1
|
Mangkalaphiban K, Ganesan R, Jacobson A. Pleiotropic effects of PAB1 deletion: Extensive changes in the yeast proteome, transcriptome, and translatome. PLoS Genet 2024; 20:e1011392. [PMID: 39236083 DOI: 10.1371/journal.pgen.1011392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 08/11/2024] [Indexed: 09/07/2024] Open
Abstract
Cytoplasmic poly(A)-binding protein (PABPC; Pab1 in yeast) is thought to be involved in multiple steps of post-transcriptional control, including translation initiation, translation termination, and mRNA decay. To understand both the direct and indirect roles of PABPC in more detail, we have employed mass spectrometry to assess the abundance of the components of the yeast proteome, as well as RNA-Seq and Ribo-Seq to analyze changes in the abundance and translation of the yeast transcriptome, in cells lacking the PAB1 gene. We find that pab1Δ cells manifest drastic changes in the proteome and transcriptome, as well as defects in translation initiation and termination. Defects in translation initiation and the stabilization of specific classes of mRNAs in pab1Δ cells appear to be partly indirect consequences of reduced levels of specific initiation factors, decapping activators, and components of the deadenylation complex in addition to the general loss of Pab1's direct role in these processes. Cells devoid of Pab1 also manifested a nonsense codon readthrough phenotype indicative of a defect in translation termination. Collectively, our results indicate that, unlike the loss of simpler regulatory proteins, elimination of cellular Pab1 is profoundly pleiotropic and disruptive to numerous aspects of post-transcriptional regulation.
Collapse
Affiliation(s)
- Kotchaphorn Mangkalaphiban
- Department of Microbiology, UMass Chan Medical School, Worcester, Massachusetts, United States of America
| | - Robin Ganesan
- Department of Microbiology, UMass Chan Medical School, Worcester, Massachusetts, United States of America
| | - Allan Jacobson
- Department of Microbiology, UMass Chan Medical School, Worcester, Massachusetts, United States of America
| |
Collapse
|
2
|
Wang J, Zhang XZ, Sun XY, Tian WJ, Wang XJ. Cellular RNA-binding proteins LARP4 and PABPC1 synergistically facilitate viral translation of coronavirus PEDV. Vet Microbiol 2024; 298:110219. [PMID: 39182469 DOI: 10.1016/j.vetmic.2024.110219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2024] [Revised: 08/10/2024] [Accepted: 08/13/2024] [Indexed: 08/27/2024]
Abstract
Coronaviruses are causing epizootic diseases and thus are a substantial threat for both domestic and wild animals. These viruses depend on the host translation machinery to complete their life cycle. The current paper identified cellular RNA-binding proteins (RBPs), La-related protein 4 (LARP4) and polyadenylate-binding protein cytoplasmic 1 (PABPC1), as critical regulators of efficient translation of the coronavirus porcine epidemic diarrhea virus (PEDV) mRNA. In Vero cells, PEDV infection caused LARP4 to migrate from the nucleus to the cytoplasm in a chromosome region maintenance1 (CRM1)-independent pathway. In the absence of the nuclear export signal of LARP4, viral translation was not promoted by LARP4. A further study unveiled that the cytoplasmic LARP4 binds to the 3'-terminal untranslated region (3'UTR) of PEDV mRNA with the assistance of PABPC1 to facilitate viral translation. LARP4 knockdown reduced the promotion of the PABPC1-induced 3'UTR translation activity. Moreover, the rabbit reticulocyte lysate (RRL) system revealed that the prokaryotic expressed protein LARP4 and PABPC1 enhance PEDV mRNA translation. To our knowledge, this is the first study demonstrating that PEDV induces nucleo-cytoplasmic shuttling of LARP4 to enhance its own replication, which broadens our insights into how viruses use host's RBPs for the efficient translation of viral mRNA.
Collapse
Affiliation(s)
- Jing Wang
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Xiu-Zhong Zhang
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Xin-Yue Sun
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Wen-Jun Tian
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Xiao-Jia Wang
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China.
| |
Collapse
|
3
|
Poonia P, Valabhoju V, Li T, Iben J, Niu X, Lin Z, Hinnebusch AG. Yeast poly(A)-binding protein (Pab1) controls translation initiation in vivo primarily by blocking mRNA decapping and decay. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.19.590253. [PMID: 38903079 PMCID: PMC11188147 DOI: 10.1101/2024.04.19.590253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
Poly(A)-binding protein (Pab1 in yeast) is involved in mRNA decay and translation initiation, but its molecular functions are incompletely understood. We found that auxin-induced degradation of Pab1 reduced bulk mRNA and polysome abundance in a manner suppressed by deleting the catalytic subunit of decapping enzyme (dcp2Δ), demonstrating that enhanced decapping/degradation is the major driver of reduced mRNA abundance and protein synthesis at limiting Pab1 levels. An increased median poly(A) tail length conferred by Pab1 depletion was also nullified by dcp2Δ, suggesting that mRNA isoforms with shorter tails are preferentially decapped/degraded at limiting Pab1. In contrast to findings on mammalian cells, the translational efficiencies (TEs) of many mRNAs were altered by Pab1 depletion; however, these changes were broadly diminished by dcp2∆, suggesting that reduced mRNA abundance is a major driver of translational reprogramming at limiting Pab1. Thus, assembly of the closed-loop mRNP via PABP-eIF4G interaction appears to be dispensable for normal translation of most yeast mRNAs in vivo. Interestingly, histone mRNAs and proteins are preferentially diminished on Pab1 depletion dependent on Dcp2, accompanied by activation of internal cryptic promoters in the manner expected for reduced nucleosome occupancies, revealing a new layer of post-transcriptional control of histone gene expression.
Collapse
Affiliation(s)
- Poonam Poonia
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Vishalini Valabhoju
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Tianwei Li
- Department of Biology, Saint Louis University, St. Louis, MO
| | - James Iben
- Department of Biology, Saint Louis University, St. Louis, MO
| | - Xiao Niu
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
- Department of Biology, Saint Louis University, St. Louis, MO
| | - Zhenguo Lin
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
- Department of Biology, Saint Louis University, St. Louis, MO
| | - Alan G Hinnebusch
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| |
Collapse
|
4
|
Wang J, Zhu H, Gan J, Liang G, Li L, Zhao Y. Engineered mRNA Delivery Systems for Biomedical Applications. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2308029. [PMID: 37805865 DOI: 10.1002/adma.202308029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 10/05/2023] [Indexed: 10/09/2023]
Abstract
Messenger RNA (mRNA)-based therapeutic strategies have shown remarkable promise in preventing and treating a staggering range of diseases. Optimizing the structure and delivery system of engineered mRNA has greatly improved its stability, immunogenicity, and protein expression levels, which has led to a wider range of uses for mRNA therapeutics. Herein, a thorough analysis of the optimization strategies used in the structure of mRNA is first provided and delivery systems are described in great detail. Furthermore, the latest advancements in biomedical engineering for mRNA technology, including its applications in combatting infectious diseases, treating cancer, providing protein replacement therapy, conducting gene editing, and more, are summarized. Lastly, a perspective on forthcoming challenges and prospects concerning the advancement of mRNA therapeutics is offered. Despite these challenges, mRNA-based therapeutics remain promising, with the potential to revolutionize disease treatment and contribute to significant advancements in the biomedical field.
Collapse
Affiliation(s)
- Ji Wang
- Department of Rheumatology and Immunology, Nanjing Drum Tower Hospital, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Haofang Zhu
- Department of Rheumatology and Immunology, Nanjing Drum Tower Hospital, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Jingjing Gan
- Department of Rheumatology and Immunology, Nanjing Drum Tower Hospital, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Gaofeng Liang
- Institute of Organoids on Chips Translational Research, Henan Academy of Sciences, Zhengzhou, 450009, China
| | - Ling Li
- Department of Endocrinology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, 210009, China
| | - Yuanjin Zhao
- Department of Rheumatology and Immunology, Nanjing Drum Tower Hospital, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
- Institute of Organoids on Chips Translational Research, Henan Academy of Sciences, Zhengzhou, 450009, China
| |
Collapse
|
5
|
Okutman O, Gürbüz AS, Büyük U, Real E, Leconte R, Chennen K, Mayer C, Muller J, Le May N, Viville S. Pathogenic missense variation in PABPC1L/EPAB causes female infertility due to oocyte maturation arrest at the germinal vesicle stage. J Assist Reprod Genet 2024; 41:311-322. [PMID: 38177974 PMCID: PMC10894787 DOI: 10.1007/s10815-023-03009-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 12/13/2023] [Indexed: 01/06/2024] Open
Abstract
Women undergoing controlled ovarian hyperstimulation prior to in vitro fertilization (IVF) are treated using various protocols to induce multiple follicular growths. Complete failure of all oocytes to mature during IVF cycles is rare; however, it is a known cause of primary female infertility. Recently, pathogenic variations in a few genes have been identified in women with oocyte maturation defects; however, the underlying genetic causes remain largely unknown.This study included a Turkish family comprising three sisters with recurring oocyte maturation arrest at the germinal vesicle stage after multiple ovarian stimulations. Exome sequencing revealed a homozygous missense variant (c.1037C>T, p.Ala346Val) in the EPAB gene (also known as PABPC1L) in all three affected sisters, which was either absent or heterozygous in the unaffected family members. Functional experiments confirming the pathogenicity of the variant were performed by transfecting HEK293T cells and demonstrated the instability and increased rate of proteolysis of the mutated PABPC1L/EPAB protein. The identified variant, located in the well-conserved fourth RNA recognition motif (RRM4), in silico 3D modelling suggested changes in the physical properties of the pathogenic variant of PABPC1L/EPAB. Our findings validate PABPC1L/EPAB as an essential genetic contributor to the oocyte maturation process in humans and have direct implications for the genetic counselling of patients and their family members.
Collapse
Affiliation(s)
- O Okutman
- Université Libre de Bruxelles (ULB), Hôpital Universitaire de Bruxelles (H.U.B), Hôpital Erasme, Service de Gynécologie-Obstetrique, Clinique de Fertilité, Route de Lennik, 808, 1070, Brussels, Belgium
| | | | - U Büyük
- Department of Molecular Biology and Genetics, Institute of Graduate Studies in Sciences, Istanbul University, Istanbul, Turkey
| | - E Real
- Laboratoire de Génétique Médicale LGM, Institut de Génétique Médicale d'Alsace IGMA, INSERM UMR 1112, Université de Strasbourg, Strasbourg, France
| | - R Leconte
- Laboratoire de Génétique Médicale LGM, Institut de Génétique Médicale d'Alsace IGMA, INSERM UMR 1112, Université de Strasbourg, Strasbourg, France
| | - K Chennen
- Complex Systems and Translational Bioinformatics, ICube UMR 7357, Université de Strasbourg, 67000, Strasbourg, France
| | - C Mayer
- Complex Systems and Translational Bioinformatics, ICube UMR 7357, Université de Strasbourg, 67000, Strasbourg, France
- UFR Sciences de La Vie, Université Paris Cité, 75013, Paris, France
| | - J Muller
- Laboratoire de Génétique Médicale LGM, Institut de Génétique Médicale d'Alsace IGMA, INSERM UMR 1112, Université de Strasbourg, Strasbourg, France
- Unité Fonctionnelle de Bioinformatique Médicale Appliquée Au Diagnostic (UF7363), Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - N Le May
- Laboratoire de Génétique Médicale LGM, Institut de Génétique Médicale d'Alsace IGMA, INSERM UMR 1112, Université de Strasbourg, Strasbourg, France
| | - S Viville
- Laboratoire de Génétique Médicale LGM, Institut de Génétique Médicale d'Alsace IGMA, INSERM UMR 1112, Université de Strasbourg, Strasbourg, France.
- Laboratoire de Diagnostic Génétique, Unité de Génétique de L'infertilité (UF3472), Hôpitaux Universitaires de Strasbourg, 67091, Strasbourg, France.
| |
Collapse
|
6
|
Mangkalaphiban K, Ganesan R, Jacobson A. Direct and indirect consequences of PAB1 deletion in the regulation of translation initiation, translation termination, and mRNA decay. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.31.543082. [PMID: 37398227 PMCID: PMC10312514 DOI: 10.1101/2023.05.31.543082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Cytoplasmic poly(A)-binding protein (PABPC; Pab1 in yeast) is thought to be involved in multiple steps of post-transcriptional control, including translation initiation, translation termination, and mRNA decay. To understand these roles of PABPC in more detail for endogenous mRNAs, and to distinguish its direct effects from indirect effects, we have employed RNA-Seq and Ribo-Seq to analyze changes in the abundance and translation of the yeast transcriptome, as well as mass spectrometry to assess the abundance of the components of the yeast proteome, in cells lacking the PAB1 gene. We observed drastic changes in the transcriptome and proteome, as well as defects in translation initiation and termination, in pab1Δ cells. Defects in translation initiation and the stabilization of specific classes of mRNAs in pab1Δ cells appear to be partly indirect consequences of reduced levels of specific initiation factors, decapping activators, and components of the deadenylation complex in addition to the general loss of Pab1's direct role in these processes. Cells devoid of Pab1 also manifested a nonsense codon readthrough phenotype indicative of a defect in translation termination, but this defect may be a direct effect of the loss of Pab1 as it could not be attributed to significant reductions in the levels of release factors.
Collapse
Affiliation(s)
- Kotchaphorn Mangkalaphiban
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, 368 Plantation Street, Worcester, MA 01655
| | - Robin Ganesan
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, 368 Plantation Street, Worcester, MA 01655
| | - Allan Jacobson
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, 368 Plantation Street, Worcester, MA 01655
| |
Collapse
|
7
|
Park J, Kim M, Yi H, Baeg K, Choi Y, Lee YS, Lim J, Kim VN. Short poly(A) tails are protected from deadenylation by the LARP1-PABP complex. Nat Struct Mol Biol 2023; 30:330-338. [PMID: 36849640 DOI: 10.1038/s41594-023-00930-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 01/10/2023] [Indexed: 03/01/2023]
Abstract
Deadenylation generally constitutes the first and pivotal step in eukaryotic messenger RNA decay. Despite its importance in posttranscriptional regulations, the kinetics of deadenylation and its regulation remain largely unexplored. Here we identify La ribonucleoprotein 1, translational regulator (LARP1) as a general decelerator of deadenylation, which acts mainly in the 30-60-nucleotide (nt) poly(A) length window. We measured the steady-state and pulse-chased distribution of poly(A)-tail length, and found that deadenylation slows down in the 30-60-nt range. LARP1 associates preferentially with short tails and its depletion results in accelerated deadenylation specifically in the 30-60-nt range. Consistently, LARP1 knockdown leads to a global reduction of messenger RNA abundance. LARP1 interferes with the CCR4-NOT-mediated deadenylation in vitro by forming a ternary complex with poly(A)-binding protein (PABP) and poly(A). Together, our work reveals a dynamic nature of deadenylation kinetics and a role of LARP1 as a poly(A) length-specific barricade that creates a threshold for deadenylation.
Collapse
Affiliation(s)
- Joha Park
- Center for RNA Research, Institute for Basic Science, Seoul, Korea
- School of Biological Sciences, Seoul National University, Seoul, Korea
- Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Myeonghwan Kim
- Center for RNA Research, Institute for Basic Science, Seoul, Korea
- School of Biological Sciences, Seoul National University, Seoul, Korea
| | - Hyerim Yi
- Center for RNA Research, Institute for Basic Science, Seoul, Korea
- School of Biological Sciences, Seoul National University, Seoul, Korea
- Stanford University School of Medicine, Stanford, CA, USA
| | - Kyungmin Baeg
- Center for RNA Research, Institute for Basic Science, Seoul, Korea
| | - Yongkuk Choi
- Center for RNA Research, Institute for Basic Science, Seoul, Korea
- School of Biological Sciences, Seoul National University, Seoul, Korea
| | - Young-Suk Lee
- Center for RNA Research, Institute for Basic Science, Seoul, Korea
- Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Korea
| | - Jaechul Lim
- Center for RNA Research, Institute for Basic Science, Seoul, Korea
- School of Biological Sciences, Seoul National University, Seoul, Korea
- Yale School of Medicine, New Haven, CT, USA
| | - V Narry Kim
- Center for RNA Research, Institute for Basic Science, Seoul, Korea.
- School of Biological Sciences, Seoul National University, Seoul, Korea.
| |
Collapse
|
8
|
Yang L, Tang L, Zhang M, Liu C. Recent Advances in the Molecular Design and Delivery Technology of mRNA for Vaccination Against Infectious Diseases. Front Immunol 2022; 13:896958. [PMID: 35928814 PMCID: PMC9345514 DOI: 10.3389/fimmu.2022.896958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 06/20/2022] [Indexed: 12/02/2022] Open
Abstract
Vaccines can prevent many millions of illnesses against infectious diseases and save numerous lives every year. However, traditional vaccines such as inactivated viral and live attenuated vaccines cannot adapt to emerging pandemics due to their time-consuming development. With the global outbreak of the COVID-19 epidemic, the virus continues to evolve and mutate, producing mutants with enhanced transmissibility and virulence; the rapid development of vaccines against such emerging global pandemics becomes more and more critical. In recent years, mRNA vaccines have been of significant interest in combating emerging infectious diseases due to their rapid development and large-scale production advantages. However, their development still suffers from many hurdles such as their safety, cellular delivery, uptake, and response to their manufacturing, logistics, and storage. More efforts are still required to optimize the molecular designs of mRNA molecules with increased protein expression and enhanced structural stability. In addition, a variety of delivery systems are also needed to achieve effective delivery of vaccines. In this review, we highlight the advances in mRNA vaccines against various infectious diseases and discuss the molecular design principles and delivery systems of associated mRNA vaccines. The current state of the clinical application of mRNA vaccine pipelines against various infectious diseases and the challenge, safety, and protective effect of associated vaccines are also discussed.
Collapse
Affiliation(s)
- Lu Yang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Lin Tang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, China
| | - Ming Zhang
- Department of Pathology, Peking University International Hospital, Beijing, China
- *Correspondence: Chaoyong Liu, ; Ming Zhang,
| | - Chaoyong Liu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, China
- *Correspondence: Chaoyong Liu, ; Ming Zhang,
| |
Collapse
|
9
|
Zhouravleva GA, Bondarev SA, Zemlyanko OM, Moskalenko SE. Role of Proteins Interacting with the eRF1 and eRF3 Release Factors in the Regulation of Translation and Prionization. Mol Biol 2022. [DOI: 10.1134/s0026893322010101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
10
|
Kajjo S, Sharma S, Chen S, Brothers WR, Cott M, Hasaj B, Jovanovic P, Larsson O, Fabian MR. PABP prevents the untimely decay of select mRNA populations in human cells. EMBO J 2022; 41:e108650. [PMID: 35156721 PMCID: PMC8922270 DOI: 10.15252/embj.2021108650] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 12/30/2021] [Accepted: 01/13/2022] [Indexed: 12/11/2022] Open
Abstract
Gene expression is tightly regulated at the levels of both mRNA translation and stability. The poly(A)-binding protein (PABP) is thought to play a role in regulating these processes by binding the mRNA 3' poly(A) tail and interacting with both the translation and mRNA deadenylation machineries. In this study, we directly investigate the impact of PABP on translation and stability of endogenous mRNAs in human cells. Remarkably, our transcriptome-wide analysis only detects marginal mRNA translation changes in PABP-depleted cells. In contrast, rapidly depleting PABP alters mRNA abundance and stability, albeit non-uniformly. Otherwise stable transcripts, including those encoding proteins with constitutive functions, are destabilized in PABP-depleted cells. In contrast, many unstable mRNAs, including those encoding proteins with regulatory functions, decay at similar rates in presence or absence of PABP. Moreover, PABP depletion-induced cell death can partially be suppressed by disrupting the mRNA decapping and 5'-3' decay machinery. Finally, we provide evidence that the LSM1-7 complex promotes decay of "stable" mRNAs in PABP-depleted cells. Taken together, these findings suggest that PABP plays an important role in preventing the untimely decay of select mRNA populations.
Collapse
Affiliation(s)
- Sam Kajjo
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada.,Division of Experimental Medicine, McGill University, Montreal, QC, Canada
| | - Sahil Sharma
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada.,Division of Experimental Medicine, McGill University, Montreal, QC, Canada
| | - Shan Chen
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - William R Brothers
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada.,Division of Experimental Medicine, McGill University, Montreal, QC, Canada
| | - Megan Cott
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada
| | - Benedeta Hasaj
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada
| | - Predrag Jovanovic
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada.,Division of Experimental Medicine, McGill University, Montreal, QC, Canada
| | - Ola Larsson
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Marc R Fabian
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada.,Division of Experimental Medicine, McGill University, Montreal, QC, Canada.,Department of Biochemistry, McGill University, Montreal, QC, Canada.,Gerald Bronfman Department of Oncology, McGill University, Montreal, QC, Canada
| |
Collapse
|
11
|
Roles of mRNA poly(A) tails in regulation of eukaryotic gene expression. Nat Rev Mol Cell Biol 2022; 23:93-106. [PMID: 34594027 PMCID: PMC7614307 DOI: 10.1038/s41580-021-00417-y] [Citation(s) in RCA: 187] [Impact Index Per Article: 93.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/16/2021] [Indexed: 02/06/2023]
Abstract
In eukaryotes, poly(A) tails are present on almost every mRNA. Early experiments led to the hypothesis that poly(A) tails and the cytoplasmic polyadenylate-binding protein (PABPC) promote translation and prevent mRNA degradation, but the details remained unclear. More recent data suggest that the role of poly(A) tails is much more complex: poly(A)-binding protein can stimulate poly(A) tail removal (deadenylation) and the poly(A) tails of stable, highly translated mRNAs at steady state are much shorter than expected. Furthermore, the rate of translation elongation affects deadenylation. Consequently, the interplay between poly(A) tails, PABPC, translation and mRNA decay has a major role in gene regulation. In this Review, we discuss recent work that is revolutionizing our understanding of the roles of poly(A) tails in the cytoplasm. Specifically, we discuss the roles of poly(A) tails in translation and control of mRNA stability and how poly(A) tails are removed by exonucleases (deadenylases), including CCR4-NOT and PAN2-PAN3. We also discuss how deadenylation rate is determined, the integration of deadenylation with other cellular processes and the function of PABPC. We conclude with an outlook for the future of research in this field.
Collapse
|
12
|
Vo JM, Mulroney L, Quick-Cleveland J, Jain M, Akeson M, Ares M. Synthesis of modified nucleotide polymers by the poly(U) polymerase Cid1: application to direct RNA sequencing on nanopores. RNA (NEW YORK, N.Y.) 2021; 27:1497-1511. [PMID: 34446532 PMCID: PMC8594468 DOI: 10.1261/rna.078898.121] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 08/23/2021] [Indexed: 05/27/2023]
Abstract
Understanding transcriptomes requires documenting the structures, modifications, and abundances of RNAs as well as their proximity to other molecules. The methods that make this possible depend critically on enzymes (including mutant derivatives) that act on nucleic acids for capturing and sequencing RNA. We tested two 3' nucleotidyl transferases, Saccharomyces cerevisiae poly(A) polymerase and Schizosaccharomyces pombe Cid1, for the ability to add base and sugar modified rNTPs to free RNA 3' ends, eventually focusing on Cid1. Although unable to polymerize ΨTP or 1meΨTP, Cid1 can use 5meUTP and 4thioUTP. Surprisingly, Cid1 can use inosine triphosphate to add poly(I) to the 3' ends of a wide variety of RNA molecules. Most poly(A) mRNAs efficiently acquire a uniform tract of about 50 inosine residues from Cid1, whereas non-poly(A) RNAs acquire longer, more heterogeneous tails. Here we test these activities for use in direct RNA sequencing on nanopores, and find that Cid1-mediated poly(I)-tailing permits detection and quantification of both mRNAs and non-poly(A) RNAs simultaneously, as well as enabling the analysis of nascent RNAs associated with RNA polymerase II. Poly(I) produces a different current trace than poly(A), enabling recognition of native RNA 3' end sequence lost by in vitro poly(A) addition. Addition of poly(I) by Cid1 offers a broadly useful alternative to poly(A) capture for direct RNA sequencing on nanopores.
Collapse
Affiliation(s)
- Jenny Mai Vo
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, California 95064, USA
| | - Logan Mulroney
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California 95064, USA
| | - Jen Quick-Cleveland
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, California 95064, USA
| | - Miten Jain
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California 95064, USA
| | - Mark Akeson
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California 95064, USA
| | - Manuel Ares
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, California 95064, USA
| |
Collapse
|
13
|
Rana A, Gupta N, Thakur A. Post-transcriptional and translational control of the morphology and virulence in human fungal pathogens. Mol Aspects Med 2021; 81:101017. [PMID: 34497025 DOI: 10.1016/j.mam.2021.101017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 08/13/2021] [Accepted: 08/20/2021] [Indexed: 11/17/2022]
Abstract
Host-pathogen interactions at the molecular level are the key to fungal pathogenesis. Fungal pathogens utilize several mechanisms such as adhesion, invasion, phenotype switching and metabolic adaptations, to survive in the host environment and respond. Post-transcriptional and translational regulations have emerged as key regulatory mechanisms ensuring the virulence and survival of fungal pathogens. Through these regulations, fungal pathogens effectively alter their protein pool, respond to various stress, and undergo morphogenesis, leading to efficient and comprehensive changes in fungal physiology. The regulation of virulence through post-transcriptional and translational regulatory mechanisms is mediated through mRNA elements (cis factors) or effector molecules (trans factors). The untranslated regions upstream and downstream of the mRNA, as well as various RNA-binding proteins involved in translation initiation or circularization of the mRNA, play pivotal roles in the regulation of morphology and virulence by influencing protein synthesis, protein isoforms, and mRNA stability. Therefore, post-transcriptional and translational mechanisms regulating the morphology, virulence and drug-resistance processes in fungal pathogens can be the target for new therapeutics. With improved "omics" technologies, these regulatory mechanisms are increasingly coming to the forefront of basic biology and drug discovery. This review aims to discuss various modes of post-transcriptional and translation regulations, and how these mechanisms exert influence in the virulence and morphogenesis of fungal pathogens.
Collapse
Affiliation(s)
- Aishwarya Rana
- Regional Centre for Biotechnology, 3rd Milestone Gurgaon-Faridabad Expressway, Faridabad 121001, India
| | - Nidhi Gupta
- Regional Centre for Biotechnology, 3rd Milestone Gurgaon-Faridabad Expressway, Faridabad 121001, India
| | - Anil Thakur
- Regional Centre for Biotechnology, 3rd Milestone Gurgaon-Faridabad Expressway, Faridabad 121001, India.
| |
Collapse
|
14
|
Xiang K, Bartel DP. The molecular basis of coupling between poly(A)-tail length and translational efficiency. eLife 2021; 10:66493. [PMID: 34213414 PMCID: PMC8253595 DOI: 10.7554/elife.66493] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 05/21/2021] [Indexed: 01/10/2023] Open
Abstract
In animal oocytes and early embryos, mRNA poly(A)-tail length strongly influences translational efficiency (TE), but later in development this coupling between tail length and TE disappears. Here, we elucidate how this coupling is first established and why it disappears. Overexpressing cytoplasmic poly(A)-binding protein (PABPC) in Xenopus oocytes specifically improved translation of short-tailed mRNAs, thereby diminishing coupling between tail length and TE. Thus, strong coupling requires limiting PABPC, implying that in coupled systems longer-tail mRNAs better compete for limiting PABPC. In addition to expressing excess PABPC, post-embryonic mammalian cell lines had two other properties that prevented strong coupling: terminal-uridylation-dependent destabilization of mRNAs lacking bound PABPC, and a regulatory regime wherein PABPC contributes minimally to TE. Thus, these results revealed three fundamental mechanistic requirements for coupling and defined the context-dependent functions for PABPC, which promotes TE but not mRNA stability in coupled systems and mRNA stability but not TE in uncoupled systems. Cells are microscopic biological factories that are constantly creating new proteins. To do so, a cell must first convert its master genetic blueprint, the DNA, into strands of messenger RNA or mRNA. These strands are subsequently translated to make proteins. Cells have two ways to adjust the number of proteins they generate so they do not produce too many or too few: by changing how many mRNA molecules are available for translation, and by regulating how efficiently they translate these mRNA molecules into proteins. In animals, both unfertilized eggs and early-stage embryos lack the ability to create or destroy mRNAs, and consequently cannot adjust the number of mRNA molecules available for translation. These cells can therefore only regulate how efficiently each mRNA is translated. They do this by changing the length of the so-called poly(A) tail at the end of each mRNA molecule, which is made up of a long stretch of repeating adenosine nucleotides. The mRNAs with longer poly(A) tails are translated more efficiently than those with shorter poly(A) tails. However, this difference disappears in older embryos, when both long and short poly(A) tails are translated with equal efficiency, and it is largely unknown why. To find out more, Xiang and Bartel studied frog eggs, and discovered that artificially raising levels of a protein that binds poly(A) tails, also known as PABPC, improved the translation of short-tailed mRNAs to create a situation in which both short- and long-tailed mRNAs were translated with near-equal efficiency. This suggested that short- and long-tailed mRNAs compete for limited amounts of the translation-enhancing PABPC, and that long-tailed mRNAs are better at it than short-tailed mRNAs. Further investigation revealed that eggs also had to establish the right conditions for PABPC to enhance translation and had to protect mRNAs not associated with PABPC from being destroyed before they could be translated. Overall, Xiang and Bartel found that in eggs and early embryos, PABPC and poly(A) tails enhanced the translation of mRNAs but did not influence their stability, whereas later in development, they enhanced mRNA stability but not translation. This research provides new insights into how protein production is controlled at different stages of animal development, from unfertilized eggs to older embryos. Understanding how this process is regulated during normal development is crucial for gaining insights into how it can become dysfunctional and cause disease. These findings may therefore have important implications for research into areas such as infertility, reproductive medicine and rare genetic diseases.
Collapse
Affiliation(s)
- Kehui Xiang
- Howard Hughes Medical Institute, Cambridge, United States.,Whitehead Institute for Biomedical Research, Cambridge, United States.,Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
| | - David P Bartel
- Howard Hughes Medical Institute, Cambridge, United States.,Whitehead Institute for Biomedical Research, Cambridge, United States.,Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
| |
Collapse
|
15
|
Zhao LW, Fan HY. Revisiting poly(A)-binding proteins: Multifaceted regulators during gametogenesis and early embryogenesis. Bioessays 2021; 43:e2000335. [PMID: 33830517 DOI: 10.1002/bies.202000335] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 03/21/2021] [Accepted: 03/24/2021] [Indexed: 12/27/2022]
Abstract
Post-transcriptional regulation faces a distinctive challenge in gametes. Transcription is limited when the germ cells enter the division phase due to condensed chromatin, while gene expression during gamete maturation, fertilization, and early cleavage depends on existing mRNA post-transcriptional coordination. The dynamics of the 3'-poly(A) tail play crucial roles in defining mRNA fate. The 3'-poly(A) tail is covered with poly(A)-binding proteins (PABPs) that help to mediate mRNA metabolism and recent work has shed light on the number and function of germ cell-specific expressed PABPs. There are two structurally different PABP groups distinguished by their cytoplasmic and nuclear localization. Both lack catalytic activity but are coupled with various roles through their interaction with multifunctional partners during mRNA metabolism. Here, we present a synopsis of PABP function during gametogenesis and early embryogenesis and describe both conventional and current models of the functions and regulation of PABPs, with an emphasis on the physiological significance of how germ cell-specific PABPs potentially affect human fertility.
Collapse
Affiliation(s)
- Long-Wen Zhao
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Heng-Yu Fan
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China.,Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province, Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| |
Collapse
|
16
|
Parnell AA, De Nobrega AK, Lyons LC. Translating around the clock: Multi-level regulation of post-transcriptional processes by the circadian clock. Cell Signal 2021; 80:109904. [PMID: 33370580 PMCID: PMC8054296 DOI: 10.1016/j.cellsig.2020.109904] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 12/20/2020] [Accepted: 12/21/2020] [Indexed: 12/11/2022]
Abstract
The endogenous circadian clock functions to maintain optimal physiological health through the tissue specific coordination of gene expression and synchronization between tissues of metabolic processes throughout the 24 hour day. Individuals face numerous challenges to circadian function on a daily basis resulting in significant incidences of circadian disorders in the United States and worldwide. Dysfunction of the circadian clock has been implicated in numerous diseases including cancer, diabetes, obesity, cardiovascular and hepatic abnormalities, mood disorders and neurodegenerative diseases. The circadian clock regulates molecular, metabolic and physiological processes through rhythmic gene expression via transcriptional and post-transcriptional processes. Mounting evidence indicates that post-transcriptional regulation by the circadian clock plays a crucial role in maintaining tissue specific biological rhythms. Circadian regulation affecting RNA stability and localization through RNA processing, mRNA degradation, and RNA availability for translation can result in rhythmic protein synthesis, even when the mRNA transcripts themselves do not exhibit rhythms in abundance. The circadian clock also targets the initiation and elongation steps of translation through multiple pathways. In this review, the influence of the circadian clock across the levels of post-transcriptional, translation, and post-translational modifications are examined using examples from humans to cyanobacteria demonstrating the phylogenetic conservation of circadian regulation. Lastly, we briefly discuss chronotherapies and pharmacological treatments that target circadian function. Understanding the complexity and levels through which the circadian clock regulates molecular and physiological processes is important for future advancement of therapeutic outcomes.
Collapse
Affiliation(s)
- Amber A Parnell
- Department of Biological Science, Program in Neuroscience, Florida State University, Tallahassee, FL 32306, USA
| | - Aliza K De Nobrega
- Department of Biological Science, Program in Neuroscience, Florida State University, Tallahassee, FL 32306, USA
| | - Lisa C Lyons
- Department of Biological Science, Program in Neuroscience, Florida State University, Tallahassee, FL 32306, USA.
| |
Collapse
|
17
|
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.
Collapse
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
| |
Collapse
|
18
|
Foot-and-Mouth Disease Virus Inhibits RIP2 Protein Expression to Promote Viral Replication. Virol Sin 2021; 36:608-622. [PMID: 33400090 DOI: 10.1007/s12250-020-00322-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 09/17/2020] [Indexed: 10/22/2022] Open
Abstract
Receptors interaction protein 2 (RIP2) is a specific adaptor molecule in the downstream of NOD2. The role of RIP2 during foot-and-mouth disease virus (FMDV) infection remains unknown. Here, our results showed that RIP2 inhibited FMDV replication and played an important role in the activation of IFN-β and NF-ĸB signal pathways during FMDV infection. FMDV infection triggered RIP2 transcription, while it reduced the expression of RIP2 protein. Detailed analysis showed that FMDV 2B, 2C, 3Cpro, and Lpro proteins were responsible for inducing the reduction of RIP2 protein. 3Cpro and Lpro are viral proteinases that can induce the cleavage or reduction of many host proteins and block host protein synthesis. The carboxyl terminal 105-114 and 135-144 regions of 2B were essential for reduction of RIP2. Our results also showed that the N terminal 1-61 region of 2C were essential for the reduction of RIP2. The 2C-induced reduction of RIP2 was dependent on inducing the reduction of poly(A)-binding protein 1 (PABPC1). The interaction between RIP2 and 2C was observed in the context of viral infection, and the residues 1-61 were required for the interaction. These data clarify novel mechanisms of reduction of RIP2 mediated by FMDV.
Collapse
|
19
|
Richard S, Gross L, Fischer J, Bendalak K, Ziv T, Urim S, Choder M. Numerous Post-translational Modifications of RNA Polymerase II Subunit Rpb4/7 Link Transcription to Post-transcriptional Mechanisms. Cell Rep 2021; 34:108578. [PMID: 33440147 DOI: 10.1016/j.celrep.2020.108578] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 07/24/2020] [Accepted: 12/09/2020] [Indexed: 01/25/2023] Open
Abstract
Rpb4/7 binds RNA polymerase II (RNA Pol II) transcripts co-transcriptionally and accompanies them throughout their lives. By virtue of its capacity to interact with key regulators (e.g., RNA Pol II, eIF3, and Pat1) temporally and spatially, Rpb4/7 regulates the major stages of the mRNA life cycle. Here we show that Rpb4/7 can undergo more than 100 combinations of post-translational modifications (PTMs). Remarkably, the Rpb4/7 PTM repertoire changes as the mRNA/Rpb4/7 complex progresses from one stage to the next. These temporal PTMs regulate Rpb4 interactions with key regulators of gene expression that control transcriptional and post-transcriptional stages. Moreover, one mutant type specifically affects mRNA synthesis, whereas the other affects mRNA synthesis and decay; both types disrupt the balance between mRNA synthesis and decay ("mRNA buffering") and the cell's capacity to respond to the environment. We propose that temporal Rpb4/7 PTMs mediate the cross-talk among the various stages of the mRNA life cycle.
Collapse
Affiliation(s)
- Stephen Richard
- Department of Molecular Microbiology, Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 31096, Israel
| | - Lital Gross
- Department of Molecular Microbiology, Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 31096, Israel
| | - Jonathan Fischer
- Computer Science Division, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Keren Bendalak
- Smoler Proteomics Center, Faculty of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Tamar Ziv
- Smoler Proteomics Center, Faculty of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Shira Urim
- Department of Molecular Microbiology, Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 31096, Israel
| | - Mordechai Choder
- Department of Molecular Microbiology, Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 31096, Israel.
| |
Collapse
|
20
|
de Rozières CM, Joseph S. Influenza A Virus NS1 Protein Binds as a Dimer to RNA-Free PABP1 but Not to the PABP1·Poly(A) RNA Complex. Biochemistry 2020; 59:4439-4448. [PMID: 33172261 DOI: 10.1021/acs.biochem.0c00666] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Influenza A virus (IAV) is a highly contagious human pathogen that is responsible for tens of thousands of deaths each year. Non-structural protein 1 (NS1) is a crucial protein expressed by IAV to evade the host immune system. Additionally, NS1 has been proposed to stimulate translation because of its ability to bind poly(A) binding protein 1 (PABP1) and eukaryotic initiation factor 4G. We analyzed the interaction of NS1 with PABP1 using quantitative techniques. Our studies show that NS1 binds as a homodimer to PABP1, and this interaction is conserved across different IAV strains. Unexpectedly, NS1 does not bind to PABP1 that is bound to poly(A) RNA. Instead, NS1 binds only to PABP1 free of RNA, suggesting that stimulation of translation does not occur by NS1 interacting with the PABP1 molecule attached to the mRNA 3'-poly(A) tail. These results suggest that the function of the NS1·PABP1 complex appears to be distinct from the classical role of PABP1 in translation initiation, when it is bound to the 3'-poly(A) tail of mRNA.
Collapse
Affiliation(s)
- Cyrus M de Rozières
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0314, United States
| | - Simpson Joseph
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0314, United States
| |
Collapse
|
21
|
Mattijssen S, Iben JR, Li T, Coon SL, Maraia RJ. Single molecule poly(A) tail-seq shows LARP4 opposes deadenylation throughout mRNA lifespan with most impact on short tails. eLife 2020; 9:e59186. [PMID: 32744499 PMCID: PMC7413741 DOI: 10.7554/elife.59186] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 08/02/2020] [Indexed: 12/22/2022] Open
Abstract
La-related protein 4 (LARP4) directly binds both poly(A) and poly(A)-binding protein (PABP). LARP4 was shown to promote poly(A) tail (PAT) lengthening and stabilization of individual mRNAs presumably by protection from deadenylation (Mattijssen et al., 2017). We developed a nucleotide resolution transcriptome-wide, single molecule SM-PAT-seq method. This revealed LARP4 effects on a wide range of PAT lengths for human mRNAs and mouse mRNAs from LARP4 knockout (KO) and control cells. LARP4 effects are clear on long PAT mRNAs but become more prominent at 30-75 nucleotides. We also analyzed time courses of PAT decay transcriptome-wide and for ~200 immune response mRNAs. This demonstrated accelerated deadenylation in KO cells on PATs < 75 nucleotides and phasing consistent with greater PABP dissociation in the absence of LARP4. Thus, LARP4 shapes PAT profiles throughout mRNA lifespan with impact on mRNA decay at short lengths known to sensitize PABP dissociation in response to deadenylation machinery.
Collapse
Affiliation(s)
- Sandy Mattijssen
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of HealthBethesdaUnited States
| | - James R Iben
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of HealthBethesdaUnited States
| | - Tianwei Li
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of HealthBethesdaUnited States
| | - Steven L Coon
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of HealthBethesdaUnited States
| | - Richard J Maraia
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of HealthBethesdaUnited States
- Commissioned Corps, U.S. Public Health ServiceRockvilleUnited States
| |
Collapse
|
22
|
Kalous J, Jansová D, Šušor A. Role of Cyclin-Dependent Kinase 1 in Translational Regulation in the M-Phase. Cells 2020; 9:cells9071568. [PMID: 32605021 PMCID: PMC7408968 DOI: 10.3390/cells9071568] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/15/2020] [Accepted: 06/24/2020] [Indexed: 12/20/2022] Open
Abstract
Cyclin dependent kinase 1 (CDK1) has been primarily identified as a key cell cycle regulator in both mitosis and meiosis. Recently, an extramitotic function of CDK1 emerged when evidence was found that CDK1 is involved in many cellular events that are essential for cell proliferation and survival. In this review we summarize the involvement of CDK1 in the initiation and elongation steps of protein synthesis in the cell. During its activation, CDK1 influences the initiation of protein synthesis, promotes the activity of specific translational initiation factors and affects the functioning of a subset of elongation factors. Our review provides insights into gene expression regulation during the transcriptionally silent M-phase and describes quantitative and qualitative translational changes based on the extramitotic role of the cell cycle master regulator CDK1 to optimize temporal synthesis of proteins to sustain the division-related processes: mitosis and cytokinesis.
Collapse
|
23
|
An T, Liu Y, Gourguechon S, Wang CC, Li Z. CDK Phosphorylation of Translation Initiation Factors Couples Protein Translation with Cell-Cycle Transition. Cell Rep 2019; 25:3204-3214.e5. [PMID: 30540951 PMCID: PMC6350937 DOI: 10.1016/j.celrep.2018.11.063] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 10/18/2018] [Accepted: 11/15/2018] [Indexed: 01/17/2023] Open
Abstract
Protein translation in eukaryotes is cell-cycle dependent, with translation rates more robust in G1 phase of the cell cycle than in mitosis. However, whether the fundamental cell-cycle control machinery directly activates protein translation during the G1/S cell-cycle transition remains unknown. Using the early divergent eukaryote Trypanosoma brucei as a model organism, we report that the G1 cyclin-dependent kinase CRK1 phosphorylates two translation initiation factors, eIF4E4 and PABP1, to promote the G1/S cell-cycle transition and global protein translation. Phosphorylation of eIF4E4 by CRK1 enhances binding to the m7G cap structure and interaction with eIF4E4 and eIF4G3, and phosphorylation of PABP1 by CRK1 promotes association with the poly(A) sequence, self-interaction, and interaction with eIF4E4. These findings demonstrate that cyclin-dependent kinase-mediated regulation of translation initiation factors couples global protein translation with the G1/S cell-cycle transition. Protein translation is cell-cycle dependent, with more robust translation rates in the G1 phase of the cell cycle than in mitosis. An et al. show that the G1 cyclin-dependent kinase CRK1 phosphorylates translation initiation factors eIF4E4 and PABP1 to couple protein translation initiation with the G1/S cell-cycle transition.
Collapse
Affiliation(s)
- Tai An
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Yi Liu
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Stéphane Gourguechon
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Ching C Wang
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Ziyin Li
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
| |
Collapse
|
24
|
Leipheimer J, Bloom ALM, Panepinto JC. Protein Kinases at the Intersection of Translation and Virulence. Front Cell Infect Microbiol 2019; 9:318. [PMID: 31572689 PMCID: PMC6749009 DOI: 10.3389/fcimb.2019.00318] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 08/26/2019] [Indexed: 12/14/2022] Open
Abstract
As free living organisms, fungi are challenged with a variety of environmental insults that threaten their cellular processes. In some cases, these challenges mimic conditions present within mammals, resulting in the accidental selection of virulence factors over evolutionary time. Be it within a host or the soil, fungi must contend with environmental challenges through the production of stress effector proteins while maintaining factors required for viability in any condition. Initiation and upkeep of this balancing act is mainly under the control of kinases that affect the propensity and selectivity of protein translation. This review will focus on kinases in pathogenic fungi that facilitate a virulence phenotype through translational control.
Collapse
Affiliation(s)
- Jay Leipheimer
- Department of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, United States
| | - Amanda L M Bloom
- Department of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, United States
| | - John C Panepinto
- Department of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, United States
| |
Collapse
|
25
|
Tang TTL, Stowell JAW, Hill CH, Passmore LA. The intrinsic structure of poly(A) RNA determines the specificity of Pan2 and Caf1 deadenylases. Nat Struct Mol Biol 2019; 26:433-442. [PMID: 31110294 PMCID: PMC6555765 DOI: 10.1038/s41594-019-0227-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 04/11/2019] [Indexed: 11/09/2022]
Abstract
The 3' poly(A) tail of messenger RNA is fundamental to regulating eukaryotic gene expression. Shortening of the poly(A) tail, termed deadenylation, reduces transcript stability and inhibits translation. Nonetheless, the mechanism for poly(A) recognition by the conserved deadenylase complexes Pan2-Pan3 and Ccr4-Not is poorly understood. Here we provide a model for poly(A) RNA recognition by two DEDD-family deadenylase enzymes, Pan2 and the Ccr4-Not nuclease Caf1. Crystal structures of Saccharomyces cerevisiae Pan2 in complex with RNA show that, surprisingly, Pan2 does not form canonical base-specific contacts. Instead, it recognizes the intrinsic stacked, helical conformation of poly(A) RNA. Using a fully reconstituted biochemical system, we show that disruption of this structure-for example, by incorporation of guanosine into poly(A)-inhibits deadenylation by both Pan2 and Caf1. Together, these data establish a paradigm for specific recognition of the conformation of poly(A) RNA by proteins that regulate gene expression.
Collapse
Affiliation(s)
| | | | - Chris H Hill
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | | |
Collapse
|
26
|
Schäfer IB, Yamashita M, Schuller JM, Schüssler S, Reichelt P, Strauss M, Conti E. Molecular Basis for poly(A) RNP Architecture and Recognition by the Pan2-Pan3 Deadenylase. Cell 2019; 177:1619-1631.e21. [PMID: 31104843 PMCID: PMC6547884 DOI: 10.1016/j.cell.2019.04.013] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 03/08/2019] [Accepted: 04/05/2019] [Indexed: 01/17/2023]
Abstract
The stability of eukaryotic mRNAs is dependent on a ribonucleoprotein (RNP) complex of poly(A)-binding proteins (PABPC1/Pab1) organized on the poly(A) tail. This poly(A) RNP not only protects mRNAs from premature degradation but also stimulates the Pan2-Pan3 deadenylase complex to catalyze the first step of poly(A) tail shortening. We reconstituted this process in vitro using recombinant proteins and show that Pan2-Pan3 associates with and degrades poly(A) RNPs containing two or more Pab1 molecules. The cryo-EM structure of Pan2-Pan3 in complex with a poly(A) RNP composed of 90 adenosines and three Pab1 protomers shows how the oligomerization interfaces of Pab1 are recognized by conserved features of the deadenylase and thread the poly(A) RNA substrate into the nuclease active site. The structure reveals the basis for the periodic repeating architecture at the 3′ end of cytoplasmic mRNAs. This illustrates mechanistically how RNA-bound Pab1 oligomers act as rulers for poly(A) tail length over the mRNAs’ lifetime. Oligomerization of PABP on the poly(A) tail creates a series of consecutive arches Pan2-Pan3 deadenylase recognizes the oligomerized state of poly(A)-bound PABP The dimerization interface of juxtaposed PABPs creates the Pan2-Pan3 docking site The poly(A) RNP arches are flexible and moldable by the interacting proteins
Collapse
Affiliation(s)
- Ingmar B Schäfer
- Department of Structural Cell Biology, MPI of Biochemistry, Munich, Germany.
| | - Masami Yamashita
- Department of Structural Cell Biology, MPI of Biochemistry, Munich, Germany
| | | | - Steffen Schüssler
- Department of Structural Cell Biology, MPI of Biochemistry, Munich, Germany
| | - Peter Reichelt
- Department of Structural Cell Biology, MPI of Biochemistry, Munich, Germany
| | - Mike Strauss
- cryoEM Facility, MPI of Biochemistry, Munich, Germany
| | - Elena Conti
- Department of Structural Cell Biology, MPI of Biochemistry, Munich, Germany.
| |
Collapse
|
27
|
Sadek J, Omer A, Hall D, Ashour K, Gallouzi IE. Alternative polyadenylation and the stress response. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1540. [DOI: 10.1002/wrna.1540] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 03/18/2019] [Accepted: 04/02/2019] [Indexed: 01/06/2023]
Affiliation(s)
- Jason Sadek
- Department of Biochemistry McGill University, Rosalind and Morris Goodman Cancer Centre Montreal Quebec Canada
| | - Amr Omer
- Department of Biochemistry McGill University, Rosalind and Morris Goodman Cancer Centre Montreal Quebec Canada
| | - Derek Hall
- Department of Biochemistry McGill University, Rosalind and Morris Goodman Cancer Centre Montreal Quebec Canada
| | - Kholoud Ashour
- Department of Biochemistry McGill University, Rosalind and Morris Goodman Cancer Centre Montreal Quebec Canada
| | - Imed Eddine Gallouzi
- Department of Biochemistry McGill University, Rosalind and Morris Goodman Cancer Centre Montreal Quebec Canada
| |
Collapse
|
28
|
A Species-Correlated Transitional Residue D132 on Human FMRP Plays a Role in Nuclear Localization via an RNA-Dependent Interaction With PABP1. Neuroscience 2019; 404:282-296. [DOI: 10.1016/j.neuroscience.2019.01.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 12/16/2018] [Accepted: 01/17/2019] [Indexed: 11/22/2022]
|
29
|
PABP Cooperates with the CCR4-NOT Complex to Promote mRNA Deadenylation and Block Precocious Decay. Mol Cell 2019; 70:1081-1088.e5. [PMID: 29932901 DOI: 10.1016/j.molcel.2018.05.009] [Citation(s) in RCA: 128] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 04/16/2018] [Accepted: 05/04/2018] [Indexed: 12/18/2022]
Abstract
Multiple deadenylases are known in vertebrates, the PAN2-PAN3 (PAN2/3) and CCR4-NOT (CNOT) complexes, and PARN, yet their differential functions remain ambiguous. Moreover, the role of poly(A) binding protein (PABP) is obscure, limiting our understanding of the deadenylation mechanism. Here, we show that CNOT serves as a predominant nonspecific deadenylase for cytoplasmic poly(A)+ RNAs, and PABP promotes deadenylation while preventing premature uridylation and decay. PAN2/3 selectively trims long tails (>∼150 nt) with minimal effect on transcriptome, whereas PARN does not affect mRNA deadenylation. CAF1 and CCR4, catalytic subunits of CNOT, display distinct activities: CAF1 trims naked poly(A) segments and is blocked by PABPC, whereas CCR4 is activated by PABPC to shorten PABPC-protected sequences. Concerted actions of CAF1 and CCR4 delineate the ∼27 nt periodic PABPC footprints along shortening tail. Our study unveils distinct functions of deadenylases and PABPC, re-drawing the view on mRNA deadenylation and regulation.
Collapse
|
30
|
Webster MW, Chen YH, Stowell JAW, Alhusaini N, Sweet T, Graveley BR, Coller J, Passmore LA. mRNA Deadenylation Is Coupled to Translation Rates by the Differential Activities of Ccr4-Not Nucleases. Mol Cell 2019; 70:1089-1100.e8. [PMID: 29932902 PMCID: PMC6024076 DOI: 10.1016/j.molcel.2018.05.033] [Citation(s) in RCA: 147] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 05/17/2018] [Accepted: 05/24/2018] [Indexed: 01/01/2023]
Abstract
Translation and decay of eukaryotic mRNAs is controlled by shortening of the poly(A) tail and release of the poly(A)-binding protein Pab1/PABP. The Ccr4-Not complex contains two exonucleases—Ccr4 and Caf1/Pop2—that mediate mRNA deadenylation. Here, using a fully reconstituted biochemical system with proteins from the fission yeast Schizosaccharomyces pombe, we show that Pab1 interacts with Ccr4-Not, stimulates deadenylation, and differentiates the roles of the nuclease enzymes. Surprisingly, Pab1 release relies on Ccr4 activity. In agreement with this, in vivo experiments in budding yeast show that Ccr4 is a general deadenylase that acts on all mRNAs. In contrast, Caf1 only trims poly(A) not bound by Pab1. As a consequence, Caf1 is a specialized deadenylase required for the selective deadenylation of transcripts with lower rates of translation elongation and reduced Pab1 occupancy. These findings reveal a coupling between the rates of translation and deadenylation that is dependent on Pab1 and Ccr4-Not. Poly(A)-binding protein is efficiently released by Ccr4-Not nuclease activity Ccr4, but not Caf1, removes poly(A) tails bound to Pab1 Ccr4 acts on all transcripts and Caf1 acts on transcripts with low codon optimality Deadenylation by Ccr4-Not connects translation with mRNA stability
Collapse
Affiliation(s)
| | - Ying-Hsin Chen
- The Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, OH 44106-4960, USA
| | | | - Najwa Alhusaini
- The Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, OH 44106-4960, USA
| | - Thomas Sweet
- The Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, OH 44106-4960, USA
| | - Brenton R Graveley
- Department of Genetics and Developmental Biology, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, CT 06030, USA
| | - Jeff Coller
- The Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, OH 44106-4960, USA.
| | | |
Collapse
|
31
|
Dynamic interaction of poly(A)-binding protein with the ribosome. Sci Rep 2018; 8:17435. [PMID: 30487538 PMCID: PMC6261967 DOI: 10.1038/s41598-018-35753-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 11/09/2018] [Indexed: 01/15/2023] Open
Abstract
Eukaryotic mRNA has a cap structure and a poly(A) tail at the 5′ and 3′ ends, respectively. The cap structure is recognized by eIF (eukaryotic translation initiation factor) 4 F, while the poly(A) tail is bound by poly(A)-binding protein (PABP). PABP has four RNA recognition motifs (RRM1–4), and RRM1-2 binds both the poly(A) tail and eIF4G component of eIF4F, resulting in enhancement of translation. Here, we show that PABP interacts with the 40S and 60S ribosomal subunits dynamically via RRM2-3 or RRM3-4. Using a reconstituted protein expression system, we demonstrate that wild-type PABP activates translation in a dose-dependent manner, while a PABP mutant that binds poly(A) RNA and eIF4G, but not the ribosome, fails to do so. From these results, functional significance of the interaction of PABP with the ribosome is discussed.
Collapse
|
32
|
Brambilla M, Martani F, Bertacchi S, Vitangeli I, Branduardi P. The Saccharomyces cerevisiae
poly (A) binding protein (Pab1): Master regulator of mRNA metabolism and cell physiology. Yeast 2018; 36:23-34. [DOI: 10.1002/yea.3347] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 06/26/2018] [Accepted: 07/06/2018] [Indexed: 12/15/2022] Open
Affiliation(s)
- Marco Brambilla
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Piazza della Scienza 2 20126 Milan Italy
| | - Francesca Martani
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Piazza della Scienza 2 20126 Milan Italy
| | - Stefano Bertacchi
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Piazza della Scienza 2 20126 Milan Italy
| | - Ilaria Vitangeli
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Piazza della Scienza 2 20126 Milan Italy
| | - Paola Branduardi
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Piazza della Scienza 2 20126 Milan Italy
| |
Collapse
|
33
|
Identification of the Novel Nup188-brr7 Allele in a Screen for Cold-Sensitive mRNA Export Mutants in Saccharomyces cerevisiae. G3-GENES GENOMES GENETICS 2018; 8:2991-3003. [PMID: 30021831 PMCID: PMC6118305 DOI: 10.1534/g3.118.200447] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The maturation and export of mRNA from the nucleus through the nuclear pore complex is critical for maintaining an appropriate proteome in all eukaryotic cells. Here we summarize a previously unpublished screen in S. cerevisiae that utilized an established dT50 in situ hybridization assay to identify cold-sensitive mutants that accumulated bulk poly A RNA in the nucleus. The screen identified seven mutants in six complementation groups, including the brr6-1 strain that we described previously. In addition to brr6-1, we identified novel alleles of the key transport gene GLE1 and NUP188, a component of the Nic96 nucleoporin complex. Notably, we show that the nup188-brr7 allele causes defects in select protein import pathways as well as mRNA export. Given recent structural and functional evidence linking the Nic96 complex to transport components, this mutant may be particularly useful to the transport community.
Collapse
|
34
|
Fernández-Pevida A, Martín-Villanueva S, Murat G, Lacombe T, Kressler D, de la Cruz J. The eukaryote-specific N-terminal extension of ribosomal protein S31 contributes to the assembly and function of 40S ribosomal subunits. Nucleic Acids Res 2016; 44:7777-91. [PMID: 27422873 PMCID: PMC5027506 DOI: 10.1093/nar/gkw641] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 07/07/2016] [Indexed: 11/12/2022] Open
Abstract
The archaea-/eukaryote-specific 40S-ribosomal-subunit protein S31 is expressed as an ubiquitin fusion protein in eukaryotes and consists of a conserved body and a eukaryote-specific N-terminal extension. In yeast, S31 is a practically essential protein, which is required for cytoplasmic 20S pre-rRNA maturation. Here, we have studied the role of the N-terminal extension of the yeast S31 protein. We show that deletion of this extension partially impairs cell growth and 40S subunit biogenesis and confers hypersensitivity to aminoglycoside antibiotics. Moreover, the extension harbours a nuclear localization signal that promotes active nuclear import of S31, which associates with pre-ribosomal particles in the nucleus. In the absence of the extension, truncated S31 inefficiently assembles into pre-40S particles and two subpopulations of mature small subunits, one lacking and another one containing truncated S31, can be identified. Plasmid-driven overexpression of truncated S31 partially suppresses the growth and ribosome biogenesis defects but, conversely, slightly enhances the hypersensitivity to aminoglycosides. Altogether, these results indicate that the N-terminal extension facilitates the assembly of S31 into pre-40S particles and contributes to the optimal translational activity of mature 40S subunits but has only a minor role in cytoplasmic cleavage of 20S pre-rRNA at site D.
Collapse
Affiliation(s)
- Antonio Fernández-Pevida
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Avda. Manuel Siurot, s/n; E-41013 Seville, Spain Departamento de Genética, Universidad de Sevilla, Seville, Spain
| | - Sara Martín-Villanueva
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Avda. Manuel Siurot, s/n; E-41013 Seville, Spain Departamento de Genética, Universidad de Sevilla, Seville, Spain
| | - Guillaume Murat
- Unit of Biochemistry, Department of Biology, University of Fribourg, Chemin du Musée 10, CH-1700 Fribourg, Switzerland
| | - Thierry Lacombe
- Department of Microbiology and Molecular Medicine, Centre Médical Universitaire, University of Geneva, Geneva, Switzerland
| | - Dieter Kressler
- Unit of Biochemistry, Department of Biology, University of Fribourg, Chemin du Musée 10, CH-1700 Fribourg, Switzerland
| | - Jesús de la Cruz
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Avda. Manuel Siurot, s/n; E-41013 Seville, Spain Departamento de Genética, Universidad de Sevilla, Seville, Spain
| |
Collapse
|
35
|
Ivanov A, Mikhailova T, Eliseev B, Yeramala L, Sokolova E, Susorov D, Shuvalov A, Schaffitzel C, Alkalaeva E. PABP enhances release factor recruitment and stop codon recognition during translation termination. Nucleic Acids Res 2016; 44:7766-76. [PMID: 27418677 PMCID: PMC5027505 DOI: 10.1093/nar/gkw635] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 07/01/2016] [Indexed: 01/01/2023] Open
Abstract
Poly(A)-binding protein (PABP) is a major component of the messenger RNA–protein complex. PABP is able to bind the poly(A) tail of mRNA, as well as translation initiation factor 4G and eukaryotic release factor 3a (eRF3a). PABP has been found to stimulate translation initiation and to inhibit nonsense-mediated mRNA decay. Using a reconstituted mammalian in vitro translation system, we show that PABP directly stimulates translation termination. PABP increases the efficiency of translation termination by recruitment of eRF3a and eRF1 to the ribosome. PABP's function in translation termination depends on its C-terminal domain and its interaction with the N-terminus of eRF3a. Interestingly, we discover that full-length eRF3a exerts a different mode of function compared to its truncated form eRF3c, which lacks the N-terminal domain. Pre-association of eRF3a, but not of eRF3c, with pre-termination complexes (preTCs) significantly increases the efficiency of peptidyl–tRNA hydrolysis by eRF1. This implicates new, additional interactions of full-length eRF3a with the ribosomal preTC. Based on our findings, we suggest that PABP enhances the productive binding of the eRF1–eRF3 complex to the ribosome, via interactions with the N-terminal domain of eRF3a which itself has an active role in translation termination.
Collapse
Affiliation(s)
- Alexandr Ivanov
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, 119991 Moscow, Russia Faculty of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Tatyana Mikhailova
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, 119991 Moscow, Russia
| | - Boris Eliseev
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Lahari Yeramala
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Elizaveta Sokolova
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, 119991 Moscow, Russia
| | - Denis Susorov
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, 119991 Moscow, Russia Faculty of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Alexey Shuvalov
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, 119991 Moscow, Russia
| | - Christiane Schaffitzel
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38042 Grenoble, France School of Biochemistry, University of Bristol, BS8 1TD, UK
| | - Elena Alkalaeva
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, 119991 Moscow, Russia
| |
Collapse
|
36
|
Suresh S, Ahn HW, Joshi K, Dakshinamurthy A, Kananganat A, Garfinkel DJ, Farabaugh PJ. Ribosomal protein and biogenesis factors affect multiple steps during movement of the Saccharomyces cerevisiae Ty1 retrotransposon. Mob DNA 2015; 6:22. [PMID: 26664557 PMCID: PMC4673737 DOI: 10.1186/s13100-015-0053-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 11/30/2015] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND A large number of Saccharomyces cerevisiae cellular factors modulate the movement of the retrovirus-like transposon Ty1. Surprisingly, a significant number of chromosomal genes required for Ty1 transposition encode components of the translational machinery, including ribosomal proteins, ribosomal biogenesis factors, protein trafficking proteins and protein or RNA modification enzymes. RESULTS To assess the mechanistic connection between Ty1 mobility and the translation machinery, we have determined the effect of these mutations on ribosome biogenesis and Ty1 transcriptional and post-transcriptional regulation. Lack of genes encoding ribosomal proteins or ribosome assembly factors causes reduced accumulation of the ribosomal subunit with which they are associated. In addition, these mutations cause decreased Ty1 + 1 programmed translational frameshifting, and reduced Gag protein accumulation despite at least normal levels of Ty1 mRNA. Several ribosome subunit mutations increase the level of both an internally initiated Ty1 transcript and its encoded truncated Gag-p22 protein, which inhibits transposition. CONCLUSIONS Together, our results suggest that this large class of cellular genes modulate Ty1 transposition through multiple pathways. The effects are largely post-transcriptional acting at a variety of levels that may include translation initiation, protein stability and subcellular protein localization.
Collapse
Affiliation(s)
- Susmitha Suresh
- />Department of Biological Sciences and Program in Molecular and Cell Biology, University of Maryland Baltimore County, Baltimore, MD 21250 USA
- />Present address: Division of Infectious Diseases, Department of Internal Medicine, Stanford University School of Medicine, Stanford, California 94305 USA
| | - Hyo Won Ahn
- />Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA 30602 USA
| | - Kartikeya Joshi
- />Department of Biological Sciences and Program in Molecular and Cell Biology, University of Maryland Baltimore County, Baltimore, MD 21250 USA
| | - Arun Dakshinamurthy
- />Department of Biological Sciences and Program in Molecular and Cell Biology, University of Maryland Baltimore County, Baltimore, MD 21250 USA
- />Present address: Department of Nanosciences and Technology, Karunya University, Karunya Nagar, Coimbatore, 641 114 Tamil Nadu India
| | - Arun Kananganat
- />Department of Biological Sciences and Program in Molecular and Cell Biology, University of Maryland Baltimore County, Baltimore, MD 21250 USA
| | - David J. Garfinkel
- />Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA 30602 USA
| | - Philip J. Farabaugh
- />Department of Biological Sciences and Program in Molecular and Cell Biology, University of Maryland Baltimore County, Baltimore, MD 21250 USA
| |
Collapse
|
37
|
Bowen AM, Musalgaonkar S, Moomau CA, Gulay SP, Mirvis M, Dinman JD. Ribosomal protein uS19 mutants reveal its role in coordinating ribosome structure and function. ACTA ACUST UNITED AC 2015; 3:e1117703. [PMID: 26824029 PMCID: PMC4721500 DOI: 10.1080/21690731.2015.1117703] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 10/15/2015] [Accepted: 11/03/2015] [Indexed: 01/16/2023]
Abstract
Prior studies identified allosteric information pathways connecting functional centers in the large ribosomal subunit to the decoding center in the small subunit through the B1a and B1b/c intersubunit bridges in yeast. In prokaryotes a single SSU protein, uS13, partners with H38 (the A-site finger) and uL5 to form the B1a and B1b/c bridges respectively. In eukaryotes, the SSU component was split into 2 separate proteins during the course of evolution. One, also known as uS13, participates in B1b/c bridge with uL5 in eukaryotes. The other, called uS19 is the SSU partner in the B1a bridge with H38. Here, polyalanine mutants of uS19 involved in the uS19/uS13 and the uS19/H38 interfaces were used to elucidate the important amino acid residues involved in these intersubunit communication pathways. Two key clusters of amino acids were identified: one located at the junction between uS19 and uS13, and a second that appears to interact with the distal tip of H38. Biochemical analyses reveal that these mutations shift the ribosomal rotational equilibrium toward the unrotated state, increasing ribosomal affinity for tRNAs in the P-site and for ternary complex in the A-site, and inhibit binding of the translocase, eEF2. These defects in turn affect specific aspects of translational fidelity. These findings suggest that uS19 plays a critical role as a conduit of information exchange between the large and small ribosomal subunits directly through the B1a, and indirectly through the B1b/c bridges.
Collapse
Affiliation(s)
- Alicia M Bowen
- Department of Chemistry and Biochemistry; University of Maryland ; College Park, MD USA
| | - Sharmishtha Musalgaonkar
- Department of Cell Biology and Molecular Genetics; University of Maryland ; College Park, MD USA
| | - Christine A Moomau
- Department of Cell Biology and Molecular Genetics; University of Maryland ; College Park, MD USA
| | - Suna P Gulay
- Department of Cell Biology and Molecular Genetics; University of Maryland ; College Park, MD USA
| | - Mary Mirvis
- Department of Cell Biology and Molecular Genetics; University of Maryland ; College Park, MD USA
| | - Jonathan D Dinman
- Department of Cell Biology and Molecular Genetics; University of Maryland ; College Park, MD USA
| |
Collapse
|
38
|
Schmid M, Olszewski P, Pelechano V, Gupta I, Steinmetz LM, Jensen TH. The Nuclear PolyA-Binding Protein Nab2p Is Essential for mRNA Production. Cell Rep 2015; 12:128-139. [PMID: 26119729 DOI: 10.1016/j.celrep.2015.06.008] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 05/13/2015] [Accepted: 06/01/2015] [Indexed: 10/23/2022] Open
Abstract
Polyadenylation of mRNA is a key step in eukaryotic gene expression. However, despite the major impact of poly(A) tails on mRNA metabolism, the precise roles of poly(A)-binding proteins (PABPs) in nuclear mRNA biogenesis remain elusive. Here, we demonstrate that rapid nuclear depletion of the S. cerevisiae PABP Nab2p leads to a global loss of cellular mRNA, but not of RNA lacking poly(A) tails. Disappearance of mRNA is a nuclear event, but not due to decreased transcription. Instead, the absence of Nab2p results in robust nuclear mRNA decay by the ribonucleolytic RNA exosome in a polyadenylation-dependent process. We conclude that Nab2p is required to protect early mRNA and therefore constitutes a crucial nuclear mRNA biogenesis factor.
Collapse
Affiliation(s)
- Manfred Schmid
- Centre for mRNP Biogenesis and Metabolism, Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Alle 3, Building 1130, 8000 Aarhus C., Denmark.
| | - Pawel Olszewski
- Centre for mRNP Biogenesis and Metabolism, Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Alle 3, Building 1130, 8000 Aarhus C., Denmark
| | - Vicent Pelechano
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | - Ishaan Gupta
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | - Lars M Steinmetz
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany; Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Torben Heick Jensen
- Centre for mRNP Biogenesis and Metabolism, Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Alle 3, Building 1130, 8000 Aarhus C., Denmark.
| |
Collapse
|
39
|
Nishimura T, Padamsi Z, Fakim H, Milette S, Dunham W, Gingras AC, Fabian M. The eIF4E-Binding Protein 4E-T Is a Component of the mRNA Decay Machinery that Bridges the 5′ and 3′ Termini of Target mRNAs. Cell Rep 2015; 11:1425-36. [DOI: 10.1016/j.celrep.2015.04.065] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 04/17/2015] [Accepted: 04/30/2015] [Indexed: 12/26/2022] Open
|
40
|
Polymenis M, Aramayo R. Translate to divide: сontrol of the cell cycle by protein synthesis. MICROBIAL CELL 2015; 2:94-104. [PMID: 28357283 PMCID: PMC5348972 DOI: 10.15698/mic2015.04.198] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Protein synthesis underpins much of cell growth and, consequently, cell multiplication. Understanding how proliferating cells commit and progress into the cell cycle requires knowing not only which proteins need to be synthesized, but also what determines their rate of synthesis during cell division.
Collapse
Affiliation(s)
- Michael Polymenis
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Rodolfo Aramayo
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
| |
Collapse
|
41
|
Costello J, Castelli LM, Rowe W, Kershaw CJ, Talavera D, Mohammad-Qureshi SS, Sims PFG, Grant CM, Pavitt GD, Hubbard SJ, Ashe MP. Global mRNA selection mechanisms for translation initiation. Genome Biol 2015; 16:10. [PMID: 25650959 PMCID: PMC4302535 DOI: 10.1186/s13059-014-0559-z] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 12/03/2014] [Indexed: 12/20/2022] Open
Abstract
Background The selection and regulation of individual mRNAs for translation initiation from a competing pool of mRNA are poorly understood processes. The closed loop complex, comprising eIF4E, eIF4G and PABP, and its regulation by 4E-BPs are perceived to be key players. Using RIP-seq, we aimed to evaluate the role in gene regulation of the closed loop complex and 4E-BP regulation across the entire yeast transcriptome. Results We find that there are distinct populations of mRNAs with coherent properties: one mRNA pool contains many ribosomal protein mRNAs and is enriched specifically with all of the closed loop translation initiation components. This class likely represents mRNAs that rely heavily on the closed loop complex for protein synthesis. Other heavily translated mRNAs are apparently under-represented with most closed loop components except Pab1p. Combined with data showing a close correlation between Pab1p interaction and levels of translation, these data suggest that Pab1p is important for the translation of these mRNAs in a closed loop independent manner. We also identify a translational regulatory mechanism for the 4E-BPs; these appear to self-regulate by inhibiting translation initiation of their own mRNAs. Conclusions Overall, we show that mRNA selection for translation initiation is not as uniformly regimented as previously anticipated. Components of the closed loop complex are highly relevant for many mRNAs, but some heavily translated mRNAs interact poorly with this machinery. Therefore, alternative, possibly Pab1p-dependent mechanisms likely exist to load ribosomes effectively onto mRNAs. Finally, these studies identify and characterize a complex self-regulatory circuit for the yeast 4E-BPs. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0559-z) contains supplementary material, which is available to authorized users.
Collapse
|
42
|
Tessier SN, Storey KB. To be or not to be: the regulation of mRNA fate as a survival strategy during mammalian hibernation. Cell Stress Chaperones 2014; 19:763-76. [PMID: 24789358 PMCID: PMC4389848 DOI: 10.1007/s12192-014-0512-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 04/13/2014] [Indexed: 12/20/2022] Open
Abstract
Mammalian hibernators undergo profound behavioral, physiological, and biochemical changes in order to cope with hypothermia, ischemia-reperfusion, and finite fuel reserves over days or weeks of continuous torpor. Against a backdrop of global reductions in energy-expensive processes such as transcription and translation, a subset of genes/proteins are strategically upregulated in order to meet challenges associated with hibernation. Consequently, hibernation involves substantial transcriptional and posttranscriptional regulatory mechanisms and provides a phenomenon with which to understand how a set of common genes/proteins can be differentially regulated in order to enhance stress tolerance beyond that which is possible for nonhibernators. The present review focuses on the involvement of messenger RNA (mRNA) interacting factors that play a role in the regulation of gene/protein expression programs that define the hibernating phenotype. These include proteins involved in mRNA processing (i.e., capping, splicing, and polyadenylation) and the possible role of alternative splicing as a means of enhancing protein diversity. Since the total pool of mRNA remains constant throughout torpor, mechanisms which enhance mRNA stability are discussed in the context of RNA binding proteins and mRNA decay pathways. Furthermore, mechanisms which control the global reduction of cap-dependent translation and the involvement of internal ribosome entry sites in mRNAs encoding stress response proteins are also discussed. Finally, the concept of regulating each of these factors in discrete subcellular compartments for enhanced efficiency is addressed. The analysis draws on recent research from several well-studied mammalian hibernators including ground squirrels, bats, and bears.
Collapse
Affiliation(s)
- Shannon N. Tessier
- Institute of Biochemistry & Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6 Canada
| | - Kenneth B. Storey
- Institute of Biochemistry & Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6 Canada
| |
Collapse
|
43
|
Tessier SN, Audas TE, Wu CW, Lee S, Storey KB. The involvement of mRNA processing factors TIA-1, TIAR, and PABP-1 during mammalian hibernation. Cell Stress Chaperones 2014; 19:813-25. [PMID: 24590458 PMCID: PMC4389841 DOI: 10.1007/s12192-014-0505-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Revised: 02/11/2014] [Accepted: 02/12/2014] [Indexed: 01/10/2023] Open
Abstract
Mammalian hibernators survive low body temperatures, ischemia-reperfusion, and restricted nutritional resources via global reductions in energy-expensive cellular processes and selective increases in stress pathways. Consequently, studies that analyze hibernation uncover mechanisms which balance metabolism and support survival by enhancing stress tolerance. We hypothesized processing factors that influence messenger ribonucleic acid (mRNA) maturation and translation may play significant roles in hibernation. We characterized the amino acid sequences of three RNA processing proteins (T cell intracellular antigen 1 (TIA-1), TIA1-related (TIAR), and poly(A)-binding proteins (PABP-1)) from thirteen-lined ground squirrels (Ictidomys tridecemlineatus), which all displayed a high degree of sequence identity with other mammals. Alternate Tia-1 and TiaR gene variants were found in the liver with higher expression of isoform b versus a in both cases. The localization of RNA-binding proteins to subnuclear structures was assessed by immunohistochemistry and confirmed by subcellular fractionation; TIA-1 was identified as a major component of subnuclear structures with up to a sevenfold increase in relative protein levels in the nucleus during hibernation. By contrast, there was no significant difference in the relative protein levels of TIARa/TIARb in the nucleus, and a decrease was observed for TIAR isoforms in cytoplasmic fractions of torpid animals. Finally, we used solubility tests to analyze the formation of reversible aggregates that are associated with TIA-1/R function during stress; a shift towards the soluble fraction (TIA-1a, TIA-1b) was observed during hibernation suggesting enhanced protein aggregation was not present during torpor. The present study identifies novel posttranscriptional regulatory mechanisms that may play a role in reducing translational rates and/or mRNA processing under unfavorable environmental conditions.
Collapse
Affiliation(s)
- Shannon N. Tessier
- />Institute of Biochemistry, Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6 Canada
| | - Timothy E. Audas
- />Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5 Canada
| | - Cheng-Wei Wu
- />Institute of Biochemistry, Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6 Canada
| | - Stephen Lee
- />Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5 Canada
| | - Kenneth B. Storey
- />Institute of Biochemistry, Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6 Canada
| |
Collapse
|
44
|
Abstract
Poly(A) tails are important regulators of mRNA stability and translational efficiency. Cytoplasmic removal of poly(A) tails by 3'→5' exonucleases (deadenylation) is the rate-limiting step in mRNA degradation. Two exonuclease complexes contribute the majority of the deadenylation activity in eukaryotes: Ccr4-Not and Pan2-Pan3. These can be specifically recruited to mRNA to regulate mRNA stability or translational efficiency, thereby fine-tuning gene expression. In the present review, we discuss the activities and roles of the Pan2-Pan3 deadenylation complex.
Collapse
|
45
|
Firczuk H, Kannambath S, Pahle J, Claydon A, Beynon R, Duncan J, Westerhoff H, Mendes P, McCarthy JE. An in vivo control map for the eukaryotic mRNA translation machinery. Mol Syst Biol 2013; 9:635. [PMID: 23340841 PMCID: PMC3564266 DOI: 10.1038/msb.2012.73] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Accepted: 12/16/2012] [Indexed: 01/16/2023] Open
Abstract
A new quantitative strategy has generated a comprehensive rate control map for protein synthesis in exponentially growing yeast cells. This analysis reveals the modularity of the system as well as highly non-stoichiometric relationships between components. ![]()
A ‘genetic titration' method has generated a map of the in vivo rate control properties of components of the protein synthesis machinery in Saccharomyces cerevisiae and has been used to parameterize a new comprehensive model of the translation pathway. The translation machinery is found to be a highly modular system in functional terms yet the intracellular concentrations of its components range from a few thousand to one million molecules per cell. This approach identifies non-intuitive features of the system such as the strongest rate control being exercised by high abundance elongation factors. The rate control analysis allows us to identify a surprising fine-control function for duplicated translation factor genes.
Rate control analysis defines the in vivo control map governing yeast protein synthesis and generates an extensively parameterized digital model of the translation pathway. Among other non-intuitive outcomes, translation demonstrates a high degree of functional modularity and comprises a non-stoichiometric combination of proteins manifesting functional convergence on a shared maximal translation rate. In exponentially growing cells, polypeptide elongation (eEF1A, eEF2, and eEF3) exerts the strongest control. The two other strong control points are recruitment of mRNA and tRNAi to the 40S ribosomal subunit (eIF4F and eIF2) and termination (eRF1; Dbp5). In contrast, factors that are found to promote mRNA scanning efficiency on a longer than-average 5′untranslated region (eIF1, eIF1A, Ded1, eIF2B, eIF3, and eIF5) exceed the levels required for maximal control. This is expected to allow the cell to minimize scanning transition times, particularly for longer 5′UTRs. The analysis reveals these and other collective adaptations of control shared across the factors, as well as features that reflect functional modularity and system robustness. Remarkably, gene duplication is implicated in the fine control of cellular protein synthesis.
Collapse
Affiliation(s)
- Helena Firczuk
- School of Life Sciences, University of Warwick, Coventry, UK
| | | | | | | | | | | | | | | | | |
Collapse
|
46
|
Xu AN, Chen XH, Tan YH, Qi XL, Xu ZF, Zhang LL, Ren FG, Bian SC, Chen Y, Wang HW. Identification of a novel circularized transcript of the AML1 gene. BMB Rep 2013; 46:163-8. [PMID: 23527860 PMCID: PMC4133869 DOI: 10.5483/bmbrep.2013.46.3.171] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The AML1 gene is an essential transcription factor regulating the differentiation of hematopoietic stem cells into mature blood cells. Though at least 12 different alternatively spliced AML1 mRNAs are generated, three splice variants (AML1a, AML1b and AML1c) have been characterized. Here, using the reverse transcription-polymerase chain reaction with outwardfacing primers, we identified a novel non-polyadenylated transcript from the AML1 gene, with exons 5 and 6 scrambled. The novel transcript resisted RNase R digestion, indicating it is a circular RNA structure that may originate from products of mRNA alternative splicing. The expression of the novel transcript in different cells or cell lines of human and a number of other species matched those of the canonical transcripts. The discovery provides additional evidence that circular RNA could stably exist in vivo in human, and may also help to understand the mechanism of the regulation of the AML1 gene transcription. [BMB Reports 2013; 46(3): 163-168]
Collapse
Affiliation(s)
- Ai-ning Xu
- Department of Hematology, The Second Hospital of Shanxi Medical University, Taiyuan 030001, China
| | | | | | | | | | | | | | | | | | | |
Collapse
|
47
|
Min EE, Roy B, Amrani N, He F, Jacobson A. Yeast Upf1 CH domain interacts with Rps26 of the 40S ribosomal subunit. RNA (NEW YORK, N.Y.) 2013; 19:1105-15. [PMID: 23801788 PMCID: PMC3708530 DOI: 10.1261/rna.039396.113] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Accepted: 05/17/2013] [Indexed: 05/18/2023]
Abstract
The central nonsense-mediated mRNA decay (NMD) regulator, Upf1, selectively targets nonsense-containing mRNAs for rapid degradation. In yeast, Upf1 preferentially associates with mRNAs that are NMD substrates, but the mechanism of its selective retention on these mRNAs has yet to be elucidated. Previously, we demonstrated that Upf1 associates with 40S ribosomal subunits. Here, we define more precisely the nature of this association using conventional and affinity-based purification of ribosomal subunits, and a two-hybrid screen to identify Upf1-interacting ribosomal proteins. Upf1 coimmunoprecipitates specifically with epitope-tagged 40S ribosomal subunits, and Upf1 association with high-salt washed or puromycin-released 40S subunits was found to occur without simultaneous eRF1, eRF3, Upf2, or Upf3 association. Two-hybrid analyses and in vitro binding assays identified a specific interaction between Upf1 and Rps26. Using mutations in domains of UPF1 known to be crucial for its function, we found that Upf1:40S association is modulated by ATP, and Upf1:Rps26 interaction is dependent on the N-terminal Upf1 CH domain. The specific association of Upf1 with the 40S subunit is consistent with the notion that this RNA helicase not only triggers rapid decay of nonsense-containing mRNAs, but may also have an important role in dissociation of the premature termination complex.
Collapse
|
48
|
Wahle E, Winkler GS. RNA decay machines: deadenylation by the Ccr4-not and Pan2-Pan3 complexes. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2013; 1829:561-70. [PMID: 23337855 DOI: 10.1016/j.bbagrm.2013.01.003] [Citation(s) in RCA: 173] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Revised: 12/14/2012] [Accepted: 01/09/2013] [Indexed: 12/20/2022]
Abstract
Shortening and removal of the 3' poly(A) tail of mature mRNA by poly(A)-specific 3' exonucleases (deadenylases) is the initial and often rate-limiting step in mRNA degradation. The majority of cytoplasmic deadenylase activity is associated with the Ccr4-Not and Pan2-Pan3 complexes. Two distinct catalytic subunits, Caf1/Pop2 and Ccr4, are associated with the Ccr4-Not complex, whereas the Pan2 enzymatic subunit forms a stable complex with Pan3. In this review, we discuss the composition and activity of these two deadenylases. In addition, we comment on generic and specific mechanisms of recruitment of Ccr4-Not and Pan2-Pan3 to mRNAs. Finally, we discuss specialised and redundant functions of the deadenylases and review the importance of Ccr4-Not subunits in the regulation of physiological processes. This article is part of a Special Issue entitled: RNA Decay mechanisms.
Collapse
Affiliation(s)
- Elmar Wahle
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany.
| | | |
Collapse
|
49
|
Abstract
Shortening of the poly(A) tail is the first and often rate-limiting step in mRNA degradation. Three poly(A)-specific 3' exonucleases have been described that can carry out this reaction: PAN, composed of two subunits; PARN, a homodimer; and the CCR4-NOT complex, a heterooligomer that contains two catalytic subunits and may have additional functions in the cell. Current evidence indicates that all three enzymes use a two-metal ion mechanism to release nucleoside monophosphates in a hydrolytic reaction. The CCR4-NOT is the main deadenylase in all organisms examined, and mutations affecting the complex can be lethal. The contribution of PAN, apparently an initial deadenylation preceding the activity of CCR4-NOT, is less important, whereas the activity of PARN seems to be restricted to specific substrates or circumstances, for example, stress conditions. Rapid deadenylation and decay of specific mRNAs can be caused by recruitment of both PAN and the CCR4-NOT complex. This function can be carried out by RNA-binding proteins, for example, members of the PUF family. Alternatively, miRNAs can recruit the deadenylase complexes with the help of their associated GW182 proteins.
Collapse
Affiliation(s)
- Christiane Harnisch
- Martin-Luther-University of Halle-Wittenberg, Institute of Biochemistry and Biotechnology, Kurt-Mothes-Strasse 3, Halle, Germany
| | - Bodo Moritz
- Martin-Luther-University of Halle-Wittenberg, Institute of Biochemistry and Biotechnology, Kurt-Mothes-Strasse 3, Halle, Germany
| | - Christiane Rammelt
- Martin-Luther-University of Halle-Wittenberg, Institute of Biochemistry and Biotechnology, Kurt-Mothes-Strasse 3, Halle, Germany
| | - Claudia Temme
- Martin-Luther-University of Halle-Wittenberg, Institute of Biochemistry and Biotechnology, Kurt-Mothes-Strasse 3, Halle, Germany
| | - Elmar Wahle
- Martin-Luther-University of Halle-Wittenberg, Institute of Biochemistry and Biotechnology, Kurt-Mothes-Strasse 3, Halle, Germany.
| |
Collapse
|
50
|
Dever TE, Green R. The elongation, termination, and recycling phases of translation in eukaryotes. Cold Spring Harb Perspect Biol 2012; 4:a013706. [PMID: 22751155 DOI: 10.1101/cshperspect.a013706] [Citation(s) in RCA: 289] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
This work summarizes our current understanding of the elongation and termination/recycling phases of eukaryotic protein synthesis. We focus here on recent advances in the field. In addition to an overview of translation elongation, we discuss unique aspects of eukaryotic translation elongation including eEF1 recycling, eEF2 modification, and eEF3 and eIF5A function. Likewise, we highlight the function of the eukaryotic release factors eRF1 and eRF3 in translation termination, and the functions of ABCE1/Rli1, the Dom34:Hbs1 complex, and Ligatin (eIF2D) in ribosome recycling. Finally, we present some of the key questions in translation elongation, termination, and recycling that remain to be answered.
Collapse
Affiliation(s)
- Thomas E Dever
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA.
| | | |
Collapse
|