1
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Xiang X, Deng Q, Zheng Y, He Y, Ji D, Vejlupkova Z, Fowler JE, Zhou L. Genome-wide investigation of the LARP gene family: focus on functional identification and transcriptome profiling of ZmLARP6c1 in maize pollen. BMC PLANT BIOLOGY 2024; 24:348. [PMID: 38684961 PMCID: PMC11057080 DOI: 10.1186/s12870-024-05054-z] [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: 01/12/2024] [Accepted: 04/19/2024] [Indexed: 05/02/2024]
Abstract
BACKGROUND The La-related proteins (LARPs) are a superfamily of RNA-binding proteins associated with regulation of gene expression. Evidence points to an important role for post-transcriptional control of gene expression in germinating pollen tubes, which could be aided by RNA-binding proteins. RESULTS In this study, a genome-wide investigation of the LARP proteins in eight plant species was performed. The LARP proteins were classified into three families based on a phylogenetic analysis. The gene structure, conserved motifs, cis-acting elements in the promoter, and gene expression profiles were investigated to provide a comprehensive overview of the evolutionary history and potential functions of ZmLARP genes in maize. Moreover, ZmLARP6c1 was specifically expressed in pollen and ZmLARP6c1 was localized to the nucleus and cytoplasm in maize protoplasts. Overexpression of ZmLARP6c1 enhanced the percentage pollen germination compared with that of wild-type pollen. In addition, transcriptome profiling analysis revealed that differentially expressed genes included PABP homologous genes and genes involved in jasmonic acid and abscisic acid biosynthesis, metabolism, signaling pathways and response in a Zmlarp6c1::Ds mutant and ZmLARP6c1-overexpression line compared with the corresponding wild type. CONCLUSIONS The findings provide a basis for further evolutionary and functional analyses, and provide insight into the critical regulatory function of ZmLARP6c1 in maize pollen germination.
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Affiliation(s)
- Xiaoqin Xiang
- College of Agronomy and Biotechnology, Maize Research Institute, Southwest University, Beibei, Chongqing, 400715, China
| | - Qianxia Deng
- College of Agronomy and Biotechnology, Maize Research Institute, Southwest University, Beibei, Chongqing, 400715, China
| | - Yi Zheng
- College of Agronomy and Biotechnology, Maize Research Institute, Southwest University, Beibei, Chongqing, 400715, China
| | - Yi He
- College of Agronomy and Biotechnology, Maize Research Institute, Southwest University, Beibei, Chongqing, 400715, China
| | - Dongpu Ji
- College of Agronomy and Biotechnology, Maize Research Institute, Southwest University, Beibei, Chongqing, 400715, China
| | - Zuzana Vejlupkova
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - John E Fowler
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - Lian Zhou
- College of Agronomy and Biotechnology, Maize Research Institute, Southwest University, Beibei, Chongqing, 400715, China.
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, 400715, China.
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2
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Abstract
The study of eukaryotic tRNA processing has given rise to an explosion of new information and insights in the last several years. We now have unprecedented knowledge of each step in the tRNA processing pathway, revealing unexpected twists in biochemical pathways, multiple new connections with regulatory pathways, and numerous biological effects of defects in processing steps that have profound consequences throughout eukaryotes, leading to growth phenotypes in the yeast Saccharomyces cerevisiae and to neurological and other disorders in humans. This review highlights seminal new results within the pathways that comprise the life of a tRNA, from its birth after transcription until its death by decay. We focus on new findings and revelations in each step of the pathway including the end-processing and splicing steps, many of the numerous modifications throughout the main body and anticodon loop of tRNA that are so crucial for tRNA function, the intricate tRNA trafficking pathways, and the quality control decay pathways, as well as the biogenesis and biology of tRNA-derived fragments. We also describe the many interactions of these pathways with signaling and other pathways in the cell.
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Affiliation(s)
- Eric M Phizicky
- Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester School of Medicine, Rochester, New York 14642, USA
| | - Anita K Hopper
- Department of Molecular Genetics and Center for RNA Biology, Ohio State University, Columbus, Ohio 43235, USA
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3
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Bayfield MA, Vinayak J, Kerkhofs K, Mansouri-Noori F. La proteins couple use of sequence-specific and non-specific binding modes to engage RNA substrates. RNA Biol 2021; 18:168-177. [PMID: 30777481 PMCID: PMC7928037 DOI: 10.1080/15476286.2019.1582955] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 02/05/2019] [Accepted: 02/05/2019] [Indexed: 12/31/2022] Open
Abstract
La shuttles between the nucleus and cytoplasm where it binds nascent RNA polymerase III (pol III) transcripts and mRNAs, respectively. La protects the 3' end of pol III transcribed RNA precursors, such as pre-tRNAs, through the use of a well-characterized UUU-3'OH binding mode. La proteins are also RNA chaperones, and La-dependent RNA chaperone activity is hypothesized to promote pre-tRNA maturation and translation at cellular and viral internal ribosome entry sites via binding sites distinct from those used for UUU-3'OH recognition. Since the publication of La-UUU-3'OH co-crystal structures, biochemical and genetic experiments have expanded our understanding of how La proteins use UUU-3'OH-independent binding modes to make sequence-independent contacts that can increase affinity for ligands and promote RNA remodeling. Other recent work has also expanded our understanding of how La binds mRNAs through contacts to the poly(A) tail. In this review, we focus on advances in the study of La protein-RNA complex surfaces beyond the description of the La-UUU-3'OH binding mode. We highlight recent advances in the functions of expected canonical nucleic acid interaction surfaces, a heightened appreciation of disordered C-terminal regions, and the nature of sequence-independent RNA determinants in La-RNA target binding. We further discuss how these RNA binding modes may have relevance to the function of the La-related proteins.
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Affiliation(s)
- Mark A. Bayfield
- Department of Biology, York University, Toronto, Ontario, Canada
| | - Jyotsna Vinayak
- Department of Biology, York University, Toronto, Ontario, Canada
| | - Kyra Kerkhofs
- Department of Biology, York University, Toronto, Ontario, Canada
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4
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Mattijssen S, Kozlov G, Fonseca BD, Gehring K, Maraia RJ. LARP1 and LARP4: up close with PABP for mRNA 3' poly(A) protection and stabilization. RNA Biol 2021; 18:259-274. [PMID: 33522422 PMCID: PMC7928012 DOI: 10.1080/15476286.2020.1868753] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 12/06/2020] [Accepted: 12/17/2020] [Indexed: 02/06/2023] Open
Abstract
La-related proteins (LARPs) share a La motif (LaM) followed by an RNA recognition motif (RRM). Together these are termed the La-module that, in the prototypical nuclear La protein and LARP7, mediates binding to the UUU-3'OH termination motif of nascent RNA polymerase III transcripts. We briefly review La and LARP7 activities for RNA 3' end binding and protection from exonucleases before moving to the more recently uncovered poly(A)-related activities of LARP1 and LARP4. Two features shared by LARP1 and LARP4 are direct binding to poly(A) and to the cytoplasmic poly(A)-binding protein (PABP, also known as PABPC1). LARP1, LARP4 and other proteins involved in mRNA translation, deadenylation, and decay, contain PAM2 motifs with variable affinities for the MLLE domain of PABP. We discuss a model in which these PABP-interacting activities contribute to poly(A) pruning of active mRNPs. Evidence that the SARS-CoV-2 RNA virus targets PABP, LARP1, LARP 4 and LARP 4B to control mRNP activity is also briefly reviewed. Recent data suggests that LARP4 opposes deadenylation by stabilizing PABP on mRNA poly(A) tails. Other data suggest that LARP1 can protect mRNA from deadenylation. This is dependent on a PAM2 motif with unique characteristics present in its La-module. Thus, while nuclear La and LARP7 stabilize small RNAs with 3' oligo(U) from decay, LARP1 and LARP4 bind and protect mRNA 3' poly(A) tails from deadenylases through close contact with PABP.Abbreviations: 5'TOP: 5' terminal oligopyrimidine, LaM: La motif, LARP: La-related protein, LARP1: La-related protein 1, MLLE: mademoiselle, NTR: N-terminal region, PABP: cytoplasmic poly(A)-binding protein (PABPC1), Pol III: RNA polymerase III, PAM2: PABP-interacting motif 2, PB: processing body, RRM: RNA recognition motif, SG: stress granule.
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Affiliation(s)
- Sandy Mattijssen
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Guennadi Kozlov
- Department of Biochemistry & Centre for Structural Biology, McGill University, Montreal, Canada
| | | | - Kalle Gehring
- Department of Biochemistry & Centre for Structural Biology, McGill University, Montreal, Canada
| | - Richard J. Maraia
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
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5
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Vinayak J, Marrella SA, Hussain RH, Rozenfeld L, Solomon K, Bayfield MA. Human La binds mRNAs through contacts to the poly(A) tail. Nucleic Acids Res 2019; 46:4228-4240. [PMID: 29447394 PMCID: PMC5934636 DOI: 10.1093/nar/gky090] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 01/31/2018] [Indexed: 12/31/2022] Open
Abstract
In addition to a role in the processing of nascent RNA polymerase III transcripts, La proteins are also associated with promoting cap-independent translation from the internal ribosome entry sites of numerous cellular and viral coding RNAs. La binding to RNA polymerase III transcripts via their common UUU-3’OH motif is well characterized, but the mechanism of La binding to coding RNAs is poorly understood. Using electromobility shift assays and cross-linking immunoprecipitation, we show that in addition to a sequence specific UUU-3’OH binding mode, human La exhibits a sequence specific and length dependent poly(A) binding mode. We demonstrate that this poly(A) binding mode uses the canonical nucleic acid interaction winged helix face of the eponymous La motif, previously shown to be vacant during uridylate binding. We also show that cytoplasmic, but not nuclear La, engages poly(A) RNA in human cells, that La entry into polysomes utilizes the poly(A) binding mode, and that La promotion of translation from the cyclin D1 internal ribosome entry site occurs in competition with cytoplasmic poly(A) binding protein (PABP). Our data are consistent with human La functioning in translation through contacts to the poly(A) tail.
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Affiliation(s)
- Jyotsna Vinayak
- Department of Biology, York University, 4700 Keele St., Life Science Building #327E, Toronto, ON M3J 1P3, Canada
| | - Stefano A Marrella
- Department of Biology, York University, 4700 Keele St., Life Science Building #327E, Toronto, ON M3J 1P3, Canada
| | - Rawaa H Hussain
- Department of Biology, York University, 4700 Keele St., Life Science Building #327E, Toronto, ON M3J 1P3, Canada
| | - Leonid Rozenfeld
- Department of Biology, York University, 4700 Keele St., Life Science Building #327E, Toronto, ON M3J 1P3, Canada
| | - Karine Solomon
- Department of Biology, York University, 4700 Keele St., Life Science Building #327E, Toronto, ON M3J 1P3, Canada
| | - Mark A Bayfield
- Department of Biology, York University, 4700 Keele St., Life Science Building #327E, Toronto, ON M3J 1P3, Canada
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6
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Shigematsu M, Kawamura T, Kirino Y. Generation of 2',3'-Cyclic Phosphate-Containing RNAs as a Hidden Layer of the Transcriptome. Front Genet 2018; 9:562. [PMID: 30538719 PMCID: PMC6277466 DOI: 10.3389/fgene.2018.00562] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 11/06/2018] [Indexed: 01/03/2023] Open
Abstract
Cellular RNA molecules contain phosphate or hydroxyl ends. A 2′,3′-cyclic phosphate (cP) is one of the 3′-terminal forms of RNAs mainly generated from RNA cleavage by ribonucleases. Although transcriptome profiling using RNA-seq has become a ubiquitous tool in biological and medical research, cP-containing RNAs (cP-RNAs) form a hidden transcriptome layer, which is infrequently recognized and characterized, because standard RNA-seq is unable to capture them. Despite cP-RNAs’ invisibility in RNA-seq data, increasing evidence indicates that they are not accumulated simply as non-functional degradation products; rather, they have physiological roles in various biological processes, designating them as noteworthy functional molecules. This review summarizes our current knowledge of cP-RNA biogenesis pathways and their catalytic enzymatic activities, discusses how the cP-RNA generation affects biological processes, and explores future directions to further investigate cP-RNA biology.
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Affiliation(s)
- Megumi Shigematsu
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, United States
| | - Takuya Kawamura
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, United States
| | - Yohei Kirino
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, United States
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7
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Blewett NH, Maraia RJ. La involvement in tRNA and other RNA processing events including differences among yeast and other eukaryotes. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2018; 1861:361-372. [PMID: 29397330 DOI: 10.1016/j.bbagrm.2018.01.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 12/29/2017] [Accepted: 01/17/2018] [Indexed: 10/25/2022]
Abstract
The conserved nuclear RNA-binding factor known as La protein arose in an ancient eukaryote, phylogenetically associated with another eukaryotic hallmark, synthesis of tRNA by RNA polymerase III (RNAP III). Because 3'-oligo(U) is the sequence-specific signal for transcription termination by RNAP III as well as the high affinity binding site for La, the latter is linked to the intranuclear posttranscriptional processing of eukaryotic precursor-tRNAs. The pre-tRNA processing pathway must accommodate a variety of substrates that are destined for both common steps as well as tRNA-specific events. The order of intranuclear pre-tRNA processing steps is mediated in part by three activities derived from interaction with La protein: 3'-end protection from untimely decay by 3' exonucleases, nuclear retention and chaperone activity that helps prevent pre-tRNA misfolding and mischanneling into offline pathways. A focus of this perspective will be on differences between yeast and mammals in the subcellular partitioning of pre-tRNA intermediates and differential interactions with La. We review how this is most relevant to pre-tRNA splicing which occurs in the cytoplasm of yeasts but in nuclei of higher eukaryotes. Also divergent is La architecture, comprised of three RNA-binding domains in organisms in all examined branches of the eukaryal tree except yeast, which have lost the C-terminal RNA recognition motif-2α (RRM2α) domain. We also review emerging data that suggest mammalian La interacts with nuclear pre-tRNA splicing intermediates and may impact this branch of the tRNA maturation pathway. Finally, because La is involved in intranuclear tRNA biogenesis we review relevant aspects of tRNA-associated neurodegenerative diseases. This article is part of a Special Issue entitled: SI: Regulation of tRNA synthesis and modification in physiological conditions and disease edited by Dr. Boguta Magdalena.
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Affiliation(s)
- Nathan H Blewett
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Richard J Maraia
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA; Commissioned Corps, U.S. Public Health Service, Rockville, MD, USA.
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8
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Maraia RJ, Mattijssen S, Cruz-Gallardo I, Conte MR. The La and related RNA-binding proteins (LARPs): structures, functions, and evolving perspectives. WILEY INTERDISCIPLINARY REVIEWS. RNA 2017; 8:10.1002/wrna.1430. [PMID: 28782243 PMCID: PMC5647580 DOI: 10.1002/wrna.1430] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 05/12/2017] [Accepted: 05/15/2017] [Indexed: 01/02/2023]
Abstract
La was first identified as a polypeptide component of ribonucleic protein complexes targeted by antibodies in autoimmune patients and is now known to be a eukaryote cell-ubiquitous protein. Structure and function studies have shown that La binds to a common terminal motif, UUU-3'-OH, of nascent RNA polymerase III (RNAP III) transcripts and protects them from exonucleolytic decay. For precursor-tRNAs, the most diverse and abundant of these transcripts, La also functions as an RNA chaperone that helps to prevent their misfolding. Related to this, we review evidence that suggests that La and its link to RNAP III were significant in the great expansions of the tRNAomes that occurred in eukaryotes. Four families of La-related proteins (LARPs) emerged during eukaryotic evolution with specialized functions. We provide an overview of the high-resolution structural biology of La and LARPs. LARP7 family members most closely resemble La but function with a single RNAP III nuclear transcript, 7SK, or telomerase RNA. A cytoplasmic isoform of La protein as well as LARPs 6, 4, and 1 function in mRNA metabolism and translation in distinct but similar ways, sometimes with the poly(A)-binding protein, and in some cases by direct binding to poly(A)-RNA. New structures of LARP domains, some complexed with RNA, provide novel insights into the functional versatility of these proteins. We also consider LARPs in relation to ancestral La protein and potential retention of links to specific RNA-related pathways. One such link may be tRNA surveillance and codon usage by LARP-associated mRNAs. WIREs RNA 2017, 8:e1430. doi: 10.1002/wrna.1430 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Richard J. Maraia
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD USA
- Commissioned Corps, U.S. Public Health Service, Rockville, MD USA
| | - Sandy Mattijssen
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD USA
| | - Isabel Cruz-Gallardo
- Randall Division of Cell and Molecular Biophysics, King's College London, Guy's Campus, London, UK
| | - Maria R. Conte
- Randall Division of Cell and Molecular Biophysics, King's College London, Guy's Campus, London, UK
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9
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Gogakos T, Brown M, Garzia A, Meyer C, Hafner M, Tuschl T. Characterizing Expression and Processing of Precursor and Mature Human tRNAs by Hydro-tRNAseq and PAR-CLIP. Cell Rep 2017; 20:1463-1475. [PMID: 28793268 PMCID: PMC5564215 DOI: 10.1016/j.celrep.2017.07.029] [Citation(s) in RCA: 146] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 06/15/2017] [Accepted: 07/13/2017] [Indexed: 12/20/2022] Open
Abstract
The participation of tRNAs in fundamental aspects of biology and disease necessitates an accurate, experimentally confirmed annotation of tRNA genes and curation of tRNA sequences. This has been challenging because RNA secondary structure, nucleotide modifications, and tRNA gene multiplicity complicate sequencing and mapping efforts. To address these issues, we developed hydro-tRNAseq, a method based on partial alkaline RNA hydrolysis that generates fragments amenable for sequencing. To identify transcribed tRNA genes, we further complemented this approach with photoactivatable crosslinking and immunoprecipitation (PAR-CLIP) of SSB/La, a conserved protein involved in pre-tRNA processing. Our results show that approximately half of all predicted tRNA genes are transcribed in human cells. We also report nucleotide modification sites and their order of introduction, and we identify tRNA leaders, trailers, and introns. By using complementary sequencing-based methodologies, we present a human tRNA atlas and determine expression levels of mature and processing intermediates of tRNAs in human cells.
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Affiliation(s)
- Tasos Gogakos
- Howard Hughes Medical Institute and Laboratory for RNA Molecular Biology, The Rockefeller University, 1230 York Avenue, Box 186, New York, NY 10065, USA
| | - Miguel Brown
- Howard Hughes Medical Institute and Laboratory for RNA Molecular Biology, The Rockefeller University, 1230 York Avenue, Box 186, New York, NY 10065, USA
| | - Aitor Garzia
- Howard Hughes Medical Institute and Laboratory for RNA Molecular Biology, The Rockefeller University, 1230 York Avenue, Box 186, New York, NY 10065, USA
| | - Cindy Meyer
- Howard Hughes Medical Institute and Laboratory for RNA Molecular Biology, The Rockefeller University, 1230 York Avenue, Box 186, New York, NY 10065, USA
| | - Markus Hafner
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute for Arthritis and Musculoskeletal and Skin Diseases, 50 South Drive, MSC 8024, Bethesda, MD 20892, USA
| | - Thomas Tuschl
- Howard Hughes Medical Institute and Laboratory for RNA Molecular Biology, The Rockefeller University, 1230 York Avenue, Box 186, New York, NY 10065, USA.
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10
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Sommer G, Fedarovich A, Kota V, Rodriguez R, Smith CD, Heise T. Applying a high-throughput fluorescence polarization assay for the discovery of chemical probes blocking La:RNA interactions in vitro and in cells. PLoS One 2017; 12:e0173246. [PMID: 28291789 PMCID: PMC5349447 DOI: 10.1371/journal.pone.0173246] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 02/18/2017] [Indexed: 12/14/2022] Open
Abstract
The RNA-binding protein La is overexpressed in a number of tumor tissues and is thought to support tumorigenesis by binding to and facilitating the expression of mRNAs encoding tumor-promoting and anti-apoptotic factors. Hence, small molecules able to block the binding of La to specific RNAs could have a therapeutic impact by reducing the expression of tumor-promoting and anti-apoptotic factors. Toward this novel therapeutic strategy, we aimed to develop a high-throughput fluorescence polarization assay to screen small compound libraries for molecules blocking the binding of La to an RNA element derived from cyclin D1 mRNA. Herein, we make use of a robust fluorescence polarization assay and the validation of primary hits by electrophoretic mobility shift assays. We showed recently that La protects cells against cisplatin treatment by stimulating the protein synthesis of the anti-apoptotic factor Bcl2. Here, we show by RNA immunoprecipitation experiments that one small compound specifically impairs the association of La with Bcl2 mRNA in cells and sensitizes cells for cipslatin-induced cell death. In summary, we report the application of a high-throughput fluorescence polarization assay to identify small compounds that impair the binding of La to target RNAs in vitro and in cells.
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Affiliation(s)
- Gunhild Sommer
- Medical University of South Carolina, Department of Biochemistry & Molecular Biology, 173 Ashley Avenue, Charleston, SC, United States of America
| | - Alena Fedarovich
- Medical University of South Carolina, Department of Biochemistry & Molecular Biology, 173 Ashley Avenue, Charleston, SC, United States of America
| | - Venkatesh Kota
- Medical University of South Carolina, Department of Biochemistry & Molecular Biology, 173 Ashley Avenue, Charleston, SC, United States of America
| | - Reycel Rodriguez
- Medical University of South Carolina, Department of Biochemistry & Molecular Biology, 173 Ashley Avenue, Charleston, SC, United States of America
| | - Charles D. Smith
- Department of Pharmaceutical and Biomedical Sciences, 173 Ashley Avenue, Charleston, SC, United States of America
| | - Tilman Heise
- Medical University of South Carolina, Department of Biochemistry & Molecular Biology, 173 Ashley Avenue, Charleston, SC, United States of America
- * E-mail:
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11
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Mattijssen S, Maraia RJ. LARP4 Is Regulated by Tumor Necrosis Factor Alpha in a Tristetraprolin-Dependent Manner. Mol Cell Biol 2016; 36:574-84. [PMID: 26644407 PMCID: PMC4751689 DOI: 10.1128/mcb.00804-15] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 09/14/2015] [Accepted: 11/20/2015] [Indexed: 01/09/2023] Open
Abstract
LARP4 is a protein with unknown function that independently binds to poly(A) RNA, RACK1, and the poly(A)-binding protein (PABPC1). Here, we report on its regulation. We found a conserved AU-rich element (ARE) in the human LARP4 mRNA 3' untranslated region (UTR). This ARE, but not its antisense version or a point-mutated version, significantly decreased the stability of β-globin reporter mRNA. We found that overexpression of tristetraprolin (TTP), but not its RNA binding mutant or the other ARE-binding proteins tested, decreased cellular LARP4 levels. RNA coimmunoprecipitation showed that TTP specifically associated with LARP4 mRNA in vivo. Consistent with this, mouse LARP4 accumulated to higher levels in TTP gene knockout (KO) cells than in control cells. Stimulation of WT cells with tumor necrosis factor alpha (TNF-α), which rapidly induces TTP, robustly decreased LARP4 with a coincident time course but had no such effect on LARP4B or La protein or on LARP4 in the TTP KO cells. The TNF-α-induced TTP pulse was followed by a transient decrease in LARP4 mRNA that was quickly followed by a subsequent transient decrease in LARP4 protein. Involvement of LARP4 as a target of TNF-α-TTP regulation provides a clue as to how its functional activity may be used in a physiologic pathway.
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Affiliation(s)
- Sandy Mattijssen
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
| | - Richard J Maraia
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA Commissioned Corps, U.S. Public Health Service, Washington, DC, USA
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12
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Stavraka C, Blagden S. The La-Related Proteins, a Family with Connections to Cancer. Biomolecules 2015; 5:2701-22. [PMID: 26501340 PMCID: PMC4693254 DOI: 10.3390/biom5042701] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 09/21/2015] [Accepted: 10/07/2015] [Indexed: 01/09/2023] Open
Abstract
The evolutionarily-conserved La-related protein (LARP) family currently comprises Genuine La, LARP1, LARP1b, LARP4, LARP4b, LARP6 and LARP7. Emerging evidence suggests each LARP has a distinct role in transcription and/or mRNA translation that is attributable to subtle sequence variations within their La modules and specific C-terminal domains. As emerging research uncovers the function of each LARP, it is evident that La, LARP1, LARP6, LARP7 and possibly LARP4a and 4b are dysregulated in cancer. Of these, LARP1 is the first to be demonstrated to drive oncogenesis. Here, we review the role of each LARP and the evidence linking it to malignancy. We discuss a future strategy of targeting members of this protein family as cancer therapy.
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Affiliation(s)
- Chara Stavraka
- Ovarian Cancer Research Centre, Institute for Reproductive and Developmental Biology, Imperial College, Du Cane Road, London W12 0HS, UK.
| | - Sarah Blagden
- Ovarian Cancer Research Centre, Institute for Reproductive and Developmental Biology, Imperial College, Du Cane Road, London W12 0HS, UK.
- Department of Oncology, University of Oxford, Churchill Hospital, Old Road, Oxford OX3 7LE, UK.
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13
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Chasapis CT, Argyriou AI, Apostolidi M, Konstantinidou P, Bentrop D, Stathopoulos C, Spyroulias GA. (1)H, (13)C and (15)N backbone and side-chain resonance assignment of the LAM-RRM1 N-terminal module of La protein from Dictyostelium discoideum. BIOMOLECULAR NMR ASSIGNMENTS 2015; 9:303-307. [PMID: 25687647 DOI: 10.1007/s12104-015-9597-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 02/09/2015] [Indexed: 06/04/2023]
Abstract
The N-terminal half of La protein consists of two concatenated motifs: La motif (LAM) and the N-terminal RNA recognition motif (RRM1) both of which are responsible for poly(U) RNA binding. Here, we present the backbone and side-chain assignments of the (1)H, (13)C and (15)N resonances of the 191-residue LAM-RRM1 region of the La protein from the lower eukaryote Dictyostelium discoideum and its secondary structure prediction.
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Affiliation(s)
| | | | - Maria Apostolidi
- Department of Biochemistry, School of Medicine, University of Patras, 26504, Patras, Greece
| | | | - Detlef Bentrop
- Institute of Physiology II, University of Freiburg, 79104, Freiburg, Germany
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14
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Argyriou AI, Chasapis CT, Apostolidi M, Konstantinidou P, Stathopoulos C, Bentrop D, Spyroulias GA. Backbone and side chain NMR assignment, along with the secondary structure prediction of RRM2 domain of La protein from a lower eukaryote exhibiting identical structural organization with its human homolog. BIOMOLECULAR NMR ASSIGNMENTS 2015; 9:219-222. [PMID: 25281001 DOI: 10.1007/s12104-014-9578-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 09/26/2014] [Indexed: 06/03/2023]
Abstract
The La protein (Lupus antigen), a key mediator during biogenesis of RNA polymerase III transcripts, contains a characteristic La motif and one or two RNA recognition motif (RRM) domains, depending on the organism of origin. The RRM1 domain is conserved in higher eukaryotes and located in the N-terminal region, whereas the C-terminal RRM2 domain is absent in most lower eukaryotes and its specific role remains, so far, uncharacterized. Here, we present the backbone and side-chain assignment of the (1)H, (13)C and (15)N resonances of RRM2 of La protein from Dictyostelium discoideum. Interestingly, the La protein in this lower eukaryote, exhibits high homology to its human counterpart. Moreover, it contains two RRM domains, instead of one, raising questions on its evolutionary origin and the putative role of RRM2 in vivo. We also provide its secondary structure as predicted by the TALOS+ online tool.
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15
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Uchikawa E, Natchiar KS, Han X, Proux F, Roblin P, Zhang E, Durand A, Klaholz BP, Dock-Bregeon AC. Structural insight into the mechanism of stabilization of the 7SK small nuclear RNA by LARP7. Nucleic Acids Res 2015; 43:3373-88. [PMID: 25753663 PMCID: PMC4381077 DOI: 10.1093/nar/gkv173] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 02/20/2015] [Indexed: 12/17/2022] Open
Abstract
The non-coding RNA 7SK is the scaffold for a small nuclear ribonucleoprotein (7SKsnRNP) which regulates the function of the positive transcription elongation factor P-TEFb in the control of RNA polymerase II elongation in metazoans. The La-related protein LARP7 is a component of the 7SKsnRNP required for stability and function of the RNA. To address the function of LARP7 we determined the crystal structure of its La module, which binds a stretch of uridines at the 3′-end of 7SK. The structure shows that the penultimate uridine is tethered by the two domains, the La-motif and the RNA-recognition motif (RRM1), and reveals that the RRM1 is significantly smaller and more exposed than in the La protein. Sequence analysis suggests that this impacts interaction with 7SK. Binding assays, footprinting and small-angle scattering experiments show that a second RRM domain located at the C-terminus binds the apical loop of the 3′ hairpin of 7SK, while the N-terminal domains bind at its foot. Our results suggest that LARP7 uses both its N- and C-terminal domains to stabilize 7SK in a closed structure, which forms by joining conserved sequences at the 5′-end with the foot of the 3′ hairpin and has thus functional implications.
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Affiliation(s)
- Emiko Uchikawa
- Department of Integrated Structural Biology, Centre for Integrative Biology (CBI), IGBMC (Institute of Genetics and of Molecular and Cellular Biology, 67404 Illkirch, France Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France Université de Strasbourg, 67000 Strasbourg, France
| | - Kundhavai S Natchiar
- Department of Integrated Structural Biology, Centre for Integrative Biology (CBI), IGBMC (Institute of Genetics and of Molecular and Cellular Biology, 67404 Illkirch, France Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France Université de Strasbourg, 67000 Strasbourg, France
| | - Xiao Han
- Department of functional genomics, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), 75005 Paris, France CNRS UMR 8197, 75005 Paris, France INSERM U1024, 75005 Paris, France Key Laboratory of Brain Functional Genomics, East China Normal University (ECNU), 200241 Shanghai, PR China
| | - Florence Proux
- Department of functional genomics, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), 75005 Paris, France CNRS UMR 8197, 75005 Paris, France INSERM U1024, 75005 Paris, France
| | - Pierre Roblin
- SOLEIL Synchrotron, 91192 Gif-sur-Yvette, France INRA-URBIA, 44316 Nantes, France
| | - Elodie Zhang
- Department of functional genomics, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), 75005 Paris, France CNRS UMR 8197, 75005 Paris, France INSERM U1024, 75005 Paris, France
| | - Alexandre Durand
- Department of Integrated Structural Biology, Centre for Integrative Biology (CBI), IGBMC (Institute of Genetics and of Molecular and Cellular Biology, 67404 Illkirch, France Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France Université de Strasbourg, 67000 Strasbourg, France
| | - Bruno P Klaholz
- Department of Integrated Structural Biology, Centre for Integrative Biology (CBI), IGBMC (Institute of Genetics and of Molecular and Cellular Biology, 67404 Illkirch, France Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France Université de Strasbourg, 67000 Strasbourg, France
| | - Anne-Catherine Dock-Bregeon
- Department of functional genomics, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), 75005 Paris, France CNRS UMR 8197, 75005 Paris, France INSERM U1024, 75005 Paris, France
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16
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Screening for antifibrotic compounds using high throughput system based on fluorescence polarization. BIOLOGY 2014; 3:281-94. [PMID: 24833510 PMCID: PMC4085608 DOI: 10.3390/biology3020281] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Revised: 02/28/2014] [Accepted: 04/01/2014] [Indexed: 02/06/2023]
Abstract
Fibroproliferative diseases are one of the leading causes of death worldwide. They are characterized by reactive fibrosis caused by uncontrolled synthesis of type I collagen. There is no cure for fibrosis and development of therapeutics that can inhibit collagen synthesis is urgently needed. Collagen α1(I) mRNA and α2(I) mRNA encode for type I collagen and they have a unique 5' stem-loop structure in their 5' untranslated regions (5'SL). Collagen 5'SL binds protein LARP6 with high affinity and specificity. The interaction between LARP6 and the 5'SL is critical for biosynthesis of type I collagen and development of fibrosis in vivo. Therefore, this interaction represents is an ideal target to develop antifibrotic drugs. A high throughput system to screen for chemical compounds that can dissociate LARP6 from 5'SL has been developed. It is based on fluorescence polarization and can be adapted to screen for inhibitors of other protein-RNA interactions. Screening of 50,000 chemical compounds yielded a lead compound that can inhibit type I collagen synthesis at nanomolar concentrations. The development, characteristics, and critical appraisal of this assay are presented.
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17
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Evolutionary conservation and expression of human RNA-binding proteins and their role in human genetic disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 825:1-55. [PMID: 25201102 DOI: 10.1007/978-1-4939-1221-6_1] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
RNA-binding proteins (RBPs) are effectors and regulators of posttranscriptional gene regulation (PTGR). RBPs regulate stability, maturation, and turnover of all RNAs, often binding thousands of targets at many sites. The importance of RBPs is underscored by their dysregulation or mutations causing a variety of developmental and neurological diseases. This chapter globally discusses human RBPs and provides a brief introduction to their identification and RNA targets. We review RBPs based on common structural RNA-binding domains, study their evolutionary conservation and expression, and summarize disease associations of different RBP classes.
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18
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Dibrov SM, Parsons J, Carnevali M, Zhou S, Rynearson KD, Ding K, Garcia Sega E, Brunn ND, Boerneke MA, Castaldi MP, Hermann T. Hepatitis C virus translation inhibitors targeting the internal ribosomal entry site. J Med Chem 2013; 57:1694-707. [PMID: 24138284 DOI: 10.1021/jm401312n] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The internal ribosome entry site (IRES) in the 5' untranslated region (UTR) of the hepatitis C virus (HCV) genome initiates translation of the viral polyprotein precursor. The unique structure and high sequence conservation of the 5' UTR render the IRES RNA a potential target for the development of selective viral translation inhibitors. Here, we provide an overview of approaches to block HCV IRES function by nucleic acid, peptide, and small molecule ligands. Emphasis will be given to the IRES subdomain IIa, which currently is the most advanced target for small molecule inhibitors of HCV translation. The subdomain IIa behaves as an RNA conformational switch. Selective ligands act as translation inhibitors by locking the conformation of the RNA switch. We review synthetic procedures for inhibitors as well as structural and functional studies of the subdomain IIa target and its ligand complexes.
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Affiliation(s)
- Sergey M Dibrov
- Department of Chemistry and Biochemistry, University of California, San Diego , 9500 Gilman Drive, La Jolla, California 92093, United States
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19
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Arias A, Emmott E, Vashist S, Goodfellow I. Progress towards the prevention and treatment of norovirus infections. Future Microbiol 2013; 8:1475-87. [PMID: 24199805 PMCID: PMC3904215 DOI: 10.2217/fmb.13.109] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Noroviruses are now recognized as the major cause of acute gastroenteritis in the developed world, yet our ability to prevent and control infection is limited. Recent work has highlighted that, while typically an acute infection in the population, immunocompromised patients often experience long-term infections that may last many years. This cohort of patients and those regularly exposed to infectious material, for example, care workers and others, would benefit greatly from the development of a vaccine or antiviral therapy. While a licensed vaccine or antiviral has yet to be developed, work over the past 10 years in this area has intensified and trials with a vaccine candidate have proven promising. Numerous antiviral targets and small molecule inhibitors that have efficacy in cell culture have now been identified; however, further studies in this area are required in order to make these suitable for clinical use.
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Affiliation(s)
- Armando Arias
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke’s Hospital, Hills Road, Cambridge, CB2 2QQ, UK
| | - Edward Emmott
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke’s Hospital, Hills Road, Cambridge, CB2 2QQ, UK
| | - Surender Vashist
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke’s Hospital, Hills Road, Cambridge, CB2 2QQ, UK
| | - Ian Goodfellow
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke’s Hospital, Hills Road, Cambridge, CB2 2QQ, UK
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20
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Hussain RH, Zawawi M, Bayfield MA. Conservation of RNA chaperone activity of the human La-related proteins 4, 6 and 7. Nucleic Acids Res 2013; 41:8715-25. [PMID: 23887937 PMCID: PMC3794603 DOI: 10.1093/nar/gkt649] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 06/28/2013] [Accepted: 07/03/2013] [Indexed: 12/22/2022] Open
Abstract
The La module is a conserved tandem arrangement of a La motif and RNA recognition motif whose function has been best characterized in genuine La proteins. The best-characterized substrates of La proteins are pre-tRNAs, and previous work using tRNA mediated suppression in Schizosaccharomyces pombe has demonstrated that yeast and human La enhance the maturation of these using two distinguishable activities: UUU-3'OH-dependent trailer binding/protection and a UUU-3'OH independent activity related to RNA chaperone function. The La module has also been identified in several conserved families of La-related proteins (LARPs) that engage other RNAs, but their mode of RNA binding and function(s) are not well understood. We demonstrate that the La modules of the human LARPs 4, 6 and 7 are also active in tRNA-mediated suppression, even in the absence of stable UUU-3'OH trailer protection. Rather, the capacity of these to enhance pre-tRNA maturation is associated with RNA chaperone function, which we demonstrate to be a conserved activity for each hLARP in vitro. Our work reveals insight into the mechanisms by which La module containing proteins discriminate RNA targets and demonstrates that RNA chaperone activity is a conserved function across representative members of the La motif-containing superfamily.
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Affiliation(s)
| | | | - Mark A. Bayfield
- Department of Biology, York University, Toronto, Ontario M3J 1P3, Canada
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21
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Maraia RJ, Lamichhane TN. 3' processing of eukaryotic precursor tRNAs. WILEY INTERDISCIPLINARY REVIEWS-RNA 2012; 2:362-75. [PMID: 21572561 DOI: 10.1002/wrna.64] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Biogenesis of eukaryotic tRNAs requires transcription by RNA polymerase III and subsequent processing. 5' processing of precursor tRNA occurs by a single mechanism, cleavage by RNase P, and usually occurs before 3' processing although some conditions allow observation of the 3'-first pathway. 3' processing is relatively complex and is the focus of this review. Precursor RNA 3'-end formation begins with pol III termination generating a variable length 3'-oligo(U) tract that represents an underappreciated and previously unreviewed determinant of processing. Evidence that the pol III-intrinsic 3'exonuclease activity mediated by Rpc11p affects 3'oligo(U) length is reviewed. In addition to multiple 3' nucleases, precursor tRNA(pre-tRNA) processing involves La and Lsm, distinct oligo(U)-binding proteins with proposed chaperone activities. 3' processing is performed by the endonuclease RNase Z or the exonuclease Rex1p (possibly others) along alternate pathways conditional on La. We review a Schizosaccharomyces pombe tRNA reporter system that has been used to distinguish two chaperone activities of La protein to its two conserved RNA binding motifs. Pre-tRNAs with structural impairments are degraded by a nuclear surveillance system that mediates polyadenylation by the TRAMP complex followed by 3'-digestion by the nuclear exosome which appears to compete with 3' processing. We also try to reconcile limited data on pre-tRNA processing and Lsm proteins which largely affect precursors but not mature tRNAs.A pathway is proposed in which 3' oligo(U) length is a primary determinant of La binding with subsequent steps distinguished by 3'-endo versus exo nucleases,chaperone activities, and nuclear surveillance.
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Affiliation(s)
- Richard J Maraia
- Intramural Research Program, Eunice Kennedy Shriver NationalInstitute of Child Health and Human Development, NationalInstitutes of Health, Bethesda, MD, USA.
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22
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Andreev DE, Hirnet J, Terenin IM, Dmitriev SE, Niepmann M, Shatsky IN. Glycyl-tRNA synthetase specifically binds to the poliovirus IRES to activate translation initiation. Nucleic Acids Res 2012; 40:5602-14. [PMID: 22373920 PMCID: PMC3384309 DOI: 10.1093/nar/gks182] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Adaptation to the host cell environment to efficiently take-over the host cell's machinery is crucial in particular for small RNA viruses like picornaviruses that come with only small RNA genomes and replicate exclusively in the cytosol. Their Internal Ribosome Entry Site (IRES) elements are specific RNA structures that facilitate the 5′ end-independent internal initiation of translation both under normal conditions and when the cap-dependent host protein synthesis is shut-down in infected cells. A longstanding issue is which host factors play a major role in this internal initiation. Here, we show that the functionally most important domain V of the poliovirus IRES uses tRNAGly anticodon stem–loop mimicry to recruit glycyl-tRNA synthetase (GARS) to the apical part of domain V, adjacent to the binding site of the key initiation factor eIF4G. The binding of GARS promotes the accommodation of the initiation region of the IRES in the mRNA binding site of the ribosome, thereby greatly enhancing the activity of the IRES at the step of the 48S initiation complex formation. Moonlighting functions of GARS that may be additionally needed for other events of the virus–host cell interaction are discussed.
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Affiliation(s)
- Dmitri E Andreev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Building 40, Moscow 119991, Russian Federation
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23
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Yang R, Gaidamakov SA, Xie J, Lee J, Martino L, Kozlov G, Crawford AK, Russo AN, Conte MR, Gehring K, Maraia RJ. La-related protein 4 binds poly(A), interacts with the poly(A)-binding protein MLLE domain via a variant PAM2w motif, and can promote mRNA stability. Mol Cell Biol 2011; 31:542-56. [PMID: 21098120 PMCID: PMC3028612 DOI: 10.1128/mcb.01162-10] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2010] [Revised: 11/05/2010] [Accepted: 11/12/2010] [Indexed: 12/19/2022] Open
Abstract
The conserved RNA binding protein La recognizes UUU-3'OH on its small nuclear RNA ligands and stabilizes them against 3'-end-mediated decay. We report that newly described La-related protein 4 (LARP4) is a factor that can bind poly(A) RNA and interact with poly(A) binding protein (PABP). Yeast two-hybrid analysis and reciprocal immunoprecipitations (IPs) from HeLa cells revealed that LARP4 interacts with RACK1, a 40S ribosome- and mRNA-associated protein. LARP4 cosediments with 40S ribosome subunits and polyribosomes, and its knockdown decreases translation. Mutagenesis of the RNA binding or PABP interaction motifs decrease LARP4 association with polysomes. Several translation and mRNA metabolism-related proteins use a PAM2 sequence containing a critical invariant phenylalanine to make direct contact with the MLLE domain of PABP, and their competition for the MLLE is thought to regulate mRNA homeostasis. Unlike all ∼150 previously analyzed PAM2 sequences, LARP4 contains a variant PAM2 (PAM2w) with tryptophan in place of the phenylalanine. Binding and nuclear magnetic resonance (NMR) studies have shown that a peptide representing LARP4 PAM2w interacts with the MLLE of PABP within the affinity range measured for other PAM2 motif peptides. A cocrystal of PABC bound to LARP4 PAM2w shows tryptophan in the pocket in PABC-MLLE otherwise occupied by phenylalanine. We present evidence that LARP4 expression stimulates luciferase reporter activity by promoting mRNA stability, as shown by mRNA decay analysis of luciferase and cellular mRNAs. We propose that LARP4 activity is integrated with other PAM2 protein activities by PABP as part of mRNA homeostasis.
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Affiliation(s)
- Ruiqing Yang
- Intramural Research Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom, Department of Biochemistry, McGill University, Montreal, QC, Canada, Commissioned Corps, U.S. Public Health Service, Washington, DC
| | - Sergei A. Gaidamakov
- Intramural Research Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom, Department of Biochemistry, McGill University, Montreal, QC, Canada, Commissioned Corps, U.S. Public Health Service, Washington, DC
| | - Jingwei Xie
- Intramural Research Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom, Department of Biochemistry, McGill University, Montreal, QC, Canada, Commissioned Corps, U.S. Public Health Service, Washington, DC
| | - Joowon Lee
- Intramural Research Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom, Department of Biochemistry, McGill University, Montreal, QC, Canada, Commissioned Corps, U.S. Public Health Service, Washington, DC
| | - Luigi Martino
- Intramural Research Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom, Department of Biochemistry, McGill University, Montreal, QC, Canada, Commissioned Corps, U.S. Public Health Service, Washington, DC
| | - Guennadi Kozlov
- Intramural Research Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom, Department of Biochemistry, McGill University, Montreal, QC, Canada, Commissioned Corps, U.S. Public Health Service, Washington, DC
| | - Amanda K. Crawford
- Intramural Research Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom, Department of Biochemistry, McGill University, Montreal, QC, Canada, Commissioned Corps, U.S. Public Health Service, Washington, DC
| | - Amy N. Russo
- Intramural Research Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom, Department of Biochemistry, McGill University, Montreal, QC, Canada, Commissioned Corps, U.S. Public Health Service, Washington, DC
| | - Maria R. Conte
- Intramural Research Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom, Department of Biochemistry, McGill University, Montreal, QC, Canada, Commissioned Corps, U.S. Public Health Service, Washington, DC
| | - Kalle Gehring
- Intramural Research Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom, Department of Biochemistry, McGill University, Montreal, QC, Canada, Commissioned Corps, U.S. Public Health Service, Washington, DC
| | - Richard J. Maraia
- Intramural Research Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom, Department of Biochemistry, McGill University, Montreal, QC, Canada, Commissioned Corps, U.S. Public Health Service, Washington, DC
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24
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Abstract
tRNA biology has come of age, revealing an unprecedented level of understanding and many unexpected discoveries along the way. This review highlights new findings on the diverse pathways of tRNA maturation, and on the formation and function of a number of modifications. Topics of special focus include the regulation of tRNA biosynthesis, quality control tRNA turnover mechanisms, widespread tRNA cleavage pathways activated in response to stress and other growth conditions, emerging evidence of signaling pathways involving tRNA and cleavage fragments, and the sophisticated intracellular tRNA trafficking that occurs during and after biosynthesis.
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Affiliation(s)
- Eric M Phizicky
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine, Rochester, New York 14642, USA.
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25
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Schäffler K, Schulz K, Hirmer A, Wiesner J, Grimm M, Sickmann A, Fischer U. A stimulatory role for the La-related protein 4B in translation. RNA (NEW YORK, N.Y.) 2010; 16:1488-99. [PMID: 20573744 PMCID: PMC2905749 DOI: 10.1261/rna.2146910] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
La-related proteins (LARPs) belong to an evolutionarily conserved family of factors with predicted roles in RNA metabolism. Here, we have analyzed the cellular interactions and function of LARP4B, a thus far uncharacterized member of the LARP family. We show that LARP4B is a cytosolic protein that accumulates upon arsenite treatment in cellular stress granules. Biochemical experiments further uncovered an interaction of LARP4B with the cytosolic poly(A) binding protein 1 (PABPC1) and the receptor for activated C Kinase (RACK1), a component of the 40S ribosomal subunit. Under physiological conditions, LARP4B co-sedimented with polysomes in cellular extracts, suggesting a role in translation. In agreement with this notion, overexpression of LARP4B stimulated protein synthesis, whereas knockdown of the factor by RNA interference impaired translation of a large number of cellular mRNAs. In sum, we identified LARP4B as a stimulatory factor of translation. We speculate that LARP4B exerts its function by bridging mRNA factors of the 3' end with initiating ribosomes.
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Affiliation(s)
- Katrin Schäffler
- Department of Biochemistry, Theodor Boveri-Institute, University of Wuerzburg, Wuerzburg D-97074, Germany
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26
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Bayfield MA, Yang R, Maraia RJ. Conserved and divergent features of the structure and function of La and La-related proteins (LARPs). BIOCHIMICA ET BIOPHYSICA ACTA 2010; 1799:365-78. [PMID: 20138158 PMCID: PMC2860065 DOI: 10.1016/j.bbagrm.2010.01.011] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2009] [Revised: 01/08/2010] [Accepted: 01/27/2010] [Indexed: 12/19/2022]
Abstract
Genuine La proteins contain two RNA binding motifs, a La motif (LAM) followed by a RNA recognition motif (RRM), arranged in a unique way to bind RNA. These proteins interact with an extensive variety of cellular RNAs and exhibit activities in two broad categories: i) to promote the metabolism of nascent pol III transcripts, including precursor-tRNAs, by binding to their common, UUU-3'OH containing ends, and ii) to modulate the translation of certain mRNAs involving an unknown binding mechanism. Characterization of several La-RNA crystal structures as well as biochemical studies reveal insight into their unique two-motif domain architecture and how the LAM recognizes UUU-3'OH while the RRM binds other parts of a pre-tRNA. Recent studies of members of distinct families of conserved La-related proteins (LARPs) indicate that some of these harbor activity related to genuine La proteins, suggesting that their UUU-3'OH binding mode has been appropriated for the assembly and regulation of a specific snRNP (e.g., 7SK snRNP assembly by hLARP7/PIP7S). Analyses of other LARP family members suggest more diverged RNA binding modes and specialization for cytoplasmic mRNA-related functions. Thus it appears that while genuine La proteins exhibit broad general involvement in both snRNA-related and mRNA-related functions, different LARP families may have evolved specialized activities in either snRNA or mRNA-related functions. In this review, we summarize recent progress that has led to greater understanding of the structure and function of La proteins and their roles in tRNA processing and RNP assembly dynamics, as well as progress on the different LARPs.
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Affiliation(s)
- Mark A Bayfield
- Department of Biology, York University, Toronto, ON, Canada.
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Bernhart E, Kollroser M, Rechberger G, Reicher H, Heinemann A, Schratl P, Hallström S, Wintersperger A, Nusshold C, DeVaney T, Zorn-Pauly K, Malli R, Graier W, Malle E, Sattler W. Lysophosphatidic acid receptor activation affects the C13NJ microglia cell line proteome leading to alterations in glycolysis, motility, and cytoskeletal architecture. Proteomics 2010; 10:141-58. [PMID: 19899077 DOI: 10.1002/pmic.200900195] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Microglia, the immunocompetent cells of the CNS, are rapidly activated in response to injury and microglia migration towards and homing at damaged tissue plays a key role in CNS regeneration. Lysophosphatidic acid (LPA) is involved in signaling events evoking microglia responses through cognate G protein-coupled receptors. Here we show that human immortalized C13NJ microglia express LPA receptor subtypes LPA(1), LPA(2), and LPA(3) on mRNA and protein level. LPA activation of C13NJ cells induced Rho and extracellular signal-regulated kinase activation and enhanced cellular ATP production. In addition, LPA induced process retraction, cell spreading, led to pronounced changes of the actin cytoskeleton and reduced cell motility, which could be reversed by inhibition of Rho activity. To get an indication about LPA-induced global alterations in protein expression patterns a 2-D DIGE/LC-ESI-MS proteomic approach was applied. On the proteome level the most prominent changes in response to LPA were observed for glycolytic enzymes and proteins regulating cell motility and/or cytoskeletal dynamics. The present findings suggest that naturally occurring LPA is a potent regulator of microglia biology. This might be of particular relevance in the pathophysiological context of neurodegenerative disorders where LPA concentrations can be significantly elevated in the CNS.
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Affiliation(s)
- Eva Bernhart
- Institute of Molecular Biology and Biochemistry, Medical University of Graz, Austria
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Cai L, Fritz D, Stefanovic L, Stefanovic B. Binding of LARP6 to the conserved 5' stem-loop regulates translation of mRNAs encoding type I collagen. J Mol Biol 2010; 395:309-26. [PMID: 19917293 PMCID: PMC2826804 DOI: 10.1016/j.jmb.2009.11.020] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2009] [Revised: 11/05/2009] [Accepted: 11/09/2009] [Indexed: 10/20/2022]
Abstract
Type I collagen is the most abundant protein in the human body, produced by folding of two alpha1(I) polypeptides and one alpha2(I) polypeptide into the triple helix. A conserved stem-loop structure is found in the 5' untranslated region of collagen mRNAs, encompassing the translation start codon. We cloned La ribonucleoprotein domain family member 6 (LARP6) as the protein that binds the collagen 5' stem-loop in a sequence-specific manner. LARP6 has a distinctive bipartite RNA binding domain not found in other members of the La superfamily. LARP6 interacts with the two single-stranded regions of the 5' stem-loop. The K(d) for binding of LARP6 to the 5' stem-loop is 1.4 nM. LARP6 binds the 5' stem-loop in both the nucleus and the cytoplasm. In the cytoplasm, LARP6 does not associate with polysomes; however, overexpression of LARP6 blocks ribosomal loading on collagen mRNAs. Knocking down LARP6 by small interfering RNA also decreased polysomal loading of collagen mRNAs, suggesting that it regulates translation. Collagen protein is synthesized at discrete regions of the endoplasmic reticulum. Using collagen-GFP (green fluorescent protein) reporter protein, we could reproduce this focal pattern of synthesis, but only when the reporter was encoded by mRNA with the 5' stem-loop and in the presence of LARP6. When the reporter was encoded by mRNA without the 5' stem-loop, or in the absence of LARP6, it accumulated diffusely throughout the endoplasmic reticulum. This indicates that LARP6 activity is needed for focal synthesis of collagen polypeptides. We postulate that the LARP6-dependent mechanism increases local concentration of collagen polypeptides for more efficient folding of the collagen heterotrimer.
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Affiliation(s)
- Le Cai
- Department of Biomedical Sciences, College of Medicine, Tallahassee, FL 32306, USA
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Huang Y, Ji L, Huang Q, Vassylyev DG, Chen X, Ma JB. Structural insights into mechanisms of the small RNA methyltransferase HEN1. Nature 2009; 461:823-7. [PMID: 19812675 PMCID: PMC5125239 DOI: 10.1038/nature08433] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2009] [Accepted: 08/17/2009] [Indexed: 12/17/2022]
Abstract
RNA silencing is a conserved regulatory mechanism in fungi, plants and animals that regulates gene expression and defence against viruses and transgenes. Small silencing RNAs of approximately 20-30 nucleotides and their associated effector proteins, the Argonaute family proteins, are the central components in RNA silencing. A subset of small RNAs, such as microRNAs and small interfering RNAs (siRNAs) in plants, Piwi-interacting RNAs in animals and siRNAs in Drosophila, requires an additional crucial step for their maturation; that is, 2'-O-methylation on the 3' terminal nucleotide. A conserved S-adenosyl-l-methionine-dependent RNA methyltransferase, HUA ENHANCER 1 (HEN1), and its homologues are responsible for this specific modification. Here we report the 3.1 A crystal structure of full-length HEN1 from Arabidopsis in complex with a 22-nucleotide small RNA duplex and cofactor product S-adenosyl-l-homocysteine. Highly cooperative recognition of the small RNA substrate by multiple RNA binding domains and the methyltransferase domain in HEN1 measures the length of the RNA duplex and determines the substrate specificity. Metal ion coordination by both 2' and 3' hydroxyls on the 3'-terminal nucleotide and four invariant residues in the active site of the methyltransferase domain suggests a novel Mg(2+)-dependent 2'-O-methylation mechanism.
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Affiliation(s)
- Ying Huang
- Department of Biochemistry and Molecular Genetics, Schools of Medicine and Dentistry, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
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Curry S, Kotik-Kogan O, Conte MR, Brick P. Getting to the end of RNA: structural analysis of protein recognition of 5' and 3' termini. BIOCHIMICA ET BIOPHYSICA ACTA 2009; 1789:653-66. [PMID: 19619683 DOI: 10.1016/j.bbagrm.2009.07.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2009] [Revised: 07/07/2009] [Accepted: 07/09/2009] [Indexed: 10/20/2022]
Abstract
The specific recognition by proteins of the 5' and 3' ends of RNA molecules is an important facet of many cellular processes, including RNA maturation, regulation of translation initiation and control of gene expression by degradation and RNA interference. The aim of this review is to survey recent structural analyses of protein binding domains that specifically bind to the extreme 5' or 3' termini of RNA. For reasons of space and because their interactions are also governed by catalytic considerations, we have excluded enzymes that modify the 5' and 3' extremities of RNA. It is clear that there is enormous structural diversity among the proteins that have evolved to bind to the ends of RNA molecules. Moreover, they commonly exhibit conformational flexibility that appears to be important for binding and regulation of the interaction. This flexibility has sometimes complicated the interpretation of structural results and presents significant challenges for future investigations.
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Affiliation(s)
- Stephen Curry
- Biophysics Section, Blackett Laboratory, Imperial College, Exhibition Road, London, SW7 2AZ, UK.
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31
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Niepmann M. Internal translation initiation of picornaviruses and hepatitis C virus. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2009; 1789:529-41. [PMID: 19439208 DOI: 10.1016/j.bbagrm.2009.05.002] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2009] [Revised: 04/29/2009] [Accepted: 05/02/2009] [Indexed: 01/02/2023]
Abstract
Picornaviruses and other positive-strand RNA viruses like hepatitis C virus (HCV) enter the cell with a single RNA genome that directly serves as the template for translation. Accordingly, the viral RNA genome needs to recruit the cellular translation machinery for viral protein synthesis. By the use of internal ribosome entry site (IRES) elements in their genomic RNAs, these viruses bypass translation competition with the bulk of capped cellular mRNAs and, moreover, establish the option to largely shut-down cellular protein synthesis. In this review, I discuss the structure and function of viral IRES elements, focusing on the recruitment of the cellular translation machinery by the IRES and on factors that may contribute to viral tissue tropism on the level of translation.
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Affiliation(s)
- Michael Niepmann
- Institute of Biochemistry, Faculty of Medicine, Justus-Liebig-University, Friedrichstrasse 24, 35392 Giessen, Germany.
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Bousquet-Antonelli C, Deragon JM. A comprehensive analysis of the La-motif protein superfamily. RNA (NEW YORK, N.Y.) 2009; 15:750-64. [PMID: 19299548 PMCID: PMC2673062 DOI: 10.1261/rna.1478709] [Citation(s) in RCA: 142] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2008] [Accepted: 01/22/2009] [Indexed: 05/24/2023]
Abstract
The extremely well-conserved La motif (LAM), in synergy with the immediately following RNA recognition motif (RRM), allows direct binding of the (genuine) La autoantigen to RNA polymerase III primary transcripts. This motif is not only found on La homologs, but also on La-related proteins (LARPs) of unrelated function. LARPs are widely found amongst eukaryotes and, although poorly characterized, appear to be RNA-binding proteins fulfilling crucial cellular functions. We searched the fully sequenced genomes of 83 eukaryotic species scattered along the tree of life for the presence of LAM-containing proteins. We observed that these proteins are absent from archaea and present in all eukaryotes (except protists from the Plasmodium genus), strongly suggesting that the LAM is an ancestral motif that emerged early after the archaea-eukarya radiation. A complete evolutionary and structural analysis of these proteins resulted in their classification into five families: the genuine La homologs and four LARP families. Unexpectedly, in each family a conserved domain representing either a classical RRM or an RRM-like motif immediately follows the LAM of most proteins. An evolutionary analysis of the LAM-RRM/RRM-L regions shows that these motifs co-evolved and should be used as a single entity to define the functional region of interaction of LARPs with their substrates. We also found two extremely well conserved motifs, named LSA and DM15, shared by LARP6 and LARP1 family members, respectively. We suggest that members of the same family are functional homologs and/or share a common molecular mode of action on different RNA baits.
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Bayfield MA, Maraia RJ. Precursor-product discrimination by La protein during tRNA metabolism. Nat Struct Mol Biol 2009; 16:430-7. [PMID: 19287396 PMCID: PMC2666094 DOI: 10.1038/nsmb.1573] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2008] [Accepted: 02/09/2009] [Indexed: 11/09/2022]
Abstract
La proteins bind pre-tRNAs at their UUU-3'OH ends, facilitating their maturation. Although the mechanism by which La binds pre-tRNA 3' trailers is known, the function of the RNA binding beta-sheet surface of the RNA-recognition motif (RRM1) is unknown. How La dissociates from UUU-3'OH-containing trailers after 3' processing is also unknown. Here we show that La preferentially binds pre-tRNAs over processed tRNAs or 3' trailer products through coupled use of two sites: one on the La motif and another on the RRM1 beta-surface that binds elsewhere on tRNA. Two sites provide stable pre-tRNA binding, whereas the processed tRNA and 3' trailer are released from their single sites relatively fast. RRM1 loop-3 mutations decrease affinity for pre-tRNA and tRNA, but not for the UUU-3'OH trailer, and impair tRNA maturation in vivo. We propose that RRM1 functions in activities that are more complex than UUU-3'OH binding. Accordingly, the RRM1 mutations also impair an RNA chaperone activity of La. The results suggest how La distinguishes precursor from product RNAs, allowing it to recycle onto a new pre-tRNA.
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Affiliation(s)
| | - Richard J. Maraia
- To whom correspondence should be directed at: 31 Center Drive, Building 31, Room 2A25, Bethesda, MD 20892-2426, Phone: 301-402-3567, Fax: 301-480-6863, E-mail:
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Michels AA, Bensaude O. RNA-driven cyclin-dependent kinase regulation: When CDK9/cyclin T subunits of P-TEFb meet their ribonucleoprotein partners. Biotechnol J 2008; 3:1022-32. [DOI: 10.1002/biot.200800104] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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Bitko V, Musiyenko A, Bayfield MA, Maraia RJ, Barik S. Cellular La protein shields nonsegmented negative-strand RNA viral leader RNA from RIG-I and enhances virus growth by diverse mechanisms. J Virol 2008; 82:7977-87. [PMID: 18550659 PMCID: PMC2519562 DOI: 10.1128/jvi.02762-07] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2007] [Accepted: 05/29/2008] [Indexed: 12/25/2022] Open
Abstract
The La antigen (SS-B) associates with a wide variety of cellular and viral RNAs to affect gene expression in multiple systems. We show that La is the major cellular protein found to be associated with the abundant 44-nucleotide viral leader RNA (leRNA) early after infection with respiratory syncytial virus (RSV), a nonsegmented negative-strand RNA virus. Consistent with this, La redistributes from the nucleus to the cytoplasm in RSV-infected cells. Upon RNA interference knockdown of La, leRNA is redirected to associate with the RNA-binding protein RIG-I, a known activator of interferon (IFN) gene expression, and this is accompanied by the early induction of IFN mRNA. These results suggest that La shields leRNA from RIG-I, abrogating the early viral activation of type I IFN. We mapped the leRNA binding function to RNA recognition motif 1 of La and showed that while wild-type La greatly enhanced RSV growth, a La mutant defective in RSV leRNA binding also did not support RSV growth. Comparative studies of RSV and Sendai virus and the use of IFN-negative Vero cells indicated that La supports the growth of nonsegmented negative-strand RNA viruses by both IFN suppression and a potentially novel IFN-independent mechanism.
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Affiliation(s)
- Vira Bitko
- Department of Biochemistry and Molecular Biology, University of South Alabama, College of Medicine, 307 University Blvd., Mobile, AL 36688-0002, USA
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36
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Kotik-Kogan O, Valentine ER, Sanfelice D, Conte MR, Curry S. Structural analysis reveals conformational plasticity in the recognition of RNA 3' ends by the human La protein. Structure 2008; 16:852-62. [PMID: 18547518 PMCID: PMC2430598 DOI: 10.1016/j.str.2008.02.021] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2008] [Revised: 02/19/2008] [Accepted: 02/24/2008] [Indexed: 01/29/2023]
Abstract
The eukaryotic La protein recognizes the 3' poly(U) sequences of nascent RNA polymerase III transcripts to assist folding and maturation. The 3' ends of such RNAs are bound by the N-terminal domain of La (LaNTD). We have solved the crystal structures of four LaNTD:RNA complexes, each containing a different single-stranded RNA oligomer, and compared them to the structure of a previously published LaNTD:RNA complex containing partially duplex RNA. The presence of purely single-stranded RNA in the binding pocket at the interface between the La motif and RRM domains allows significantly closer contact with the 3' end of the RNA. Comparison of the different LaNTD:RNA complexes identifies a conserved set of interactions with the last two nucleotides at the 3' end of the RNA ligand that are key to binding. Strikingly, we also observe two alternative conformations of bound ssRNA, indicative of an unexpected degree of plasticity in the modes of RNA binding.
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Affiliation(s)
- Olga Kotik-Kogan
- Biophysics Section, Blackett Laboratory, Imperial College, Exhibition Road, London SW7 2AZ, United Kingdom
| | - Elizabeth R. Valentine
- Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, United Kingdom
| | - Domenico Sanfelice
- Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, United Kingdom
| | - Maria R. Conte
- Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, United Kingdom
| | - Stephen Curry
- Biophysics Section, Blackett Laboratory, Imperial College, Exhibition Road, London SW7 2AZ, United Kingdom
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He N, Jahchan NS, Hong E, Li Q, Bayfield MA, Maraia RJ, Luo K, Zhou Q. A La-related protein modulates 7SK snRNP integrity to suppress P-TEFb-dependent transcriptional elongation and tumorigenesis. Mol Cell 2008; 29:588-99. [PMID: 18249148 PMCID: PMC6239424 DOI: 10.1016/j.molcel.2008.01.003] [Citation(s) in RCA: 196] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2007] [Revised: 10/03/2007] [Accepted: 01/02/2008] [Indexed: 11/18/2022]
Abstract
The general transcription factor P-TEFb stimulates RNA polymerase II elongation and cotranscriptional processing of pre-mRNA. Contributing to a functional equilibrium important for growth control, a reservoir of P-TEFb is maintained in an inactive snRNP where 7SK snRNA is a central scaffold. Here, we identify PIP7S as a La-related protein stably associated with and required for 7SK snRNP integrity. PIP7S binds and stabilizes nearly all the nuclear 7SK via 3' -UUU-OH, leading to the sequestration and inactivation of P-TEFb. This function requires its La domain and intact C terminus. The latter is frequently deleted in human tumors due to microsatellite instability-associated mutations. Consistent with the tumor suppressor role of a Drosophila homolog of PIP7S, loss of PIP7S function shifts the P-TEFb equilibrium toward the active state, disrupts epithelial differentiation, and causes P-TEFb-dependent malignant transformation. Through PIP7S modulation of P-TEFb, our data thus link a general elongation factor to growth control and tumorigenesis.
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Affiliation(s)
- Nanhai He
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Nadine S. Jahchan
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Eunmee Hong
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Qiang Li
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Mark A. Bayfield
- Intramural Research Program, Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Richard J. Maraia
- Intramural Research Program, Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kunxin Luo
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Qiang Zhou
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
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Krueger BJ, Jeronimo C, Roy BB, Bouchard A, Barrandon C, Byers SA, Searcey CE, Cooper JJ, Bensaude O, Cohen EA, Coulombe B, Price DH. LARP7 is a stable component of the 7SK snRNP while P-TEFb, HEXIM1 and hnRNP A1 are reversibly associated. Nucleic Acids Res 2008; 36:2219-29. [PMID: 18281698 PMCID: PMC2367717 DOI: 10.1093/nar/gkn061] [Citation(s) in RCA: 189] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Regulation of the elongation phase of RNA polymerase II transcription by P-TEFb is a critical control point for gene expression. The activity of P-TEFb is regulated, in part, by reversible association with one of two HEXIMs and the 7SK snRNP. A recent proteomics survey revealed that P-TEFb and the HEXIMs are tightly connected to two previously-uncharacterized proteins, the methyphosphate capping enzyme, MEPCE, and a La-related protein, LARP7. Glycerol gradient sedimentation analysis of lysates from cells treated with P-TEFb inhibitors, suggested that the 7SK snRNP reorganized such that LARP7 and 7SK remained associated after P-TEFb and HEXIM1 were released. Immunodepletion of LARP7 also depleted most of the 7SK regardless of the presence of P-TEFb, HEXIM or hnRNP A1 in the complex. Small interfering RNA knockdown of LARP7 in human cells decreased the steady-state level of 7SK, led to an initial increase in free P-TEFb and increased Tat transactivation of the HIV-1 LTR. Knockdown of LARP7 or 7SK ultimately caused a decrease in total P-TEFb protein levels. Our studies have identified LARP7 as a 7SK-binding protein and suggest that free P-TEFb levels are determined by a balance between release from the large form and reduction of total P-TEFb.
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Affiliation(s)
- Brian J Krueger
- Molecular and Cellular Biology Program, University of Iowa, Iowa City, Iowa, USA
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Abstract
During the past decade, numerous ncRNAs (non-coding RNAs) have been identified as regulators of transcription. This review focuses on a few examples of ncRNAs that directly interact with and regulate components of the transcription machinery. Artificial RNA aptamers have been selected against components of the transcriptional machinery. The bacterial 6S RNA and the eukaryotic B2 RNA directly target RNA polymerases. The 7SK RNA, U1 snRNA (small nuclear RNA) and SRA (steroid receptor RNA activator) RNA bind to and regulate the activity of transcription factors. Xist (X-inactive-specific transcript) and roX (RNA on the X) RNAs are involved in epigenetic regulation of transcription through the recruitment of histone-modifying enzymes.
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Identification of novel posttranscriptional targets of the BCR/ABL oncoprotein by ribonomics: requirement of E2F3 for BCR/ABL leukemogenesis. Blood 2007; 111:816-28. [PMID: 17925491 DOI: 10.1182/blood-2007-05-090472] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Several RNA binding proteins (RBPs) have been implicated in the progression of chronic myelogenous leukemia (CML) from the indolent chronic phase to the aggressively fatal blast crisis. In the latter phase, expression and function of specific RBPs are aberrantly regulated at transcriptional or posttranslational levels by the constitutive kinase activity of the BCR/ABL oncoprotein. As a result, altered expression/function of RBPs leads to increased resistance to apoptotic stimuli, enhanced survival, growth advantage, and differentiation arrest of CD34+ progenitors from patients in CML blast crisis. Here, we identify the mRNAs bound to the hnRNP-A1, hnRNP-E2, hnRNP-K, and La/SSB RBPs in BCR/ABLtransformed myeloid cells. Interestingly, we found that the mRNA encoding the transcription factor E2F3 associates to hnRNP-A1 through a conserved binding site located in the E2F3 3' untranslated region (UTR). E2F3 levels were up-regulated in CML-BCCD34+ in a BCR/ABL kinase- and hnRNP-A1 shuttling-dependent manner. Moreover, by using shRNA-mediated E2F3 knock-down and BCR/ABL-transduced lineage-negative bone marrow cells from E2F3+/+ and E2F3-/- mice, we show that E2F3 expression is important for BCR/ABL clonogenic activity and in vivo leukemogenic potential. Thus, the complexity of the mRNA/RBP network, together with the discovery of E2F3 as an hnRNP-A1-regulated factor, outlines the relevant role played by RBPs in posttranscriptional regulation of CML development and progression.
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van Niekerk EA, Willis DE, Chang JH, Reumann K, Heise T, Twiss JL. Sumoylation in axons triggers retrograde transport of the RNA-binding protein La. Proc Natl Acad Sci U S A 2007; 104:12913-8. [PMID: 17646655 PMCID: PMC1937566 DOI: 10.1073/pnas.0611562104] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
A surprisingly large population of mRNAs has been shown to localize to sensory axons, but few RNA-binding proteins have been detected in these axons. These axonal mRNAs include several potential binding targets for the La RNA chaperone protein. La is transported into axonal processes in both culture and peripheral nerve. Interestingly, La is posttranslationally modified in sensory neurons by sumoylation. In axons, small ubiquitin-like modifying polypeptides (SUMO)-La interacts with dynein, whereas native La interacts with kinesin. Lysine 41 is required for sumoylation, and sumoylation-incompetent La(K41R) shows only anterograde transport, whereas WT La shows both anterograde and retrograde transport in axons. Thus, sumoylation of La determines the directionality of its transport within the axonal compartment, with SUMO-La likely recycling to the cell body.
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Affiliation(s)
- Erna A. van Niekerk
- *Department of Biological Sciences, University of Delaware, Newark, DE 19713
| | - Dianna E. Willis
- Nemours Biomedical Research, Alfred I. duPont Hospital for Children, Wilmington, DE 19803
| | - Jay H. Chang
- Neural Development and Plasticity Section, Laboratory of Cellular and Synaptic Neurophysiology, National Institute of Child Health and Human Development–National Institutes of Health, Bethesda, MD 20892
| | - Kerstin Reumann
- Heinrich Pette Institute for Experimental Virology and Immunology, University of Hamburg, D-20251 Hamburg, Germany; and
| | - Tilman Heise
- Heinrich Pette Institute for Experimental Virology and Immunology, University of Hamburg, D-20251 Hamburg, Germany; and
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425
| | - Jeffery L. Twiss
- *Department of Biological Sciences, University of Delaware, Newark, DE 19713
- Nemours Biomedical Research, Alfred I. duPont Hospital for Children, Wilmington, DE 19803
- To whom correspondence should be addressed. E-mail:
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Bayfield MA, Kaiser TE, Intine RV, Maraia RJ. Conservation of a masked nuclear export activity of La proteins and its effects on tRNA maturation. Mol Cell Biol 2007; 27:3303-12. [PMID: 17308035 PMCID: PMC1899964 DOI: 10.1128/mcb.00026-07] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2007] [Revised: 02/01/2007] [Accepted: 02/14/2007] [Indexed: 11/20/2022] Open
Abstract
La is an RNA-processing-associated phosphoprotein so highly conserved that the human La protein (hLa) can replace the tRNA-processing function of the fission yeast La protein (Sla1p) in vivo. La proteins contain multiple trafficking elements that support interactions with RNAs in different subcellular locations. Prior data indicate that deletion of a nuclear retention element (NRE) causes nuclear export of La and dysfunctional processing of associated pre-tRNAs that are spliced but 5' and 3' unprocessed, with an accompanying decrease in tRNA-mediated suppression, in fission yeast. To further pursue these observations, we first identified conserved residues in the NREs of hLa and Sla1p that when substituted mimic the NRE deletion phenotype. NRE-defective La proteins then deleted of other motifs indicated that RNA recognition motif 1 (RRM1) is required for nuclear export. Mutations of conserved RRM1 residues restored nuclear accumulation of NRE-defective La proteins. Some RRM1 mutations restored nuclear accumulation, prevented disordered pre-tRNA processing, and restored suppression, indicating that the tRNA-related activity of RRM1 and its nuclear export activity could be functionally separated. When mapped onto an hLa structure, the export-sensitive residues comprised surfaces distinct from the RNA-binding surface of RRM1. The data indicate that the NRE has been conserved to mask or functionally override an equally conserved nuclear export activity of RRM1. The data suggest that conserved elements mediate nuclear retention, nuclear export, and RNA-binding activities of the multifunctional La protein and that their interrelationship contributes to the ability of La to engage its different classes of RNA ligands in different cellular locations.
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Affiliation(s)
- Mark A Bayfield
- Intramural Research Program, National Institute of Child Health and Human Development, U.S. National Institutes of Health, Bethesda, MD 20892-2426, USA
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Fleurdépine S, Deragon JM, Devic M, Guilleminot J, Bousquet-Antonelli C. A bona fide La protein is required for embryogenesis in Arabidopsis thaliana. Nucleic Acids Res 2007; 35:3306-21. [PMID: 17459889 PMCID: PMC1904278 DOI: 10.1093/nar/gkm200] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2007] [Revised: 03/21/2007] [Accepted: 03/21/2007] [Indexed: 01/28/2023] Open
Abstract
Searches in the Arabidopsis thaliana genome using the La motif as query revealed the presence of eight La or La-like proteins. Using structural and phylogenetic criteria, we identified two putative genuine La proteins (At32 and At79) and showed that both are expressed throughout plant development but at different levels and under different regulatory conditions. At32, but not At79, restores Saccharomyces cerevisiae La nuclear functions in non-coding RNAs biogenesis and is able to bind to plant 3'-UUU-OH RNAs. We conclude that these La nuclear functions are conserved in Arabidopsis and supported by At32, which we renamed as AtLa1. Consistently, AtLa1 is predominantly localized to the plant nucleoplasm and was also detected in the nucleolar cavity. The inactivation of AtLa1 in Arabidopsis leads to an embryonic-lethal phenotype with deficient embryos arrested at early globular stage of development. In addition, mutant embryonic cells display a nucleolar hypertrophy suggesting that AtLa1 is required for normal ribosome biogenesis. The identification of two distantly related proteins with all structural characteristics of genuine La proteins suggests that these factors evolved to a certain level of specialization in plants. This unprecedented situation provides a unique opportunity to dissect the very different aspects of this crucial cellular activity.
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Affiliation(s)
- Sophie Fleurdépine
- CNRS UMR6547 GEEM, Université Blaise Pascal, 63177 Aubière, France and CNRS UMR5096 LGDP, Université de Perpignan Via Domitia, 66860 Perpignan, France
| | - Jean-Marc Deragon
- CNRS UMR6547 GEEM, Université Blaise Pascal, 63177 Aubière, France and CNRS UMR5096 LGDP, Université de Perpignan Via Domitia, 66860 Perpignan, France
| | - Martine Devic
- CNRS UMR6547 GEEM, Université Blaise Pascal, 63177 Aubière, France and CNRS UMR5096 LGDP, Université de Perpignan Via Domitia, 66860 Perpignan, France
| | - Jocelyne Guilleminot
- CNRS UMR6547 GEEM, Université Blaise Pascal, 63177 Aubière, France and CNRS UMR5096 LGDP, Université de Perpignan Via Domitia, 66860 Perpignan, France
| | - Cécile Bousquet-Antonelli
- CNRS UMR6547 GEEM, Université Blaise Pascal, 63177 Aubière, France and CNRS UMR5096 LGDP, Université de Perpignan Via Domitia, 66860 Perpignan, France
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Park JM, Intine RV, Maraia RJ. Mouse and human La proteins differ in kinase substrate activity and activation mechanism for tRNA processing. Gene Expr 2007; 14:71-81. [PMID: 18257391 PMCID: PMC6042041 DOI: 10.3727/105221607783417619] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The La protein interacts with a variety of small RNAs as well as certain growth-associated mRNAs such as Mdm2 mRNA. Human La (hLa) phosphoprotein is so highly conserved that it can replace the tRNA processing function of the fission yeast La protein in vivo. We used this system, which is based on tRNA-mediated suppression (TMS) of ade6-704 in S. pombe, to compare the activities of mouse and human La proteins. Prior studies indicate that hLa is activated by phosphorylation of serine-366 by protein kinase CK2, neutralizing a negative effect of a short basic motif (SBM). First, we report the sequence mapping of the UGA stop codon that requires suppressor tRNA for TMS, to an unexpected site in S. pombe ade6-704. Next, we show that, unlike hLa, native mLa is unexpectedly inactive for TMS, although its intrinsic activity is revealed by deletion of its SBM. We then show that mLa is not phosphorylated by CK2, accounting for the mechanistic difference between mLa and hLa. We found a PKA/PKG target sequence in mLa (S199) that is not present in hLa, and show that PKA/PKG efficiently phosphorylates mLa S199 in vitro. A noteworthy conclusion that comes from this work is that this fission yeast system can be used to gain insight into differences in control mechanisms used by La proteins of different mammalian species. Finally, RNA binding assays indicate that while mutation of mLa S199 has little effect on pre-tRNA binding, it substantially decreases binding to a probe derived from Mdm2 mRNA. In closing, we note that species-specific signaling through La may be relevant to the La-dependent Mdm2 pathways of p53 metabolism and cancer progression in mice and humans.
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Affiliation(s)
- Jung-Min Park
- Intramural Research Program, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Robert V. Intine
- Intramural Research Program, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Richard J. Maraia
- Intramural Research Program, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
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Huang Y, Bayfield MA, Intine RV, Maraia RJ. Separate RNA-binding surfaces on the multifunctional La protein mediate distinguishable activities in tRNA maturation. Nat Struct Mol Biol 2006; 13:611-8. [PMID: 16799560 DOI: 10.1038/nsmb1110] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2006] [Accepted: 05/15/2006] [Indexed: 11/08/2022]
Abstract
By sequence-specific binding to 3' UUU-OH, the La protein shields precursor (pre)-RNAs from 3' end digestion and is required to protect defective pre-transfer RNAs from decay. Although La is comprised of a La motif and an RNA-recognition motif (RRM), a recent structure indicates that the RRM beta-sheet surface is not involved in UUU-OH recognition, raising questions as to its function. Progressively defective suppressor tRNAs in Schizosaccharomyces pombe reveal differential sensitivities to La and Rrp6p, a 3' exonuclease component of pre-tRNA decay. 3' end protection is compromised by mutations to the La motif but not the RRM surface. The most defective pre-tRNAs require a second activity of La, in addition to 3' protection, that requires an intact RRM surface. The two activities of La in tRNA maturation map to its two conserved RNA-binding surfaces and suggest a modular model that has implications for its other ligands.
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Affiliation(s)
- Ying Huang
- Laboratory of Molecular Growth Regulation, National Institute of Child Health and Human Development, US National Institutes of Health, 31 Center Dr., Rm. 2A25, Bethesda, Maryland 20892, USA
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Curry S, Conte MR. A terminal affair: 3'-end recognition by the human La protein. Trends Biochem Sci 2006; 31:303-5. [PMID: 16679019 DOI: 10.1016/j.tibs.2006.04.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2006] [Revised: 03/15/2006] [Accepted: 04/25/2006] [Indexed: 10/24/2022]
Abstract
The La protein, an autoantigen in rheumatic disease, orchestrates several aspects of the metabolism of noncoding RNA molecules. More than 20 years ago it was shown that La primarily binds the 3' UUU-OH tails of nascent transcripts of RNA polymerase III. A recent study now reveals how the structure of the amino-terminal domain of the human La protein achieves specific 3'-end recognition.
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Affiliation(s)
- Stephen Curry
- Biophysics Section, Blackett Laboratory, Faculty of Natural Sciences, Imperial College, Exhibition Road, London SW7 2AZ, UK
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Kiss T, Fayet E, Jády BE, Richard P, Weber M. Biogenesis and intranuclear trafficking of human box C/D and H/ACA RNPs. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2006; 71:407-17. [PMID: 17381323 DOI: 10.1101/sqb.2006.71.025] [Citation(s) in RCA: 133] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Box C/D and H/ACA snoRNAs represent two abundant groups of small noncoding RNAs. The majority of box C/D and H/ACA snoRNAs function as guide RNAs in the site-specific 2'-O-methylation and pseudouridylation of rRNAs, respectively. The box C/D snoRNAs associate with fibrillarin, Nop56, Nop58, and 15.5K/NHPX proteins to form functional snoRNP particles, whereas all box H/ACA snoRNAs form complexes with the dyskerin, Nop10, Nhp2, and Gar1 snoRNP proteins. Recent studies demonstrate that the biogenesis of mammalian snoRNPs is a complex process that requires numerous trans-acting factors. Most vertebrate snoRNAs are posttranscriptionally processed from pre-mRNA introns, and the early steps of snoRNP assembly are physically and functionally coupled with the synthesis or splicing of the host pre-mRNA. The maturing snoRNPs follow a complicated intranuclear trafficking process that is directed by transport factors also involved in nucleocytoplasmic RNA transport. The human telomerase RNA (hTR) carries a box H/ACA RNA domain that shares a common Cajal-body-specific localization element with a subclass of box H/ACA RNAs, which direct pseudouridylation of spliceosomal snRNAs in the Cajal body. However, besides concentrating in Cajal bodies, hTR also accumulates at a small, structurally distinct subset of telomeres during S phase. This suggests that a cell-cycle-dependent, dynamic localization of hTR to telomeres may play an important regulatory role in human telomere synthesis.
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MESH Headings
- Active Transport, Cell Nucleus
- Coiled Bodies/metabolism
- Humans
- Introns
- Models, Biological
- Nucleic Acid Conformation
- RNA/genetics
- RNA/metabolism
- RNA Polymerase II/metabolism
- RNA Splicing
- RNA, Small Nucleolar/chemistry
- RNA, Small Nucleolar/genetics
- RNA, Small Nucleolar/metabolism
- Ribonucleoproteins/chemistry
- Ribonucleoproteins/genetics
- Ribonucleoproteins/metabolism
- Ribonucleoproteins, Small Nucleolar/chemistry
- Ribonucleoproteins, Small Nucleolar/genetics
- Ribonucleoproteins, Small Nucleolar/metabolism
- Telomerase/genetics
- Telomerase/metabolism
- Transcription, Genetic
- RNA, Small Untranslated
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Affiliation(s)
- T Kiss
- Laboratoire de Biologie Moléculaire Eucaryote du CNRS, UMR5099, IFR109, Toulouse, France
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