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Jing S, Yang J, Liu Y, Wang F, Zheng F, Ren A, Yu B, Zhao Y, Jia B, Chen R, Yu B, Liu Q, Xu J. Functional Analysis of CPSF30 in Nilaparvata lugens Using RNA Interference Reveals Its Essential Role in Development and Survival. INSECTS 2024; 15:860. [PMID: 39590459 PMCID: PMC11594811 DOI: 10.3390/insects15110860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2024] [Revised: 10/27/2024] [Accepted: 11/01/2024] [Indexed: 11/28/2024]
Abstract
The brown planthopper (Nilaparvata lugens) is a major pest threatening global rice production, significantly reducing yields annually. As N. lugens increasingly develops resistance to conventional control methods, such as chemical pesticides, there is an urgent need for innovative and sustainable pest management strategies. Cleavage and Polyadenylation Specificity Factor 30 (CPSF30) is a key protein involved in mRNA 3' end processing, yet its function in N. lugens remains poorly understood. This study aims to elucidate the role of CPSF30 in the growth and development of N. lugens and evaluate its potential as a target for RNA interference (RNAi)-based pest control strategies. We cloned and characterized the cDNA sequence of NlCPSF30, which encodes a protein of 341 amino acids containing five CCCH zinc-finger domains and two CCHC zinc-knuckle domains. Sequence alignment revealed that NlCPSF30 is highly conserved among insect species, particularly in the zinc-finger domains essential for RNA binding and processing. Phylogenetic analysis showed that NlCPSF30 is closely related to CPSF30 proteins from other hemipteran species. Expression analysis indicated that NlCPSF30 is most highly expressed in the fat body and during the adult stage, with significantly higher expression in females than in males. RNAi-mediated silencing of NlCPSF30 in third-instar nymphs resulted in severe phenotypic abnormalities, including disrupted molting and increased mortality following injection of double-stranded RNA (dsRNA) targeting NlCPSF30. Moreover, it influenced the expression of genes associated with hormone regulation, namely NlHry, NlE93, and NlKr-h1. These results suggest that NlCPSF30 is integral to critical physiological processes, with its disruption leading to increased mortality. Our findings identify NlCPSF30 as an essential gene for N. lugens' survival and a promising target for RNAi-based pest management strategies. This study provides a valuable molecular target and theoretical insights for developing RNAi-based control methods against N. lugens.
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Affiliation(s)
- Shengli Jing
- College of Life Sciences, Xinyang Normal University, Xinyang 464000, China; (S.J.); (J.Y.); (Y.L.); (F.W.); (F.Z.); (A.R.); (B.Y.); (Y.Z.); (B.J.); (R.C.); (B.Y.); (Q.L.)
| | - Jing Yang
- College of Life Sciences, Xinyang Normal University, Xinyang 464000, China; (S.J.); (J.Y.); (Y.L.); (F.W.); (F.Z.); (A.R.); (B.Y.); (Y.Z.); (B.J.); (R.C.); (B.Y.); (Q.L.)
| | - Yali Liu
- College of Life Sciences, Xinyang Normal University, Xinyang 464000, China; (S.J.); (J.Y.); (Y.L.); (F.W.); (F.Z.); (A.R.); (B.Y.); (Y.Z.); (B.J.); (R.C.); (B.Y.); (Q.L.)
| | - Feifei Wang
- College of Life Sciences, Xinyang Normal University, Xinyang 464000, China; (S.J.); (J.Y.); (Y.L.); (F.W.); (F.Z.); (A.R.); (B.Y.); (Y.Z.); (B.J.); (R.C.); (B.Y.); (Q.L.)
| | - Fang Zheng
- College of Life Sciences, Xinyang Normal University, Xinyang 464000, China; (S.J.); (J.Y.); (Y.L.); (F.W.); (F.Z.); (A.R.); (B.Y.); (Y.Z.); (B.J.); (R.C.); (B.Y.); (Q.L.)
| | - Aobo Ren
- College of Life Sciences, Xinyang Normal University, Xinyang 464000, China; (S.J.); (J.Y.); (Y.L.); (F.W.); (F.Z.); (A.R.); (B.Y.); (Y.Z.); (B.J.); (R.C.); (B.Y.); (Q.L.)
| | - Bingbing Yu
- College of Life Sciences, Xinyang Normal University, Xinyang 464000, China; (S.J.); (J.Y.); (Y.L.); (F.W.); (F.Z.); (A.R.); (B.Y.); (Y.Z.); (B.J.); (R.C.); (B.Y.); (Q.L.)
| | - Yue Zhao
- College of Life Sciences, Xinyang Normal University, Xinyang 464000, China; (S.J.); (J.Y.); (Y.L.); (F.W.); (F.Z.); (A.R.); (B.Y.); (Y.Z.); (B.J.); (R.C.); (B.Y.); (Q.L.)
| | - Bing Jia
- College of Life Sciences, Xinyang Normal University, Xinyang 464000, China; (S.J.); (J.Y.); (Y.L.); (F.W.); (F.Z.); (A.R.); (B.Y.); (Y.Z.); (B.J.); (R.C.); (B.Y.); (Q.L.)
| | - Ruixian Chen
- College of Life Sciences, Xinyang Normal University, Xinyang 464000, China; (S.J.); (J.Y.); (Y.L.); (F.W.); (F.Z.); (A.R.); (B.Y.); (Y.Z.); (B.J.); (R.C.); (B.Y.); (Q.L.)
| | - Bin Yu
- College of Life Sciences, Xinyang Normal University, Xinyang 464000, China; (S.J.); (J.Y.); (Y.L.); (F.W.); (F.Z.); (A.R.); (B.Y.); (Y.Z.); (B.J.); (R.C.); (B.Y.); (Q.L.)
| | - Qingsong Liu
- College of Life Sciences, Xinyang Normal University, Xinyang 464000, China; (S.J.); (J.Y.); (Y.L.); (F.W.); (F.Z.); (A.R.); (B.Y.); (Y.Z.); (B.J.); (R.C.); (B.Y.); (Q.L.)
- State Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Jingang Xu
- College of Life Sciences, Xinyang Normal University, Xinyang 464000, China; (S.J.); (J.Y.); (Y.L.); (F.W.); (F.Z.); (A.R.); (B.Y.); (Y.Z.); (B.J.); (R.C.); (B.Y.); (Q.L.)
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Dutta S, Srivatsan SG. Enzymatic Functionalization of RNA Oligonucleotides by Terminal Uridylyl Transferase Using Fluorescent and Clickable Nucleotide Analogs. Chem Asian J 2024; 19:e202400475. [PMID: 38949615 DOI: 10.1002/asia.202400475] [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: 04/26/2024] [Revised: 06/27/2024] [Accepted: 07/01/2024] [Indexed: 07/02/2024]
Abstract
We report a systematic study on controlling the enzyme activity of a terminal uridylyl transferase (TUTase) called SpCID1, which provides methods to effect site-specific incorporation of a single modified nucleotide analog at the 3'-end of an RNA oligonucleotide (ON). Responsive heterocycle-modified fluorescent UTP probes that are useful in analyzing non-canonical nucleic acid structures and azide- and alkyne-modified UTP analogs that are compatible for chemoenzymatic functionalization were used as study systems. In the first strategy, we balanced the concentration of essential metal ion cofactors (Mg2+ and Mn2+ ions) to restrict the processivity of the enzyme, which gave a very good control on the incorporation of clickable nucleotide analogs. In the second approach, borate that complexes with 2' and 3' oxygen atoms of a ribose sugar was used as a reversibly binding chelator to block repeated addition of nucleotide analogs. Notably, in the presence of heterocycle-modified fluorescent UTPs, we obtained single-nucleotide incorporated RNA products in reasonable yields, while with clickable nucleotides yields were very good. Further, 3'-end azide- and alkyne-labeled RNA ONs were post-enzymatically functionalized by CuAAC and SPAAC reactions with fluorescent probes. These strategies broaden the scope of TUTase in site-specifically installing modifications of different types onto RNA for various applications.
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Affiliation(s)
- Swagata Dutta
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune Dr. Homi Bhabha Road, Pune, 411008, India
| | - Seergazhi G Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune Dr. Homi Bhabha Road, Pune, 411008, India
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Ni Z, Ahmed N, Nabeel-Shah S, Guo X, Pu S, Song J, Marcon E, Burke G, Tong AH, Chan K, Ha KH, Blencowe B, Moffat J, Greenblatt J. Identifying human pre-mRNA cleavage and polyadenylation factors by genome-wide CRISPR screens using a dual fluorescence readthrough reporter. Nucleic Acids Res 2024; 52:4483-4501. [PMID: 38587191 PMCID: PMC11077057 DOI: 10.1093/nar/gkae240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 01/29/2024] [Accepted: 04/02/2024] [Indexed: 04/09/2024] Open
Abstract
Messenger RNA precursors (pre-mRNA) generally undergo 3' end processing by cleavage and polyadenylation (CPA), which is specified by a polyadenylation site (PAS) and adjacent RNA sequences and regulated by a large variety of core and auxiliary CPA factors. To date, most of the human CPA factors have been discovered through biochemical and proteomic studies. However, genetic identification of the human CPA factors has been hampered by the lack of a reliable genome-wide screening method. We describe here a dual fluorescence readthrough reporter system with a PAS inserted between two fluorescent reporters. This system enables measurement of the efficiency of 3' end processing in living cells. Using this system in combination with a human genome-wide CRISPR/Cas9 library, we conducted a screen for CPA factors. The screens identified most components of the known core CPA complexes and other known CPA factors. The screens also identified CCNK/CDK12 as a potential core CPA factor, and RPRD1B as a CPA factor that binds RNA and regulates the release of RNA polymerase II at the 3' ends of genes. Thus, this dual fluorescence reporter coupled with CRISPR/Cas9 screens reliably identifies bona fide CPA factors and provides a platform for investigating the requirements for CPA in various contexts.
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Affiliation(s)
- Zuyao Ni
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Nujhat Ahmed
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada
| | - Syed Nabeel-Shah
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada
| | - Xinghua Guo
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Shuye Pu
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Jingwen Song
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Edyta Marcon
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Giovanni L Burke
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada
| | - Amy Hin Yan Tong
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada
| | - Katherine Chan
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada
| | - Kevin C H Ha
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada
| | - Benjamin J Blencowe
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada
| | - Jason Moffat
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada
- Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON Canada
| | - Jack F Greenblatt
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada
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Krochtová K, Janovec L, Bogárová V, Halečková A, Kožurková M. Interaction of 3,9-disubstituted acridine with single stranded poly(rA), double stranded poly(rAU) and triple stranded poly(rUAU): molecular docking - A spectroscopic tandem study. Chem Biol Interact 2024; 394:110965. [PMID: 38552767 DOI: 10.1016/j.cbi.2024.110965] [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: 01/26/2024] [Revised: 03/12/2024] [Accepted: 03/16/2024] [Indexed: 04/10/2024]
Abstract
RNA plays an important role in many biological processes which are crucial for cell survival, and it has been suggested that it may be possible to inhibit individual processes involved in many diseases by targeting specific sequences of RNA. The aim of this work is to determine the affinity of novel 3,9-disubstited acridine derivative 1 with three different RNA molecules, namely single stranded poly(rA), double stranded homopolymer poly(rAU) and triple stranded poly(rUAU). The results of the absorption titration assays show that the binding constant of the novel derivative to the RNA molecules was in the range of 1.7-6.2 × 104 mol dm-3. The fluorescence and circular dichroism titration assays revealed considerable changes. The most significant results in terms of interpreting the nature of the interactions were the melting temperatures of the RNA samples in complexes with the 1. In the case of poly(rA), denaturation resulted in a self-structure formation; increased stabilization was observed for poly(rAU), while the melting points of the ligand-poly(rUAU) complex showed significant destabilization as a result of the interaction. The principles of molecular mechanics were applied to propose the non-bonded interactions within the binding complex, pentariboadenylic acid and acridine ligand as the study model. Initial molecular docking provided the input structure for advanced simulation techniques. Molecular dynamics simulation and cluster analysis reveal π - π stacking and the hydrogen bonds formation as the main forces that can stabilize the binding complex. Subsequent MM-GBSA calculations showed negative binding enthalpy accompanied the complex formation and proposed the most preferred conformation of the interaction complex.
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Affiliation(s)
- Kristína Krochtová
- Department of Biochemistry, Institute of Chemistry, Faculty of Science, Pavol Jozef Šafárik University in Košice, Šrobárova 2, 041 54, Košice, Slovak Republic
| | - Ladislav Janovec
- Department of Organic Chemistry, Institute of Chemistry, Faculty of Science, Pavol Jozef Šafárik University in Košice, Šrobárova 2, 041 54, Košice, Slovak Republic
| | - Viktória Bogárová
- Department of Biochemistry, Institute of Chemistry, Faculty of Science, Pavol Jozef Šafárik University in Košice, Šrobárova 2, 041 54, Košice, Slovak Republic
| | - Annamária Halečková
- Department of Organic Chemistry, Institute of Chemistry, Faculty of Science, Pavol Jozef Šafárik University in Košice, Šrobárova 2, 041 54, Košice, Slovak Republic
| | - Mária Kožurková
- Department of Biochemistry, Institute of Chemistry, Faculty of Science, Pavol Jozef Šafárik University in Košice, Šrobárova 2, 041 54, Košice, Slovak Republic.
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Cheuka PM, Njaria P, Mayoka G, Funjika E. Emerging Drug Targets for Antimalarial Drug Discovery: Validation and Insights into Molecular Mechanisms of Function. J Med Chem 2024; 67:838-863. [PMID: 38198596 DOI: 10.1021/acs.jmedchem.3c01828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
Approximately 619,000 malaria deaths were reported in 2021, and resistance to recommended drugs, including artemisinin-combination therapies (ACTs), threatens malaria control. Treatment failure with ACTs has been found to be as high as 93% in northeastern Thailand, and parasite mutations responsible for artemisinin resistance have already been reported in some African countries. Therefore, there is an urgent need to identify alternative treatments with novel targets. In this Perspective, we discuss some promising antimalarial drug targets, including enzymes involved in proteolysis, DNA and RNA metabolism, protein synthesis, and isoprenoid metabolism. Other targets discussed are transporters, Plasmodium falciparum acetyl-coenzyme A synthetase, N-myristoyltransferase, and the cyclic guanosine monophosphate-dependent protein kinase G. We have outlined mechanistic details, where these are understood, underpinning the biological roles and hence druggability of such targets. We believe that having a clear understanding of the underlying chemical interactions is valuable to medicinal chemists in their quest to design appropriate inhibitors.
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Affiliation(s)
- Peter Mubanga Cheuka
- Department of Chemistry, School of Natural Sciences, University of Zambia, P.O. Box 32379, Lusaka 10101, Zambia
| | - Paul Njaria
- Department of Pharmacognosy and Pharmaceutical Chemistry, Kenyatta University, P.O. Box 14548-00400, Nairobi 00100, Kenya
| | - Godfrey Mayoka
- Department of Pharmacology and Pharmacognosy, School of Pharmacy, Jomo Kenyatta University of Agriculture and Technology, P.O. Box 62000-00200, Nairobi 00100, Kenya
| | - Evelyn Funjika
- Department of Chemistry, School of Natural Sciences, University of Zambia, P.O. Box 32379, Lusaka 10101, Zambia
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Zhou L, Li K, Hunt AG. Natural variation in the plant polyadenylation complex. FRONTIERS IN PLANT SCIENCE 2024; 14:1303398. [PMID: 38317838 PMCID: PMC10839035 DOI: 10.3389/fpls.2023.1303398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 12/22/2023] [Indexed: 02/07/2024]
Abstract
Messenger RNA polyadenylation, the process wherein the primary RNA polymerase II transcript is cleaved and a poly(A) tract added, is a key step in the expression of genes in plants. Moreover, it is a point at which gene expression may be regulated by determining the functionality of the mature mRNA. Polyadenylation is mediated by a complex (the polyadenylation complex, or PAC) that consists of between 15 and 20 subunits. While the general functioning of these subunits may be inferred by extending paradigms established in well-developed eukaryotic models, much remains to be learned about the roles of individual subunits in the regulation of polyadenylation in plants. To gain further insight into this, we conducted a survey of variability in the plant PAC. For this, we drew upon a database of naturally-occurring variation in numerous geographic isolates of Arabidopsis thaliana. For a subset of genes encoding PAC subunits, the patterns of variability included the occurrence of premature stop codons in some Arabidopsis accessions. These and other observations lead us to conclude that some genes purported to encode PAC subunits in Arabidopsis are actually pseudogenes, and that others may encode proteins with dispensable functions in the plant. Many subunits of the PAC showed patterns of variability that were consistent with their roles as essential proteins in the cell. Several other PAC subunits exhibit patterns of variability consistent with selection for new or altered function. We propose that these latter subunits participate in regulatory interactions important for differential usage of poly(A) sites.
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Affiliation(s)
| | | | - Arthur G. Hunt
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, United States
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Sebastião MJ, Hoffman M, Escandell J, Tousi F, Zhang J, Figueroa B, DeMaria C, Gomes-Alves P. Identification of Mispairing Omic Signatures in Chinese Hamster Ovary (CHO) Cells Producing a Tri-Specific Antibody. Biomedicines 2023; 11:2890. [PMID: 38001891 PMCID: PMC10669571 DOI: 10.3390/biomedicines11112890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/16/2023] [Accepted: 10/20/2023] [Indexed: 11/26/2023] Open
Abstract
Monoclonal antibody-based therapy has shown efficacy against cancer, autoimmune, infectious, and inflammatory diseases. Multispecific antibodies (MsAbs), including trispecifics (tsAbs), offer enhanced therapeutic potential by targeting different epitopes. However, when co-expressed from three or more different polypeptide chains, MsAb production can lead to incorrect chain assembly and co-production of mispaired species with impaired biological activity. Moreover, mispairing carries significant challenges for downstream purification, decreasing yields and increasing the cost of bioprocess development. In this study, quantitative transcriptomics and proteomics analyses were employed to investigate which signaling pathways correlated with low and high mispairing clone signatures. Gene and protein expression profiles of Chinese hamster ovary (CHO) clones producing an tsAb were analyzed in the exponential growth and stationary (tsAb production) phase of fed-batch culture. Functional analysis revealed activated endoplasmic reticulum stress in high mispairing clones in both culture phases, while low mispairing clones exhibited expression profiles indicative of activated protein translation, as well as higher endocytosis and target protein degradation, suggesting the clearance of unfolded proteins through ubiquitin-mediated mechanisms. In addition, through transcriptomic profiling, we identified a group of genes that have the potential to be used as a biomarker panel tool for identifying high mispairing levels in the early stages of bioprocess development.
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Affiliation(s)
- Maria João Sebastião
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2780-901 Oeiras, Portugal; (M.J.S.)
- ITQB-NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Michael Hoffman
- Sanofi Cell Line and Cell Bank Development, Mammalian Platform, Global CMC Development, Framingham, MA 01701, USA (B.F.)
| | - José Escandell
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2780-901 Oeiras, Portugal; (M.J.S.)
- ITQB-NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Fatemeh Tousi
- Sanofi Bioanalytics Development, Global CMC Development, Framingham, MA 01701, USA
| | - Jin Zhang
- Sanofi Cell Line and Cell Bank Development, Mammalian Platform, Global CMC Development, Framingham, MA 01701, USA (B.F.)
| | - Bruno Figueroa
- Sanofi Cell Line and Cell Bank Development, Mammalian Platform, Global CMC Development, Framingham, MA 01701, USA (B.F.)
| | - Christine DeMaria
- Sanofi Cell Line and Cell Bank Development, Mammalian Platform, Global CMC Development, Framingham, MA 01701, USA (B.F.)
| | - Patrícia Gomes-Alves
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2780-901 Oeiras, Portugal; (M.J.S.)
- ITQB-NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
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Wen X, Irshad A, Jin H. The Battle for Survival: The Role of RNA Non-Canonical Tails in the Virus-Host Interaction. Metabolites 2023; 13:1009. [PMID: 37755289 PMCID: PMC10537345 DOI: 10.3390/metabo13091009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 09/09/2023] [Accepted: 09/12/2023] [Indexed: 09/28/2023] Open
Abstract
Terminal nucleotidyltransferases (TENTs) could generate a 'mixed tail' or 'U-rich tail' consisting of different nucleotides at the 3' end of RNA by non-templated nucleotide addition to protect or degrade cellular messenger RNA. Recently, there has been increasing evidence that the decoration of virus RNA terminus with a mixed tail or U-rich tail is a critical way to affect viral RNA stability in virus-infected cells. This paper first briefly introduces the cellular function of the TENT family and non-canonical tails, then comprehensively reviews their roles in virus invasion and antiviral immunity, as well as the significance of the TENT family in antiviral therapy. This review will contribute to understanding the role and mechanism of non-canonical RNA tailing in survival competition between the virus and host.
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Affiliation(s)
| | | | - Hua Jin
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing 100081, China; (X.W.); (A.I.)
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Dai XX, Pi SB, Zhao LW, Wu YW, Shen JL, Zhang SY, Sha QQ, Fan HY. PABPN1 functions as a hub in the assembly of nuclear poly(A) domains that are essential for mouse oocyte development. SCIENCE ADVANCES 2022; 8:eabn9016. [PMID: 36306357 PMCID: PMC9616507 DOI: 10.1126/sciadv.abn9016] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 09/12/2022] [Indexed: 06/16/2023]
Abstract
Growing oocytes store a large amount of maternal mRNA to support the subsequent "maternal-zygotic transition" process. At present, it is not clear how the growing oocytes store and process the newly transcribed mRNA under physiological conditions. In this study, we report non-membrane-bound compartments, nuclear poly(A) domains (NPADs), as the hub for newly transcribed mRNA, in developing mouse oocytes. The RNA binding protein PABPN1 promotes the formation of NPAD through its N-terminal disordered domain and RNA-recognized motif by means of liquid phase separation. Pabpn1-null growing oocytes cannot form NPAD normally in vivo and have defects in stability of oocyte growing-related transcripts and formation of long 3' untranslated region isoform transcripts. Ultimately, Pabpn1fl/fl;Gdf9-Cre mice are completely sterile with primary ovarian insufficiency. These results demonstrate that NPAD formed by the phase separation properties of PABPN1-mRNA are the hub of the newly transcribed mRNA and essential for the development of oocytes and female reproduction.
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Affiliation(s)
- Xing-Xing Dai
- MOE Key Laboratory for Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Shuai-Bo Pi
- MOE Key Laboratory for Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Long-Wen Zhao
- MOE Key Laboratory for Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Yun-Wen Wu
- MOE Key Laboratory for Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Jing-Ling Shen
- Institute of Life Sciences, College of Life and Environmental Sciences, Wenzhou University, Wenzhou 325035, China
| | - Song-Ying Zhang
- Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Qian-Qian Sha
- Fertility Preservation Laboratory, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, 510317 Guangzhou, China
| | - Heng-Yu Fan
- MOE Key Laboratory for Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
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10
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Wang Y, Feng T, Zhu M, Shi X, Wang Z, Liu S, Zhang X, Zhang J, Zhao S, Zhang J, Ling X, Liu M. PABPN1L assemble into "ring-like" aggregates in the cytoplasm of MII oocytes and is associated with female infertility†. Biol Reprod 2021; 106:83-94. [PMID: 34726234 DOI: 10.1093/biolre/ioab203] [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: 05/24/2021] [Revised: 09/20/2021] [Accepted: 10/27/2021] [Indexed: 11/14/2022] Open
Abstract
Infertility affects 10% - 15% of families worldwide. However, the pathogenesis of female infertility caused by abnormal early embryonic development is not clear. A resent study showed that PABPN1L recruited BTG4 to mRNA 3'-poly(A) tails and was essential for maternal mRNA degradation. Here, we generated an PABPN1L-antibody and found "ring-like" PABPN1L aggregates in the cytoplasm of MII oocytes. PABPN1L-EGFP proteins spontaneously formed"ring-like" aggregates in vitro. This phenomenon is similar with CCR4-NOT catalytic subunit, CNOT7, when it starts deadenylation process in vitro. We constructed two mouse model (Pabpn1l -/- and Pabpn1l tm1a/tm1a) simulating the intron1-exon2 abnormality of human PABPN1L and found that the female was sterile and the male was fertile. Using RNA-Seq, we observed a large-scale up-regulation of RNA in zygotes derived from Pabpn1l-/- MII oocytes. We found that 9222 genes were up-regulated instead of being degraded in the Pabpn1l-♀/+♂zygote. Both the Btg4 and Cnot61 genes are necessary for the deadenylation process and Pabpn1l -/- resembled both the Btg4 and Cnot6l knockouts, where 71.2% genes stabilized in the Btg4-♀/+♂ zygote and 84.2% genes stabilized in the Cnot6l-♀/+♂zygote were also stabilized in Pabpn1l-♀/+♂ zygote. BTG4/CNOT7/CNOT6L was partially co-located with PABPN1L in MII oocytes. The above results suggest that PABPN1L is widely associated with CCR4-NOT-mediated maternal mRNA degradation and PABPN1L variants on intron1-exon2 could be a genetic marker of female infertility. Summary sentence. "Ring-like" PABPN1L aggregates was found in the cytoplasm of MII oocytes and in vitro; intron1-exon2 abnormality of Pabpn1l leads female sterile in mice.
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Affiliation(s)
- Ying Wang
- State Key Laboratory of Reproductive Medicine, Department of Reproduction, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, 210004, China
| | - Tianhao Feng
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, 211166, China
| | - Mingcong Zhu
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, 211166, China
| | - Xiaodan Shi
- State Key Laboratory of Reproductive Medicine, Department of Reproduction, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, 210004, China
| | - Zerui Wang
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, 211166, China
| | - Siyu Liu
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, 211166, China
| | - Xin Zhang
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, 211166, China
| | - Jintao Zhang
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, 211166, China
| | - Shuqin Zhao
- State Key Laboratory of Reproductive Medicine, Animal Core Facility of Nanjing Medical University, Nanjing 211166, China
| | - Junqiang Zhang
- State Key Laboratory of Reproductive Medicine, Department of Reproduction, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, 210004, China
| | - Xiufeng Ling
- State Key Laboratory of Reproductive Medicine, Department of Reproduction, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, 210004, China
| | - Mingxi Liu
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, 211166, China
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11
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Wang H, Li G, Zhong C, Mo J, Sun Y, Shi J, Zhou R, Li Z, Wu Z, Liu D, Zhang X. Generation of Multi-Transgenic Pigs Using PiggyBac Transposons Co-expressing Pectinase, Xylanase, Cellulase, β-1.3-1.4-Glucanase and Phytase. Front Genet 2020; 11:597841. [PMID: 33329743 PMCID: PMC7734351 DOI: 10.3389/fgene.2020.597841] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 11/09/2020] [Indexed: 11/29/2022] Open
Abstract
The current challenges facing the pork industry are to maximize feed efficiency and minimize fecal emissions. Unlike ruminants, pigs lack several digestive enzymes such as pectinase, xylanase, cellulase, β-1.3-1.4-glucanase, and phytase which are essential to hydrolyze the cell walls of grains to release endocellular nutrients into their digestive tracts. Herein, we synthesized multiple cellulase and pectinase genes derived from lower organisms and then codon-optimized these genes to be expressed in pigs. These genes were then cloned into our previously optimized XynB (xylanase)- EsAPPA (phytase) bicistronic construct. We then successfully generated transgenic pigs that expressed the four enzymes [Pg7fn (pectinase), XynB (xylanase), EsAPPA (phytase), and TeEGI (cellulase and β-glucanase)] using somatic cell cloning. The expression of these genes was parotid gland specific. Enzymatic assays using the saliva of these founders demonstrated high levels of phytase (2.0∼3.4 U/mL) and xylanase (0.25∼0.42 U/mL) activities, but low levels of pectinase (0.06∼0.08 U/mL) activity. These multi-transgenic pigs are expected to contribute to enhance feed utilization and reduce environmental impact.
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Affiliation(s)
- Haoqiang Wang
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Guoling Li
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Cuili Zhong
- Wens Foodstuff Group Co., Ltd., Yunfu, China
| | - Jianxin Mo
- Wens Foodstuff Group Co., Ltd., Yunfu, China
| | - Yue Sun
- Wens Foodstuff Group Co., Ltd., Yunfu, China
| | - Junsong Shi
- Wens Foodstuff Group Co., Ltd., Yunfu, China
| | - Rong Zhou
- Wens Foodstuff Group Co., Ltd., Yunfu, China
| | - Zicong Li
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Zhenfang Wu
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China
- Wens Foodstuff Group Co., Ltd., Yunfu, China
| | - Dewu Liu
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Xianwei Zhang
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China
- Wens Foodstuff Group Co., Ltd., Yunfu, China
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12
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Aguilar LC, Paul B, Reiter T, Gendron L, Arul Nambi Rajan A, Montpetit R, Trahan C, Pechmann S, Oeffinger M, Montpetit B. Altered rRNA processing disrupts nuclear RNA homeostasis via competition for the poly(A)-binding protein Nab2. Nucleic Acids Res 2020; 48:11675-11694. [PMID: 33137177 PMCID: PMC7672433 DOI: 10.1093/nar/gkaa964] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 10/06/2020] [Accepted: 10/12/2020] [Indexed: 12/13/2022] Open
Abstract
RNA-binding proteins (RBPs) are key mediators of RNA metabolism. Whereas some RBPs exhibit narrow transcript specificity, others function broadly across both coding and non-coding RNAs. Here, in Saccharomyces cerevisiae, we demonstrate that changes in RBP availability caused by disruptions to distinct cellular processes promote a common global breakdown in RNA metabolism and nuclear RNA homeostasis. Our data shows that stabilization of aberrant ribosomal RNA (rRNA) precursors in an enp1-1 mutant causes phenotypes similar to RNA exosome mutants due to nucleolar sequestration of the poly(A)-binding protein (PABP) Nab2. Decreased nuclear PABP availability is accompanied by genome-wide changes in RNA metabolism, including increased pervasive transcripts levels and snoRNA processing defects. These phenotypes are mitigated by overexpression of PABPs, inhibition of rDNA transcription, or alterations in TRAMP activity. Our results highlight the need for cells to maintain poly(A)-RNA levels in balance with PABPs and other RBPs with mutable substrate specificity across nucleoplasmic and nucleolar RNA processes.
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Affiliation(s)
- Lisbeth-Carolina Aguilar
- Department for Systems Biology, Institut de recherches cliniques de Montréal (IRCM), Montréal, QC, Canada
| | - Biplab Paul
- Department of Cell Biology, University of Alberta, Edmonton, Canada
| | - Taylor Reiter
- Food Science Graduate Group, University of California Davis, Davis, CA, USA
| | - Louis Gendron
- Département de biochimie et médecine moléculaire, Université de Montréal, Montréal, QC, Canada
| | - Arvind Arul Nambi Rajan
- Biochemistry, Molecular, Cellular and Developmental Biology Graduate Group, University of California Davis, Davis, CA, USA
| | - Rachel Montpetit
- Department of Viticulture and Enology, University of California Davis, Davis, CA, USA
| | - Christian Trahan
- Department for Systems Biology, Institut de recherches cliniques de Montréal (IRCM), Montréal, QC, Canada
| | - Sebastian Pechmann
- Département de biochimie et médecine moléculaire, Université de Montréal, Montréal, QC, Canada
| | - Marlene Oeffinger
- Department for Systems Biology, Institut de recherches cliniques de Montréal (IRCM), Montréal, QC, Canada
- Département de biochimie et médecine moléculaire, Université de Montréal, Montréal, QC, Canada
- Division of Experimental Medicine, McGill University, Montreal, QC, Canada
| | - Ben Montpetit
- Department of Cell Biology, University of Alberta, Edmonton, Canada
- Food Science Graduate Group, University of California Davis, Davis, CA, USA
- Biochemistry, Molecular, Cellular and Developmental Biology Graduate Group, University of California Davis, Davis, CA, USA
- Department of Viticulture and Enology, University of California Davis, Davis, CA, USA
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13
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Ma XY, Zhang H, Feng JX, Hu JL, Yu B, Luo L, Cao YL, Liao S, Wang J, Gao S. Structures of mammalian GLD-2 proteins reveal molecular basis of their functional diversity in mRNA and microRNA processing. Nucleic Acids Res 2020; 48:8782-8795. [PMID: 32633758 PMCID: PMC7470959 DOI: 10.1093/nar/gkaa578] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 05/20/2020] [Accepted: 07/03/2020] [Indexed: 11/12/2022] Open
Abstract
The stability and processing of cellular RNA transcripts are efficiently controlled via non-templated addition of single or multiple nucleotides, which is catalyzed by various nucleotidyltransferases including poly(A) polymerases (PAPs). Germline development defective 2 (GLD-2) is among the first reported cytoplasmic non-canonical PAPs that promotes the translation of germline-specific mRNAs by extending their short poly(A) tails in metazoan, such as Caenorhabditis elegans and Xenopus. On the other hand, the function of mammalian GLD-2 seems more diverse, which includes monoadenylation of certain microRNAs. To understand the structural basis that underlies the difference between mammalian and non-mammalian GLD-2 proteins, we determine crystal structures of two rodent GLD-2s. Different from C. elegans GLD-2, mammalian GLD-2 is an intrinsically robust PAP with an extensively positively charged surface. Rodent and C. elegans GLD-2s have a topological difference in the β-sheet region of the central domain. Whereas C. elegans GLD-2 prefers adenosine-rich RNA substrates, mammalian GLD-2 can work on RNA oligos with various sequences. Coincident with its activity on microRNAs, mammalian GLD-2 structurally resembles the mRNA and miRNA processor terminal uridylyltransferase 7 (TUT7). Our study reveals how GLD-2 structurally evolves to a more versatile nucleotidyltransferase, and provides important clues in understanding its biological function in mammals.
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Affiliation(s)
- Xiao-Yan Ma
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong 510060, China
| | - Hong Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong 510060, China
| | - Jian-Xiong Feng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong 510060, China
| | - Jia-Li Hu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong 510060, China
| | - Bing Yu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong 510060, China
| | - Li Luo
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong 510060, China
| | - Yu-Lu Cao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong 510060, China
| | - Shuang Liao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong 510060, China
| | - Jichang Wang
- Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China.,Department of histology and embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Song Gao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong 510060, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou 510530, China
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14
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Sudheesh AP, Mohan N, Francis N, Laishram RS, Anderson RA. Star-PAP controlled alternative polyadenylation coupled poly(A) tail length regulates protein expression in hypertrophic heart. Nucleic Acids Res 2020; 47:10771-10787. [PMID: 31598705 PMCID: PMC6847588 DOI: 10.1093/nar/gkz875] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 09/08/2019] [Accepted: 10/05/2019] [Indexed: 12/31/2022] Open
Abstract
Alternative polyadenylation (APA)-mediated 3′-untranslated region (UTR) shortening is known to increase protein expression due to the loss of miRNA regulatory sites. Yet, mRNAs with longer 3′-UTR also show enhanced protein expression. Here, we identify a mechanism by which longer transcripts generated by the distal-most APA site leads to increased protein expression compared to the shorter transcripts and the longer transcripts are positioned to regulate heart failure (HF). A Star-PAP target gene, NQO1 has three poly(A) sites (PA-sites) at the terminal exon on the pre-mRNA. Star-PAP selects the distal-most site that results in the expression of the longest isoform. We show that the NQO1 distal-specific mRNA isoform accounts for the majority of cellular NQO1 protein. Star-PAP control of the distal-specific isoform is stimulated by oxidative stress and the toxin dioxin. The longest NQO1 transcript has increased poly(A) tail (PA-tail) length that accounts for the difference in translation potentials of the three NQO1 isoforms. This mechanism is involved in the regulation of cardiac hypertrophy (CH), an antecedent condition to HF where NQO1 downregulation stems from the loss of the distal-specific transcript. The loss of NQO1 during hypertrophy was rescued by ectopic expression of the distal- but not the proximal- or middle-specific NQO1 mRNA isoforms in the presence of Star-PAP expression, and reverses molecular events of hypertrophy in cardiomyocytes.
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Affiliation(s)
- A P Sudheesh
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum-014, India.,Manipal Academy of Higher Education, Manipal 576104, India
| | - Nimmy Mohan
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum-014, India.,Manipal Academy of Higher Education, Manipal 576104, India
| | - Nimmy Francis
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum-014, India.,Manipal Academy of Higher Education, Manipal 576104, India
| | - Rakesh S Laishram
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum-014, India
| | - Richard A Anderson
- School of Medicine and Public Health, University of Wisconsin, MD 53726, USA
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15
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Duan A, Kong L, An T, Zhou H, Yu C, Li Y. Star-PAP regulates tumor protein D52 through modulating miR-449a/34a in breast cancer. Biol Open 2019; 8:bio.045914. [PMID: 31649118 PMCID: PMC6899025 DOI: 10.1242/bio.045914] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Tumor protein D52 (TPD52) is an oncogene amplified and overexpressed in various cancers. Tumor-suppressive microRNA-449a and microRNA-34a (miR-449a/34a) were recently reported to inhibit breast cancer cell migration and invasion via targeting TPD52. However, the upstream events are not clearly defined. Star-PAP is a non-canonical poly (A) polymerase which could regulate the expression of many miRNAs and mRNAs, but its biological functions are not well elucidated. The present study aimed to explore the regulative roles of Star-PAP in miR-449a/34a and TPD52 expression in breast cancer. We observed a negative correlation between the expression of TPD52 and Star-PAP in breast cancer. Overexpression of Star-PAP inhibited TPD52 expression, while endogenous Star-PAP knockdown led to increased TPD52. Furthermore, RNA immunoprecipitation assay suggested that Star-PAP could not bind to TPD52, independent of the 3′-end processing. RNA pull-down assay showed that Star-PAP could bind to 3′region of miR-449a. In line with these results, blunted cell proliferation or cell apoptosis caused by Star-PAP was rescued by overexpression of TPD52 or downregulation of miR-449a/34a. Our findings identified that Star-PAP regulates TPD52 by modulating miR-449a/34a, which may be an important molecular mechanism underlying the tumorigenesis of breast cancer and provide a rational therapeutic target for breast cancer treatment. Summary: Star-PAP is an important regulator of miR-449a/34a and was first identified indirectly regulating TPD52 via modulating miR-449a/34a. Furthermore, Star-PAP-miR-449a/34a-TPD52 axis is involved in proliferation and apoptosis of breast cancer cells.
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Affiliation(s)
- Aizhu Duan
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, P.R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P.R. China
| | - Lingmei Kong
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, P.R. China
| | - Tao An
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, P.R. China
| | - Hongyu Zhou
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, P.R. China
| | - Chunlei Yu
- Institute of Materia Medica, School of Pharmacy, North Sichuan Medical College, Nanchong, Sichuan, 637100, P.R. China
| | - Yan Li
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, P.R. China
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16
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Ke Y, Zhang J, Lv X, Zeng X, Ba X. Novel insights into PARPs in gene expression: regulation of RNA metabolism. Cell Mol Life Sci 2019; 76:3283-3299. [PMID: 31055645 PMCID: PMC6697709 DOI: 10.1007/s00018-019-03120-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 04/13/2019] [Accepted: 04/29/2019] [Indexed: 12/15/2022]
Abstract
Poly(ADP-ribosyl)ation (PARylation) is an important post-translational modification in which an ADP-ribose group is transferred to the target protein by poly(ADP-riboses) polymerases (PARPs). Since the discovery of poly-ADP-ribose (PAR) 50 years ago, its roles in cellular processes have been extensively explored. Although research initially focused on the functions of PAR and PARPs in DNA damage detection and repair, our understanding of the roles of PARPs in various nuclear and cytoplasmic processes, particularly in gene expression, has increased significantly. In this review, we discuss the current advances in understanding the roles of PARylation with a particular emphasis in gene expression through RNA biogenesis and processing. In addition to updating PARP's significance in transcriptional regulation, we specifically focus on how PARPs and PARylation affect gene expression, especially inflammation-related genes, at the post-transcriptional levels by modulating RNA processing and degrading. Increasing evidence suggests that PARP inhibition is a promising treatment for inflammation-related diseases besides conventional chemotherapy for cancer.
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Affiliation(s)
- Yueshuang Ke
- The Key Laboratory of Molecular Epigenetics of the Ministry of Education, Institute of Genetics and Cytology, School of Life Science, Northeast Normal University, Changchun, 130024, Jilin, China
| | - Jing Zhang
- The Key Laboratory of Molecular Epigenetics of the Ministry of Education, Institute of Genetics and Cytology, School of Life Science, Northeast Normal University, Changchun, 130024, Jilin, China
| | - Xueping Lv
- The Key Laboratory of Molecular Epigenetics of the Ministry of Education, Institute of Genetics and Cytology, School of Life Science, Northeast Normal University, Changchun, 130024, Jilin, China
| | - Xianlu Zeng
- The Key Laboratory of Molecular Epigenetics of the Ministry of Education, Institute of Genetics and Cytology, School of Life Science, Northeast Normal University, Changchun, 130024, Jilin, China
| | - Xueqing Ba
- The Key Laboratory of Molecular Epigenetics of the Ministry of Education, Institute of Genetics and Cytology, School of Life Science, Northeast Normal University, Changchun, 130024, Jilin, China.
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, China.
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17
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Toompuu M, Tuomela T, Laine P, Paulin L, Dufour E, Jacobs HT. Polyadenylation and degradation of structurally abnormal mitochondrial tRNAs in human cells. Nucleic Acids Res 2019. [PMID: 29518244 PMCID: PMC6007314 DOI: 10.1093/nar/gky159] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
RNA 3' polyadenylation is known to serve diverse purposes in biology, in particular, regulating mRNA stability and translation. Here we determined that, upon exposure to high levels of the intercalating agent ethidium bromide (EtBr), greater than those required to suppress mitochondrial transcription, mitochondrial tRNAs in human cells became polyadenylated. Relaxation of the inducing stress led to rapid turnover of the polyadenylated tRNAs. The extent, kinetics and duration of tRNA polyadenylation were EtBr dose-dependent, with mitochondrial tRNAs differentially sensitive to the stress. RNA interference and inhibitor studies indicated that ongoing mitochondrial ATP synthesis, plus the mitochondrial poly(A) polymerase and SUV3 helicase were required for tRNA polyadenylation, while polynucleotide phosphorylase counteracted the process and was needed, along with SUV3, for degradation of the polyadenylated tRNAs. Doxycycline treatment inhibited both tRNA polyadenylation and turnover, suggesting a possible involvement of the mitoribosome, although other translational inhibitors had only minor effects. The dysfunctional tRNALeu(UUR) bearing the pathological A3243G mutation was constitutively polyadenylated at a low level, but this was markedly enhanced after doxycycline treatment. We propose that polyadenylation of structurally and functionally abnormal mitochondrial tRNAs entrains their PNPase/SUV3-mediated destruction, and that this pathway could play an important role in mitochondrial diseases associated with tRNA mutations.
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Affiliation(s)
- Marina Toompuu
- Faculty of Medicine and Life Sciences, BioMediTech Institute and Tampere University Hospital, FI-33014 University of Tampere, Finland
| | - Tea Tuomela
- Faculty of Medicine and Life Sciences, BioMediTech Institute and Tampere University Hospital, FI-33014 University of Tampere, Finland
| | - Pia Laine
- Institute of Biotechnology, FI-00014 University of Helsinki, Finland
| | - Lars Paulin
- Institute of Biotechnology, FI-00014 University of Helsinki, Finland
| | - Eric Dufour
- Faculty of Medicine and Life Sciences, BioMediTech Institute and Tampere University Hospital, FI-33014 University of Tampere, Finland
| | - Howard T Jacobs
- Faculty of Medicine and Life Sciences, BioMediTech Institute and Tampere University Hospital, FI-33014 University of Tampere, Finland.,Institute of Biotechnology, FI-00014 University of Helsinki, Finland
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18
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Ozturk S. The translational functions of embryonic poly(A)‐binding protein during gametogenesis and early embryo development. Mol Reprod Dev 2019; 86:1548-1560. [DOI: 10.1002/mrd.23253] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Accepted: 07/26/2019] [Indexed: 12/27/2022]
Affiliation(s)
- Saffet Ozturk
- Department of Histology and EmbryologyAkdeniz University School of MedicineAntalya Turkey
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19
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Duan TL, He GJ, Hu LD, Yan YB. The Intrinsically Disordered C-Terminal Domain Triggers Nucleolar Localization and Function Switch of PARN in Response to DNA Damage. Cells 2019; 8:cells8080836. [PMID: 31387300 PMCID: PMC6721724 DOI: 10.3390/cells8080836] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 07/23/2019] [Accepted: 07/29/2019] [Indexed: 12/11/2022] Open
Abstract
Poly(A)-specific ribonuclease (PARN), a multifunctional multi-domain deadenylase, is crucial to the regulation of mRNA turnover and the maturation of various non-coding RNAs. Despite extensive studies of the well-folding domains responsible for PARN catalysis, the structure and function of the C-terminal domain (CTD) remains elusive. PARN is a cytoplasm-nucleus shuttle protein with concentrated nucleolar distribution. Here, we identify the nuclear and nucleolar localization signals in the CTD of PARN. Spectroscopic studies indicated that PARN-CTD is intrinsically disordered with loosely packed local structures/tertiary structure. Phosphorylation-mimic mutation S557D disrupted the local structure and facilitated the binding of the CTD with the well-folded domains, with no impact on PARN deadenylase activity. Under normal conditions, the nucleolus-residing PARN recruited CBP80 into the nucleoli to repress its deadenylase activity, while DNA damage-induced phosphorylation of PARN-S557 expelled CBP80 from the nucleoli to discharge activity inhibition and attracted nucleoplasm-located CstF-50 into the nucleoli to activate deadenylation. The structure switch-induced function switch of PARN reshaped the profile of small nuclear non-coding RNAs to respond to DNA damage. Our findings highlight that the structure switch of the CTD induced by posttranslational modifications redefines the subset of binding partners, and thereby the RNA targets in the nucleoli.
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Affiliation(s)
- Tian-Li Duan
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Guang-Jun He
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Li-Dan Hu
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yong-Bin Yan
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.
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20
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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: 65] [Impact Index Per Article: 10.8] [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
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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.
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21
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Kulkarni P, Uversky VN. Intrinsically Disordered Proteins and the Janus Challenge. Biomolecules 2018; 8:biom8040179. [PMID: 30567293 PMCID: PMC6315817 DOI: 10.3390/biom8040179] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 12/13/2018] [Indexed: 12/24/2022] Open
Abstract
To gain a new insight into the role of proteins in the origin of life on Earth, we present the Janus Challenge: identify an intrinsically disordered protein (IDP), naturally occurring or synthetic, that has catalytic activity. For example, such a catalytic IDP may perform condensation reactions to catalyze a peptide bond or a phosphodiester bond formation utilizing natural/un-natural amino acids or nucleotides, respectively. The IDP may also have autocatalytic, de novo synthesis, or self-replicative activity. Meeting this challenge may not only shed new light and provide an alternative to the RNA world hypothesis, but it may also serve as an impetus for technological advances with important biomedical applications.
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Affiliation(s)
- Prakash Kulkarni
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010, USA.
| | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA.
- Laboratory of New methods in Biology, Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino 142290, Moscow Region, Russia.
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22
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Yashiro Y, Tomita K. Function and Regulation of Human Terminal Uridylyltransferases. Front Genet 2018; 9:538. [PMID: 30483311 PMCID: PMC6240794 DOI: 10.3389/fgene.2018.00538] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 10/24/2018] [Indexed: 11/21/2022] Open
Abstract
RNA uridylylation plays a pivotal role in the biogenesis and metabolism of functional RNAs, and regulates cellular gene expression. RNA uridylylation is catalyzed by a subset of proteins from the non-canonical terminal nucleotidyltransferase family. In human, three proteins (TUT1, TUT4, and TUT7) have been shown to exhibit template-independent uridylylation activity at 3′-end of specific RNAs. TUT1 catalyzes oligo-uridylylation of U6 small nuclear (sn) RNA, which catalyzes mRNA splicing. Oligo-uridylylation of U6 snRNA is required for U6 snRNA maturation, U4/U6-di-snRNP formation, and U6 snRNA recycling during mRNA splicing. TUT4 and TUT7 catalyze mono- or oligo-uridylylation of precursor let-7 (pre–let-7). Let-7 RNA is broadly expressed in somatic cells and regulates cellular proliferation and differentiation. Mono-uridylylation of pre–let-7 by TUT4/7 promotes subsequent Dicer processing to up-regulate let-7 biogenesis. Oligo-uridylylation of pre–let-7 by TUT4/7 is dependent on an RNA-binding protein, Lin28. Oligo-uridylylated pre–let-7 is less responsive to processing by Dicer and degraded by an exonuclease DIS3L2. As a result, let-7 expression is repressed. Uridylylation of pre–let-7 depends on the context of the 3′-region of pre–let-7 and cell type. In this review, we focus on the 3′ uridylylation of U6 snRNA and pre-let-7, and describe the current understanding of mechanism of activity and regulation of human TUT1 and TUT4/7, based on their crystal structures that have been recently solved.
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Affiliation(s)
- Yuka Yashiro
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Kozo Tomita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
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23
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Tudek A, Lloret-Llinares M, Jensen TH. The multitasking polyA tail: nuclear RNA maturation, degradation and export. Philos Trans R Soc Lond B Biol Sci 2018; 373:rstb.2018.0169. [PMID: 30397105 DOI: 10.1098/rstb.2018.0169] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/20/2018] [Indexed: 12/17/2022] Open
Abstract
A polyA (pA) tail is an essential modification added to the 3' ends of a wide range of RNAs at different stages of their metabolism. Here, we describe the main sources of polyadenylation and outline their underlying biochemical interactions within the nuclei of budding yeast Saccharomyces cerevisiae, human cells and, when relevant, the fission yeast Schizosaccharomyces pombe Polyadenylation mediated by the S. cerevisiae Trf4/5 enzymes, and their human homologues PAPD5/7, typically leads to the 3'-end trimming or complete decay of non-coding RNAs. By contrast, the primary function of canonical pA polymerases (PAPs) is to produce stable and nuclear export-competent mRNAs. However, this dichotomy is becoming increasingly blurred, at least in S. pombe and human cells, where polyadenylation mediated by canonical PAPs may also result in transcript decay.This article is part of the theme issue '5' and 3' modifications controlling RNA degradation'.
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Affiliation(s)
- Agnieszka Tudek
- Department of Molecular Biology and Genetics, Aarhus University, C. F. Møllers Allé 3, building 1130, 8000 Aarhus C, Denmark
| | - Marta Lloret-Llinares
- Department of Molecular Biology and Genetics, Aarhus University, C. F. Møllers Allé 3, building 1130, 8000 Aarhus C, Denmark
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, C. F. Møllers Allé 3, building 1130, 8000 Aarhus C, Denmark
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24
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Hunter M, Yuan P, Vavilala D, Fox M. Optimization of Protein Expression in Mammalian Cells. ACTA ACUST UNITED AC 2018; 95:e77. [DOI: 10.1002/cpps.77] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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25
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Characterization of mRNA polyadenylation in the apicomplexa. PLoS One 2018; 13:e0203317. [PMID: 30161237 PMCID: PMC6117058 DOI: 10.1371/journal.pone.0203317] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 08/18/2018] [Indexed: 11/19/2022] Open
Abstract
Messenger RNA polyadenylation is a universal aspect of gene expression in eukaryotes. In well-established model organisms, this process is mediated by a conserved complex of 15–20 subunits. To better understand this process in apicomplexans, a group of unicellular parasites that causes serious disease in humans and livestock, a computational and high throughput sequencing study of the polyadenylation complex and poly(A) sites in several species was conducted. BLAST-based searches for orthologs of the human polyadenylation complex yielded clear matches to only two—poly(A) polymerase and CPSF73—of the 19 proteins used as queries in this analysis. As the human subunits that recognize the AAUAAA polyadenylation signal (PAS) were not immediately obvious, a computational analysis of sequences adjacent to experimentally-determined apicomplexan poly(A) sites was conducted. The results of this study showed that there exists in apicomplexans an A-rich region that corresponds in position to the AAUAAA PAS. The set of experimentally-determined sites in one species, Sarcocystis neurona, was further analyzed to evaluate the extent and significance of alternative poly(A) site choice in this organism. The results showed that almost 80% of S. neurona genes possess more than one poly(A) site, and that more than 780 sites showed differential usage in the two developmental stages–extracellular merozoites and intracellular schizonts–studied. These sites affected more than 450 genes, and included a disproportionate number of genes that encode membrane transporters and ribosomal proteins. Taken together, these results reveal that apicomplexan species seem to possess a poly(A) signal analogous to AAUAAA even though genes that may encode obvious counterparts of the AAUAAA-recognizing proteins are absent in these organisms. They also indicate that, as is the case in other eukaryotes, alternative polyadenylation is a widespread phenomenon in S. neurona that has the potential to impact growth and development.
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26
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Xu C, Zhang J. Alternative Polyadenylation of Mammalian Transcripts Is Generally Deleterious, Not Adaptive. Cell Syst 2018; 6:734-742.e4. [PMID: 29886108 DOI: 10.1016/j.cels.2018.05.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 03/27/2018] [Accepted: 05/09/2018] [Indexed: 01/07/2023]
Abstract
Alternative polyadenylation (APA) produces from the same gene multiple mature RNAs with varying 3' ends. Although APA is commonly believed to generate beneficial functional diversity and be adaptive, we hypothesize that most genes have one optimal polyadenylation site and that APA is caused largely by deleterious polyadenylation errors. The error hypothesis, but not the adaptive hypothesis, predicts that, as the expression level of a gene increases, its polyadenylation diversity declines, relative use of the major (presumably optimal) polyadenylation site increases, and that of each minor (presumably nonoptimal) site decreases. It further predicts that the number of polyadenylation signals per gene is smaller than the random expectation and that polyadenylation signals for major but not minor sites are under purifying selection. All of these predictions are confirmed in mammals, suggesting that numerous defective RNAs are produced in normal cells, many phenotypic variations at the molecular level are nonadaptive, and cellular life is noisier than is appreciated.
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Affiliation(s)
- Chuan Xu
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China; Department of Ecology and Evolutionary Biology, University of Michigan, 4018 Biological Science Building, 1105 North University Avenue, Ann Arbor, MI 48109, USA
| | - Jianzhi Zhang
- Department of Ecology and Evolutionary Biology, University of Michigan, 4018 Biological Science Building, 1105 North University Avenue, Ann Arbor, MI 48109, USA.
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27
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Song Y, Xu Y, Deng J, Chen M, Lu Y, Wang Y, Yao H, Zhou L, Liu Z, Lai L, Li Z. CRISPR/Cas9-mediated mutation of tyrosinase (Tyr) 3' UTR induce graying in rabbit. Sci Rep 2017; 7:1569. [PMID: 28484254 PMCID: PMC5431497 DOI: 10.1038/s41598-017-01727-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 04/03/2017] [Indexed: 01/08/2023] Open
Abstract
The 3' untranslated regions (UTRs), located at the end of mRNA molecules, are believed to play a role in RNA replication and/or protein translation. Mutations in the tyrosinase (Tyr) gene are known to cause recessive albinism in humans and other species. In this study, to test whether the CRISPR/Cas9 system works on the mutation of the UTRs regulatory region in rabbit, the 3' UTR of the rabbit Tyr gene was deleted by a dual sgRNA directed CRISPR/Cas9 system. As expected, gray coat color and reduced melanin in hair follicles and irises was found in the mutated rabbit, thus increasing confidence in the association of the mutation of the Tyr 3' UTR with graying in rabbit. The graying phenotype was also found in the F1 generation, suggesting that the mutated allele can be stably inherited by the offspring. Thus, we provide the first evidence that reduced melanin and graying can be caused by deletion of the Tyr 3' UTR in rabbits. Additionally, CRISPR/Cas9-mediated large fragment deletions can facilitate genotype to phenotype studies of UTRs or non-coding RNAs in future.
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Affiliation(s)
- Yuning Song
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Jilin University, Changchun, 130062, China
| | - Yuxin Xu
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Jilin University, Changchun, 130062, China
| | - Jichao Deng
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Jilin University, Changchun, 130062, China
| | - Mao Chen
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Jilin University, Changchun, 130062, China
| | - Yi Lu
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Jilin University, Changchun, 130062, China
| | - Yong Wang
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Jilin University, Changchun, 130062, China
| | - Haobin Yao
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Jilin University, Changchun, 130062, China
| | - Lina Zhou
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Jilin University, Changchun, 130062, China
| | - Zhiquan Liu
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Jilin University, Changchun, 130062, China
| | - Liangxue Lai
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Jilin University, Changchun, 130062, China.
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
| | - Zhanjun Li
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Jilin University, Changchun, 130062, China.
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28
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Hu W, Li S, Park JY, Boppana S, Ni T, Li M, Zhu J, Tian B, Xie Z, Xiang M. Dynamic landscape of alternative polyadenylation during retinal development. Cell Mol Life Sci 2016; 74:1721-1739. [PMID: 27990575 DOI: 10.1007/s00018-016-2429-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 11/24/2016] [Accepted: 12/01/2016] [Indexed: 10/20/2022]
Abstract
The development of the central nervous system (CNS) is a complex process that must be exquisitely controlled at multiple levels to ensure the production of appropriate types and quantity of neurons. RNA alternative polyadenylation (APA) contributes to transcriptome diversity and gene regulation, and has recently been shown to be widespread in the CNS. However, the previous studies have been primarily focused on the tissue specificity of APA and developmental APA change of whole model organisms; a systematic survey of APA usage is lacking during CNS development. Here, we conducted global analysis of APA during mouse retinal development, and identified stage-specific polyadenylation (pA) sites that are enriched for genes critical for retinal development and visual perception. Moreover, we demonstrated 3'UTR (untranslated region) lengthening and increased usage of intronic pA sites over development that would result in gaining many different RBP (RNA-binding protein) and miRNA target sites. Furthermore, we showed that a considerable number of polyadenylated lncRNAs are co-expressed with protein-coding genes involved in retinal development and functions. Together, our data indicate that APA is highly and dynamically regulated during retinal development and maturation, suggesting that APA may serve as a crucial mechanism of gene regulation underlying the delicate process of CNS development.
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Affiliation(s)
- Wenyan Hu
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 500040, China
| | - Shengguo Li
- Center for Advanced Biotechnology and Medicine and Department of Pediatrics, Rutgers University-Robert Wood Johnson Medical School, 679 Hoes Lane West, Piscataway, NJ, 08854, USA
| | - Ji Yeon Park
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, 07101, USA
| | - Sridhar Boppana
- Center for Advanced Biotechnology and Medicine and Department of Pediatrics, Rutgers University-Robert Wood Johnson Medical School, 679 Hoes Lane West, Piscataway, NJ, 08854, USA
| | - Ting Ni
- State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Miaoxin Li
- Department of Medical Genetics, Center for Genome Research, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Jun Zhu
- Systems Biology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Bin Tian
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, 07101, USA
| | - Zhi Xie
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 500040, China.
| | - Mengqing Xiang
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 500040, China. .,Center for Advanced Biotechnology and Medicine and Department of Pediatrics, Rutgers University-Robert Wood Johnson Medical School, 679 Hoes Lane West, Piscataway, NJ, 08854, USA.
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29
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Rangel L, Lospitao E, Ruiz-Sáenz A, Alonso MA, Correas I. Alternative polyadenylation in a family of paralogous EPB41 genes generates protein 4.1 diversity. RNA Biol 2016; 14:236-244. [PMID: 27981895 DOI: 10.1080/15476286.2016.1270003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Alternative polyadenylation (APA) is a step in mRNA 3'-end processing that contributes to the complexity of the transcriptome by generating isoforms that differ in either their coding sequence or their 3'-untranslated regions (UTRs). The EPB41 genes, EPB41, EPB41L2, EPB41L3 and EPB41L1, encode an impressively complex array of structural adaptor proteins (designated 4.1R, 4.1G, 4.1B and 4.1N, respectively) by using alternative transcriptional promoters and tissue-specific alternative pre-mRNA splicing. The great variety of 4.1 proteins mainly results from 5'-end and internal processing of the EPB41 pre-mRNAs. Thus, 4.1 proteins can vary in their N-terminal extensions but all contain a highly homologous C-terminal domain (CTD). Here we study a new group of EPB41-related mRNAs that originate by APA and lack the exons encoding the CTD characteristic of prototypical 4.1 proteins, thereby encoding a new type of 4.1 protein. For the EPB41 gene, this type of processing was observed in all 11 human tissues analyzed. Comparative genomic analysis of EPB41 indicates that APA is conserved in various mammals. In addition, we show that APA also functions for the EPB41L2, EPB41L3 and EPB41L1 genes, but in a more restricted manner in the case of the latter 2 than it does for the EPB41 and EPB41L2 genes. Our study shows alternative polyadenylation to be an additional mechanism for the generation of 4.1 protein diversity in the already complex EPB41-related genes. Understanding the diversity of EPB41 RNA processing is essential for a full appreciation of the many 4.1 proteins expressed in normal and pathological tissues.
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Affiliation(s)
- Laura Rangel
- a Departamento de Biología Molecular , Universidad Autónoma de Madrid (UAM), Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas (CSIC), Nicolás Cabrera , Cantoblanco, Madrid , Spain
| | - Eva Lospitao
- a Departamento de Biología Molecular , Universidad Autónoma de Madrid (UAM), Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas (CSIC), Nicolás Cabrera , Cantoblanco, Madrid , Spain
| | - Ana Ruiz-Sáenz
- a Departamento de Biología Molecular , Universidad Autónoma de Madrid (UAM), Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas (CSIC), Nicolás Cabrera , Cantoblanco, Madrid , Spain
| | - Miguel A Alonso
- a Departamento de Biología Molecular , Universidad Autónoma de Madrid (UAM), Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas (CSIC), Nicolás Cabrera , Cantoblanco, Madrid , Spain
| | - Isabel Correas
- a Departamento de Biología Molecular , Universidad Autónoma de Madrid (UAM), Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas (CSIC), Nicolás Cabrera , Cantoblanco, Madrid , Spain
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30
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Widespread 3'-end uridylation in eukaryotic RNA viruses. Sci Rep 2016; 6:25454. [PMID: 27151171 PMCID: PMC4858684 DOI: 10.1038/srep25454] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 04/15/2016] [Indexed: 01/08/2023] Open
Abstract
RNA 3′ uridylation occurs pervasively in eukaryotes, but is poorly characterized in viruses. In this study, we demonstrate that a broad array of RNA viruses, including mycoviruses, plant viruses and animal viruses, possess a novel population of RNA species bearing nontemplated oligo(U) or (U)-rich tails, suggesting widespread 3′ uridylation in eukaryotic viruses. Given the biological relevance of 3′ uridylation to eukaryotic RNA degradation, we propose a conserved but as-yet-unknown mechanism in virus-host interaction.
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31
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Kandala DT, Mohan N, A V, A P S, G R, Laishram RS. CstF-64 and 3'-UTR cis-element determine Star-PAP specificity for target mRNA selection by excluding PAPα. Nucleic Acids Res 2015; 44:811-23. [PMID: 26496945 PMCID: PMC4737136 DOI: 10.1093/nar/gkv1074] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 10/06/2015] [Indexed: 01/02/2023] Open
Abstract
Almost all eukaryotic mRNAs have a poly (A) tail at the 3′-end. Canonical PAPs (PAPα/γ) polyadenylate nuclear pre-mRNAs. The recent identification of the non-canonical Star-PAP revealed specificity of nuclear PAPs for pre-mRNAs, yet the mechanism how Star-PAP selects mRNA targets is still elusive. Moreover, how Star-PAP target mRNAs having canonical AAUAAA signal are not regulated by PAPα is unclear. We investigate specificity mechanisms of Star-PAP that selects pre-mRNA targets for polyadenylation. Star-PAP assembles distinct 3′-end processing complex and controls pre-mRNAs independent of PAPα. We identified a Star-PAP recognition nucleotide motif and showed that suboptimal DSE on Star-PAP target pre-mRNA 3′-UTRs inhibit CstF-64 binding, thus preventing PAPα recruitment onto it. Altering 3′-UTR cis-elements on a Star-PAP target pre-mRNA can switch the regulatory PAP from Star-PAP to PAPα. Our results suggest a mechanism of poly (A) site selection that has potential implication on the regulation of alternative polyadenylation.
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Affiliation(s)
- Divya T Kandala
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Trivandrum 695014, India
| | - Nimmy Mohan
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Trivandrum 695014, India
| | - Vivekanand A
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Trivandrum 695014, India
| | - Sudheesh A P
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Trivandrum 695014, India
| | - Reshmi G
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Trivandrum 695014, India
| | - Rakesh S Laishram
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Trivandrum 695014, India
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32
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Viegas SC, Silva IJ, Apura P, Matos RG, Arraiano CM. Surprises in the 3'-end: 'U' can decide too! FEBS J 2015; 282:3489-99. [PMID: 26183531 DOI: 10.1111/febs.13377] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Revised: 06/22/2015] [Accepted: 07/10/2015] [Indexed: 12/27/2022]
Abstract
RNA molecules are subjected to post-transcriptional modifications that might determine their maturation, activity, localization and stability. These alterations can occur within the RNA molecule or at its 5'- or 3'- extremities, and are essential for gene regulation and proper function of the RNA. One major type of modification is the 3'-end addition of nontemplated nucleotides. Polyadenylation is the most well studied type of 3'-RNA modification, both in eukaryotes and prokaryotes. The importance of 3'-oligouridylation has recently gained attention through the discovery of several types of uridylated-RNAs, by the existence of enzymes that specifically add poly(U) tails and others that preferentially degrade these tails. Namely, Dis3L2 is a 3'-5' exoribonuclease from the RNase II/RNB family that has been shown to act preferentially on oligo(U)-tailed transcripts. Our understanding of this process is still at the beginning, but it is already known to interfere in the regulation of diverse RNA species in most eukaryotes. Now that we are aware of the prevalence of RNA uridylation and the techniques available to globally evaluate the 3'-terminome, we can expect to make rapid progress in determining the extent of terminal oligouridylation in different RNA populations and unravel its impact on RNA decay mechanisms. Here, we sum up what is known about 3'-RNA modification in the different cellular compartments of eukaryotic cells, the conserved enzymes that perform this 3'-end modification and the effectors that are selectively activated by this process.
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Affiliation(s)
- Sandra C Viegas
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Inês J Silva
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Patricia Apura
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Rute G Matos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Cecilia M Arraiano
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
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Mohan N, Sudheesh AP, Francis N, Anderson R, Laishram RS. Phosphorylation regulates the Star-PAP-PIPKIα interaction and directs specificity toward mRNA targets. Nucleic Acids Res 2015; 43:7005-20. [PMID: 26138484 PMCID: PMC4538844 DOI: 10.1093/nar/gkv676] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 06/19/2015] [Indexed: 11/14/2022] Open
Abstract
Star-PAP is a nuclear non-canonical poly(A) polymerase (PAP) that shows specificity toward mRNA targets. Star-PAP activity is stimulated by lipid messenger phosphatidyl inositol 4,5 bisphoshate (PI4,5P2) and is regulated by the associated Type I phosphatidylinositol-4-phosphate 5-kinase that synthesizes PI4,5P2 as well as protein kinases. These associated kinases act as coactivators of Star-PAP that regulates its activity and specificity toward mRNAs, yet the mechanism of control of these interactions are not defined. We identified a phosphorylated residue (serine 6, S6) on Star-PAP in the zinc finger region, the domain required for PIPKIα interaction. We show that S6 is phosphorylated by CKIα within the nucleus which is required for Star-PAP nuclear retention and interaction with PIPKIα. Unlike the CKIα mediated phosphorylation at the catalytic domain, Star-PAP S6 phosphorylation is insensitive to oxidative stress suggesting a signal mediated regulation of CKIα activity. S6 phosphorylation together with coactivator PIPKIα controlled select subset of Star-PAP target messages by regulating Star-PAP-mRNA association. Our results establish a novel role for phosphorylation in determining Star-PAP target mRNA specificity and regulation of 3'-end processing.
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Affiliation(s)
- Nimmy Mohan
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Thycaud Post, Poojappura, Trivandrum 695014, India
| | - A P Sudheesh
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Thycaud Post, Poojappura, Trivandrum 695014, India
| | - Nimmy Francis
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Thycaud Post, Poojappura, Trivandrum 695014, India
| | - Richard Anderson
- School of Medicine and Public Health, University of Wisconsin-Madison, WI 53706, USA
| | - Rakesh S Laishram
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Thycaud Post, Poojappura, Trivandrum 695014, India
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Ospina-Villa JD, Zamorano-Carrillo A, Lopez-Camarillo C, Castañon-Sanchez CA, Soto-Sanchez J, Ramirez-Moreno E, Marchat LA. Amino acid residues Leu135 and Tyr236 are required for RNA binding activity of CFIm25 in Entamoeba histolytica. Biochimie 2015; 115:44-51. [PMID: 25941172 DOI: 10.1016/j.biochi.2015.04.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 04/22/2015] [Indexed: 11/29/2022]
Abstract
Pre-mRNA 3' end processing in the nucleus is essential for mRNA stability, efficient nuclear transport, and translation in eukaryotic cells. In Human, the cleavage/polyadenylation machinery contains the 25 kDa subunit of the Cleavage Factor Im (CFIm25), which specifically recognizes two UGUA elements and regulates the assembly of polyadenylation factors, poly(A) site selection and polyadenylation. In Entamoeba histolytica, the protozoan parasite responsible for human amoebiasis, EhCFIm25 has been reported as a RNA binding protein that interacts with the Poly(A) Polymerase. Here, we follow-up with the study of EhCFIm25 to characterize its interaction with RNA. Using in silico strategy, we identified Leu135 and Tyr236 in EhCFIm25 as conserved amino acids among CFIm25 homologues. We therefore generated mutant EhCFIm25 proteins to investigate the role of these residues for RNA interaction. Results showed that RNA binding activity was totally abrogated when Leu135 and Tyr236 were replaced with Ala residue, and Tyr236 was changed for Phe. In contrast, RNA binding activity was less affected when Leu135 was substituted by Thr. Our data revealed for the first time -until we know-the functional relevance of the conserved Leu135 and Tyr236 in EhCFIm25 for RNA binding activity. They also gave some insights about the possible chemical groups that could be interacting with the RNA molecule.
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Affiliation(s)
| | - Absalom Zamorano-Carrillo
- Biotechnology Program, ENMH-IPN, Mexico City, Mexico; Molecular Biomedicine Program, ENMH-IPN, Mexico City, Mexico
| | | | - Carlos A Castañon-Sanchez
- Subdirección de Enseñanza e Investigación, Hospital Regional de Alta Especialidad de Oaxaca, Oaxaca, Mexico
| | | | - Esther Ramirez-Moreno
- Biotechnology Program, ENMH-IPN, Mexico City, Mexico; Molecular Biomedicine Program, ENMH-IPN, Mexico City, Mexico
| | - Laurence A Marchat
- Biotechnology Program, ENMH-IPN, Mexico City, Mexico; Molecular Biomedicine Program, ENMH-IPN, Mexico City, Mexico.
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Shelomi M, Jasper WC, Atallah J, Kimsey LS, Johnson BR. Differential expression of endogenous plant cell wall degrading enzyme genes in the stick insect (Phasmatodea) midgut. BMC Genomics 2014; 15:917. [PMID: 25331961 PMCID: PMC4221708 DOI: 10.1186/1471-2164-15-917] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 10/01/2014] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Stick and leaf insects (Phasmatodea) are an exclusively leaf-feeding order of insects with no record of omnivory, unlike other "herbivorous" Polyneoptera. They represent an ideal system for investigating the adaptations necessary for obligate folivory, including plant cell wall degrading enzymes (PCWDEs). However, their physiology and internal anatomy is poorly understood, with limited genomic resources available. RESULTS We de novo assembled transcriptomes for the anterior and posterior midguts of six diverse Phasmatodea species, with RNA-Seq on one exemplar species, Peruphasma schultei. The latter's assembly yielded >100,000 transcripts, with over 4000 transcripts uniquely or more highly expressed in specific midgut sections. Two to three dozen PCWDE encoding gene families, including cellulases and pectinases, were differentially expressed in the anterior midgut. These genes were also found in genomic DNA from phasmid brain tissue, suggesting endogenous production. Sequence alignments revealed catalytic sites on most PCWDE transcripts. While most phasmid PCWDE genes showed homology with those of other insects, the pectinases were homologous to bacterial genes. CONCLUSIONS We identified a large and diverse PCWDE repertoire endogenous to the phasmids. If these expressed genes are translated into active enzymes, then phasmids can theoretically break plant cell walls into their monomer components independently of microbial symbionts. The differential gene expression between the two midgut sections provides the first molecular hints as to their function in living phasmids. Our work expands the resources available for industrial applications of animal-derived PCWDEs, and facilitates evolutionary analysis of lower Polyneopteran digestive enzymes, including the pectinases whose origin in Phasmatodea may have been a horizontal transfer event from bacteria.
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Affiliation(s)
- Matan Shelomi
- />Department of Entomology and Nematology, University of California-Davis, Davis, CA 95616 USA
- />Department of Entomology, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
| | - W Cameron Jasper
- />Department of Entomology and Nematology, University of California-Davis, Davis, CA 95616 USA
| | - Joel Atallah
- />Department of Entomology and Nematology, University of California-Davis, Davis, CA 95616 USA
| | - Lynn S Kimsey
- />Department of Entomology and Nematology, University of California-Davis, Davis, CA 95616 USA
| | - Brian R Johnson
- />Department of Entomology and Nematology, University of California-Davis, Davis, CA 95616 USA
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Laishram RS. Poly(A) polymerase (PAP) diversity in gene expression--star-PAP vs canonical PAP. FEBS Lett 2014; 588:2185-97. [PMID: 24873880 PMCID: PMC6309179 DOI: 10.1016/j.febslet.2014.05.029] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 05/02/2014] [Accepted: 05/15/2014] [Indexed: 01/09/2023]
Abstract
Almost all eukaryotic mRNAs acquire a poly(A) tail at the 3'-end by a concerted RNA processing event: cleavage and polyadenylation. The canonical PAP, PAPα, was considered the only nuclear PAP involved in general polyadenylation of mRNAs. A phosphoinositide-modulated nuclear PAP, Star-PAP, was then reported to regulate a select set of mRNAs in the cell. In addition, several non-canonical PAPs have been identified with diverse cellular functions. Further, canonical PAP itself exists in multiple isoforms thus illustrating the diversity of PAPs. In this review, we compare two nuclear PAPs, Star-PAP and PAPα with a general overview of PAP diversity in the cell. Emerging evidence suggests distinct niches of target pre-mRNAs for the two PAPs and that modulation of these PAPs regulates distinct cellular functions.
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Affiliation(s)
- Rakesh S Laishram
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, India.
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Li W, Zhang Y, Zhang C, Pei X, Wang Z, Jia S. Presence of poly(A) and poly(A)-rich tails in a positive-strand RNA virus known to lack 3׳ poly(A) tails. Virology 2014; 454-455:1-10. [PMID: 24725926 DOI: 10.1016/j.virol.2014.02.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Revised: 12/08/2013] [Accepted: 02/01/2014] [Indexed: 01/08/2023]
Abstract
Here we show that Tobacco mosaic virus (TMV), a positive-strand RNA virus known to end with 3׳ tRNA-like structures, does possess a small fraction of gRNA bearing polyadenylate tails. Particularly, many tails are at sites corresponding to the 3׳ end of near full length gRNA, and are composed of poly(A)-rich sequences containing the other nucleotides in addition to adenosine, resembling the degradation-stimulating poly(A) tails observed in all biological kingdoms. Further investigations demonstrate that these polyadenylated RNA species are not enriched in chloroplasts. Silencing of cpPNPase, a chloroplast-localized polynucleotide polymerase known to not only polymerize the poly(A)-rich tails but act as a 3׳ to 5׳ exoribonuclease, does not change the profile of polyadenylate tails associated with TMV RNA. Nevertheless, because similar tails were also detected in other phylogenetically distinct positive-strand RNA viruses lacking poly(A) tails, such kind of polyadenylation may reflect a common but as-yet-unknown interface between hosts and viruses.
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Affiliation(s)
- Weimin Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Yongqiang Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chao Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xinwu Pei
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhixing Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shirong Jia
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
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Lutz CS, Cornett AL. Regulation of genes in the arachidonic acid metabolic pathway by RNA processing and RNA-mediated mechanisms. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 4:593-605. [PMID: 23956046 DOI: 10.1002/wrna.1183] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Revised: 05/28/2013] [Accepted: 05/29/2013] [Indexed: 01/22/2023]
Abstract
Arachidonic acid (AA) is converted by enzymes in an important metabolic pathway to produce molecules known collectively as eicosanoids, 20 carbon molecules with significant physiological and pathological functions in the human body. Cyclooxygenase (COX) enzymes work in one arm of the pathway to produce prostaglandins (PGs) and thromboxanes (TXs), while the actions of 5-lipoxygenase (ALOX5 or 5LO) and its associated protein (ALOX5AP or FLAP) work in the other arm of the metabolic pathway to produce leukotrienes (LTs). The expression of the COX and ALOX5 enzymes that convert AA to eicosanoids is highly regulated at the post- or co-transcriptional level by alternative mRNA splicing, alternative mRNA polyadenylation, mRNA stability, and microRNA (miRNA) regulation. This review article will highlight these mechanisms of mRNA modulation.
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Affiliation(s)
- Carol S Lutz
- Department of Biochemistry and Molecular Biology, New Jersey Medical School and the Graduate School of Biomedical Sciences, Rutgers, NJ, USA.
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A small portion of plastid transcripts is polyadenylated in the flagellate Euglena gracilis. FEBS Lett 2014; 588:783-8. [PMID: 24492004 DOI: 10.1016/j.febslet.2014.01.034] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Revised: 01/08/2014] [Accepted: 01/09/2014] [Indexed: 12/21/2022]
Abstract
Euglena gracilis possesses secondary plastids of green algal origin. In this study, E. gracilis expressed sequence tags (ESTs) derived from polyA-selected mRNA were searched and several ESTs corresponding to plastid genes were found. PCR experiments failed to detect SL sequence at the 5'-end of any of these transcripts, suggesting plastid origin of these polyadenylated molecules. Quantitative PCR experiments confirmed that polyadenylation of transcripts occurs in the Euglena plastids. Such transcripts have been previously observed in primary plastids of plants and algae as low-abundance intermediates of transcript degradation. Our results suggest that a similar mechanism exists in secondary plastids.
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40
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Hockert JA, MacDonald CC. The stem-loop luciferase assay for polyadenylation (SLAP) method for determining CstF-64-dependent polyadenylation activity. Methods Mol Biol 2014; 1125:109-17. [PMID: 24590783 PMCID: PMC5417545 DOI: 10.1007/978-1-62703-971-0_9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Polyadenylation is an essential cellular process in eukaryotic cells (Edmonds M and Abrams R, J Biol Chem 235, 1142-1149, 1960; Zhao J et al., Microbiol Mol Biol Rev 63, 405-445, 1999; Edmonds M, Progr Nucleic Acid Res Mol Biol 71, 285-389, 2002). For this reason, it has been difficult to examine the functions of specific polyadenylation proteins in vivo. Here, we describe a cell culture assay that allows structure-function experiments on CstF-64, a protein that binds to pre-mRNAs downstream of the cleavage site for accurate and efficient polyadenylation. We also demonstrate that the stem-loop luciferase assay for polyadenylation (SLAP) accurately reflects CstF-64-dependent polyadenylation. This assay could be easily adapted to the study of other important RNA-binding proteins in polyadenylation.
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41
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Hoque M, Li W, Tian B. Accurate mapping of cleavage and polyadenylation sites by 3' region extraction and deep sequencing. Methods Mol Biol 2014; 1125:119-29. [PMID: 24590784 DOI: 10.1007/978-1-62703-971-0_10] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Deep sequencing of RNA (RNA-seq) is becoming a standard method to study gene expression. While RNA-seq reads cover most regions of an mRNA sequence, they are often depleted in the 3' end region, making them less amenable for mapping the cleavage and polyadenylation site (pA). A major problem in identification of pA is mispriming at internal A-rich regions and oligo(A) tails when an oligo(dT) primer is used for reverse transcription or sequencing. We recently developed a method named 3' region extraction and deep sequencing (3'READS), which completely addresses mispriming issues and is straightforward to use. The method accurately maps pAs and allows quantitative analysis of alternative cleavage and polyadenylation (APA) isoforms and gene expression.
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Affiliation(s)
- Mainul Hoque
- Department of Biochemistry and Molecular Biology, University of Medicine and Dentistry of New Jersey (UMDNJ)-New Jersey Medical School, Newark, NJ, USA
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42
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Pezet-Valdez M, Fernández-Retana J, Ospina-Villa JD, Ramírez-Moreno ME, Orozco E, Charcas-López S, Soto-Sánchez J, Mendoza-Hernández G, López-Casamicha M, López-Camarillo C, Marchat LA. The 25 kDa subunit of cleavage factor Im Is a RNA-binding protein that interacts with the poly(A) polymerase in Entamoeba histolytica. PLoS One 2013; 8:e67977. [PMID: 23840799 PMCID: PMC3695940 DOI: 10.1371/journal.pone.0067977] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2013] [Accepted: 05/23/2013] [Indexed: 01/03/2023] Open
Abstract
In eukaryotes, polyadenylation of pre-mRNA 3´ end is essential for mRNA export, stability and translation. Taking advantage of the knowledge of genomic sequences of Entamoeba histolytica, the protozoan responsible for human amoebiasis, we previously reported the putative polyadenylation machinery of this parasite. Here, we focused on the predicted protein that has the molecular features of the 25 kDa subunit of the Cleavage Factor Im (CFIm25) from other organisms, including the Nudix (nucleoside diphosphate linked to another moiety X) domain, as well as the RNA binding domain and the PAP/PAB interacting region. The recombinant EhCFIm25 protein (rEhCFIm25) was expressed in bacteria and used to generate specific antibodies in rabbit. Subcellular localization assays showed the presence of the endogenous protein in nuclear and cytoplasmic fractions. In RNA electrophoretic mobility shift assays, rEhCFIm25 was able to form specific RNA-protein complexes with the EhPgp5 mRNA 3´ UTR used as probe. In addition, Pull-Down and LC/ESI-MS/MS tandem mass spectrometry assays evidenced that the putative EhCFIm25 was able to interact with the poly(A) polymerase (EhPAP) that is responsible for the synthesis of the poly(A) tail in other eukaryotic cells. By Far-Western experiments, we confirmed the interaction between the putative EhCFIm25 and EhPAP in E. histolytica. Taken altogether, our results showed that the putative EhCFIm25 is a conserved RNA binding protein that interacts with the poly(A) polymerase, another member of the pre-mRNA 3´ end processing machinery in this protozoan parasite.
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Affiliation(s)
- Marisol Pezet-Valdez
- Programa Institucional de Biomedicina Molecular, Escuela Nacional de Medicina y Homeopatía del IPN, Guillermo Massieu Helguera #239, Fracc. La Escalera, Ticomán, México D.F., Mexico
| | - Jorge Fernández-Retana
- Programa Institucional de Biomedicina Molecular, Escuela Nacional de Medicina y Homeopatía del IPN, Guillermo Massieu Helguera #239, Fracc. La Escalera, Ticomán, México D.F., Mexico
| | - Juan David Ospina-Villa
- Programa Institucional de Biomedicina Molecular, Escuela Nacional de Medicina y Homeopatía del IPN, Guillermo Massieu Helguera #239, Fracc. La Escalera, Ticomán, México D.F., Mexico
| | - María Esther Ramírez-Moreno
- Programa Institucional de Biomedicina Molecular, Escuela Nacional de Medicina y Homeopatía del IPN, Guillermo Massieu Helguera #239, Fracc. La Escalera, Ticomán, México D.F., Mexico
- Doctorado en Biotecnología en Red, Escuela Nacional de Medicina y Homeopatía del IPN, Guillermo Massieu Helguera #239, Fracc. La Escalera, Ticomán, México D.F., Mexico
| | - Esther Orozco
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados, Instituto Politécnico Nacional, México D.F., Mexico
| | - Socorro Charcas-López
- Programa Institucional de Biomedicina Molecular, Escuela Nacional de Medicina y Homeopatía del IPN, Guillermo Massieu Helguera #239, Fracc. La Escalera, Ticomán, México D.F., Mexico
| | - Jacqueline Soto-Sánchez
- Programa Institucional de Biomedicina Molecular, Escuela Nacional de Medicina y Homeopatía del IPN, Guillermo Massieu Helguera #239, Fracc. La Escalera, Ticomán, México D.F., Mexico
| | - Guillermo Mendoza-Hernández
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, México D.F., Mexico
| | - Mavil López-Casamicha
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, México D.F., Mexico
| | - César López-Camarillo
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, México D.F., Mexico
| | - Laurence A. Marchat
- Programa Institucional de Biomedicina Molecular, Escuela Nacional de Medicina y Homeopatía del IPN, Guillermo Massieu Helguera #239, Fracc. La Escalera, Ticomán, México D.F., Mexico
- Doctorado en Biotecnología en Red, Escuela Nacional de Medicina y Homeopatía del IPN, Guillermo Massieu Helguera #239, Fracc. La Escalera, Ticomán, México D.F., Mexico
- * E-mail:
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43
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Lee CY, Chen L. Alternative polyadenylation sites reveal distinct chromatin accessibility and histone modification in human cell lines. Bioinformatics 2013; 29:1713-7. [PMID: 23740743 DOI: 10.1093/bioinformatics/btt288] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION In addition to alternative splicing, alternative polyadenylation has also been identified as a critical and prevalent regulatory mechanism in human gene expression. However, the mechanism of alternative polyadenylation selection and the involved factors is still largely unknown. RESULTS We use the ENCODE data to scan DNA functional elements, including chromatin accessibility and histone modification, around transcript cleavage sites. Our results demonstrate that polyadenylation sites tend to be less sensitive to DNase I. However, these polyadenylation sites have preference in nucleosome-depleted regions, indicating the involvement of chromatin higher-order structure rather than nucleosomes in the resultant lower chromatin accessibility. More interestingly, for genes using two polyadenylation sites, the distal sites show even lower chromatin accessibility compared with the proximal sites or the unique sites of genes using only one polyadenylation site. We also observe that the histone modification mark, histone H3 lysine 36 tri-methylation (H3K36Me3), exhibits different patterns around the cleavage sites of genes using multiple polyadenylation sites from those of genes using a single polyadenylation site. Surprisingly, the H3K36Me3 levels are comparable among the alternative polyadenylation sites themselves. In summary, polyadenylation and alternative polyadenylation are closely related to functional elements on the DNA level. CONTACT liang.chen@usc.edu.
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Affiliation(s)
- Che-yu Lee
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
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44
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Zhuang Y, Zhang H, Lin S. Polyadenylation of 18S rRNA in algae(1). JOURNAL OF PHYCOLOGY 2013; 49:570-579. [PMID: 27007045 DOI: 10.1111/jpy.12068] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Accepted: 12/23/2012] [Indexed: 06/05/2023]
Abstract
Polyadenylation is best known for occurring to mRNA of eukaryotes transcribed by RNA polymerase II to stabilize mRNA molecules and promote their translation. rRNAs transcribed by RNA polymerase I or III are typically believed not to be polyadenylated. However, there is increasing evidence that polyadenylation occurs to nucleus-encoded rRNAs as part of the RNA degradation pathway. To examine whether the same polyadenylation-assisted degradation pathway occurs in algae, we surveyed representative species of algae including diatoms, chlorophytes, dinoflagellates and pelagophytes using oligo (dT)-primed reversed transcription PCR (RT-PCR). In all the algal species examined, truncated 18S rRNA or its precursor molecules with homo- or hetero-polymeric poly(A) tails were detected. Mining existing algal expressed sequence tag (EST) data revealed polyadenylated truncated 18S rRNA in four additional phyla of algae. rRNA polyadenylation occurred at various internal positions along the 18S rRNA and its precursor sequences. Moreover, putative homologs of noncanonical poly(A) polymerase (ncPAP) Trf4p, which is responsible for polyadenylating nuclear-encoded RNA and targeting it for degradation, were detected from the genomes and transcriptomes of five phyla of algae. Our results suggest that polyadenylation-assisted RNA degradation mechanism widely exists in algae, particularly for the nucleus-encoded rRNA and its precursors.
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Affiliation(s)
- Yunyun Zhuang
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut, 06340, USA
- Marine Biodiversity and Global Change Research Center and State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361005, China
| | - Huan Zhang
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut, 06340, USA
| | - Senjie Lin
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut, 06340, USA
- Marine Biodiversity and Global Change Research Center and State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361005, China
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45
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Sibbritt T, Patel HR, Preiss T. Mapping and significance of the mRNA methylome. WILEY INTERDISCIPLINARY REVIEWS-RNA 2013; 4:397-422. [PMID: 23681756 DOI: 10.1002/wrna.1166] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 03/20/2013] [Accepted: 03/22/2013] [Indexed: 12/25/2022]
Abstract
Internal methylation of eukaryotic mRNAs in the form of N6-methyladenosine (m(6)A) and 5-methylcytidine (m(5)C) has long been known to exist, but progress in understanding its role was hampered by difficulties in identifying individual sites. This was recently overcome by high-throughput sequencing-based methods that mapped thousands of sites for both modifications throughout mammalian transcriptomes, with most sites found in mRNAs. The topology of m(6)A in mouse and human revealed both conserved and variable sites as well as plasticity in response to extracellular cues. Within mRNAs, m(5)C and m(6)A sites were relatively depleted in coding sequences and enriched in untranslated regions, suggesting functional interactions with post-transcriptional gene control. Finer distribution analyses and preexisting literature point toward roles in the regulation of mRNA splicing, translation, or decay, through an interplay with RNA-binding proteins and microRNAs. The methyltransferase (MTase) METTL3 'writes' m(6)A marks on mRNA, whereas the demethylase FTO can 'erase' them. The RNA:m(5)C MTases NSUN2 and TRDMT1 have roles in tRNA methylation but they also act on mRNA. Proper functioning of these enzymes is important in development and there are clear links to human disease. For instance, a common variant of FTO is a risk allele for obesity carried by 1 billion people worldwide and mutations cause a lethal syndrome with growth retardation and brain deficits. NSUN2 is linked to cancer and stem cell biology and mutations cause intellectual disability. In this review, we summarize the advances, open questions, and intriguing possibilities in this emerging field that might be called RNA modomics or epitranscriptomics.
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Affiliation(s)
- Tennille Sibbritt
- Genome Biology Department, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
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Li H, Li C, Zhou S, Poulos TL, Gershon PD. Domain-level rocking motion within a polymerase that translocates on single-stranded nucleic acid. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:617-24. [PMID: 23519670 PMCID: PMC3606039 DOI: 10.1107/s0907444913000346] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2012] [Accepted: 01/04/2013] [Indexed: 11/10/2022]
Abstract
Vaccinia virus poly(A) polymerase (VP55) is the only known polymerase that can translocate independently with respect to single-stranded nucleic acid (ssNA). Previously, its structure has only been solved in the context of the VP39 processivity factor. Here, a crystal structure of unliganded monomeric VP55 has been solved to 2.86 Å resolution, showing the first backbone structural isoforms among either VP55 or its processivity factor (VP39). Backbone differences between the two molecules of VP55 in the asymmetric unit indicated that unliganded monomeric VP55 can undergo a `rocking' motion of the N-terminal domain with respect to the other two domains, which may be `rigidified' upon VP39 docking. This observation is consistent with previously demonstrated experimental molecular dynamics of the monomer during translocation with respect to nucleic acid and with different mechanisms of translocation in the presence and absence of processivity factor VP39. Side-chain conformational changes in the absence of ligand were observed at a key primer contact site and at the catalytic center of VP55. The current structure completes the trio of possible structural forms for VP55 and VP39, namely the VP39 monomer, the VP39-VP55 heterodimer and the VP55 monomer.
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Affiliation(s)
- Huiyung Li
- Department of Molecular Biology and Biochemistry, Xinxiang Medical University, Xinxiang, Henan 453003, People’s Republic of China
| | - Changzheng Li
- Department of Molecular Biology and Biochemistry, Xinxiang Medical University, Xinxiang, Henan 453003, People’s Republic of China
- Department of Molecular Biology and Biochemistry, UC-Irvine, Irvine, USA
| | - Sufeng Zhou
- Department of Molecular Biology and Biochemistry, Xinxiang Medical University, Xinxiang, Henan 453003, People’s Republic of China
- Department of Molecular Biology and Biochemistry, UC-Irvine, Irvine, USA
| | - Thomas L. Poulos
- Department of Molecular Biology and Biochemistry, UC-Irvine, Irvine, USA
- Department of Pharmaceutical Sciences, UC-Irvine, Irvine, USA
- Department of Chemistry, UC-Irvine, Irvine, USA
| | - Paul David Gershon
- Department of Molecular Biology and Biochemistry, UC-Irvine, Irvine, USA
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Régnier P, Hajnsdorf E. The interplay of Hfq, poly(A) polymerase I and exoribonucleases at the 3' ends of RNAs resulting from Rho-independent termination: A tentative model. RNA Biol 2013; 10:602-9. [PMID: 23392248 DOI: 10.4161/rna.23664] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Discovered in eukaryotes as a modification essential for mRNA function, polyadenylation was then identified as a means used by all cells to destabilize RNA. In Escherichia coli, most accessible 3' RNA extremities are believed to be potential targets of poly(A) polymerase I. However, some RNAs might be preferentially adenylated. After a short statement of the current knowledge of poly(A) metabolism, we discuss how Hfq could affect recognition and polyadenylation of RNA terminated by Rho-independent terminators. Comparison of RNA terminus leads to the proposal that RNAs harboring 3' terminal features required for Hfq binding are not polyadenylated, whereas those lacking these structural elements can gain the oligo(A) tails that initiate exonucleolytic degradation. We also speculate that Hfq stimulates the synthesis of longer tails that could be used as Hfq-binding sites involved in non-characterized functions of Hfq-dependent sRNAs.
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Affiliation(s)
- Philippe Régnier
- University Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, Paris, France.
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Mohanty BK, Kushner SR. Deregulation of poly(A) polymerase I in Escherichia coli inhibits protein synthesis and leads to cell death. Nucleic Acids Res 2013; 41:1757-66. [PMID: 23241393 PMCID: PMC3561954 DOI: 10.1093/nar/gks1280] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Revised: 11/07/2012] [Accepted: 11/08/2012] [Indexed: 11/13/2022] Open
Abstract
Polyadenylation plays important roles in RNA metabolism in both prokaryotes and eukaryotes. Surprisingly, deregulation of polyadenylation by poly(A) polymerase I (PAP I) in Escherichia coli leads to toxicity and cell death. We show here that mature tRNAs, which are normally not substrates for PAP I in wild-type cells, are rapidly polyadenylated as PAP I levels increase, leading to dramatic reductions in the fraction of aminoacylated tRNAs, cessation of protein synthesis and cell death. The toxicity associated with PAP I is exacerbated by the absence of either RNase T and/or RNase PH, the two major 3' → 5' exonucleases involved in the final step of tRNA 3'-end maturation, confirming their role in the regulation of tRNA polyadenylation. Furthermore, our data demonstrate that regulation of PAP I is critical not for preventing the decay of mRNAs, but rather for maintaining normal levels of functional tRNAs and protein synthesis in E. coli, a function for polyadenylation that has not been observed previously in any organism.
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Affiliation(s)
| | - Sidney R. Kushner
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
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Chang JH, Tong L. Mitochondrial poly(A) polymerase and polyadenylation. BIOCHIMICA ET BIOPHYSICA ACTA 2012; 1819:992-7. [PMID: 22172994 PMCID: PMC3307840 DOI: 10.1016/j.bbagrm.2011.10.012] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2011] [Revised: 10/25/2011] [Accepted: 10/27/2011] [Indexed: 01/22/2023]
Abstract
Polyadenylation of mitochondrial RNAs in higher eukaryotic organisms have diverse effects on their function and metabolism. Polyadenylation completes the UAA stop codon of a majority of mitochondrial mRNAs in mammals, regulates the translation of the mRNAs, and has diverse effects on their stability. In contrast, polyadenylation of most mitochondrial mRNAs in plants leads to their degradation, consistent with the bacterial origin of this organelle. PAPD1 (mtPAP, TUTase1), a noncanonical poly(A) polymerase (ncPAP), is responsible for producing the poly(A) tails in mammalian mitochondria. The crystal structure of human PAPD1 was reported recently, offering molecular insights into its catalysis. This article is part of a Special Issue entitled: Mitochondrial Gene Expression.
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Affiliation(s)
- Jeong Ho Chang
- Department of Biological Sciences, Columbia University, New York, NY10027, USA
| | - Liang Tong
- Department of Biological Sciences, Columbia University, New York, NY10027, USA
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Berkovits BD, Wang L, Guarnieri P, Wolgemuth DJ. The testis-specific double bromodomain-containing protein BRDT forms a complex with multiple spliceosome components and is required for mRNA splicing and 3'-UTR truncation in round spermatids. Nucleic Acids Res 2012; 40:7162-75. [PMID: 22570411 PMCID: PMC3424537 DOI: 10.1093/nar/gks342] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Revised: 04/05/2012] [Accepted: 04/10/2012] [Indexed: 12/02/2022] Open
Abstract
Members of the BET (bromodomain and extra terminal motif) family of proteins have been shown to be chromatin-interacting regulators of transcription. We previously generated a mutation in the testis-specific mammalian BET gene Brdt (bromodomain, testis-specific) that yields protein lacking the first bromodomain (BRDT(ΔBD1)) and observed disrupted spermiogenesis and male sterility. To determine whether BRDT(ΔBD1) protein results in altered transcription, we analyzed the transcriptomes of control versus Brdt(ΔBD1/ΔBD1) round spermatids. Over 400 genes showed statistically significant differential expression, and among the up-regulated genes, there was an enrichment of RNA splicing genes. Over 60% of these splicing genes had transcripts that lacked truncation of their 3'-untranslated region (UTR) typical of round spermatids. We selected four of these genes to characterize: Srsf2, Ddx5, Hnrnpk and Tardbp. The 3'-UTRs of Srsf2, Ddx5 and Hnrnpk mRNAs were longer in mutant round spermatids and resulted in reduced protein levels. Tardbp was transcriptionally up-regulated and a splicing shift toward the longer variant was observed. All four splicing proteins were found to complex with BRDT in control and mutant testes. We thus suggest that, along with modulating transcription, BRDT modulates gene expression as part of the splicing machinery. These modulations alter 3'-UTR processing in round spermatids; importantly, the BD1 is essential for these functions.
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Affiliation(s)
- Binyamin D. Berkovits
- Department of Genetics and Development, Biomedical Informatics Shared Resources, Bioinformatics Division, The Herbert Irving Comprehensive Cancer Center, The Institute of Human Nutrition and Department of Obstetrics and Gynecology, Columbia University Medical Center, New York, NY 10032, USA
| | - Li Wang
- Department of Genetics and Development, Biomedical Informatics Shared Resources, Bioinformatics Division, The Herbert Irving Comprehensive Cancer Center, The Institute of Human Nutrition and Department of Obstetrics and Gynecology, Columbia University Medical Center, New York, NY 10032, USA
| | - Paolo Guarnieri
- Department of Genetics and Development, Biomedical Informatics Shared Resources, Bioinformatics Division, The Herbert Irving Comprehensive Cancer Center, The Institute of Human Nutrition and Department of Obstetrics and Gynecology, Columbia University Medical Center, New York, NY 10032, USA
| | - Debra J. Wolgemuth
- Department of Genetics and Development, Biomedical Informatics Shared Resources, Bioinformatics Division, The Herbert Irving Comprehensive Cancer Center, The Institute of Human Nutrition and Department of Obstetrics and Gynecology, Columbia University Medical Center, New York, NY 10032, USA
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