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Magg V, Manetto A, Kopp K, Wu CC, Naghizadeh M, Lindner D, Eke L, Welsch J, Kallenberger SM, Schott J, Haucke V, Locker N, Stoecklin G, Ruggieri A. Turnover of PPP1R15A mRNA encoding GADD34 controls responsiveness and adaptation to cellular stress. Cell Rep 2024; 43:114069. [PMID: 38602876 DOI: 10.1016/j.celrep.2024.114069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 01/25/2024] [Accepted: 03/21/2024] [Indexed: 04/13/2024] Open
Abstract
The integrated stress response (ISR) is a key cellular signaling pathway activated by environmental alterations that represses protein synthesis to restore homeostasis. To prevent sustained damage, the ISR is counteracted by the upregulation of growth arrest and DNA damage-inducible 34 (GADD34), a stress-induced regulatory subunit of protein phosphatase 1 that mediates translation reactivation and stress recovery. Here, we uncover a novel ISR regulatory mechanism that post-transcriptionally controls the stability of PPP1R15A mRNA encoding GADD34. We establish that the 3' untranslated region of PPP1R15A mRNA contains an active AU-rich element (ARE) recognized by proteins of the ZFP36 family, promoting its rapid decay under normal conditions and stabilization for efficient expression of GADD34 in response to stress. We identify the tight temporal control of PPP1R15A mRNA turnover as a component of the transient ISR memory, which sets the threshold for cellular responsiveness and mediates adaptation to repeated stress conditions.
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Affiliation(s)
- Vera Magg
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Disease Research, 69120 Heidelberg, Germany
| | - Alessandro Manetto
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Disease Research, 69120 Heidelberg, Germany
| | - Katja Kopp
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Disease Research, 69120 Heidelberg, Germany
| | - Chia Ching Wu
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Disease Research, 69120 Heidelberg, Germany
| | - Mohsen Naghizadeh
- Heidelberg University, Medical Faculty Mannheim, Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3) and Mannheim Cancer Center (MCC), 68167 Mannheim, Germany
| | - Doris Lindner
- Heidelberg University, Medical Faculty Mannheim, Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3) and Mannheim Cancer Center (MCC), 68167 Mannheim, Germany
| | - Lucy Eke
- Faculty of Health and Medical Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, UK
| | - Julia Welsch
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Disease Research, 69120 Heidelberg, Germany
| | - Stefan M Kallenberger
- Digital Health Center, Berlin Institute of Health (BIH) and Charité, 10178 Berlin, Germany; Medical Oncology, National Center for Tumor Diseases, Heidelberg University, 69120 Heidelberg, Germany
| | - Johanna Schott
- Heidelberg University, Medical Faculty Mannheim, Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3) and Mannheim Cancer Center (MCC), 68167 Mannheim, Germany
| | - Volker Haucke
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, 13125 Berlin, Germany; Freie Universität Berlin, Faculty of Biology, Chemistry, and Pharmacy, 14195 Berlin, Germany
| | - Nicolas Locker
- Faculty of Health and Medical Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, UK; The Pirbright Institute, GU24 0NF Pirbright, UK
| | - Georg Stoecklin
- Heidelberg University, Medical Faculty Mannheim, Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3) and Mannheim Cancer Center (MCC), 68167 Mannheim, Germany; Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany.
| | - Alessia Ruggieri
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Disease Research, 69120 Heidelberg, Germany.
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Huynh TN, Parker R. The PARN, TOE1, and USB1 RNA deadenylases and their roles in non-coding RNA regulation. J Biol Chem 2023; 299:105139. [PMID: 37544646 PMCID: PMC10493513 DOI: 10.1016/j.jbc.2023.105139] [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: 05/13/2023] [Revised: 07/28/2023] [Accepted: 07/29/2023] [Indexed: 08/08/2023] Open
Abstract
The levels of non-coding RNAs (ncRNAs) are regulated by transcription, RNA processing, and RNA degradation pathways. One mechanism for the degradation of ncRNAs involves the addition of oligo(A) tails by non-canonical poly(A) polymerases, which then recruit processive sequence-independent 3' to 5' exonucleases for RNA degradation. This pathway of decay is also regulated by three 3' to 5' exoribonucleases, USB1, PARN, and TOE1, which remove oligo(A) tails and thereby can protect ncRNAs from decay in a manner analogous to the deubiquitination of proteins. Loss-of-function mutations in these genes lead to premature degradation of some ncRNAs and lead to specific human diseases such as Poikiloderma with Neutropenia (PN) for USB1, Dyskeratosis Congenita (DC) for PARN and Pontocerebellar Hypoplasia type 7 (PCH7) for TOE1. Herein, we review the biochemical properties of USB1, PARN, and TOE1, how they modulate ncRNA levels, and their roles in human diseases.
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Affiliation(s)
- Thao Ngoc Huynh
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado, USA
| | - Roy Parker
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado, USA; Howard Hughes Medical Institute, Chevy Chase, Maryland, USA.
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Tietz KT, Gallagher TL, Mannings MC, Morrow ZT, Derr NL, Amacher SL. Pumilio response and AU-rich elements drive rapid decay of Pnrc2-regulated cyclic gene transcripts. Dev Biol 2020; 462:129-140. [PMID: 32246943 DOI: 10.1016/j.ydbio.2020.03.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 02/18/2020] [Accepted: 03/20/2020] [Indexed: 01/06/2023]
Abstract
Vertebrate segmentation is regulated by the segmentation clock, a biological oscillator that controls periodic formation of somites, or embryonic segments, which give rise to many mesodermal tissue types. This molecular oscillator generates cyclic gene expression with the same periodicity as somite formation in the presomitic mesoderm (PSM), an area of mesenchymal cells that give rise to mature somites. Molecular components of the clock include the Hes/her family of genes that encode transcriptional repressors, but additional genes cycle. Cyclic gene transcripts are cleared rapidly, and clearance depends upon the pnrc2 (proline-rich nuclear receptor co-activator 2) gene that encodes an mRNA decay adaptor. Previously, we showed that the her1 3'UTR confers instability to otherwise stable transcripts in a Pnrc2-dependent manner, however, the molecular mechanism(s) by which cyclic gene transcripts are cleared remained largely unknown. To identify features of the her1 3'UTR that are critical for Pnrc2-mediated decay, we developed an array of transgenic inducible reporter lines carrying different regions of the 3'UTR. We find that the terminal 179 nucleotides (nts) of the her1 3'UTR are necessary and sufficient to confer rapid instability. Additionally, we show that the 3'UTR of another cyclic gene, deltaC (dlc), also confers Pnrc2-dependent instability. Motif analysis reveals that both her1 and dlc 3'UTRs contain terminally-located Pumilio response elements (PREs) and AU-rich elements (AREs), and we show that the PRE and ARE in the last 179 nts of the her1 3'UTR drive rapid turnover of reporter mRNA. Finally, we show that mutation of Pnrc2 residues and domains that are known to facilitate interaction of human PNRC2 with decay factors DCP1A and UPF1 reduce the ability of Pnrc2 to restore normal cyclic gene expression in pnrc2 mutant embryos. Our findings suggest that Pnrc2 interacts with decay machinery components and cooperates with Pumilio (Pum) proteins and ARE-binding proteins to promote rapid turnover of cyclic gene transcripts during somitogenesis.
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Affiliation(s)
- Kiel T Tietz
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA; Interdisciplinary Graduate Program in Molecular, Cellular and Developmental Biology, The Ohio State University, Columbus, OH, 43210, USA
| | - Thomas L Gallagher
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA
| | - Monica C Mannings
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA; Interdisciplinary Graduate Program in Molecular, Cellular and Developmental Biology, The Ohio State University, Columbus, OH, 43210, USA
| | - Zachary T Morrow
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, 43210, USA
| | - Nicolas L Derr
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, 43210, USA
| | - Sharon L Amacher
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA; Interdisciplinary Graduate Program in Molecular, Cellular and Developmental Biology, The Ohio State University, Columbus, OH, 43210, USA; Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, 43210, USA; Center for Muscle Health and Neuromuscular Disorders, The Ohio State University, Columbus, OH, 43210, USA.
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Direct and Indirect Effects on Viral Translation and RNA Replication Are Required for AUF1 Restriction of Enterovirus Infections in Human Cells. mBio 2018; 9:mBio.01669-18. [PMID: 30181254 PMCID: PMC6123441 DOI: 10.1128/mbio.01669-18] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Picornaviruses primarily infect the gastrointestinal or upper respiratory tracts of humans and animals and may disseminate to tissues of the central nervous system, heart, skin, liver, or pancreas. Many common human pathogens belong to the Picornaviridae family, which includes viruses known to cause paralytic poliomyelitis (poliovirus); myocarditis (coxsackievirus B3 [CVB3]); the common cold (human rhinovirus [HRV]); and hand, foot, and mouth disease (enterovirus 71 [EV71]), among other illnesses. There are no specific treatments for infection, and vaccines exist for only two picornaviruses: poliovirus and hepatitis A virus. Given the worldwide distribution and prevalence of picornaviruses, it is important to gain insight into the host mechanisms used to restrict infection. Other than proteins involved in the innate immune response, few host factors have been identified that restrict picornavirus replication. The work presented here seeks to define the mechanism of action for the host restriction factor AUF1 during infection by poliovirus and CVB3. The cellular mRNA decay protein AUF1 acts as a restriction factor during infection by picornaviruses, including poliovirus, coxsackievirus, and human rhinovirus. AUF1 relocalizes from the nucleus to the cytoplasm during infection by these viruses due to the disruption of nucleocytoplasmic trafficking by viral proteinases. Previous studies have demonstrated that AUF1 binds to poliovirus and coxsackievirus B3 (CVB3) RNA during infection, with binding shown to occur within the internal ribosome entry site (IRES) of the 5′ noncoding region (NCR) or the 3′ NCR, respectively. Binding to different sites within the viral RNA suggests that AUF1 may negatively regulate infection by these viruses using different mechanisms. The work presented here addresses the mechanism of AUF1 inhibition of the replication of poliovirus and CVB3. We demonstrate that AUF1 knockdown in human cells results in increased viral translation, RNA synthesis, and virus production. AUF1 is shown to negatively regulate translation of a poliovirus and CVB3 IRES reporter RNA during infection but not in uninfected cells. We found that this inhibitory activity is not mediated through destabilization of viral genomic RNA; however, it does require virus-induced relocalization of AUF1 from the nucleus to the cytoplasm during the early phases of infection. Our findings suggest that AUF1 restriction of poliovirus and CVB3 replication uses a common mechanism through the viral IRES, which is distinct from the canonical role that AUF1 plays in regulated mRNA decay in uninfected host cells.
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Gallie DR. Plant growth and fertility requires functional interactions between specific PABP and eIF4G gene family members. PLoS One 2018; 13:e0191474. [PMID: 29381712 PMCID: PMC5790229 DOI: 10.1371/journal.pone.0191474] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 01/07/2018] [Indexed: 11/19/2022] Open
Abstract
The initiation of protein synthesis requires the involvement of the eukaryotic translation initiation factor (eIF) 4G to promote assembly of the factors needed to recruit a 40S ribosomal subunit to an mRNA. Although many eukaryotes express two eIF4G isoforms that are highly similar, those in plants, referred to as eIF4G and eIFiso4G, are highly divergent in size, sequence, and domain organization. Species of the Brassicaceae and the Cleomaceae also express a divergent eIFiso4G isoform, referred to as eIFiso4G2, not found elsewhere in the plant kingdom. Despite their divergence, eIF4G and eIFiso4G interact with eIF4A, eIF4B, and eIF4E isoforms needed for binding an mRNA. eIF4G and eIFiso4G also interact with the poly(A)-binding protein (PABP) which promotes ribosome recruitment to an mRNA. Increasing the complexity of such an interaction, however, Arabidopsis also expresses three PABP isoforms (PAB2, PAB4, and PAB8) in vegetative and reproductive tissues. In this study, the functional interactions among the eIF4G and the widely-expressed PABP isoforms were examined. Loss of PAB2 or PAB8 in combination with loss of eIF4G or eIFiso4G had little to no effect on growth or fertility whereas pab2 pab8 eif4g or pab2 pab8 eifiso4g1/2 mutants exhibited smaller stature and reduced fertility. Although the pab4 eifiso4g1 mutant grows normally and is fertile, pab4 eif4g or pab4 eifiso4g2 mutants could not be isolated. Even pab4/PAB4 eif4g/eIF4G heterozygous plants exhibited growth defects and low fertility. Mutant co-inheritance analysis in reciprocal crosses with wild-type plants revealed that most ovaries and pollen from pab4/PAB4 eif4g/eIF4G plants were PAB4 eif4g. Similarly, co-inheritance studies with pab4/PAB4 eifiso4g2/eIFiso4G2 plants suggested most ovaries were PAB4 eifiso4g2. These results suggest that a functional interaction between PAB4 and eIF4G and between PAB4 and eIFiso4G2 is required for growth and normal fertility.
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Affiliation(s)
- Daniel R. Gallie
- Department of Biochemistry, University of California, Riverside, CA, United States of America
- * E-mail:
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Lee M, Rey K, Besler K, Wang C, Choy J. Immunobiology of Nitric Oxide and Regulation of Inducible Nitric Oxide Synthase. Results Probl Cell Differ 2017; 62:181-207. [PMID: 28455710 DOI: 10.1007/978-3-319-54090-0_8] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Nitric oxide (NO) is a bioactive gas that has multiple roles in innate and adaptive immune responses. In macrophages, nitric oxide is produced by inducible nitric oxide synthase upon microbial and cytokine stimulation. It is needed for host defense against pathogens and for immune regulation. This review will summarize the role of NO and iNOS in inflammatory and immune responses and will discuss the regulatory mechanisms that control inducible nitric oxide synthase expression and activity.
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Affiliation(s)
- Martin Lee
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Kevin Rey
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Katrina Besler
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Christine Wang
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Jonathan Choy
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada.
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Gallie DR. Class II members of the poly(A) binding protein family exhibit distinct functions during Arabidopsis growth and development. ACTA ACUST UNITED AC 2017; 5:e1295129. [PMID: 28702277 DOI: 10.1080/21690731.2017.1295129] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 01/20/2017] [Accepted: 02/09/2017] [Indexed: 10/20/2022]
Abstract
The poly(A)-binding protein (PABP) binds to the poly(A) tail of eukaryotic cellular mRNAs and contributes to their stability and translational efficiency. In plants, PABP is expressed from an unusually large gene family grouped into 3 classes that expanded during the evolution of land plants. Subsequent to expansion of the family, members diverged in their primary sequence and in expression. Further expansion of the family and divergence of its members in the Brassicaceae demonstrate the continued dynamic evolution of PABP in plants. In this study, the function of the widely-expressed class II PABP family members was examined to determine how individual class II members contribute to plant growth and development. Of the 3 class II PABP members, PAB2 and PAB4 contribute most to vegetative growth and vegetative-to-floral transition whereas PAB2, and the recently-evolved third class II member, PAB8, contribute to inflorescence and silique growth. Interestingly, although class I and class III PABP members are expressed specifically in reproductive organs, class II PABP members are also necessary for fertility in that the combinatorial loss of PAB2 and either PAB4 or PAB8 expression resulted in reduced fertility. Although all 3 class II members are required for protein expression, PAB4 contributes most to the steady-state level of a reporter mRNA and to protein expression. These findings suggest that class II PABP members are partially overlapping in function but also involved in distinct aspects of plant growth and development.
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Affiliation(s)
- Daniel R Gallie
- Department of Biochemistry, University of California, Riverside, CA, USA
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Diverse Strategies Used by Picornaviruses to Escape Host RNA Decay Pathways. Viruses 2016; 8:v8120335. [PMID: 27999393 PMCID: PMC5192396 DOI: 10.3390/v8120335] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Revised: 12/07/2016] [Accepted: 12/09/2016] [Indexed: 12/24/2022] Open
Abstract
To successfully replicate, viruses protect their genomic material from degradation by the host cell. RNA viruses must contend with numerous destabilizing host cell processes including mRNA decay pathways and viral RNA (vRNA) degradation resulting from the antiviral response. Members of the Picornaviridae family of small RNA viruses have evolved numerous diverse strategies to evade RNA decay, including incorporation of stabilizing elements into vRNA and re-purposing host stability factors. Viral proteins are deployed to disrupt and inhibit components of the decay machinery and to redirect decay machinery to the advantage of the virus. This review summarizes documented interactions of picornaviruses with cellular RNA decay pathways and processes.
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9
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White MR, Garcin ED. The sweet side of RNA regulation: glyceraldehyde-3-phosphate dehydrogenase as a noncanonical RNA-binding protein. WILEY INTERDISCIPLINARY REVIEWS-RNA 2015; 7:53-70. [PMID: 26564736 DOI: 10.1002/wrna.1315] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 09/30/2015] [Accepted: 10/01/2015] [Indexed: 01/26/2023]
Abstract
The glycolytic protein, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), has a vast array of extraglycolytic cellular functions, including interactions with nucleic acids. GAPDH has been implicated in the translocation of transfer RNA (tRNA), the regulation of cellular messenger RNA (mRNA) stability and translation, as well as the regulation of replication and gene expression of many single-stranded RNA viruses. A growing body of evidence supports GAPDH-RNA interactions serving as part of a larger coordination between intermediary metabolism and RNA biogenesis. Despite the established role of GAPDH in nucleic acid regulation, it is still unclear how and where GAPDH binds to its RNA targets, highlighted by the absence of any conserved RNA-binding sequences. This review will summarize our current understanding of GAPDH-mediated regulation of RNA function. WIREs RNA 2016, 7:53-70. doi: 10.1002/wrna.1315 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Michael R White
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD, USA
| | - Elsa D Garcin
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD, USA
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Laver JD, Marsolais AJ, Smibert CA, Lipshitz HD. Regulation and Function of Maternal Gene Products During the Maternal-to-Zygotic Transition in Drosophila. Curr Top Dev Biol 2015; 113:43-84. [PMID: 26358870 DOI: 10.1016/bs.ctdb.2015.06.007] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Drosophila late-stage oocytes and early embryos are transcriptionally silent. Thus, control of gene expression during these developmental periods is posttranscriptional and posttranslational. Global changes in the transcriptome and proteome occur during oocyte maturation, after egg activation and fertilization, and upon zygotic genome activation. We review the scale, content, and dynamics of these global changes; the factors that regulate these changes; and the mechanisms by which they are accomplished. We highlight the intimate relationship between the clearance of maternal gene products and the activation of the embryo's own genome, and discuss the fact that each of these complementary components of the maternal-to-zygotic transition can be subdivided into several phases that serve different biological roles and are regulated by distinct factors.
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Affiliation(s)
- John D Laver
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | | | - Craig A Smibert
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada; Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Howard D Lipshitz
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
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Placentation, maternal-fetal interface, and conceptus loss in swine. Theriogenology 2015; 85:135-44. [PMID: 26324112 DOI: 10.1016/j.theriogenology.2015.08.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 07/29/2015] [Accepted: 08/02/2015] [Indexed: 12/20/2022]
Abstract
Pregnancy is a delicate yet complex physiological process that requires fine-tuning of many factors (hormones, growth factors, cytokines, and receptors) between the mother and the conceptus to ensure the survival of the conceptus(es) to term. Any disturbance in the maternal-conceptus dialog can have detrimental effects on the affected conceptus or even the outcome of pregnancy as a whole. Being a litter-bearing species, such disruptions can lead to a loss of up to 45% of the totally healthy offspring during early (periattachment) and midgestation to late gestation in pigs. Although the exact mechanism is not entirely understood, several factors have been associated with the fetal loss including but not limited to uterine capacity, placental efficiency, genetics, nutrition, and deficits in vascularization at the maternal-fetal interface. Over the years, we investigated how immune cells are recruited to the porcine maternal-fetal interface and whether they contribute to vascularization. We also delineated how cytokines, chemokines, and cytokine destabilizing factors fine-tune inflammation and whether the cytokine shift from early to midpregnancy exists at the porcine maternal-fetal interface. Finally, we evaluated the role of microRNAs in regulating immune cell recruitment and their angiogenic functions during pregnancy. Collectively our research points out that the immune-angiogenesis axis at the porcine maternal interface is significantly involved in promoting new blood vessel development, regulating inflammatory responses and ultimately contributing to pregnancy success. In this review, we summarized current knowledge on spontaneous fetal loss in swine, with special attention to the mechanisms in immune reactivity and interplay at the maternal-fetal interface.
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12
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Gallie DR, Liu R. Phylogenetic analysis reveals dynamic evolution of the poly(A)-binding protein gene family in plants. BMC Evol Biol 2014; 14:238. [PMID: 25421536 PMCID: PMC4252990 DOI: 10.1186/s12862-014-0238-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 11/07/2014] [Indexed: 01/05/2023] Open
Abstract
Background The poly(A)-binding protein (PABP) binds the poly(A) tail of eukaryotic mRNAs and functions to maintain the integrity of the mRNA while promoting protein synthesis through its interaction with eukaryotic translation initiation factor (eIF) 4G and eIF4B. PABP is encoded by a single gene in yeast and marine algae but during plant evolution the PABP gene family expanded substantially, underwent sequence divergence into three subclasses, and acquired tissue-specificity in gene family member expression. Although such changes suggest functional specialization, the size of the family and its sequence divergence have complicated an understanding of which gene family members may be foundational and which may represent more recent expansions of the family to meet the specific needs of speciation. Here, we examine the evolution of the plant PABP gene family to provide insight into these aspects of the family that may yield clues into the function of individual family members. Results The PABP gene family had expanded to two members by the appearance of fresh water algae and four members in non-vascular plants. In lycophytes, the first sequence divergence yielding a specific class member occurs. The earliest members of the gene family share greatest similarity to those modern members whose expression is confined to reproductive tissues, suggesting that supporting reproductive-associated gene expression is the most conserved function of this family. A family member sharing similarity to modern vegetative-associated members first appears in gymnosperms. Further elaboration of the reproductive-associated and vegetative-associated members occurred during the evolution of flowering plants. Conclusions Expansion of the plant PABP gene family began prior to the colonization of land. By the evolution of lycophytes, the first class member whose expression is confined to reproductive tissues in higher plants had appeared. A second class member whose expression is vegetative-associated appeared in gymnosperms and all three modern classes had fully evolved by the appearance of the first known basal angiosperm. The size of each PABP class underwent further expansion during subsequent evolution, especially in the Brassicaceae, suggesting that the family is undergoing dynamic evolution. Electronic supplementary material The online version of this article (doi:10.1186/s12862-014-0238-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daniel R Gallie
- Department of Biochemistry, University of California, Riverside, CA, 92521-0129, USA.
| | - Renyi Liu
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521-0129, USA.
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Chafin CB, Regna NL, Dai R, Caudell DL, Reilly CM. MicroRNA-let-7a expression is increased in the mesangial cells of NZB/W mice and increases IL-6 production in vitro. Autoimmunity 2014; 46:351-62. [PMID: 24001203 DOI: 10.3109/08916934.2013.773976] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Recent evidence supports a role for epigenetic alterations in the pathogenesis of systemic lupus erythematosus (SLE). MicroRNAs (miRNAs or miRs) are endogenous epigenetic regulators whose expression is altered in many diseases, including SLE. IL-6 is an inflammatory cytokine produced by mesangial cells during lupus nephritis (LN). IL-6 contains a potential binding site for miRNA-let-7a (let-7a) in its 3' untranslated region (UTR). We found let-7a expression was significantly increased in the mesangial cells of pre-diseased and actively diseased New Zealand Black/White (NZB/W) mice compared to age-matched New Zealand White (NZW) mice. Overexpression of let-7a in vitro increased IL-6 production in stimulated mesangial cells compared to non-transfected controls. Inhibition of let-7a did not significantly affect immune-stimulated IL-6 production. When stimulated mesangial cells overexpressing let-7a were treated with the transcription inhibitor Actinomycin D (ActD), IL-6 was degraded faster, consistent with the direct targeting of the 3' UTR of IL-6 by let-7a. Overexpression of let-7a increased the expression of tristetraprolin (TTP), an RNA-binding protein (RBP) that has 5 potential binding regions in the 3' UTR of IL-6. ActD inhibited the transcription of proteins including TTP that may contribute to the let-7a-mediated increase in immune-stimulated IL-6 production. These data show that NZB/W mice have higher let-7a expression than NZW mice and that increased let-7a expression in vitro increases IL-6 production in stimulated mesangial cells. Further studies examining the role of let-7a expression in inflammation are warranted.
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Affiliation(s)
- Cristen B Chafin
- Department of Biomedical Sciences & Pathobiology, Virginia-Maryland Regional College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA.
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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: 1.6] [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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15
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Maryati M, Kaur I, Jadhav GP, Olotu-Umoren L, Oveh B, Hashmi L, Fischer PM, Winkler GS. A fluorescence-based assay suitable for quantitative analysis of deadenylase enzyme activity. Nucleic Acids Res 2013; 42:e30. [PMID: 24170810 PMCID: PMC3950723 DOI: 10.1093/nar/gkt972] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
In eukaryotic cells, the shortening and removal of the poly(A) tail of cytoplasmic mRNA by deadenylase enzymes is a critical step in post-transcriptional gene regulation. The ribonuclease activity of deadenylase enzymes is attributed to either a DEDD (Asp-Glu-Asp-Asp) or an endonuclease–exonuclease–phosphatase domain. Both domains require the presence of two Mg2+ ions in the active site. To facilitate the biochemical analysis of deadenylase enzymes, we have developed a fluorescence-based deadenylase assay. The assay is based on end-point measurement, suitable for quantitative analysis and can be adapted for 96- and 384-well microplate formats. We demonstrate the utility of the assay by screening a chemical compound library, resulting in the identification of non-nucleoside inhibitors of the Caf1/CNOT7 enzyme, a catalytic subunit of the Ccr4–Not deadenylase complex. These compounds may be useful tools for the biochemical analysis of the Caf1/CNOT7 deadenylase subunit of the Ccr4–Not complex and indicate the feasibility of developing selective inhibitors of deadenylase enzymes using the fluorescence-based assay.
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Affiliation(s)
- Maryati Maryati
- School of Pharmacy and Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK
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16
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Casper I, Nowag S, Koch K, Hubrich T, Bollmann F, Henke J, Schmitz K, Kleinert H, Pautz A. Post-transcriptional regulation of the human inducible nitric oxide synthase (iNOS) expression by the cytosolic poly(A)-binding protein (PABP). Nitric Oxide 2013; 33:6-17. [DOI: 10.1016/j.niox.2013.05.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Revised: 05/14/2013] [Accepted: 05/16/2013] [Indexed: 12/21/2022]
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17
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Abstract
The addition of poly(A) tails to eukaryotic nuclear mRNAs promotes their stability, export to the cytoplasm and translation. Subsequently, the balance between exonucleolytic deadenylation and selective re-establishment of translation-competent poly(A) tails by cytoplasmic poly(A) polymerases is essential for the appropriate regulation of gene expression from oocytes to neurons. In recent years, surprising roles for cytoplasmic poly(A) polymerase-related enzymes that add uridylyl, rather than adenylyl, residues to RNA 3' ends have also emerged. These terminal uridylyl transferases promote the turnover of certain mRNAs but also modify microRNAs, their precursors and other small RNAs to modulate their stability or biological functions.
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Affiliation(s)
- Chris J Norbury
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
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Vlasova-St Louis I, Dickson AM, Bohjanen PR, Wilusz CJ. CELFish ways to modulate mRNA decay. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2013; 1829:695-707. [PMID: 23328451 DOI: 10.1016/j.bbagrm.2013.01.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Revised: 01/03/2013] [Accepted: 01/05/2013] [Indexed: 12/14/2022]
Abstract
The CELF family of RNA-binding proteins regulates many steps of mRNA metabolism. Although their best characterized function is in pre-mRNA splice site choice, CELF family members are also powerful modulators of mRNA decay. In this review we focus on the different modes of regulation that CELF proteins employ to mediate mRNA decay by binding to GU-rich elements. After starting with an overview of the importance of CELF proteins during development and disease pathogenesis, we then review the mRNA networks and cellular pathways these proteins regulate and the mechanisms by which they influence mRNA decay. Finally, we discuss how CELF protein activity is modulated during development and in response to cellular signals. We conclude by highlighting the priorities for new experiments in this field. This article is part of a Special Issue entitled: RNA Decay mechanisms.
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Palusa S, Ndaluka C, Bowen RA, Wilusz CJ, Wilusz J. The 3' untranslated region of the rabies virus glycoprotein mRNA specifically interacts with cellular PCBP2 protein and promotes transcript stability. PLoS One 2012; 7:e33561. [PMID: 22438951 PMCID: PMC3306424 DOI: 10.1371/journal.pone.0033561] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2011] [Accepted: 02/14/2012] [Indexed: 12/25/2022] Open
Abstract
Viral polymerase entry and pausing at intergenic junctions is predicted to lead to a defined polarity in the levels of rhabdovirus gene expression. Interestingly, we observed that the rabies virus glycoprotein mRNA is differentially over-expressed based on this model relative to other transcripts during infection of 293T cells. During infection, the rabies virus glycoprotein mRNA also selectively interacts with the cellular poly(rC)-binding protein 2 (PCBP2), a factor known to influence mRNA stability. Reporter assays performed both in electroporated cells and in a cell-free RNA decay system indicate that the conserved portion of the 3' UTR of the rabies virus glycoprotein mRNA contains an RNA stability element. PCBP2 specifically interacts with reporter transcripts containing this 72 base 3' UTR sequence. Furthermore, the PCBP2 interaction is directly associated with the stability of reporter transcripts. Therefore, we conclude that PCBP2 specifically and selectively interacts with the rabies virus glycoprotein mRNA and that this interaction may contribute to the post-transcriptional regulation of glycoprotein expression.
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Affiliation(s)
- Saiprasad Palusa
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Christina Ndaluka
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
- Department of Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - Richard A. Bowen
- Department of Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - Carol J. Wilusz
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Jeffrey Wilusz
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
- * E-mail:
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20
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Schott J, Stoecklin G. Networks controlling mRNA decay in the immune system. WILEY INTERDISCIPLINARY REVIEWS-RNA 2012; 1:432-56. [PMID: 21956941 DOI: 10.1002/wrna.13] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The active control of mRNA degradation has emerged as a key regulatory mechanism required for proper gene expression in the immune system. An adenosine/uridine (AU)-rich element (ARE) is at the heart of a first regulatory system that promotes the rapid degradation of a multitude of cytokine and chemokine mRNAs. AREs serve as binding sites for a number of regulatory proteins that either destabilize or stabilize the mRNA. Several kinase pathways regulate the activity of ARE-binding proteins and thereby coordinate the expression of their target mRNAs. Small regulatory micro (mi)-RNAs represent a second system that enhances the degradation of several mRNAs encoding important components of signal transduction cascades that are activated during adaptive and innate immune responses. Specific miRNAs are important for the differentiation of T helper cells, class switch recombination in B cells, and the maturation of dendritic cells. Excitement in this area of research is fueled by the discovery of novel RNA elements and regulatory proteins that exert control over specific mRNAs, as exemplified by an endonuclease that was found to directly cleave interleukin-6 mRNA. Together, these systems make up an extensive regulatory network that controls decay rates of individual mRNAs in a precise manner and thereby orchestrates the dynamic expression of many factors essential for adaptive and innate immune responses. In this review, we provide an overview of relevant factors regulated at the level of mRNA stability, summarize RNA-binding proteins and miRNAs that control their degradation rates, and discuss signaling pathways operating within this regulatory network.
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Affiliation(s)
- Johanna Schott
- Helmholtz Junior Research Group Posttranscriptional Control of Gene Expression, German Cancer Research Center, DKFZ-ZMBH Alliance, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
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21
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Balatsos N, Vlachakis D, Chatzigeorgiou V, Manta S, Komiotis D, Vlassi M, Stathopoulos C. Kinetic and in silico analysis of the slow-binding inhibition of human poly(A)-specific ribonuclease (PARN) by novel nucleoside analogues. Biochimie 2012; 94:214-21. [DOI: 10.1016/j.biochi.2011.10.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Accepted: 10/17/2011] [Indexed: 11/16/2022]
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22
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Pieper D, Schirmer S, Prechtel AT, Kehlenbach RH, Hauber J, Chemnitz J. Functional characterization of the HuR:CD83 mRNA interaction. PLoS One 2011; 6:e23290. [PMID: 21829725 PMCID: PMC3150423 DOI: 10.1371/journal.pone.0023290] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2011] [Accepted: 07/12/2011] [Indexed: 01/15/2023] Open
Abstract
Maturation of dendritic cells (DC) is characterized by expression of CD83, a surface protein that appears to be necessary for the effective activation of naïve T-cells and T-helper cells by DC. Lately it was shown that CD83 expression is regulated on the posttranscriptional level by interaction of the shuttle protein HuR with a novel posttranscriptional regulatory RNA element (PRE), which is located in the coding region of the CD83 transcript. Interestingly, this interaction commits the CD83 mRNA to efficient nuclear export via the CRM1 pathway. To date, however, the structural basis of this interaction, which potentially involves three distinct RNA recognition motifs (RRM1–3) in HuR and a complex three-pronged RNA stem-loop element in CD83 mRNA, has not been investigated in detail. In the present work we analyzed this interaction in vitro and in vivo using various HuR- and CD83 mRNA mutants. We are able to demonstrate that both, RRM1 and RRM2 are crucial for binding, whereas RRM3 as well as the HuR hinge region contributed only marginally to this protein∶RNA interaction. Furthermore, mutation of uridine rich patches within the PRE did not disturb HuR:CD83 mRNA complex formation while, in contrast, the deletion of specific PRE subfragments from the CD83 mRNA prevented HuR binding in vitro and in vivo. Interestingly, the observed inhibition of HuR binding to CD83 mRNA does not lead to a nuclear trapping of the transcript but rather redirected this transcript from the CRM1- towards the NXF1/TAP-specific nuclear export pathway. Thus, the presence of a functional PRE permits nucleocytoplasmic trafficking of the CD83 transcript via the CRM1 pathway.
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Affiliation(s)
- Dorothea Pieper
- Department of Cell Biology and Virology, Heinrich Pette Institute - Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Susann Schirmer
- Department of Cell Biology and Virology, Heinrich Pette Institute - Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Alexander T. Prechtel
- Department of Cell Biology and Virology, Heinrich Pette Institute - Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Ralph H. Kehlenbach
- Zentrum für Biochemie und Molekulare Zellbiologie, Universität Göttingen, Göttingen, Germany
| | - Joachim Hauber
- Department of Cell Biology and Virology, Heinrich Pette Institute - Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Jan Chemnitz
- Department of Cell Biology and Virology, Heinrich Pette Institute - Leibniz Institute for Experimental Virology, Hamburg, Germany
- * E-mail:
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23
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Walser CB, Lipshitz HD. Transcript clearance during the maternal-to-zygotic transition. Curr Opin Genet Dev 2011; 21:431-43. [PMID: 21497081 DOI: 10.1016/j.gde.2011.03.003] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Accepted: 03/21/2011] [Indexed: 02/04/2023]
Abstract
In all animals, a key event in the transition from maternal control of development to control by products of the zygotic genome is the elimination of a significant fraction of the mRNAs loaded into the egg by the mother. Clearance of these maternal mRNAs is accomplished by two activities: the first is maternally encoded while the second requires zygotic transcription. Recent advances include identification of RNA-binding proteins that function as specificity factors to direct the maternal degradation machinery to its target mRNAs; small RNAs-most notably microRNAs-that function as components of the zygotically encoded activity; signaling pathways that trigger production and/or activation of the clearance mechanism in early embryos; and mechanisms for spatial control of transcript clearance.
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Affiliation(s)
- Claudia B Walser
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada M5S 1A8
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24
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Li Y, Song M, Kiledjian M. Differential utilization of decapping enzymes in mammalian mRNA decay pathways. RNA (NEW YORK, N.Y.) 2011; 17:419-428. [PMID: 21224379 PMCID: PMC3039142 DOI: 10.1261/rna.2439811] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2010] [Accepted: 12/09/2010] [Indexed: 05/30/2023]
Abstract
mRNA decapping is a crucial step in the regulation of mRNA stability and gene expression. Dcp2 is an mRNA decapping enzyme that has been widely studied. We recently reported the presence of a second mammalian cytoplasmic decapping enzyme, Nudt16. Here we address the differential utilization of the two decapping enzymes in specified mRNA decay processes. Using mouse embryonic fibroblast (MEF) cell lines derived from a hypomorphic knockout of the Dcp2 gene with undetectable levels of Dcp2 or MEF cell lines harboring a Nudt16-directed shRNA to generate reduced levels of Nudt16, we demonstrate the distinct roles for Dcp2 and Nudt16 in nonsense-mediated mRNA decay (NMD), decay of ARE-containing mRNA and miRNA-mediated silencing. Our results indicated that NMD preferentially utilizes Dcp2 rather than Nudt16; Dcp2 and Nudt16 are redundant in miRNA-mediated silencing; and Dcp2 and Nudt16 are differentially utilized for ARE-mRNA decay. These data demonstrate that the two distinct decapping enzymes can uniquely function in specific mRNA decay processes in mammalian cells.
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Affiliation(s)
- You Li
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, New Jersey 08854-8082, USA
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25
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Sandler H, Kreth J, Timmers HTM, Stoecklin G. Not1 mediates recruitment of the deadenylase Caf1 to mRNAs targeted for degradation by tristetraprolin. Nucleic Acids Res 2011; 39:4373-86. [PMID: 21278420 PMCID: PMC3105394 DOI: 10.1093/nar/gkr011] [Citation(s) in RCA: 173] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The carbon catabolite repressor protein 4 (Ccr4)–Negative on TATA (Not) complex controls gene expression at two levels. In the nucleus, it regulates the basal transcription machinery, nuclear receptor-mediated transcription and histone modifications. In the cytoplasm, the complex is required for messenger RNA (mRNA) turnover through its two associated deadenylases, Ccr4 and Caf1. Not1 is the largest protein of the Ccr4–Not complex and serves as a scaffold for other subunits of the complex. Here, we provide evidence that human Not1 in the cytoplasm associates with the C-terminal domain of tristetraprolin (TTP), an RNA binding protein that mediates rapid degradation of mRNAs containing AU-rich elements (AREs). Not1 shows extensive interaction through its central region with TTP, whereas binding of Caf1 is restricted to a smaller central domain within Not1. Importantly, Not1 is required for the rapid decay of ARE-mRNAs, and TTP can recruit the Caf1 deadenylase only in presence of Not1. Thus, cytoplasmic Not1 provides a platform that allows a specific RNA binding protein to recruit the Caf1 deadenylase and thereby trigger decay of its target mRNAs.
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Affiliation(s)
- Heike Sandler
- Helmholtz Junior Research Group Posttranscriptional Control of Gene Expression, German Cancer Research Center, DKFZ-ZMBH Alliance, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
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26
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Song MG, Li Y, Kiledjian M. Multiple mRNA decapping enzymes in mammalian cells. Mol Cell 2010; 40:423-32. [PMID: 21070968 DOI: 10.1016/j.molcel.2010.10.010] [Citation(s) in RCA: 119] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2010] [Revised: 07/10/2010] [Accepted: 08/25/2010] [Indexed: 01/18/2023]
Abstract
Regulation of RNA degradation plays an important role in the control of gene expression. One mechanism of eukaryotic mRNA decay proceeds through an initial deadenylation followed by 5' end decapping and exonucleolytic decay. Dcp2 is currently believed to be the only cytoplasmic decapping enzyme responsible for decapping of all mRNAs. Here we report that Dcp2 protein modestly contributes to bulk mRNA decay and surprisingly is not detectable in a subset of mouse and human tissues. Consistent with these findings, a hypomorphic knockout of Dcp2 had no adverse consequences in mice. In contrast, the previously reported Xenopus nucleolar decapping enzyme, Nudt16, is an ubiquitous cytoplasmic decapping enzyme in mammalian cells. Like Dcp2, Nudt16 also regulates the stability of a subset of mRNAs including a member of the motin family of proteins involved in angiogenesis, Angiomotin-like 2. These data demonstrate mammalian cells possess multiple mRNA decapping enzymes, including Nudt16 to regulate mRNA turnover.
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Affiliation(s)
- Man-Gen Song
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ 08854, USA
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27
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Ling SHM, Qamra R, Song H. Structural and functional insights into eukaryotic mRNA decapping. WILEY INTERDISCIPLINARY REVIEWS-RNA 2010; 2:193-208. [PMID: 21957006 DOI: 10.1002/wrna.44] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The control of messenger RNA (mRNA) translation and degradation is important in regulation of eukaryotic gene expression. In the general and specialized mRNA decay pathways which involve 5(') →3(') decay, decapping is the central step because it is the controlling gate preceding the actual degradation of mRNA and is a site of numerous control inputs. Removal of the cap structure is catalyzed by a decapping holoenzyme composed of the catalytic Dcp2 subunit and the coactivator Dcp1. Decapping is regulated by decapping activators and inhibitors. Recent structural and kinetics studies indicated that Dcp1 and the substrate RNA promote the closed form of the enzyme and the catalytic step of decapping is rate limiting and accelerated by Dcp1. The conformational change between the open and closed decapping enzyme is important for controlling decapping, and regulation of this transition has been proposed to be a checkpoint for determining the fate of mRNAs. Here we summarize the past and recent advances on the structural and functional studies of protein factors involved in regulating mRNA decapping.
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Affiliation(s)
- Sharon H M Ling
- Laboratory of Macromolecular Structure, Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673
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28
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Ishimaru D, Zuraw L, Ramalingam S, Sengupta TK, Bandyopadhyay S, Reuben A, Fernandes DJ, Spicer EK. Mechanism of regulation of bcl-2 mRNA by nucleolin and A+U-rich element-binding factor 1 (AUF1). J Biol Chem 2010; 285:27182-27191. [PMID: 20571027 PMCID: PMC2930717 DOI: 10.1074/jbc.m109.098830] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2009] [Revised: 05/28/2010] [Indexed: 11/06/2022] Open
Abstract
The antiapoptotic Bcl-2 protein is overexpressed in a variety of cancers, particularly leukemias. In some cell types this is the result of enhanced stability of bcl-2 mRNA, which is controlled by elements in its 3'-untranslated region. Nucleolin is one of the proteins that binds to bcl-2 mRNA, thereby increasing its half-life. Here, we examined the site on the bcl-2 3'-untranslated region that is bound by nucleolin as well as the protein binding domains important for bcl-2 mRNA recognition. RNase footprinting and RNA fragment binding assays demonstrated that nucleolin binds to a 40-nucleotide region at the 5' end of the 136-nucleotide bcl-2 AU-rich element (ARE(bcl-2)). The first two RNA binding domains of nucleolin were sufficient for high affinity binding to ARE(bcl-2). In RNA decay assays, ARE(bcl-2) transcripts were protected from exosomal decay by the addition of nucleolin. AUF1 has been shown to recruit the exosome to mRNAs. When MV-4-11 cell extracts were immunodepleted of AUF1, the rate of decay of ARE(bcl-2) transcripts was reduced, indicating that nucleolin and AUF1 have opposing roles in bcl-2 mRNA turnover. When the function of nucleolin in MV-4-11 cells was impaired by treatment with the nucleolin-targeting aptamer AS1411, association of AUF1 with bcl-2 mRNA was increased. This suggests that the degradation of bcl-2 mRNA induced by AS1411 results from both interference with nucleolin protection of bcl-2 mRNA and recruitment of the exosome by AUF1. Based on our findings, we propose a model that illustrates the opposing roles of nucleolin and AUF1 in regulating bcl-2 mRNA stability.
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Affiliation(s)
- Daniella Ishimaru
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina 29425
| | - Lisa Zuraw
- Department of Chemistry, The Citadel, Charleston, South Carolina 29409
| | - Sivakumar Ramalingam
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina 29425
| | - Tapas K Sengupta
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina 29425
| | - Sumita Bandyopadhyay
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina 29425
| | - Adrian Reuben
- Division of Gastroenterology and Hepatology, Department of Medicine, Medical University of South Carolina, Charleston, South Carolina 29425
| | - Daniel J Fernandes
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina 29425
| | - Eleanor K Spicer
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina 29425.
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29
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Stumpo DJ, Lai WS, Blackshear PJ. Inflammation: cytokines and RNA-based regulation. WILEY INTERDISCIPLINARY REVIEWS-RNA 2010; 1:60-80. [PMID: 21956907 DOI: 10.1002/wrna.1] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The outcome of an inflammatory response depends upon the coordinated regulation of a variety of both pro-inflammatory and anti-inflammatory cytokines and other proteins. Regulation of these inflammation mediators can occur at multiple levels, including transcription, mRNA translation, post-translational modifications, and mRNA degradation. Post-transcriptional regulation has been shown to play an important role in controlling the expression of these mediators, allowing for normal initiation and resolution of the inflammatory response. Many inflammatory mediators have unstable mRNAs due, in part, to the presence of AU-rich elements in their 3'-untranslated regions. Increasing numbers of RNA-binding proteins have been identified that can bind to these AU-rich elements and then regulate the stability and/or translation of the mRNA. This review summarizes current knowledge about the role of several RNA-binding proteins that act through AU-rich elements to post-transcriptionally regulate the biosynthesis of proteins involved in inflammation.
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Affiliation(s)
- Deborah J Stumpo
- Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
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30
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Li Y, Kiledjian M. Regulation of mRNA decapping. WILEY INTERDISCIPLINARY REVIEWS-RNA 2010; 1:253-65. [PMID: 21935889 DOI: 10.1002/wrna.15] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Decapping is a critical step in the control of mRNA stability and the regulation of gene expression. Two major decapping enzymes involved in mRNA turnover have been identified, each functioning in one of the two exonucleolytic mRNA decay pathways in eukaryotic cells. The Dcp2 protein cleaves capped mRNA and initiates 5' to 3' degradation; the scavenger decapping enzyme, DcpS, hydrolyzes the cap structure generated by the 3' to 5' decay pathway. Consistent with the important role of decapping in gene expression, cap hydrolysis is exquisitely controlled by multiple regulators that influence association with the cap and the catalytic step. In this review, we will discuss the functions of the two different decapping enzymes, their regulation by cis-elements and trans-factors, and the potential role of the decapping enzymes in human neurological disorders.
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Affiliation(s)
- You Li
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ 08854-8082, USA
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Nuclear deadenylation/polyadenylation factors regulate 3' processing in response to DNA damage. EMBO J 2010; 29:1674-87. [PMID: 20379136 DOI: 10.1038/emboj.2010.59] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2009] [Accepted: 03/05/2010] [Indexed: 12/23/2022] Open
Abstract
We previously showed that mRNA 3' end cleavage reaction in cell extracts is strongly but transiently inhibited under DNA-damaging conditions. The cleavage stimulation factor-50 (CstF-50) has a role in this response, providing a link between transcription-coupled RNA processing and DNA repair. In this study, we show that CstF-50 interacts with nuclear poly(A)-specific ribonuclease (PARN) using in vitro and in extracts of UV-exposed cells. The CstF-50/PARN complex formation has a role in the inhibition of 3' cleavage and activation of deadenylation upon DNA damage. Extending these results, we found that the tumour suppressor BARD1, which is involved in the UV-induced inhibition of 3' cleavage, strongly activates deadenylation by PARN in the presence of CstF-50, and that CstF-50/BARD1 can revert the cap-binding protein-80 (CBP80)-mediated inhibition of PARN activity. We also provide evidence that PARN along with the CstF/BARD1 complex participates in the regulation of endogenous transcripts under DNA-damaging conditions. We speculate that the interplay between polyadenylation, deadenylation and tumour-suppressor factors might prevent the expression of prematurely terminated messengers, contributing to control of gene expression under different cellular conditions.
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Chowdhury A, Tharun S. Activation of decapping involves binding of the mRNA and facilitation of the post-binding steps by the Lsm1-7-Pat1 complex. RNA (NEW YORK, N.Y.) 2009; 15:1837-1848. [PMID: 19643916 PMCID: PMC2743039 DOI: 10.1261/rna.1650109] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2009] [Accepted: 06/25/2009] [Indexed: 05/28/2023]
Abstract
Decapping is a critical step in the conserved 5'-to-3' mRNA decay pathway of eukaryotes. The hetero-octameric Lsm1-7-Pat1 complex is required for normal rates of decapping in this pathway. This complex also protects the mRNA 3'-ends from trimming in vivo. To elucidate the mechanism of decapping, we analyzed multiple lsm1 mutants, lsm1-6, lsm1-8, lsm1-9, and lsm1-14, all of which are defective in decapping and 3'-end protection but unaffected in Lsm1-7-Pat1 complex integrity. The RNA binding ability of the mutant complex was found to be almost completely lost in the lsm1-8 mutant but only partially impaired in the other mutants. Importantly, overproduction of the Lsm1-9p- or Lsm1-14p-containing (but not Lsm1-8p-containing) mutant complexes in wild-type cells led to a dominant inhibition of mRNA decay. Further, the mRNA 3'-end protection defect of lsm1-9 and lsm1-14 cells, but not the lsm1-8 cells, could be partly suppressed by overproduction of the corresponding mutant complexes in those cells. These results suggest the following: (1) Decapping requires both binding of the Lsm1-7-Pat1 complex to the mRNA and facilitation of the post-binding events, while binding per se is sufficient for 3'-end protection. (2) A major block exists at the post-binding steps in the lsm1-9 and lsm1-14 mutants and at the binding step in the lsm1-8 mutant. Consistent with these ideas, the lsm1-9, 14 allele generated by combining the mutations of lsm1-9 and lsm1-14 alleles had almost fully lost the RNA binding activity of the complex and behaved like the lsm1-8 mutant.
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Affiliation(s)
- Ashis Chowdhury
- Department of Biochemistry, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814-4799, USA
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33
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Curry S, Kotik-Kogan O, Conte MR, Brick P. Getting to the end of RNA: structural analysis of protein recognition of 5' and 3' termini. BIOCHIMICA ET BIOPHYSICA ACTA 2009; 1789:653-66. [PMID: 19619683 DOI: 10.1016/j.bbagrm.2009.07.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2009] [Revised: 07/07/2009] [Accepted: 07/09/2009] [Indexed: 10/20/2022]
Abstract
The specific recognition by proteins of the 5' and 3' ends of RNA molecules is an important facet of many cellular processes, including RNA maturation, regulation of translation initiation and control of gene expression by degradation and RNA interference. The aim of this review is to survey recent structural analyses of protein binding domains that specifically bind to the extreme 5' or 3' termini of RNA. For reasons of space and because their interactions are also governed by catalytic considerations, we have excluded enzymes that modify the 5' and 3' extremities of RNA. It is clear that there is enormous structural diversity among the proteins that have evolved to bind to the ends of RNA molecules. Moreover, they commonly exhibit conformational flexibility that appears to be important for binding and regulation of the interaction. This flexibility has sometimes complicated the interpretation of structural results and presents significant challenges for future investigations.
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Affiliation(s)
- Stephen Curry
- Biophysics Section, Blackett Laboratory, Imperial College, Exhibition Road, London, SW7 2AZ, UK.
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34
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Balatsos NAA, Vlachakis D, Maragozidis P, Manta S, Anastasakis D, Kyritsis A, Vlassi M, Komiotis D, Stathopoulos C. Competitive inhibition of human poly(A)-specific ribonuclease (PARN) by synthetic fluoro-pyranosyl nucleosides. Biochemistry 2009; 48:6044-51. [PMID: 19472977 DOI: 10.1021/bi900236k] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Poly(A)-specific ribonuclease (PARN) is a cap-interacting deadenylase that mediates, together with other exonucleases, the eukaryotic mRNA turnover and thus is actively involved in the regulation of gene expression. Aminoglycosides and natural nucleotides are the only reported modulators of human PARN activity, so far. In the present study, we show that synthetic nucleoside analogues bearing a fluoro-glucopyranosyl sugar moiety and benzoyl-modified cytosine or adenine as a base can effectively inhibit human PARN. Such nucleoside analogues exhibited substantial inhibitory effects, when tested against various cancer cell lines, as has been previously reported. Kinetic analysis showed that the inhibition of PARN is competitive and could not be released by altering Mg(II) concentration. Moreover, substitution of the 2', 4', or 6'-OH of the sugar moiety with acetyl and/or trityl groups was crucial for inhibitory efficacy. To understand how the nucleosides fit into the active site of PARN, we performed molecular docking experiments followed by molecular dynamics simulations. The in silico analysis showed that these compounds can efficiently dock into the active site of PARN. Our results support the idea that the sugar moiety mediates the stabilization of the nucleoside into the active site through interactions with catalytic amino acid residues. Taken together, our in vitro and in silico data suggest that human PARN is among the molecular targets of these compounds and could act therapeutically by lowering the mRNA turnover rate, thus explaining their known in vivo inhibitory effect at the molecular level.
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Affiliation(s)
- Nikolaos A A Balatsos
- Department of Biochemistry & Biotechnology, University of Thessaly, 26 Ploutonos Street, 412 21 Larissa, Greece
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35
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Balatsos NAA, Anastasakis D, Stathopoulos C. Inhibition of human poly(A)-specific ribonuclease (PARN) by purine nucleotides: kinetic analysis. J Enzyme Inhib Med Chem 2009; 24:516-23. [PMID: 18763168 DOI: 10.1080/14756360802218763] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Poly(A)-specific ribonuclease (PARN) is a cap-interacting and poly(A)-specific 3'-exoribonuclease that efficiently degrades mRNA poly(A) tails. Based on the enzyme's preference for its natural substrates, we examined the role of purine nucleotides as potent effectors of human PARN activity. We found that all purine nucleotides tested can reduce poly(A) degradation by PARN. Detailed kinetic analysis revealed that RTP nucleotides behave as non-competitive inhibitors while RDP and RMP exhibit competitive inhibition. Mg(2 + ) which is a catalytically important mediator of PARN activity can release inhibition of RTP and RDP but not RMP. Although many strategies have been proposed for the regulation of PARN activity, very little is known about the modulation of PARN activity by small molecule effectors, such as nucleotides. Our data imply that PARN activity can be modulated by purine nucleotides in vitro, providing an additional simple regulatory mechanism.
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Affiliation(s)
- Nikolaos A A Balatsos
- Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
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36
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Franks TM, Lykke-Andersen J. The control of mRNA decapping and P-body formation. Mol Cell 2009; 32:605-15. [PMID: 19061636 DOI: 10.1016/j.molcel.2008.11.001] [Citation(s) in RCA: 321] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2008] [Indexed: 01/24/2023]
Abstract
mRNA decapping is a critical step in eukaryotic cytoplasmic mRNA turnover. Cytoplasmic mRNA decapping is catalyzed by Dcp2 in conjunction with its coactivator Dcp1 and is stimulated by decapping enhancer proteins. mRNAs associated with the decapping machinery can assemble into cytoplasmic mRNP granules called processing bodies (PBs). Evidence suggests that PB-associated mRNPs are translationally repressed and can be degraded or stored for subsequent translation. However, whether mRNP assembly into a PB is important for translational repression, decapping, or decay has remained controversial. Here, we discuss the regulation of decapping machinery recruitment to specific mRNPs and how their assembly into PBs is governed by the relative rates of translational repression, mRNP multimerization, and mRNA decay.
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Affiliation(s)
- Tobias M Franks
- Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
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37
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Cherry J, Jones H, Karschner VA, Pekala PH. Post-transcriptional control of CCAAT/enhancer-binding protein beta (C/EBPbeta) expression: formation of a nuclear HuR-C/EBPbeta mRNA complex determines the amount of message reaching the cytosol. J Biol Chem 2008; 283:30812-20. [PMID: 18678862 PMCID: PMC2576548 DOI: 10.1074/jbc.m805659200] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2008] [Indexed: 12/27/2022] Open
Abstract
In 3T3-L1 cells, HuR is constitutively expressed and prior to induction of differentiation localized predominantly to the nucleus. Within minutes of induction of differentiation, nuclear HuR binds to its target ligand mRNAs, and the complexes appear to move to the cytosol. One ligand mRNA is the CCAAT/enhancer-binding protein beta (C/EBPbeta) message. To examine the function and importance of the HuR-C/EBPbeta interaction, retroviral expression constructs were created in which the HuR binding site was altered by deletion (betadel) or deletion and substitution (betad/s). Expression of these constructs in murine embryonic fibroblasts resulted in significant adipose conversion relative to those cells expressing wild type C/EBPbeta. C/EBPbeta protein content was increased markedly in both betadel and betad/s, which correlated with the acquisition of the adipocyte phenotype. Analysis of the betad/s cell line demonstrated a robust expression of C/EBPalpha coincident with peroxisome proliferator-activated receptor gamma expression. Total C/EBPbeta mRNA accumulation indicated no difference between cells harboring either the wild type C/EBPbeta cDNA or betad/s construct. However, cytosolic C/EBPbeta mRNA in the cells expressing the betad/s construct was maintained at levels between 2- and 7-fold greater than in the cells expressing the wild type construct. Alteration in mRNA half-life was not responsible for the increased accumulation. Mechanistically, these data suggest that HuR binding results in nuclear retention of the C/EBPbeta mRNA and is consistent with HuR control, at least in part, of mRNA processing.
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Affiliation(s)
- Joy Cherry
- Department of Biochemistry and Molecular Biology, The Brody School of Medicine at East Carolina University, Greenville, North Carolina 27858, USA
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38
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Guo YS, Chen Z, Wen XD, Ko TC, Townsend CM, Hellmich MR. Synergistic regulation of COX-2 expression by bombesin and transforming growth factor-beta. Dig Dis Sci 2008; 53:2045-52. [PMID: 18095163 DOI: 10.1007/s10620-007-0122-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2007] [Accepted: 11/09/2007] [Indexed: 12/09/2022]
Abstract
Overexpression of cyclooxygenase-2 (COX-2), an inducible enzyme regulating prostaglandin release, is mechanistically linked to the development, growth, and spread of gastrointestinal (GI) cancers. GI peptide bombesin (BBS) was reported to stimulate COX-2 gene expression. Here we show that TGF-beta1 dramatically enhances the BBS-induced expression of COX-2 mRNA and protein, and the release of PGE2 in the model rat intestinal epithelial cell (RIE-1) line. The synergistic increase in COX-2 levels results from a combination of enhanced COX-2 transcription and reduced mRNA degradation. BBS, but not TGF-beta1, stimulated COX-2 promoter activity, and TGF-beta1 enhanced COX-2 mRNA stability through a p38(MAPK)-dependent pathway. The synergistic regulation of COX-2 expression by TGF-beta1 and BBS may contribute to the upregulation of COX-2 in GI cancers.
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Affiliation(s)
- Yan-Shi Guo
- Department of Surgery, The University of Texas Medical Branch, Galveston, TX 77555-0722, USA.
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39
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Monecke T, Schell S, Dickmanns A, Ficner R. Crystal structure of the RRM domain of poly(A)-specific ribonuclease reveals a novel m(7)G-cap-binding mode. J Mol Biol 2008; 382:827-34. [PMID: 18694759 DOI: 10.1016/j.jmb.2008.07.073] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2008] [Revised: 06/26/2008] [Accepted: 07/23/2008] [Indexed: 10/21/2022]
Abstract
Poly(A)-specific ribonuclease (PARN) is a processive 3'-exoribonuclease involved in the decay of eukaryotic mRNAs. Interestingly, PARN interacts not only with the 3' end of the mRNA but also with its 5' end as PARN contains an RRM domain that specifically binds both the poly(A) tail and the 7-methylguanosine (m(7)G) cap. The interaction of PARN with the 5' cap of mRNAs stimulates the deadenylation activity and enhances the processivity of this reaction. We have determined the crystal structure of the PARN-RRM domain with a bound m(7)G triphosphate nucleotide, revealing a novel binding mode for the m(7)G cap. The structure of the m(7)G binding pocket is located outside of the canonical RNA-binding surface of the RRM domain and differs significantly from that of other m(7)G-cap-binding proteins. The crystal structure also shows a remarkable conformational flexibility of the RRM domain, leading to a perfect exchange of two alpha-helices with an adjacent protein molecule in the crystal lattice.
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Affiliation(s)
- Thomas Monecke
- Abteilung für Molekulare Strukturbiologie, Institut für Mikrobiologie und Genetik, GZMB, Georg-August-Universität Göttingen, 37077 Göttingen, Germany
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40
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Chaperone Hsp27, a novel subunit of AUF1 protein complexes, functions in AU-rich element-mediated mRNA decay. Mol Cell Biol 2008; 28:5223-37. [PMID: 18573886 DOI: 10.1128/mcb.00431-08] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Controlled, transient cytokine production by monocytes depends heavily upon rapid mRNA degradation, conferred by 3' untranslated region-localized AU-rich elements (AREs) that associate with RNA-binding proteins. The ARE-binding protein AUF1 forms a complex with cap-dependent translation initiation factors and heat shock proteins to attract the mRNA degradation machinery. We refer to this protein assembly as the AUF1- and signal transduction-regulated complex, ASTRC. Rapid degradation of ARE-bearing mRNAs (ARE-mRNAs) requires ubiquitination of AUF1 and its destruction by proteasomes. Activation of monocytes by adhesion to capillary endothelium at sites of tissue damage and subsequent proinflammatory cytokine induction are prominent features of inflammation, and ARE-mRNA stabilization plays a critical role in the induction process. Here, we demonstrate activation-induced subunit rearrangements within ASTRC and identify chaperone Hsp27 as a novel subunit that is itself an ARE-binding protein essential for rapid ARE-mRNA degradation. As Hsp27 has well-characterized roles in protein ubiquitination as well as in adhesion-induced cytoskeletal remodeling and cell motility, its association with ASTRC may provide a sensing mechanism to couple proinflammatory cytokine induction with monocyte adhesion and motility.
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41
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Zhang L, Lee JE, Wilusz J, Wilusz CJ. The RNA-binding protein CUGBP1 regulates stability of tumor necrosis factor mRNA in muscle cells: implications for myotonic dystrophy. J Biol Chem 2008; 283:22457-63. [PMID: 18559347 DOI: 10.1074/jbc.m802803200] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Type I myotonic dystrophy (DM1) is caused by a triplet repeat expansion in the 3'-untranslated region (UTR) of the dystrophia myotonia protein kinase (DMPK) gene. Pathogenesis is closely linked with production of a toxic RNA from the mutant allele, which interferes with function of several RNA-binding proteins, including CUGBP1. Here we show that expression of a mutant DMPK 3'-UTR containing 960 CUG repeats is sufficient to increase expression and stability of an mRNA encoding the potent proinflammatory cytokine, tumor necrosis factor (TNF). CUGBP1 specifically recognizes sequences within the TNF 3'-UTR that are dissimilar from its canonical UG-rich binding site. Depletion of CUGBP1 from mouse myoblasts results in increased abundance of TNF mRNA through stabilization of the transcript. Moreover, activation of the protein kinase C pathway by treatment with phorbol ester, which has been shown previously to result in CUGBP1 phosphorylation, also causes TNF mRNA stabilization. Our results suggest that the elevated serum TNF seen in DM1 patients may be derived from muscle where it is induced by expression of toxic DMPK RNA. Importantly, overexpression of this potent cytokine could contribute to the muscle wasting and insulin resistance that are characteristic of this debilitating disease.
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Affiliation(s)
- Libin Zhang
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523, USA
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42
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Moulton VR, Kyttaris VC, Juang YT, Chowdhury B, Tsokos GC. The RNA-stabilizing protein HuR regulates the expression of zeta chain of the human T cell receptor-associated CD3 complex. J Biol Chem 2008; 283:20037-44. [PMID: 18505733 DOI: 10.1074/jbc.m710434200] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
T cell dysfunction is crucial to the pathogenesis of systemic lupus erythematosus (SLE); however, the molecular mechanisms involved in the deficient expression of the T cell receptor-associated CD3zeta chain in SLE are not clear. SLE T cells express abnormally increased levels of an alternatively spliced isoform of CD3zeta that lacks a 562-bp region in its 3'-untranslated region (UTR). We showed previously that two adenosine/uridine-rich elements (ARE) in this splice-deleted region of CD3zeta transcript are critical for the mRNA stability and protein expression of CD3zeta. In this study we show for the first time that the mRNA-stabilizing protein HuR binds to these two ARE bearing regions of CD3zeta 3'-UTR. Knockdown of HuR resulted in decreased expression of the CD3zeta chain, whereas overexpression led to the increase of CD3zeta chain levels. Additionally, overexpression of HuR in human T cells resulted in increased mRNA stability of CD3zeta. Our results identify the 3'-UTR of CD3zeta as a novel target for the mRNA-stabilizing protein HuR. Thus, the absence of two critical AREs in the alternatively spliced CD3zeta 3'-UTR found in SLE T cells may result in decreased HuR binding, representing a possible molecular mechanism contributing to the reduced stability and expression of CD3zeta in SLE.
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Affiliation(s)
- Vaishali R Moulton
- Department of Medicine, Division of Rheumatology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
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Tharun S. Roles of eukaryotic Lsm proteins in the regulation of mRNA function. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2008; 272:149-89. [PMID: 19121818 DOI: 10.1016/s1937-6448(08)01604-3] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The eukaryotic Lsm proteins belong to the large family of Sm-like proteins, which includes members from all organisms ranging from archaebacteria to humans. The Sm and Lsm proteins typically exist as hexameric or heptameric complexes in vivo and carry out RNA-related functions. Multiple complexes made up of different combinations of Sm and Lsm proteins are known in eukaryotes and these complexes are involved in a variety of functions such as mRNA decay in the cytoplasm, mRNA and pre-mRNA decay in the nucleus, pre-mRNA splicing, replication dependent histone mRNA 3'-end processing, etc. While most Lsm proteins function in the form of heteromeric complexes that include other Lsm proteins, some Lsm proteins are also known that do not behave in that manner. Abnormal expression of some Lsm proteins has also been implicated in human diseases. The various roles of eukaryotic Lsm complexes impacting mRNA function are discussed in this review.
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Affiliation(s)
- Sundaresan Tharun
- Department of Biochemistry, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
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Abstract
The abundance of a cytoplasmic mRNA in eukaryotes often determines the level of the encoded protein product. The rates at which an mRNA is synthesized, exported, and degraded collectively contribute to its abundance in all cell types. Numerous mRNAs, particularly those encoding structural proteins, are very stable, with half-lives in the order of many hours. In contrast, mRNAs encoding regulatory proteins, including oncoproteins, cytokines, and signaling proteins, are relatively unstable with half-lives of an hour or less. As a result, modest changes in their decay rates affect their levels over a relatively short time period. This is particularly important to ensure rapid responses to extracellular signaling events. Messenger RNAs often harbor sequence elements that dictate their degradation rates. Adenylate uridylate (A+U)-rich elements (AREs), first identified in 1986, are perhaps the best characterized sequences that promote rapid mRNA degradation. These elements, localized within 3'-untranslated regions, sometimes contain AUUUA pentamers within an overall U-rich sequence, but this does not always define a bona fide ARE. Thus, experimental validation is essential before bestowing upon a suspected A+U-rich sequence the title of "ARE." This chapter describes a reporter gene system that permits quantitative assessment of the effects of candidate A+U-rich sequences on mRNA half-life. This system employs tetracycline-controlled transcriptional silencing of the reporter gene, isolation of total-cell RNA at selected time points, quantitative reverse transcriptase polymerase chain reaction analysis of reporter mRNA levels, and nonlinear regression analysis of mRNA level as a function of time to quantitatively define parameters describing mRNA decay kinetics. Finally, this chapter describes more specialized assays to characterize ARE-mediated mRNA decay pathways, including deadenylation, and discusses decapping.
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Song MG, Kiledjian M. 3' Terminal oligo U-tract-mediated stimulation of decapping. RNA (NEW YORK, N.Y.) 2007; 13:2356-65. [PMID: 17942740 PMCID: PMC2080602 DOI: 10.1261/rna.765807] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Decapping is a critical step in the control of gene expression and is regulated by both positive and negative trans factors. Less is known about cis elements that promote decapping. In plants, following microRNA (miRNA)-directed cleavage of an mRNA, a uridine tract can be added onto the exposed 3' end of the resulting 5' fragment, which can promote 5' end decay. We now demonstrate that in mammalian cell extract, addition of five uridine residues to the 3' end of an RNA (U5) promotes decapping relative to an RNA lacking the uridines (U0). Although the decapping stimulation observed in extract required hDcp2, recombinant hDcp2 was unable to support differential decapping of the U0 and U5 RNAs, indicating that the stimulation was likely due to an indirect recruitment of hDcp2 to the RNA. Consistent with the promotion of 5' end decapping by the uridine tract, affinity purification with the U5 RNA revealed the presence of a decapping subcomplex at least consisting of hDcp2, Dcp1a, Edc4, LSm1, and LSm4 that were specifically bound to the U5 RNA but not the U0 RNA. In addition to promoting decapping, the U-tract stabilized the 3' end of the RNA by preventing 3' to 5' exonucleolytic decay to ensure 5' end directional degradation. These data suggest that following post-transcriptional oligo uridylation of an mRNA or mRNA fragment, the U-tract has the capacity to specifically stimulate 5' end decapping to expedite mRNA decay.
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Affiliation(s)
- Man-Gen Song
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, New Jersey 08854-8082, USA
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46
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Transcript-specific decapping and regulated stability by the human Dcp2 decapping protein. Mol Cell Biol 2007; 28:939-48. [PMID: 18039849 DOI: 10.1128/mcb.01727-07] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
mRNA decapping is a critical step in the control of mRNA stability and gene expression and is carried out by the Dcp2 decapping enzyme. Dcp2 is an RNA binding protein that must bind RNA in order to recognize the cap for hydrolysis. We demonstrate that human Dcp2 (hDcp2) preferentially binds to a subset of mRNAs and identify sequences at the 5' terminus of the mRNA encoding Rrp41, a core subunit component of the RNA exosome, as a specific hDcp2 substrate. A 60-nucleotide element at the 5' end of Rrp41 mRNA was identified and shown to confer more efficient decapping on a heterologous RNA both in vitro and upon transfection into cells. Moreover, reduction of hDcp2 protein levels in cells resulted in a selective stabilization of the Rrp41 mRNA, confirming it as a downstream target of hDcp2 regulation. These findings demonstrate that hDcp2 can specifically bind to and regulate the stability of a subset of mRNAs, and its intriguing regulation of the 3'-to-5' exonuclease exosome subunit suggests a potential interplay between 5'-end mRNA decapping and 3'-end mRNA decay.
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Chowdhury A, Mukhopadhyay J, Tharun S. The decapping activator Lsm1p-7p-Pat1p complex has the intrinsic ability to distinguish between oligoadenylated and polyadenylated RNAs. RNA (NEW YORK, N.Y.) 2007; 13:998-1016. [PMID: 17513695 PMCID: PMC1894922 DOI: 10.1261/rna.502507] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2007] [Accepted: 04/19/2007] [Indexed: 05/15/2023]
Abstract
Decapping is a critical step in mRNA decay. In the 5'-to-3' mRNA decay pathway conserved in all eukaryotes, decay is initiated by poly(A) shortening, and oligoadenylated mRNAs (but not polyadenylated mRNAs) are selectively decapped allowing their subsequent degradation by 5' to 3' exonucleolysis. The highly conserved heptameric Lsm1p-7p complex (made up of the seven Sm-like proteins, Lsm1p-Lsm7p) and its interacting partner Pat1p activate decapping by an unknown mechanism and localize with other decapping factors to the P-bodies in the cytoplasm. The Lsm1p-7p-Pat1p complex also protects the 3'-ends of mRNAs in vivo from trimming, presumably by binding to the 3'-ends. In order to determine the intrinsic RNA-binding properties of this complex, we have purified it from yeast and carried out in vitro analyses. Our studies revealed that it directly binds RNA at/near the 3'-end. Importantly, it possesses the intrinsic ability to distinguish between oligoadenylated and polyadenylated RNAs such that the former are bound with much higher affinity than the latter. These results indicate that the intrinsic RNA-binding characteristics of this complex form a critical determinant of its in vivo interactions and functions.
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Affiliation(s)
- Ashis Chowdhury
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814-4799, USA
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Morita M, Suzuki T, Nakamura T, Yokoyama K, Miyasaka T, Yamamoto T. Depletion of mammalian CCR4b deadenylase triggers elevation of the p27Kip1 mRNA level and impairs cell growth. Mol Cell Biol 2007; 27:4980-90. [PMID: 17452450 PMCID: PMC1951489 DOI: 10.1128/mcb.02304-06] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The stability of mRNA influences the abundance of cellular transcripts and proteins. Deadenylases play critical roles in mRNA turnover and thus are important for the regulation of various biological events. Here, we report the identification and characterization of CCR4b/CNOT6L, which is homologous to yeast CCR4 mRNA deadenylase. CCR4b is localized mainly in the cytoplasm and displays deadenylase activity both in vitro and in vivo. CCR4b forms a multisubunit complex similar to the yeast CCR4-NOT complex. Suppression of CCR4b by RNA interference results in growth retardation of NIH 3T3 cells accompanied by elevation of both p27(Kip1) mRNA and p27(Kip1) protein. Reintroduction of wild-type CCR4b, but not mutant CCR4b lacking deadenylase activity, restores the growth of CCR4b-depleted NIH 3T3 cells. The data suggest that CCR4b regulates cell growth in a manner dependent on its deadenylase activity. We also show that p27(Kip1) mRNA is stabilized and its poly(A) tail is preserved in CCR4b-depleted cells. Our findings provide evidence that CCR4b deadenylase is a constituent of the mammalian CCR4-NOT complex and regulates the turnover rate of specific target mRNAs. Thus, CCR4b may be involved in various cellular events that include cell proliferation.
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Affiliation(s)
- Masahiro Morita
- Division of Oncology, Department of Cancer Biology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
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Stefanizzi I, Cañete-Soler R. Coregulation of light neurofilament mRNA by poly(A)-binding protein and aldolase C: Implications for neurodegeneration. Brain Res 2007; 1139:15-28. [PMID: 17276415 DOI: 10.1016/j.brainres.2006.12.092] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2006] [Revised: 12/14/2006] [Accepted: 12/31/2006] [Indexed: 11/16/2022]
Abstract
The multifunctional proteins aldolase C and poly (A)-binding protein (PABP) undergo competitive interactions in cells coexpressing aldolase C and NF-L. A specific in vivo interaction between aldolase C and NF-L mRNA had been localized to a 68 nt segment of the transcript spanning the translation termination signal. It is shown here that the poly (A)-binding protein (PABP) binds the body of the NF-L transcript and increases its levels of expression when an excess of PABP is transiently provided in trans. Immunoprecipitation of PABP-associated ribonucleoprotein complexes of human spinal cord pulls down the dimeric form of aldolase C suggesting that their co-regulation of NF-L expression could be linked to the oligomerization status of aldolase C. An ex vivo model of mRNA decay has assessed mechanisms whereby aldolase C and PABP control NF-L expression. This model shows that aldolase C is a zinc-activated ribonuclease that cleaves the transcript at sites closed to the end-terminal structures. Immunological and biochemical depletion of endogenous PABP increases the instability of the transcript suggesting that PABP shields the NF-L mRNA from aldolase attack. An in vitro model shows that a mutant NF-L 68, in which the 45 nt of proximal 3'-UTR is replaced with unrelated sequence, is not degraded by aldolase C. Taken together, the findings might have important consequences for understanding causal mechanisms underlying neurodegeneration.
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Affiliation(s)
- Ida Stefanizzi
- Division of Neuropathology, Department of Pathology and Laboratory Medicine, 608 Stellar Chance, University of Pennsylvania Medical Center, Philadelphia, PA 19104, USA
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