CMTR1. When DHX15 is bound, CMTR1 activity is repressed and the methyltransferase does not bind to RNA pol II. Conversely, CMTR1 activates DHX15 helicase activity, which is likely to impact several nuclear functions. In HCC1806 breast carcinoma cell line, the DHX15–CMTR1 interaction controls ribosome loading of a subset of mRNAs and regulates cell proliferation. The impact of the CMTR1–DHX15 interaction is complex and will depend on the relative expression of these enzymes and their interactors, and the cellular dependency on different RNA processing pathways.
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Affiliation(s)
- Francisco Inesta-Vaquera
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Viduth K Chaugule
- Institute of Molecular, Cell and Systems Biology, School of Life Sciences, University of Glasgow, Glasgow, UK
| | - Alison Galloway
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Laurel Chandler
- Nuffield Department of Clinical Neurosciences, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Alejandro Rojas-Fernandez
- Center for Interdisciplinary Studies on the Nervous System and Institute of Medicine, Universidad Austral de Chile, Valdivia, Chile
| | - Simone Weidlich
- Division of Signal Transduction Therapies, School of Life Sciences, University of Dundee, Dundee, UK
| | - Mark Peggie
- Division of Signal Transduction Therapies, School of Life Sciences, University of Dundee, Dundee, UK
| | - Victoria H Cowling
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
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10
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Murakami K, Nakano K, Shimizu T, Ohto U. The crystal structure of human DEAH-box RNA helicase 15 reveals a domain organization of the mammalian DEAH/RHA family. Acta Crystallogr F Struct Biol Commun 2017; 73:347-355. [PMID: 28580923 PMCID: PMC5458392 DOI: 10.1107/s2053230x17007336] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 05/17/2017] [Indexed: 12/31/2022] Open
Abstract
DEAH-box RNA helicase 15 (DHX15) plays important roles in RNA metabolism, including in splicing and in ribosome biogenesis. In addition, mammalian DHX15 also mediates the innate immune sensing of viral RNA. However, structural information on this protein is not available, although the structure of the fungal orthologue of this protein, Prp43, has been elucidated. Here, the crystal structure of the ADP-bound form of human DHX15 is reported at a resolution of 2.0 Å. This is the first structure to be revealed of a member of the mammalian DEAH-box RNA helicase (DEAH/RHA) family in a nearly complete form, including the catalytic core consisting of the two N-terminal RecA domains and the C-terminal regulatory domains (CTD). The ADP-bound form of DHX15 displayed a compact structure, in which the RecA domains made extensive contacts with the CTD. Notably, a potential RNA-binding site was found on the surface of a RecA domain with positive electrostatic potential. Almost all structural features were conserved between the fungal Prp43 and the human DHX15, suggesting that they share a fundamentally common mechanism of action and providing a better understanding of the specific mammalian functions of DHX15.
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Affiliation(s)
- Karin Murakami
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kenji Nakano
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Toshiyuki Shimizu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Saitama 332-0012, Japan
| | - Umeharu Ohto
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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11
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Hernando CE, Romanowski A, Yanovsky MJ. Transcriptional and post-transcriptional control of the plant circadian gene regulatory network. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1860:84-94. [PMID: 27412912 DOI: 10.1016/j.bbagrm.2016.07.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 06/30/2016] [Accepted: 07/03/2016] [Indexed: 11/16/2022]
Abstract
The circadian clock drives rhythms in multiple physiological processes allowing plants to anticipate and adjust to periodic changes in environmental conditions. These physiological rhythms are associated with robust oscillations in the expression of thousands of genes linked to the control of photosynthesis, cell elongation, biotic and abiotic stress responses, developmental processes such as flowering, and the clock itself. Given its pervasive effects on plant physiology, it is not surprising that circadian clock genes have played an important role in the domestication of crop plants and in the improvement of crop productivity. Therefore, identifying the principles governing the dynamics of the circadian gene regulatory network in plants could strongly contribute to further speed up crop improvement. Here we provide an historical as well as a current description of our knowledge of the molecular mechanisms underlying circadian rhythms in plants. This work focuses on the transcriptional and post-transcriptional regulatory layers that control the very core of the circadian clock, and some of its complex interactions with signaling pathways that help synchronize plant growth and development to daily and seasonal changes in the environment. This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks, edited by Dr. Erich Grotewold and Dr. Nathan Springer.
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Affiliation(s)
- C Esteban Hernando
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Técnicas de Argentina, Av. Patricias Argentinas 435, C1405BWE Ciudad de Buenos Aires, Argentina.
| | - Andrés Romanowski
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Técnicas de Argentina, Av. Patricias Argentinas 435, C1405BWE Ciudad de Buenos Aires, Argentina.
| | - Marcelo J Yanovsky
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Técnicas de Argentina, Av. Patricias Argentinas 435, C1405BWE Ciudad de Buenos Aires, Argentina.
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12
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Nolte C, Staiger D. RNA around the clock - regulation at the RNA level in biological timing. FRONTIERS IN PLANT SCIENCE 2015; 6:311. [PMID: 25999975 PMCID: PMC4419606 DOI: 10.3389/fpls.2015.00311] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 04/19/2015] [Indexed: 05/21/2023]
Abstract
The circadian timing system in plants synchronizes their physiological functions with the environment. This is achieved by a global control of gene expression programs with a considerable part of the transcriptome undergoing 24-h oscillations in steady-state abundance. These circadian oscillations are driven by a set of core clock proteins that generate their own 24-h rhythm through periodic feedback on their own transcription. Additionally, post-transcriptional events are instrumental for oscillations of core clock genes and genes in clock output. Here we provide an update on molecular events at the RNA level that contribute to the 24-h rhythm of the core clock proteins and shape the circadian transcriptome. We focus on the circadian system of the model plant Arabidopsis thaliana but also discuss selected regulatory principles in other organisms.
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Affiliation(s)
| | - Dorothee Staiger
- *Correspondence: Dorothee Staiger, Molecular Cell Physiology, Faculty of Biology, Bielefeld University, Universitaetsstrasse 25, Bielefeld D-33615, Germany
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Cui Z, Xu Q, Wang X. Regulation of the circadian clock through pre-mRNA splicing in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:1973-80. [PMID: 24604736 DOI: 10.1093/jxb/eru085] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Alternative splicing plays an important role in regulating gene functions and enhancing the diversity of the proteome in plants. Most of the genes are interrupted by introns in Arabidopsis. More than half of the intron-split genes involved in multiple biological processes including the circadian clock are alternatively spliced. In this review, we focus on the involvement of alternative splicing in the regulation of the circadian clock.
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Affiliation(s)
- Zhibo Cui
- Rice Research Institute; Key Laboratory of Northeast Rice Biology and Breeding, Ministry of Agriculture; Key Laboratory of Northern Japonica Super Rice Breeding, Ministry of Education; Shenyang Agricultural University, Shenyang 110866, China
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Hu L, Yang F, Liu X, Xu D, Dai W. Nuclear protein IK undergoes dynamic subcellular translocation and forms unique nuclear bodies during the cell cycle. Biomark Res 2013; 1:11. [PMID: 24252166 PMCID: PMC4177551 DOI: 10.1186/2050-7771-1-11] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Accepted: 01/27/2013] [Indexed: 02/06/2023] Open
Abstract
IK is a nuclear protein containing a unique domain named RED due to the presence of a repetitive arginine (R), aspartic (E), and glutamic acid (D) sequence. To date, the function of this protein remains largely unknown despite of a couple of previous studies in the literature. Here we report that depletion of IK via RNA interference results in mitotic arrest. We also demonstrate that IK undergoes dynamic translocation during interphase and mitosis. In particular, IK is primarily present in some interphase cells as nuclear foci/bodies which do not co-localize with nucleoli, PMA bodies and Cajal bodies. Pull-down analysis coupled with mass spectrometry reveals that IK is associated with DHX15, a putative ATP-dependent RNA helicase. Our results strongly suggest that IK may participate in pre-mRNA splicing and that it may be a useful biomarker for a new nuclear structure in the cell.
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Affiliation(s)
- Liyan Hu
- Department of Environmental Medicine, New York University Langone Medical Center, Tuxedo, NY, 10987, USA.
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15
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Abstract
The circadian clock is an endogenous timing system responsible for coordinating an organism's biological processes with its environment. Interlocked transcriptional feedback loops constitute the fundamental architecture of the circadian clock. In Arabidopsis, three feedback loops, the core loop, morning loop and evening loop, comprise a network that is the basis of the circadian clock. The components of these three loops are regulated in distinct ways, including transcriptional, post-transcriptional and posttranslational mechanisms. The discovery of the DNA-binding and repressive activities of TOC1 has overturned our initial concept of its function in the circadian clock. The alternative splicing of circadian clock-related genes plays an essential role in normal functioning of the clock and enables organisms to sense environmental changes. In this review, we describe the regulatory mechanisms of the circadian clock that have been identified in Arabidopsis.
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Affiliation(s)
- Xiaoxue Wang
- College of Agronomy; Rice Research Institute; Shenyang Agricultural University; Shenyang, P.R. China
| | - Ligeng Ma
- College of Biological Sciences; Capital Normal University; Beijing, P.R. China
- Corresponding author: Ligeng Ma;
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16
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Jones MA, Williams BA, McNicol J, Simpson CG, Brown JW, Harmer SL. Mutation of Arabidopsis spliceosomal timekeeper locus1 causes circadian clock defects. THE PLANT CELL 2012; 24:4066-82. [PMID: 23110899 PMCID: PMC3517236 DOI: 10.1105/tpc.112.104828] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2012] [Revised: 09/08/2012] [Accepted: 10/10/2012] [Indexed: 05/18/2023]
Abstract
The circadian clock plays a crucial role in coordinating plant metabolic and physiological functions with predictable environmental variables, such as dusk and dawn, while also modulating responses to biotic and abiotic challenges. Much of the initial characterization of the circadian system has focused on transcriptional initiation, but it is now apparent that considerable regulation is exerted after this key regulatory step. Transcript processing, protein stability, and cofactor availability have all been reported to influence circadian rhythms in a variety of species. We used a genetic screen to identify a mutation within a putative RNA binding protein (spliceosomal timekeeper locus1 [STIPL1]) that induces a long circadian period phenotype under constant conditions. STIPL1 is a homolog of the spliceosomal proteins TFP11 (Homo sapiens) and Ntr1p (Saccharomyces cerevisiae) involved in spliceosome disassembly. Analysis of general and alternative splicing using a high-resolution RT-PCR system revealed that mutation of this protein causes less efficient splicing of most but not all of the introns analyzed. In particular, the altered accumulation of circadian-associated transcripts may contribute to the observed mutant phenotype. Interestingly, mutation of a close homolog of STIPL1, STIP-LIKE2, does not cause a circadian phenotype, which suggests divergence in function between these family members. Our work highlights the importance of posttranscriptional control within the clock mechanism.
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Affiliation(s)
- Matthew A. Jones
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, California, 95616
| | - Brian A. Williams
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, California, 95616
| | - Jim McNicol
- Biomathematics and Statistics Scotland at Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, Scotland, United Kingdom
| | - Craig G. Simpson
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, United Kingdom
| | - John W.S. Brown
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, United Kingdom
- Division of Plant Sciences, University of Dundee at James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, United Kingdom
| | - Stacey L. Harmer
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, California, 95616
- Address correspondence to
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Shimizu T, Ho B, Deeley K, Briseño-Ruiz J, Faraco IM, Schupack BI, Brancher JA, Pecharki GD, Küchler EC, Tannure PN, Lips A, Vieira TCS, Patir A, Yildirim M, Poletta FA, Mereb JC, Resick JM, Brandon CA, Orioli IM, Castilla EE, Marazita ML, Seymen F, Costa MC, Granjeiro JM, Trevilatto PC, Vieira AR. Enamel formation genes influence enamel microhardness before and after cariogenic challenge. PLoS One 2012; 7:e45022. [PMID: 23028741 PMCID: PMC3454391 DOI: 10.1371/journal.pone.0045022] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Accepted: 08/11/2012] [Indexed: 11/19/2022] Open
Abstract
There is evidence for a genetic component in caries susceptibility, and studies in humans have suggested that variation in enamel formation genes may contribute to caries. For the present study, we used DNA samples collected from 1,831 individuals from various population data sets. Single nucleotide polymorphism markers were genotyped in selected genes (ameloblastin, amelogenin, enamelin, tuftelin, and tuftelin interacting protein 11) that influence enamel formation. Allele and genotype frequencies were compared between groups with distinct caries experience. Associations with caries experience can be detected but they are not necessarily replicated in all population groups and the most expressive results was for a marker in AMELX (p=0.0007). To help interpret these results, we evaluated if enamel microhardness changes under simulated cariogenic challenges are associated with genetic variations in these same genes. After creating an artificial caries lesion, associations could be seen between genetic variation in TUFT1 (p=0.006) and TUIP11 (p=0.0006) with enamel microhardness. Our results suggest that the influence of genetic variation of enamel formation genes may influence the dynamic interactions between the enamel surface and the oral cavity.
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Affiliation(s)
- Takehiko Shimizu
- Department of Pediatric Dentistry, Nihon University of Dentistry at Matsudo, Matsudo, Chiba, Japan
| | - Bao Ho
- Department of Oral Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Kathleen Deeley
- Department of Oral Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Jessica Briseño-Ruiz
- Department of Oral Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Italo M. Faraco
- Department of Oral Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Brett I. Schupack
- Department of Oral Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - João A. Brancher
- Center for Health and Biological Sciences, Pontifical Catholic University of Paraná (PUCPR), Curitiba, Brazil
| | - Giovana D. Pecharki
- Center for Health and Biological Sciences, Pontifical Catholic University of Paraná (PUCPR), Curitiba, Brazil
| | - Erika C. Küchler
- Clinical Research Unit, Biology Institute, Fluminense Federal University, Niterói, Rio de Janeiro, Brazil
| | - Patricia N. Tannure
- Discipline of Pediatric Dentistry, Veiga de Almeida University, Rio de Janeiro, Brazil
| | - Andrea Lips
- Department of Pediatric Dentistry and Orthodontics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Thays C. S. Vieira
- Clinical Research Unit, Biology Institute, Fluminense Federal University, Niterói, Rio de Janeiro, Brazil
| | - Asli Patir
- Department of Pedodontics, Istanbul Medipol University, Istanbul, Turkey
| | - Mine Yildirim
- Department of Pedodontics, Faculty of Dentistry, Istanbul University, Istanbul, Turkey
| | - Fernando A. Poletta
- Latin American Collaborative Study of Congenital Malformations (ECLAMC), Center for Medical Education and Clinical Research (CEMIC), Buenos Aires, Argentina
| | - Juan C. Mereb
- Latin American Collaborative Study of Congenital Malformations (ECLAMC), Hospital de Area El Bolsón, Río Negro, Argentina
| | - Judith M. Resick
- Department of Oral Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Carla A. Brandon
- Department of Oral Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Iêda M. Orioli
- Latin American Collaborative Study of Congenital Malformations (ECLAMC), National Institute of Population Medical Genetics (INAGEMP-CNPq), Department of Genetics, Institute of Biology, Center of Health Sciences, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Eduardo E. Castilla
- Latin American Collaborative Study of Congenital Malformations (ECLAMC), Center for Medical Education and Clinical Research (CEMIC), Buenos Aires, Argentina
- Latin American Collaborative Study of Congenital Malformations (ECLAMC), National Institute of Population Medical Genetics (INAGEMP-CNPq), Department of Genetics, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Mary L. Marazita
- Department of Oral Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Center for Craniofacial and Dental Genetics, Department of Human Genetics, and Clinical and Translational Science, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Figen Seymen
- Department of Pedodontics, Faculty of Dentistry, Istanbul University, Istanbul, Turkey
| | - Marcelo C. Costa
- Department of Pediatric Dentistry and Orthodontics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - José M. Granjeiro
- Clinical Research Unit, Biology Institute, Fluminense Federal University, Niterói, Rio de Janeiro, Brazil
| | - Paula C. Trevilatto
- Center for Health and Biological Sciences, Pontifical Catholic University of Paraná (PUCPR), Curitiba, Brazil
| | - Alexandre R. Vieira
- Department of Oral Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Center for Craniofacial and Dental Genetics, Department of Pediatric Dentistry, School of Dental Medicine, and Clinical and Translational Science, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
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The G-patch domain of Mason-Pfizer monkey virus is a part of reverse transcriptase. J Virol 2011; 86:1988-98. [PMID: 22171253 DOI: 10.1128/jvi.06638-11] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Mason-Pfizer monkey virus (M-PMV), like some other betaretroviruses, encodes a G-patch domain (GPD). This glycine-rich domain, which has been predicted to be an RNA binding module, is invariably localized at the 3' end of the pro gene upstream of the pro-pol ribosomal frameshift sequence of genomic RNAs of betaretroviruses. Following two ribosomal frameshift events and the translation of viral mRNA, the GPD is present in both Gag-Pro and Gag-Pro-Pol polyproteins. During the maturation of the Gag-Pro polyprotein, the GPD transiently remains a C-terminal part of the protease (PR), from which it is then detached by PR itself. The destiny of the Gag-Pro-Pol-encoded GPD remains to be determined. The function of the GPD in the retroviral life cycle is unknown. To elucidate the role of the GPD in the M-PMV replication cycle, alanine-scanning mutational analysis of its most highly conserved residues was performed. A series of individual mutations as well as the deletion of the entire GPD had no effect on M-PMV assembly, polyprotein processing, and RNA incorporation. However, a reduction of the reverse transcriptase (RT) activity, resulting in a drop in M-PMV infectivity, was determined for all GPD mutants. Immunoprecipitation experiments suggested that the GPD is a part of RT and participates in its function. These data indicate that the M-PMV GPD functions as a part of reverse transcriptase rather than protease.
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Aksaas AK, Larsen AC, Rogne M, Rosendal K, Kvissel AK, Skålhegg BS. G-patch domain and KOW motifs-containing protein, GPKOW; a nuclear RNA-binding protein regulated by protein kinase A. J Mol Signal 2011; 6:10. [PMID: 21880142 PMCID: PMC3179746 DOI: 10.1186/1750-2187-6-10] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2011] [Accepted: 08/31/2011] [Indexed: 12/28/2022] Open
Abstract
Background Post-transcriptional processing of pre-mRNA takes place in several steps and requires involvement of a number of RNA-binding proteins. How pre-mRNA processing is regulated is in large enigmatic. The catalytic (C) subunit of protein kinase A (PKA) is a serine/threonine kinase, which regulates numerous cellular processes including pre-mRNA splicing. Despite that a significant fraction of the C subunit is found in splicing factor compartments in the nucleus, there are no indications of a direct interaction between RNA and PKA. Based on this we speculate if the specificity of the C subunit in regulating pre-mRNA splicing may be mediated indirectly through other nuclear proteins. Results Using yeast two-hybrid screening with the PKA C subunit Cbeta2 as bait, we identified the G-patch domain and KOW motifs-containing protein (GPKOW), also known as the T54 protein or MOS2 homolog, as an interaction partner for Cbeta2. We demonstrate that GPKOW, which contains one G-patch domain and two KOW motifs, is a nuclear RNA-binding protein conserved between species. GPKOW contains two sites that are phosphorylated by PKA in vitro. By RNA immunoprecipitation and site directed mutagenesis of the PKA phosphorylation sites we revealed that GPKOW binds RNA in vivo in a PKA sensitive fashion. Conclusion GPKOW is a RNA-binding protein that binds RNA in a PKA regulated fashion. Together with our previous results demonstrating that PKA regulates pre-mRNA splicing, our results suggest that PKA phosphorylation is involved in regulating RNA processing at several steps.
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