1
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Biziaev N, Shuvalov A, Salman A, Egorova T, Shuvalova E, Alkalaeva E. The impact of mRNA poly(A) tail length on eukaryotic translation stages. Nucleic Acids Res 2024; 52:7792-7808. [PMID: 38874498 PMCID: PMC11260481 DOI: 10.1093/nar/gkae510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 05/08/2024] [Accepted: 06/06/2024] [Indexed: 06/15/2024] Open
Abstract
The poly(A) tail plays an important role in maintaining mRNA stability and influences translation efficiency via binding with PABP. However, the impact of poly(A) tail length on mRNA translation remains incompletely understood. This study explores the effects of poly(A) tail length on human translation. We determined the translation rates in cell lysates using mRNAs with different poly(A) tails. Cap-dependent translation was stimulated by the poly(A) tail, however, it was largely independent of poly(A) tail length, with an exception observed in the case of the 75 nt poly(A) tail. Conversely, cap-independent translation displayed a positive correlation with poly(A) tail length. Examination of translation stages uncovered the dependence of initiation and termination on the presence of the poly(A) tail, but the efficiency of initiation remained unaffected by poly(A) tail extension. Further study unveiled that increased binding of eRFs to the ribosome with the poly(A) tail extension induced more efficient hydrolysis of peptidyl-tRNA. Building upon these findings, we propose a crucial role for the 75 nt poly(A) tail in orchestrating the formation of a double closed-loop mRNA structure within human cells which couples the initiation and termination phases of translation.
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Affiliation(s)
- Nikita Biziaev
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, 119991 Moscow, Russia
| | - Alexey Shuvalov
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, 119991 Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, 119991 Moscow, Russia
| | - Ali Salman
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, 119991 Moscow, Russia
| | - Tatiana Egorova
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, 119991 Moscow, Russia
| | - Ekaterina Shuvalova
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, 119991 Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, 119991 Moscow, Russia
| | - Elena Alkalaeva
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, 119991 Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, 119991 Moscow, Russia
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2
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Perzanowska O, Smietanski M, Jemielity J, Kowalska J. Chemically Modified Poly(A) Analogs Targeting PABP: Structure Activity Relationship and Translation Inhibitory Properties. Chemistry 2022; 28:e202201115. [PMID: 35575378 PMCID: PMC9400960 DOI: 10.1002/chem.202201115] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Indexed: 11/13/2022]
Abstract
Poly(A)‐binding protein (PABP) is an essential element of cellular translational machinery. Recent studies have revealed that poly(A) tail modifications can modulate mRNA stability and translational potential, and that oligoadenylate‐derived PABP ligands can act as effective translational inhibitors with potential applications in pain management. Although extensive research has focused on protein‐RNA and protein‐protein interactions involving PABPs, further studies are required to examine the ligand specificity of PABP. In this study, we developed a microscale thermophoresis‐based assay to probe the interactions between PABP and oligoadenylate analogs containing different chemical modifications. Using this method, we evaluated oligoadenylate analogs modified with nucleobase, ribose, and phosphate moieties to identify modification hotspots. In addition, we determined the susceptibility of the modified oligos to CNOT7 to identify those with the potential for increased cellular stability. Consequently, we selected two enzymatically stable oligoadenylate analogs that inhibit translation in rabbit reticulocyte lysates with a higher potency than a previously reported PABP ligand. We believe that the results presented in this study and the implemented methodology can be capitalized upon in the future development of RNA‐based biological tools.
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Affiliation(s)
- Olga Perzanowska
- Division of Biophysics Faculty of Physics University of Warsaw Ludwika Pasteura 5 02-093 Warsaw Poland
- Centre of New Technologies University of Warsaw Stefana Banacha 2c 02-097 Warsaw Poland
| | - Miroslaw Smietanski
- Centre of New Technologies University of Warsaw Stefana Banacha 2c 02-097 Warsaw Poland
| | - Jacek Jemielity
- Centre of New Technologies University of Warsaw Stefana Banacha 2c 02-097 Warsaw Poland
| | - Joanna Kowalska
- Division of Biophysics Faculty of Physics University of Warsaw Ludwika Pasteura 5 02-093 Warsaw Poland
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3
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ATP-Independent Initiation during Cap-Independent Translation of m 6A-Modified mRNA. Int J Mol Sci 2021; 22:ijms22073662. [PMID: 33915887 PMCID: PMC8036370 DOI: 10.3390/ijms22073662] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 03/21/2021] [Accepted: 03/26/2021] [Indexed: 11/16/2022] Open
Abstract
The methylation of adenosine in the N6 position (m6A) is a widely used modification of eukaryotic mRNAs. Its importance for the regulation of mRNA translation was put forward recently, essentially due to the ability of methylated mRNA to be translated in conditions of inhibited cap-dependent translation initiation, e.g., under stress. However, the peculiarities of translation initiation on m6A-modified mRNAs are not fully known. In this study, we used toeprinting and translation in a cell-free system to confirm that m6A-modified mRNAs can be translated in conditions of suppressed cap-dependent translation. We show for the first time that m6A-modified mRNAs display not only decreased elongation, but also a lower efficiency of translation initiation. Additionally, we report relative resistance of m6A-mRNA translation initiation in the absence of ATP and inhibited eIF4A activity. Our novel findings indicate that the scanning of m6A-modified leader sequences is performed by a noncanonical mechanism.
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4
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Lyabin DN, Smolin EA, Budkina KS, Eliseeva IA, Ovchinnikov LP. Towards the mechanism(s) of YB-3 synthesis regulation by YB-1. RNA Biol 2020; 18:1630-1641. [PMID: 33280507 DOI: 10.1080/15476286.2020.1859243] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
Y-box binding proteins are members of the family of proteins containing the evolutionarily conserved cold shock domain. Their cellular functions are quite diverse, including transcription and translation regulation, participation in pre-mRNA splicing, mRNA stabilization and packaging into mRNPs, involvement in DNA repair, and some others. To date, we know little about the plausible functional interchangeability of Y-box binding proteins. Our previous finding was that in YB-1-null HEK293T cells the synthesis of YB-3 is enhanced, thus enabling YB-3 to interact with a larger set of mRNAs and compensate for the YB-1 absence. We suggested the existence of a mechanism of YB-3 synthesis regulation by its paralog, YB-1. Here we demonstrate that YB-1 participates in the translational control and stabilization of YB-3 mRNA through untranslated regions of YB-3 mRNA.
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Affiliation(s)
- D N Lyabin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia
| | - E A Smolin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia
| | - K S Budkina
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia
| | - I A Eliseeva
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia
| | - L P Ovchinnikov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia
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5
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Lyabin DN, Eliseeva IA, Smolin EA, Doronin AN, Budkina KS, Kulakovskiy IV, Ovchinnikov LP. YB-3 substitutes YB-1 in global mRNA binding. RNA Biol 2020; 17:487-499. [PMID: 31944153 PMCID: PMC7237157 DOI: 10.1080/15476286.2019.1710050] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Y-box binding proteins are DNA- and RNA-binding proteins with an evolutionarily ancient and conserved cold shock domain. The Y-box binding protein 1 (YB-1) is the most studied due to its abundance in somatic cells. YB-1 is involved in a variety of cellular processes, including proliferation, differentiation and stress response. Here, using Ribo-Seq and RIP-Seq we confirm that YB-1 binds a wide range of mRNAs and globally acts as a translation inhibitor. Surprisingly, YBX1 knockout results in only minor alterations in the expression of other genes, mostly caused by changes in RNA abundance. But YB-3 mRNA is an exception: it is better translated in the absence of YB-1, thereby producing an increased amount of YB-3 and thus suggesting that its synthesis is under YB-1 negative control. We have shown that the set of mRNAs bound to YB-3 is strikingly similar to that of YB-1, and that the mRNA-binding by YB-3 is enhanced in the absence of YB-1, resulting in a similar global reduction of translation of bound mRNAs in YB-1-null cells. Thus, YB-3 acts as a substitute for YB-1 in mRNA binding and, probably, in global translational control.
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Affiliation(s)
- D N Lyabin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia
| | - I A Eliseeva
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia
| | - E A Smolin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia
| | - A N Doronin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia.,Department of Bioengineering, BIOCAD, Lyubuchany, Russia.,Faculty of Molecular and Cellular Biotechnology, Pushchino State Institute of Natural Science, Pushchino, Russia
| | - K S Budkina
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia
| | - I V Kulakovskiy
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia.,Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,Institute of Mathematical Problems of Biology RAS - the Branch of Keldysh Institute of Applied Mathematics, Russian Academy of Sciences, Pushchino, Russia
| | - L P Ovchinnikov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia
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6
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Byun JY, Lee KH, Shin YB, Kim DM. Cascading Amplification of Immunoassay Signal by Cell-Free Expression of Firefly Luciferase from Detection Antibody-Conjugated DNA in an Escherichia coli Extract. ACS Sens 2019; 4:93-99. [PMID: 30582797 DOI: 10.1021/acssensors.8b00949] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An expression immunoassay is a powerful technique that combines unique features of immunosorbent assays and cell-free protein synthesis. The main advantage of the expression immunoassay is a greatly amplified signal, whereas a conventional enzyme-linked immunosorbent assay (ELISA) employs a single enzyme molecule conjugated to a detection antibody to produce a measurable signal. Expression immunoassays utilize a DNA molecule conjugated to a target-bound antibody to generate multiple enzyme molecules that then produce the signal. To date, expression immunoassays have not been widely adopted due to the limited availability of efficient methods for translating antibody-conjugated DNA. We developed a highly efficient translation module for expression immunoassays using an Escherichia coli extract-based cell-free protein synthesis system. When we used our immunoassay technique to detect α-fetoprotein, we achieved a limit of detection of 7 fM. Given the outstanding sensitivity that can be obtained with only minimal modifications to the procedure of standard ELISA, we believe that this method will open up new possibilities for widespread application of expression immunoassays to ultrasensitive detection and diagnostics.
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Affiliation(s)
- Ju-Young Byun
- Hazards Monitoring BioNano Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon 34141, Korea
| | - Kyung-Ho Lee
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, Daejeon 34134, Korea
| | - Yong-Beom Shin
- Hazards Monitoring BioNano Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon 34141, Korea
- BioNano Health Guard Research Center (H-GUARD), Daejeon 34141, Korea
| | - Dong-Myung Kim
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, Daejeon 34134, Korea
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7
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Feng Q, Shao S. In vitro reconstitution of translational arrest pathways. Methods 2018; 137:20-36. [DOI: 10.1016/j.ymeth.2017.12.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 12/18/2017] [Accepted: 12/19/2017] [Indexed: 01/17/2023] Open
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8
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Lyabin DN, Nigmatullina LF, Doronin AN, Eliseeva IA, Ovchinnikov LP. Identification of proteins specifically interacting with YB-1 mRNA 3' UTR and the effect of hnRNP Q on YB-1 mRNA translation. BIOCHEMISTRY (MOSCOW) 2014; 78:651-9. [PMID: 23980891 DOI: 10.1134/s0006297913060102] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In this study, proteins specifically interacting with the 3' untranslated region (UTR) of mRNA of the multifunctional Y-box-binding protein 1 (YB-1) were identified. One of these, hnRNP Q, was shown to specifically interact with the regulatory element (RE) in YB-1 mRNA 3' UTR and to inhibit translation of this mRNA. Its binding to the RE was accompanied by displacement from this element of the poly(A)-binding protein (PABP), a positive regulator of YB-1 mRNA translation, and by enhanced binding of the negative YB-1 mRNA translation regulator - YB-1 itself.
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Affiliation(s)
- D N Lyabin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
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9
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Sagar V, Murray KE. The mammalian orthoreovirus bicistronic M3 mRNA initiates translation using a 5' end-dependent, scanning mechanism that does not require interaction of 5'-3' untranslated regions. Virus Res 2014; 183:30-40. [PMID: 24486484 DOI: 10.1016/j.virusres.2014.01.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Revised: 01/15/2014] [Accepted: 01/16/2014] [Indexed: 12/12/2022]
Abstract
Mammalian orthoreovirus mRNAs possess short 5' UTR, lack 3' poly(A) tails, and may lack 5' cap structures at late times post-infection. As such, the mechanisms by which these viral mRNAs recruit ribosomes remain completely unknown. Toward addressing this question, we used bicistronic MRV M3 mRNA to analyze the role of 5' and 3' UTRs during MRV protein synthesis. The 5' UTR was found to be dispensable for translation initiation; however, reducing its length promoted increased downstream initiation. Modifying start site Kozak context altered the ratio of upstream to downstream initiation, whereas mutations in the 3' UTR did not. Moreover, an M3 mRNA lacking a 3' UTR was able to rescue MRV infection to WT levels in an siRNA trans-complementation assay. Together, these data allow us to propose a model in which the MRV M3 mRNA initiates translation using a 5' end-dependent, scanning mechanism that does not require the viral mRNA 3' UTR or 5'-3' UTRs interaction.
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Affiliation(s)
- Vidya Sagar
- Department of Biological Sciences, Florida International University, Miami, FL 33199, United States.
| | - Kenneth E Murray
- Department of Biological Sciences, Florida International University, Miami, FL 33199, United States
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10
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Arima H, Morishita Y, Hagiwara D, Hayashi M, Oiso Y. Endoplasmic reticulum stress in vasopressin neurons of familial diabetes insipidus model mice: aggregate formation and mRNA poly(A) tail shortening. Exp Physiol 2013; 99:66-71. [PMID: 24121282 DOI: 10.1113/expphysiol.2013.072553] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The immunoglobulin heavy chain binding protein (BiP) is an endoplasmic reticulum (ER) chaperone, which binds to newly synthesized secretory and transmembrane proteins to facilitate protein folding. BiP mRNA is expressed in the arginine vasopressin (AVP) neurons in the supraoptic nucleus of wild-type mice even in basal conditions, and the expression levels increase in response to dehydration. These data suggest that AVP neurons are subjected to ER stress. Familial neurohypophysial diabetes insipidus (FNDI) is caused by mutations in the gene locus of AVP. The mutant proteins could accumulate in the ER and possibly increase ER stress in the AVP neurons. We bred mice possessing a mutation causing FNDI, which manifested progressive polyuria, as do the patients with FNDI. Electron microscopic analyses demonstrated that aggregates accumulated in the ER of AVP neurons in FNDI mice. Despite polyuria, which could potentially induce dehydration, AVP mRNA expression was decreased in the supraoptic nucleus, and the AVP mRNA poly(A) tail length was shortened in FNDI mice compared with wild-type mice. Incubation of hypothalamic explants of wild-type mice with ER stressors caused shortening of the poly(A) tail length of AVP mRNA, accompanied by decreases in the expression. These data revealed a mechanism by which ER stress decreases poly(A) tail length of AVP mRNA, and this reduces the load of unfolded proteins that form the aggregates in ER of the AVP neurons in FNDI mice.
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Affiliation(s)
- Hiroshi Arima
- H. Arima: 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan.
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11
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Svitkin YV, Yanagiya A, Karetnikov AE, Alain T, Fabian MR, Khoutorsky A, Perreault S, Topisirovic I, Sonenberg N. Control of translation and miRNA-dependent repression by a novel poly(A) binding protein, hnRNP-Q. PLoS Biol 2013; 11:e1001564. [PMID: 23700384 PMCID: PMC3660254 DOI: 10.1371/journal.pbio.1001564] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Accepted: 04/10/2013] [Indexed: 02/05/2023] Open
Abstract
The heterogeneous nuclear ribonucleoprotein Q2 competitively binds mRNA poly(A) tails to regulate translational and miRNA-related functions of PABP. Translation control often operates via remodeling of messenger ribonucleoprotein particles. The poly(A) binding protein (PABP) simultaneously interacts with the 3′ poly(A) tail of the mRNA and the eukaryotic translation initiation factor 4G (eIF4G) to stimulate translation. PABP also promotes miRNA-dependent deadenylation and translational repression of target mRNAs. We demonstrate that isoform 2 of the mouse heterogeneous nuclear protein Q (hnRNP-Q2/SYNCRIP) binds poly(A) by default when PABP binding is inhibited. In addition, hnRNP-Q2 competes with PABP for binding to poly(A) in vitro. Depleting hnRNP-Q2 from translation extracts stimulates cap-dependent and IRES-mediated translation that is dependent on the PABP/poly(A) complex. Adding recombinant hnRNP-Q2 to the extracts inhibited translation in a poly(A) tail-dependent manner. The displacement of PABP from the poly(A) tail by hnRNP-Q2 impaired the association of eIF4E with the 5′ m7G cap structure of mRNA, resulting in the inhibition of 48S and 80S ribosome initiation complex formation. In mouse fibroblasts, silencing of hnRNP-Q2 stimulated translation. In addition, hnRNP-Q2 impeded let-7a miRNA-mediated deadenylation and repression of target mRNAs, which require PABP. Thus, by competing with PABP, hnRNP-Q2 plays important roles in the regulation of global translation and miRNA-mediated repression of specific mRNAs. The regulation of mRNA translation and stability is of paramount importance for almost every cellular function. In eukaryotes, the poly(A) binding protein (PABP) is a central regulator of both global and mRNA-specific translation. PABP simultaneously interacts with the 3′ poly(A) tail of the mRNA and the eukaryotic translation initiation factor 4G (eIF4G). These interactions circularize the mRNA and stimulate translation. PABP also regulates specific mRNAs by promoting miRNA-dependent deadenylation and translational repression. A key step in understanding PABP's functions is to identify factors that affect its association with the poly(A) tail. Here we show that the cytoplasmic isoform of the mouse heterogeneous nuclear ribonucleoprotein Q (hnRNP-Q2/SYNCRIP), which exhibits binding preference to poly(A), interacts with the poly(A) tail by default when PABP binding is inhibited. In addition, hnRNP-Q2 competes with PABP for binding to the poly(A) tail. Depleting hnRNP-Q2 stimulates translation in cell-free extracts and in cultured cells, in agreement with its function as translational repressor. In addition, hnRNP-Q2 impeded miRNA-mediated deadenylation and repression of target mRNAs, which requires PABP. Thus, competition from hnRNP-Q2 provides a novel mechanism by which multiple functions of PABP are regulated. This regulation could play important roles in various biological processes, such as development, viral infection, and human disease.
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Affiliation(s)
- Yuri V. Svitkin
- Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada
| | - Akiko Yanagiya
- Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada
| | - Alexey E. Karetnikov
- Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada
| | - Tommy Alain
- Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada
| | - Marc R. Fabian
- Lady Davis Institute for Medical Research, Jewish General Hospital, Department of Oncology, McGill University, Montreal, Quebec, Canada
| | - Arkady Khoutorsky
- Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada
| | - Sandra Perreault
- Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada
| | - Ivan Topisirovic
- Lady Davis Institute for Medical Research, Jewish General Hospital, Department of Oncology, McGill University, Montreal, Quebec, Canada
| | - Nahum Sonenberg
- Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada
- * E-mail:
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12
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Lyabin DN, Eliseeva IA, Ovchinnikov LP. YB-1 synthesis is regulated by mTOR signaling pathway. PLoS One 2012; 7:e52527. [PMID: 23285076 PMCID: PMC3527543 DOI: 10.1371/journal.pone.0052527] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Accepted: 11/16/2012] [Indexed: 02/07/2023] Open
Abstract
YB-1 is a eukaryotic protein with numerous intra- and extracellular functions based on its ability to interact with RNA, DNA, and many proteins. In spite of achievements in studying its functions, regulation of YB-1 synthesis in the cell remains poorly understood. In the current study Western and Northern blotting were used to determine the amounts of YB-1 and YB-1 mRNA in rabbit organs and several cell lines. As found, in the majority of studied eukaryotic cells a considerable proportion of YB-1 mRNA was stored in free mRNPs, i.e., was poorly translated. Also, we demonstrated that YB-1 synthesis depended on conditions that determined the rate of cell division. Specific suppression of YB-1 synthesis resulted from inhibition of the mTOR signaling pathway with inhibitor PP242, but not rapamycin. Experiments on reporter constructs showed that dependence of YB-1 mRNA translation on activity of the mTOR signaling pathway was dictated by 5′ untranslated regions of this mRNA, irrelatively of the TOP-like sequences at the beginning of 5′ UTR.
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Affiliation(s)
- Dmitry N. Lyabin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation
| | - Irina A. Eliseeva
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation
| | - Lev P. Ovchinnikov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation
- * E-mail:
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13
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Eliseeva IA, Ovchinnikov LP, Lyabin DN. Specific PABP effect on translation of YB-1 mRNA is neutralized by polyadenylation through a "mini-loop" at 3' UTR. RNA Biol 2012; 9:1473-87. [PMID: 23134843 DOI: 10.4161/rna.22711] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
YB-1 is a multifunctional cold shock domain containing protein that is involved virtually in all DNA- and mRNA-dependent cellular events. Its amount is regulated at the level of both transcription and translation. We showed previously that translation of poly A(-) YB-1 mRNA in vitro is selectively controlled by two proteins, YB-1 and PABP, through their specific and competitive binding to a regulatory element (RE) within 3' UTR of this mRNA. Here, we describe effects of these two proteins on translation of poly A(+) as compared with poly A(-) YB-1 mRNA in a rabbit reticulocyte cell-free translation system. We have found that YB-1 inhibits translation of both poly A(+) and poly A(-) YB-1 mRNAs at the same comparatively low YB-1/mRNA ratio. PABP has no positive effect on translation of poly A(+) YB-1 mRNA, although it has a stimulating effect on translation of poly A(-) YB-1 mRNA. A positive PABP effect on translation of poly A(+) YB-1 mRNA arose after removal of a portion of the sequence between RE and the poly(A) tail and disappeared after its replacement by another non-specific sequence of the same length. We also report that the RE fragment forms a complex with the poly(A) fragment in the presence of rabbit reticulocyte lysate (RRL) proteins. For its formation PABP is necessary but not sufficient. These results are in agreement with the proposed model implying formation of a mini-loop at 3' UTR of YB-1 mRNA that includes RE, RRL proteins and the poly(A) tail.
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Affiliation(s)
- Irina A Eliseeva
- Institute of Protein Research; Russian Academy of Sciences; Pushchino, Moscow Region, Russian Federation
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14
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Morishita Y, Arima H, Hiroi M, Hayashi M, Hagiwara D, Asai N, Ozaki N, Sugimura Y, Nagasaki H, Shiota A, Takahashi M, Oiso Y. Poly(A) tail length of neurohypophysial hormones is shortened under endoplasmic reticulum stress. Endocrinology 2011; 152:4846-55. [PMID: 21971157 DOI: 10.1210/en.2011-1415] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Familial neurohypophysial diabetes insipidus (FNDI) is caused by mutations in the gene locus of arginine vasopressin (AVP), an antidiuretic hormone. Although the carriers are normal at birth, polyuria and polydipsia appear several months or years later. Previously, we made mice possessing a mutation causing FNDI and reported that the mice manifested progressive polyuria as do the patients with FNDI. Here, we report that decreases in AVP mRNA expression in the supraoptic nucleus were accompanied by shortening of the AVP mRNA poly(A) tail length in the FNDI mice, a case in which aggregates accumulated in the endoplasmic reticulum (ER) of the hypothalamic AVP neurons. Expression levels of AVP heteronuclear RNA in the supraoptic nucleus, a sensitive indicator for gene transcription, were not significantly different between FNDI and wild-type mice. Incubation of hypothalamic explants of wild-type mice with ER stressors (thapsigargin and tunicamycin) caused shortening of the poly(A) tail length of AVP and oxytocin mRNA, accompanied by decreases in their expression. On the other hand, an ER stress-reducing molecule (tauroursodeoxycholate) increased the poly(A) tail length as well as the expression levels of AVP and oxytocin mRNA. These data reveal a novel mechanism by which ER stress decreases poly(A) tail length of neurohypophysial hormones, probably to reduce the load of unfolded proteins.
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Affiliation(s)
- Yoshiaki Morishita
- Department of Endocrinology and Diabetes, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
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15
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General RNA-binding proteins have a function in poly(A)-binding protein-dependent translation. EMBO J 2008; 28:58-68. [PMID: 19078965 DOI: 10.1038/emboj.2008.259] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2008] [Accepted: 11/12/2008] [Indexed: 12/29/2022] Open
Abstract
The interaction between the poly(A)-binding protein (PABP) and eukaryotic translational initiation factor 4G (eIF4G), which brings about circularization of the mRNA, stimulates translation. General RNA-binding proteins affect translation, but their role in mRNA circularization has not been studied before. Here, we demonstrate that the major mRNA ribonucleoprotein YB-1 has a pivotal function in the regulation of eIF4F activity by PABP. In cell extracts, the addition of YB-1 exacerbated the inhibition of 80S ribosome initiation complex formation by PABP depletion. Rabbit reticulocyte lysate in which PABP weakly stimulates translation is rendered PABP-dependent after the addition of YB-1. In this system, eIF4E binding to the cap structure is inhibited by YB-1 and stimulated by a nonspecific RNA. Significantly, adding PABP back to the depleted lysate stimulated eIF4E binding to the cap structure more potently if this binding had been downregulated by YB-1. Conversely, adding nonspecific RNA abrogated PABP stimulation of eIF4E binding. These data strongly suggest that competition between YB-1 and eIF4G for mRNA binding is required for efficient stimulation of eIF4F activity by PABP.
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16
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Tanaka H, Mielke SP, Benham CJ, Kawai T. Visualization of the Detailed Structure of Plasmid DNA. J Phys Chem B 2008; 112:16788-92. [DOI: 10.1021/jp804634s] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hiroyuki Tanaka
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan, and UC Davis Genome Center, University of California, One Shields Avenue, Davis, California 95616
| | - Steven P. Mielke
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan, and UC Davis Genome Center, University of California, One Shields Avenue, Davis, California 95616
| | - Craig J. Benham
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan, and UC Davis Genome Center, University of California, One Shields Avenue, Davis, California 95616
| | - Tomoji Kawai
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan, and UC Davis Genome Center, University of California, One Shields Avenue, Davis, California 95616
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17
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Alekhina OM, Vassilenko KS, Spirin AS. Translation of non-capped mRNAs in a eukaryotic cell-free system: acceleration of initiation rate in the course of polysome formation. Nucleic Acids Res 2007; 35:6547-59. [PMID: 17897963 PMCID: PMC2095793 DOI: 10.1093/nar/gkm725] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2007] [Revised: 08/28/2007] [Accepted: 08/31/2007] [Indexed: 11/14/2022] Open
Abstract
Real-time monitoring of the translation of non-capped luciferase mRNA in a wheat germ cell-free system has been performed by continuous in situ measurement of the luminescence increase in the translation mixture. The phenomenon of acceleration of translation has been revealed. It has been shown that the acceleration is accompanied by the loading of translating polysomes with additional ribosomes, and thus is caused mainly by a rise in the initiation rate, rather than the stimulation of elongation or the involvement of additional mRNA molecules in translation. The acceleration requires a sufficient concentration of mRNA and depends on the sequence of the 5' untranslated region (UTR). It can be abolished by the addition of excess cap analog (m(7)GpppGm). As the acceleration does not depend on the preliminary translation of other mRNAs in the same extract, the conclusion has been made that the effect is not due to activation of the ribosome population or other components of the system during translation, but rather it is the consequence of intra-polysomal events. The acceleration observed is discussed in terms of the model of two overlapping initiation pathways in eukaryotic polysomes: translation of non-capped mRNAs starts with eIF4F-independent initiation at 5' UTR, and after the formation of sufficiently loaded polysomes, they rearrange in such a way that a mechanism of re-initiation of terminating ribosomes switches on. The eIF4F-mediated circularization of polysomes may be considered as a possible event that leads to the re-initiation switch and the resultant acceleration effect.
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Affiliation(s)
| | | | - Alexander S. Spirin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
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18
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Hino M, Kataoka M, Kajimoto K, Yamamoto T, Kido JI, Shinohara Y, Baba Y. Efficiency of cell-free protein synthesis based on a crude cell extract from Escherichia coli, wheat germ, and rabbit reticulocytes. J Biotechnol 2007; 133:183-9. [PMID: 17826860 DOI: 10.1016/j.jbiotec.2007.08.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2007] [Revised: 07/05/2007] [Accepted: 08/01/2007] [Indexed: 11/18/2022]
Abstract
The efficiency of protein synthesis for glyceraldehyde-3-phosphate dehydrogenase (G3PDH) was examined with several in vitro coupled transcription/translation protein synthesis systems based on Escherichia coli lysate, wheat germ, or reticulocyte lysate, and an in vitro translation system based on wheat germ extract. A significant amount of protein synthesis was observed only in systems based on E. coli using pET/G3PDH as the expression vector. A remarkable increase of protein synthesis was obtained in wheat germ using a pT(N)T expression vector which contains a 5'-globin leader sequence and a synthetic poly(A)(30) tail instead of pET. A significant difference of T7 RNA polymerase presence by Western blot analysis was not observed in the first four systems, and the difference of total RNA presence in each reaction mixture by Northern blot analysis seemed unrelated to protein synthesis. Although a small amount of protein was synthesized using RNA-encoding G3PDH transcribed in vitro with pET/G3PDH by an in vitro translation system, an extreme increase was observed using transcribed RNA with pEU/G3PDH, which contains T7 RNA promoter and a translation enhancer, Omega sequence. These results suggest that the presence of an enhancer sequence for translation is one of the critical steps for protein synthesis by a eukaryotic cell-free protein synthesis system.
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Affiliation(s)
- Mami Hino
- Biomarker Analysis Team, Health Technology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Takamatsu, Japan
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19
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Svitkin YV, Sonenberg N. Translational control by the poly(A) binding protein: A check for mRNA integrity. Mol Biol 2006. [DOI: 10.1134/s0026893306040133] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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20
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Mockey M, Gonçalves C, Dupuy FP, Lemoine FM, Pichon C, Midoux P. mRNA transfection of dendritic cells: synergistic effect of ARCA mRNA capping with Poly(A) chains in cis and in trans for a high protein expression level. Biochem Biophys Res Commun 2005; 340:1062-8. [PMID: 16403444 DOI: 10.1016/j.bbrc.2005.12.105] [Citation(s) in RCA: 118] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2005] [Accepted: 12/16/2005] [Indexed: 11/26/2022]
Abstract
The occurrence of translation mechanism in the cytosol offers advantages to mRNA transfer over DNA-based transfection in non-dividing cells. Here, we sought to optimize mRNA constructs allowing a high level of protein upon lipofection. We found that luciferase into mouse dendritic cells (JAWSII cells) was approximately 20-fold higher when the luciferase mRNA was capped with 3'-O-methyl-m7(5')Gppp5'G (anti-reverse cap analogue; ARCA) than with m7(5')Gppp5'G (CAP). Adding a Poly(A) tail of 100 instead of 64 adenosines in cis increased by approximately 35-fold more the protein level. Finally, ARCA-Luc-mRNA-A100 construct was 700-fold better efficient than the CAP-Luc-mRNA-A64 one. Moreover, co-transfection with free Poly(A) chains in trans enhanced by 100% the luciferase level. The efficiency of ARCA-mRNA-A100 construct was validated in immature and mature human CD34-derived dendritic cells. Such mRNA construct was also successful to obtain high level of MART-1 tumor antigen.
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Affiliation(s)
- Michael Mockey
- Centre de Biophysique Moléculaire, UPR4301 CNRS, affiliated to the University of Orléans and INSERM, rue Charles Sadron, 45071 Orléans cedex 2, France
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21
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Skabkina OV, Lyabin DN, Skabkin MA, Ovchinnikov LP. YB-1 autoregulates translation of its own mRNA at or prior to the step of 40S ribosomal subunit joining. Mol Cell Biol 2005; 25:3317-23. [PMID: 15798215 PMCID: PMC1069629 DOI: 10.1128/mcb.25.8.3317-3323.2005] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
YB-1 is a member of the numerous families of proteins with an evolutionary ancient cold-shock domain. It is involved in many DNA- and RNA-dependent events and regulates gene expression at different levels. Previously, we found a regulatory element within the 3' untranslated region (UTR) of YB-1 mRNA that specifically interacted with YB-1 and poly(A)-binding protein (PABP); we also showed that PABP positively affected YB-1 mRNA translation in a poly(A) tail-independent manner (O. V. Skabkina, M. A. Skabkin, N. V. Popova, D. N. Lyabin, L. O. Penalva, and L. P. Ovchinnikov, J. Biol. Chem. 278:18191-18198, 2003). Here, YB-1 is shown to strongly and specifically inhibit its own synthesis at the stage of initiation, with accumulation of its mRNA in the form of free mRNPs. YB-1 and PABP binding sites have been mapped on the YB-1 mRNA regulatory element. These were UCCAG/ACAA for YB-1 and a approximately 50-nucleotide A-rich sequence for PABP that overlapped each other. PABP competes with YB-1 for binding to the YB-1 mRNA regulatory element and restores translational activity of YB-1 mRNA that has been inhibited by YB-1. Thus, YB-1 negatively regulates its own synthesis, presumably by specific interaction with the 3'UTR regulatory element, whereas PABP restores translational activity of YB-1 mRNA by displacing YB-1 from this element.
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Affiliation(s)
- Olga V Skabkina
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290 Russia
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22
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Skabkina OV, Skabkin MA, Popova NV, Lyabin DN, Penalva LO, Ovchinnikov LP. Poly(A)-binding protein positively affects YB-1 mRNA translation through specific interaction with YB-1 mRNA. J Biol Chem 2003; 278:18191-8. [PMID: 12646583 DOI: 10.1074/jbc.m209073200] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The major protein of cytoplasmic mRNPs from rabbit reticulocytes, YB-1, is a member of an ancient family of proteins containing a common structural feature, cold-shock domain. In eukaryotes, this family is represented by multifunctional mRNA/Y-box DNA-binding proteins that control gene expression at different stages. To address possible post-transcriptional regulation of YB-1 gene expression, we examined effects of exogenous 5'- and 3'-untranslatable region-containing fragments of YB-1 mRNA on its translation and stability in a cell-free system. The addition of the 3' mRNA fragment as well as its subfragment I shut off protein synthesis at the initiation stage without affecting mRNA stability. UV cross-linking revealed four proteins (69, 50, 46, and 44 kDa) that specifically interacted with the 3' mRNA fragment; the inhibitory subfragment I bound two of them, 69- and 50-kDa proteins. We have identified these proteins as PABP (poly(A)-binding protein) (69 kDa) and YB-1 (50 kDa) and demonstrated that titrating out of PABP by poly(A) strongly and specifically inhibits YB-1 mRNA cap(+)poly(A)(-) translation in a cell-free system. Thus, PABP is capable of positively affecting YB-1 mRNA translation in a poly(A) tail-independent manner.
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Affiliation(s)
- Olga V Skabkina
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russian Federation
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23
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Wakiyama M, Suzuki A, Saigoh M, Sakai N, Miyoshi H, Kojima S, Miura K. Analysis of the isoform of Xenopus euakryotic translation initiation factor 4E. Biosci Biotechnol Biochem 2001; 65:232-5. [PMID: 11272840 DOI: 10.1271/bbb.65.232] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We have found two isoforms of the eukaryotic translation initiation factor 4E (eIF4E) in Xenopus laevis. These proteins differ in length by 18 amino acids. Overexpression of either of the two eIF4E proteins modestly increase translation in Xenopus oocytes. The results suggest that both of these two isoforms function in translation.
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Affiliation(s)
- M Wakiyama
- Institute for Biomolecular Science, Gakushuin University, Tokyo, Japan
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24
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Edelmann A, Kirchberger J, Naumann M, Kopperschläger G. Generation of catalytically active 6-phosphofructokinase from Saccharomyces cerevisiae in a cell-free system. EUROPEAN JOURNAL OF BIOCHEMISTRY 2000; 267:4825-30. [PMID: 10903517 DOI: 10.1046/j.1432-1327.2000.01540.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
PFK1 and PFK2 coding for the subunits of 6-phosphofructokinase from Saccharomyces cerevisiae were cloned into plasmids suitable for runoff transcription. In vitro translation products of both kinds of subunit were obtained using rabbit reticulocyte lysate as the synthesis and folding system. They were monitored by chemiluminescent Western-blot analysis. Folding and assembly of the alpha-subunit and beta-subunit of 6-phosphofructokinase were found to occur in the cell-free system resulting in an enzymatically active protein. The in vitro generated enzyme exhibits a folding state that is similar to that of the heterooctameric form of 6-phosphofructokinase in the presence of fructose 6-phosphate, ATP and ammonium sulfate, as demonstrated by size-exclusion HPLC followed by ELISA.
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Affiliation(s)
- A Edelmann
- Institut für Biochemie der Medizinischen Fakultät, Universität Leipzig, Germany.
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25
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Kuraishi T, Sun Y, Aoki F, Imakawa K, Sakai S. The poly(A) tail length of casein mRNA in the lactating mammary gland changes depending upon the accumulation and removal of milk. Biochem J 2000; 347:579-83. [PMID: 10749689 PMCID: PMC1220992 DOI: 10.1042/0264-6021:3470579] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The length of casein mRNA from the lactating mouse mammary gland, as assessed on Northern blots, is shorter after weaning, but is elongated following the removal of milk. In order to investigate this phenomenon, the molecular structures of beta- and gamma-casein mRNAs were analysed. The coding and non-coding regions of the two forms were the same length, but the long form of casein mRNA had a longer poly(A) tail than the short form (P<0.05). In order to examine the stability of casein mRNA under identical conditions, casein mRNAs with the long and short poly(A) tails were incubated in the rabbit reticulocyte lysate (RRL) cell-free translation system. Casein mRNA with the long poly(A) tail had a longer half-life than that with the short tail (P<0.05). The beta- and gamma-casein mRNAs were first degraded into 0.92 and 0.81 kb fragments respectively. With undegraded mRNA, the poly(A) tail shortening by exoribonuclease was not observed until the end of the incubation. Northern blot analysis showed that casein mRNA with the long poly(A) tail was protected efficiently from endoribonucleases. We conclude that the length of the poly(A) tail of casein mRNA in the lactating mammary gland changes depending upon the accumulation and removal of the gland's milk, and we show that the longer poly(A) tail potentially protects the mRNA from degradation by endoribonucleases.
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Affiliation(s)
- T Kuraishi
- Department of Animal Breeding, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
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