1
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Chen R, Glauninger H, Kahan DN, Shangguan J, Sachleben JR, Riback JA, Drummond DA, Sosnick TR. HDX-MS finds that partial unfolding with sequential domain activation controls condensation of a cellular stress marker. Proc Natl Acad Sci U S A 2024; 121:e2321606121. [PMID: 38513106 PMCID: PMC10990091 DOI: 10.1073/pnas.2321606121] [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: 12/12/2023] [Accepted: 01/29/2024] [Indexed: 03/23/2024] Open
Abstract
Eukaryotic cells form condensates to sense and adapt to their environment [S. F. Banani, H. O. Lee, A. A. Hyman, M. K. Rosen, Nat. Rev. Mol. Cell Biol. 18, 285-298 (2017), H. Yoo, C. Triandafillou, D. A. Drummond, J. Biol. Chem. 294, 7151-7159 (2019)]. Poly(A)-binding protein (Pab1), a canonical stress granule marker, condenses upon heat shock or starvation, promoting adaptation [J. A. Riback et al., Cell 168, 1028-1040.e19 (2017)]. The molecular basis of condensation has remained elusive due to a dearth of techniques to probe structure directly in condensates. We apply hydrogen-deuterium exchange/mass spectrometry to investigate the mechanism of Pab1's condensation. Pab1's four RNA recognition motifs (RRMs) undergo different levels of partial unfolding upon condensation, and the changes are similar for thermal and pH stresses. Although structural heterogeneity is observed, the ability of MS to describe populations allows us to identify which regions contribute to the condensate's interaction network. Our data yield a picture of Pab1's stress-triggered condensation, which we term sequential activation (Fig. 1A), wherein each RRM becomes activated at a temperature where it partially unfolds and associates with other likewise activated RRMs to form the condensate. Subsequent association is dictated more by the underlying free energy surface than specific interactions, an effect we refer to as thermodynamic specificity. Our study represents an advance for elucidating the interactions that drive condensation. Furthermore, our findings demonstrate how condensation can use thermodynamic specificity to perform an acute response to multiple stresses, a potentially general mechanism for stress-responsive proteins.
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Affiliation(s)
- Ruofan Chen
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL60637
| | - Hendrik Glauninger
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL60637
- Graduate Program in Biophysical Sciences, Division of Physical Sciences, University of Chicago, Chicago, IL60637
| | - Darren N. Kahan
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL60637
| | - Julia Shangguan
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL60637
| | | | - Joshua A. Riback
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL60637
- Graduate Program in Biophysical Sciences, Division of Physical Sciences, University of Chicago, Chicago, IL60637
| | - D. Allan Drummond
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL60637
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL60637
| | - Tobin R. Sosnick
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL60637
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL60637
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL60637
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2
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Roles of mRNA poly(A) tails in regulation of eukaryotic gene expression. Nat Rev Mol Cell Biol 2022; 23:93-106. [PMID: 34594027 PMCID: PMC7614307 DOI: 10.1038/s41580-021-00417-y] [Citation(s) in RCA: 186] [Impact Index Per Article: 93.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/16/2021] [Indexed: 02/06/2023]
Abstract
In eukaryotes, poly(A) tails are present on almost every mRNA. Early experiments led to the hypothesis that poly(A) tails and the cytoplasmic polyadenylate-binding protein (PABPC) promote translation and prevent mRNA degradation, but the details remained unclear. More recent data suggest that the role of poly(A) tails is much more complex: poly(A)-binding protein can stimulate poly(A) tail removal (deadenylation) and the poly(A) tails of stable, highly translated mRNAs at steady state are much shorter than expected. Furthermore, the rate of translation elongation affects deadenylation. Consequently, the interplay between poly(A) tails, PABPC, translation and mRNA decay has a major role in gene regulation. In this Review, we discuss recent work that is revolutionizing our understanding of the roles of poly(A) tails in the cytoplasm. Specifically, we discuss the roles of poly(A) tails in translation and control of mRNA stability and how poly(A) tails are removed by exonucleases (deadenylases), including CCR4-NOT and PAN2-PAN3. We also discuss how deadenylation rate is determined, the integration of deadenylation with other cellular processes and the function of PABPC. We conclude with an outlook for the future of research in this field.
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3
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Eliseeva IA, Sogorina EM, Smolin EA, Kulakovskiy IV, Lyabin DN. Diverse Regulation of YB-1 and YB-3 Abundance in Mammals. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:S48-S167. [PMID: 35501986 DOI: 10.1134/s000629792214005x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/13/2021] [Accepted: 09/17/2021] [Indexed: 06/14/2023]
Abstract
YB proteins are DNA/RNA binding proteins, members of the family of proteins with cold shock domain. Role of YB proteins in the life of cells, tissues, and whole organisms is extremely important. They are involved in transcription regulation, pre-mRNA splicing, mRNA translation and stability, mRNA packaging into mRNPs, including stress granules, DNA repair, and many other cellular events. Many processes, from embryonic development to aging, depend on when and how much of these proteins have been synthesized. Here we discuss regulation of the levels of YB-1 and, in part, of its homologs in the cell. Because the amount of YB-1 is immediately associated with its functioning, understanding the mechanisms of regulation of the protein amount invariably reveals the events where YB-1 is involved. Control over the YB-1 abundance may allow using this gene/protein as a therapeutic target in cancers, where an increased expression of the YBX1 gene often correlates with the disease severity and poor prognosis.
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Affiliation(s)
- Irina A Eliseeva
- Institute of Protein Research, Pushchino, Moscow Region, 142290, Russia.
| | | | - Egor A Smolin
- Institute of Protein Research, Pushchino, Moscow Region, 142290, Russia.
| | - Ivan V Kulakovskiy
- Institute of Protein Research, Pushchino, Moscow Region, 142290, Russia.
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Moscow, 119991, Russia
| | - Dmitry N Lyabin
- Institute of Protein Research, Pushchino, Moscow Region, 142290, Russia.
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4
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Guo AX, Cui JJ, Wang LY, Yin JY. The role of CSDE1 in translational reprogramming and human diseases. Cell Commun Signal 2020; 18:14. [PMID: 31987048 PMCID: PMC6986143 DOI: 10.1186/s12964-019-0496-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 12/16/2019] [Indexed: 02/06/2023] Open
Abstract
Abstract CSDE1 (cold shock domain containing E1) plays a key role in translational reprogramming, which determines the fate of a number of RNAs during biological processes. Interestingly, the role of CSDE1 is bidirectional. It not only promotes and represses the translation of RNAs but also increases and decreases the abundance of RNAs. However, the mechanisms underlying this phenomenon are still unknown. In this review, we propose a “protein-RNA connector” model to explain this bidirectional role and depict its three versions: sequential connection, mutual connection and facilitating connection. As described in this molecular model, CSDE1 binds to RNAs and cooperates with other protein regulators. CSDE1 connects with different RNAs and their regulators for different purposes. The triple complex of CSDE1, a regulator and an RNA reprograms translation in different directions for each transcript. Meanwhile, a number of recent studies have found important roles for CSDE1 in human diseases. This model will help us to understand the role of CSDE1 in translational reprogramming and human diseases. Video Abstract
Graphical abstract ![]()
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Affiliation(s)
- Ao-Xiang Guo
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410078, People's Republic of China.,Institute of Clinical Pharmacology, Central South University; Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078, People's Republic of China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, People's Republic of China.,National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, People's Republic of China
| | - Jia-Jia Cui
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410078, People's Republic of China.,Institute of Clinical Pharmacology, Central South University; Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078, People's Republic of China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, People's Republic of China.,National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, People's Republic of China
| | - Lei-Yun Wang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410078, People's Republic of China.,Institute of Clinical Pharmacology, Central South University; Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078, People's Republic of China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, People's Republic of China.,National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, People's Republic of China
| | - Ji-Ye Yin
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410078, People's Republic of China. .,Institute of Clinical Pharmacology, Central South University; Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078, People's Republic of China. .,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, People's Republic of China. .,National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, People's Republic of China. .,Hunan Provincial Gynecological Cancer Diagnosis and Treatment Engineering Research Center, Changsha, 410078, People's Republic of China. .,Hunan Key Laboratory of Precise Diagnosis and Treatment of Gastrointestinal Tumor, Changsha, 410078, People's Republic of China.
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5
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Wang L, Romano MC, Davidson FA. Translational control of gene expression via interacting feedback loops. Phys Rev E 2019; 100:050402. [PMID: 31869996 DOI: 10.1103/physreve.100.050402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Indexed: 11/07/2022]
Abstract
Translation is a key step in the synthesis of proteins. Accordingly, cells have evolved an intricate array of control mechanisms to regulate this process. By constructing a multicomponent mathematical framework we uncover how translation may be controlled via interacting feedback loops. Our results reveal that this interplay gives rise to a remarkable range of protein synthesis dynamics, including oscillations, step change, and bistability. This suggests that cells may have recourse to a much richer set of control mechanisms than was previously understood.
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Affiliation(s)
- Liang Wang
- Division of Mathematics, School of Science and Engineering, University of Dundee, Dundee DD1 4HN, United Kingdom
| | - M Carmen Romano
- SUPA, Institute for Complex Systems and Mathematical Biology, Department of Physics, Aberdeen AB24 3UE, United Kingdom and Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB24 3FX, United Kingdom
| | - Fordyce A Davidson
- Division of Mathematics, School of Science and Engineering, University of Dundee, Dundee DD1 4HN, United Kingdom
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6
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Smirnova VV, Shestakova ED, Bikmetov DV, Chugunova AA, Osterman IA, Serebryakova MV, Sergeeva OV, Zatsepin TS, Shatsky IN, Terenin IM. eIF4G2 balances its own mRNA translation via a PCBP2-based feedback loop. RNA (NEW YORK, N.Y.) 2019; 25:757-767. [PMID: 31010886 PMCID: PMC6573783 DOI: 10.1261/rna.065623.118] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 03/18/2019] [Indexed: 06/09/2023]
Abstract
Poly(rC)-binding protein 2 (PCBP2, hnRNP E2) is one of the most abundant RNA-binding proteins in mammalian cells. In humans, it exists in seven isoforms, which are assumed to play similar roles in cells. The protein is shown to bind 3'-untranslated regions (3'-UTRs) of many mRNAs and regulate their translation and/or stability, but nothing is known about the functional consequences of PCBP2 binding to 5'-UTRs. Here we show that the PCBP2 isoform f interacts with the 5'-UTRs of mRNAs encoding eIF4G2 (a translation initiation factor with a yet unknown mechanism of action, also known as DAP5) and Cyclin I, and inhibits their translation in vitro and in cultured cells, while the PCBP2 isoform e only affects Cyclin I translation. Furthermore, eIF4G2 participates in a cap-dependent translation of the PCBP2 mRNA. Thus, PCBP2 and eIF4G2 seem to regulate one another's expression via a novel type of feedback loop formed by the translation initiation factor and the RNA-binding protein.
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Affiliation(s)
- Victoria V Smirnova
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskie Gory, 119234 Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, Moscow 119992, Russia
| | - Ekaterina D Shestakova
- Department of Biochemistry, School of Biology, Lomonosov Moscow State University, Leninskie Gory, Moscow, 119234, Russian Federation
| | - Dmitry V Bikmetov
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskie Gory, 119234 Moscow, Russia
| | - Anastasia A Chugunova
- Chemistry Department, Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow Region 143026, Russia
| | - Ilya A Osterman
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, Moscow 119992, Russia
- Chemistry Department, Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow Region 143026, Russia
| | - Marina V Serebryakova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, Moscow 119992, Russia
| | - Olga V Sergeeva
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow Region 143026, Russia
| | - Timofey S Zatsepin
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow Region 143026, Russia
| | - Ivan N Shatsky
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, Moscow 119992, Russia
| | - Ilya M Terenin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, Moscow 119992, Russia
- Sechenov First Moscow State Medical University, Institute of Molecular Medicine, 119991, Moscow, Russian Federation
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7
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Xia X. Translation Control of HAC1 by Regulation of Splicing in Saccharomyces cerevisiae. Int J Mol Sci 2019; 20:ijms20122860. [PMID: 31212749 PMCID: PMC6627864 DOI: 10.3390/ijms20122860] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 05/30/2019] [Accepted: 06/10/2019] [Indexed: 12/19/2022] Open
Abstract
Hac1p is a key transcription factor regulating the unfolded protein response (UPR) induced by abnormal accumulation of unfolded/misfolded proteins in the endoplasmic reticulum (ER) in Saccharomyces cerevisiae. The accumulation of unfolded/misfolded proteins is sensed by protein Ire1p, which then undergoes trans-autophosphorylation and oligomerization into discrete foci on the ER membrane. HAC1 pre-mRNA, which is exported to the cytoplasm but is blocked from translation by its intron sequence looping back to its 5’UTR to form base-pair interaction, is transported to the Ire1p foci to be spliced, guided by a cis-acting bipartite element at its 3’UTR (3’BE). Spliced HAC1 mRNA can be efficiently translated. The resulting Hac1p enters the nucleus and activates, together with coactivators, a large number of genes encoding proteins such as protein chaperones to restore and maintain ER homeostasis and secretary protein quality control. This review details the translation regulation of Hac1p production, mediated by the nonconventional splicing, in the broad context of translation control and summarizes the evolution and diversification of the UPR signaling pathway among fungal, metazoan and plant lineages.
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Affiliation(s)
- Xuhua Xia
- Department of Biology, University of Ottawa, Marie-Curie Private, Ottawa, ON K1N 9A7, Canada.
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8
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Gilbertson S, Federspiel JD, Hartenian E, Cristea IM, Glaunsinger B. Changes in mRNA abundance drive shuttling of RNA binding proteins, linking cytoplasmic RNA degradation to transcription. eLife 2018; 7:37663. [PMID: 30281021 PMCID: PMC6203436 DOI: 10.7554/elife.37663] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 09/28/2018] [Indexed: 12/21/2022] Open
Abstract
Alterations in global mRNA decay broadly impact multiple stages of gene expression, although signals that connect these processes are incompletely defined. Here, we used tandem mass tag labeling coupled with mass spectrometry to reveal that changing the mRNA decay landscape, as frequently occurs during viral infection, results in subcellular redistribution of RNA binding proteins (RBPs) in human cells. Accelerating Xrn1-dependent mRNA decay through expression of a gammaherpesviral endonuclease drove nuclear translocation of many RBPs, including poly(A) tail-associated proteins. Conversely, cells lacking Xrn1 exhibited changes in the localization or abundance of numerous factors linked to mRNA turnover. Using these data, we uncovered a new role for relocalized cytoplasmic poly(A) binding protein in repressing recruitment of TATA binding protein and RNA polymerase II to promoters. Collectively, our results show that changes in cytoplasmic mRNA decay can directly impact protein localization, providing a mechanism to connect seemingly distal stages of gene expression. The nucleus of a cell harbors DNA, which contains all information needed to build an organism. The instructions are stored as a genetic code that serves as a blueprint for making proteins – molecules that are important for almost every process in the body – and to assemble cells. But first, the code on the DNA needs to be translated with the help of a ‘middle man’, known as messenger RNA. These molecules carry information to other parts of the cell, wherever it is needed. Messenger RNA is produced in the nucleus of a cell, and then exported into the material within a cell, called the cytoplasm, as a template to produce proteins. Once this process has finished, the template is destroyed. The rate at which the messenger RNA is made affects the flow of genetic information. However, recent evidence suggests that the speed at which messenger RNA is destroyed in the cytoplasm can influence how much of it is made in the nucleus, i.e., if high levels of RNA are destroyed, the production is stopped. For example, it has been shown that certain viruses possess proteins that speed up the destruction of messenger RNA to gain control over the host cell. Here, Gilbertson et al. wanted to find out more about how the breakdown of RNA can signal the nucleus to stop producing these molecules. Messenger RNAs are coated with proteins, which are released when the RNA is destroyed. To test if some of those proteins travel back to the nucleus to influence the production of messenger RNA, proteins in human cells grown in the laboratory were labeled with specific trackers. RNA destruction was induced, in a way that is similar to what happens during a virus attack. The experiments revealed that many RNA-binding proteins indeed return to the nucleus when RNA is destroyed. One of these proteins, named cytoplasmic poly(A)-binding protein, played a key role in transmitting the signal between the cytoplasm and the nucleus to control the production messenger RNA. The amount of messenger RNA can change in many ways throughout the life of a cell. For example, viral infections can lower it and limit the growth and health of cells. A drop in these molecules could act as an early warning of ill health in cells and trigger responses in the nucleus. This new link between messenger RNA destruction and production may help to shed new light on how cells use different signals to control the production of their own genes while restricting pathogens from taking over. A next step will be to determine how these signals communicate with the RNA production machinery in the nucleus and how certain viruses can subvert this process to activate their own genes.
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Affiliation(s)
- Sarah Gilbertson
- Department of Molecular and Cell Biology, University of California, Berkeley, United States
| | - Joel D Federspiel
- Department of Molecular Biology, Princeton University, Princeton, United States
| | - Ella Hartenian
- Department of Molecular and Cell Biology, University of California, Berkeley, United States
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Princeton, United States
| | - Britt Glaunsinger
- Department of Molecular and Cell Biology, University of California, Berkeley, United States.,Department of Plant & Microbial Biology, University of California, Berkeley, United States.,Howard Hughes Medical Institute, United States
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9
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Ozturk S, Uysal F. Poly(A)-binding proteins are required for translational regulation in vertebrate oocytes and early embryos. Reprod Fertil Dev 2018; 29:1890-1901. [PMID: 28103468 DOI: 10.1071/rd16283] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 12/01/2016] [Indexed: 12/22/2022] Open
Abstract
Poly(A)-binding proteins (PABPs) function in the timely regulation of gene expression during oocyte maturation, fertilisation and early embryo development in vertebrates. To this end, PABPs bind to poly(A) tails or specific sequences of maternally stored mRNAs to protect them from degradation and to promote their translational activities. To date, two structurally different PABP groups have been identified: (1) cytoplasmic PABPs, including poly(A)-binding protein, cytoplasmic 1 (PABPC1), embryonic poly(A)-binding protein (EPAB), induced PABP and poly(A)-binding protein, cytoplasmic 3; and (2) nuclear PABPs, namely embryonic poly(A)-binding protein 2 and nuclear poly(A)-binding protein 1. Many studies have been undertaken to characterise the spatial and temporal expression patterns and subcellular localisations of PABPC1 and EPAB in vertebrate oocytes and early embryos. In the present review, we comprehensively evaluate and discuss the expression patterns and particular functions of the EPAB and PABPC1 genes, especially in mouse and human oocytes and early embryos.
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Affiliation(s)
- Saffet Ozturk
- Department of Histology and Embryology, Akdeniz University, School of Medicine, Campus, 07070, Antalya, Turkey
| | - Fatma Uysal
- Department of Histology and Embryology, Akdeniz University, School of Medicine, Campus, 07070, Antalya, Turkey
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10
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Andreev DE, Dmitriev SE, Loughran G, Terenin IM, Baranov PV, Shatsky IN. Translation control of mRNAs encoding mammalian translation initiation factors. Gene 2018; 651:174-182. [PMID: 29414693 DOI: 10.1016/j.gene.2018.02.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 01/25/2018] [Accepted: 02/04/2018] [Indexed: 10/18/2022]
Abstract
Eukaryotic cells evolved highly complex and accurate protein synthesis machinery that is finely tuned by various signaling pathways. Dysregulation of translation is a hallmark of many diseases, including cancer, and thus pharmacological approaches to modulate translation become very promising. While there has been much progress in our understanding of mammalian mRNA-specific translation control, surprisingly, relatively little is known about whether and how the protein components of the translation machinery shape translation of their own mRNAs. Here we analyze mammalian mRNAs encoding components of the translation initiation machinery for potential regulatory features such as 5'TOP motifs, TISU motifs, poor start codon nucleotide context and upstream open reading frames.
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Affiliation(s)
- Dmitri E Andreev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.
| | - Sergey E Dmitriev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia; Department of Biochemistry, Biological Faculty, Lomonosov Moscow State University, Moscow, Russia
| | - Gary Loughran
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Ilya M Terenin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Pavel V Baranov
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Ivan N Shatsky
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.
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11
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Brandariz-Núñez A, Zeng F, Lam QN, Jin H. Sbp1 modulates the translation of Pab1 mRNA in a poly(A)- and RGG-dependent manner. RNA (NEW YORK, N.Y.) 2018; 24:43-55. [PMID: 28986506 PMCID: PMC5733569 DOI: 10.1261/rna.062547.117] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 09/29/2017] [Indexed: 05/13/2023]
Abstract
RNA-binding protein Sbp1 facilitates the decapping pathway in mRNA metabolism and inhibits global mRNA translation by an unclear mechanism. Here we report molecular interactions responsible for Sbp1-mediated translation inhibition of mRNA encoding the polyadenosine-binding protein (Pab1), an essential translation factor that stimulates mRNA translation and inhibits mRNA decapping in eukaryotic cells. We demonstrate that the two distal RRMs of Sbp1 bind to the poly(A) sequence in the 5'UTR of the Pab1 mRNA specifically and cooperatively while the central RGG domain of the protein interacts directly with Pab1. Furthermore, methylation of arginines in the RGG domain abolishes the protein-protein interaction and the inhibitory effect of Sbp1 on translation initiation of Pab1 mRNA. Based on these results, the underlying mechanism for Sbp1-specific translational regulation is proposed. The functional differences of Sbp1 and RGG repeats alone on transcript-specific translation were observed, and a comparison of the results suggests the importance of remodeling the 5'UTR by RNA-binding proteins in mRNA translation.
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Affiliation(s)
- Alberto Brandariz-Núñez
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Champaign, Illinois 61801, USA
| | - Fuxing Zeng
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Champaign, Illinois 61801, USA
| | - Quan Ngoc Lam
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Champaign, Illinois 61801, USA
| | - Hong Jin
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Champaign, Illinois 61801, USA
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Champaign, Illinois 61801, USA
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12
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Fagg WS, Liu N, Fair JH, Shiue L, Katzman S, Donohue JP, Ares M. Autogenous cross-regulation of Quaking mRNA processing and translation balances Quaking functions in splicing and translation. Genes Dev 2017; 31:1894-1909. [PMID: 29021242 PMCID: PMC5695090 DOI: 10.1101/gad.302059.117] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 09/11/2017] [Indexed: 12/18/2022]
Abstract
Quaking protein isoforms arise from a single Quaking gene and bind the same RNA motif to regulate splicing, translation, decay, and localization of a large set of RNAs. However, the mechanisms by which Quaking expression is controlled to ensure that appropriate amounts of each isoform are available for such disparate gene expression processes are unknown. Here we explore how levels of two isoforms, nuclear Quaking-5 (Qk5) and cytoplasmic Qk6, are regulated in mouse myoblasts. We found that Qk5 and Qk6 proteins have distinct functions in splicing and translation, respectively, enforced through differential subcellular localization. We show that Qk5 and Qk6 regulate distinct target mRNAs in the cell and act in distinct ways on their own and each other's transcripts to create a network of autoregulatory and cross-regulatory feedback controls. Morpholino-mediated inhibition of Qk translation confirms that Qk5 controls Qk RNA levels by promoting accumulation and alternative splicing of Qk RNA, whereas Qk6 promotes its own translation while repressing Qk5. This Qk isoform cross-regulatory network responds to additional cell type and developmental controls to generate a spectrum of Qk5/Qk6 ratios, where they likely contribute to the wide range of functions of Quaking in development and cancer.
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Affiliation(s)
- W Samuel Fagg
- Sinsheimer Laboratories, Department of Molecular, Cell, and Developmental Biology, Center for Molecular Biology of RNA, University of California at Santa Cruz. Santa Cruz, California 95064, USA.,Department of Surgery, Transplant Division, Shriners Hospital for Children, University of Texas Medical Branch, Galveston, Texas 77555, USA
| | - Naiyou Liu
- Department of Surgery, Transplant Division, Shriners Hospital for Children, University of Texas Medical Branch, Galveston, Texas 77555, USA
| | - Jeffrey Haskell Fair
- Department of Surgery, Transplant Division, Shriners Hospital for Children, University of Texas Medical Branch, Galveston, Texas 77555, USA
| | - Lily Shiue
- Sinsheimer Laboratories, Department of Molecular, Cell, and Developmental Biology, Center for Molecular Biology of RNA, University of California at Santa Cruz. Santa Cruz, California 95064, USA
| | - Sol Katzman
- Sinsheimer Laboratories, Department of Molecular, Cell, and Developmental Biology, Center for Molecular Biology of RNA, University of California at Santa Cruz. Santa Cruz, California 95064, USA
| | - John Paul Donohue
- Sinsheimer Laboratories, Department of Molecular, Cell, and Developmental Biology, Center for Molecular Biology of RNA, University of California at Santa Cruz. Santa Cruz, California 95064, USA
| | - Manuel Ares
- Sinsheimer Laboratories, Department of Molecular, Cell, and Developmental Biology, Center for Molecular Biology of RNA, University of California at Santa Cruz. Santa Cruz, California 95064, USA
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13
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Chorghade S, Seimetz J, Emmons R, Yang J, Bresson SM, Lisio MD, Parise G, Conrad NK, Kalsotra A. Poly(A) tail length regulates PABPC1 expression to tune translation in the heart. eLife 2017; 6. [PMID: 28653618 PMCID: PMC5487213 DOI: 10.7554/elife.24139] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 05/18/2017] [Indexed: 12/13/2022] Open
Abstract
The rate of protein synthesis in the adult heart is one of the lowest in mammalian tissues, but it increases substantially in response to stress and hypertrophic stimuli through largely obscure mechanisms. Here, we demonstrate that regulated expression of cytosolic poly(A)-binding protein 1 (PABPC1) modulates protein synthetic capacity of the mammalian heart. We uncover a poly(A) tail-based regulatory mechanism that dynamically controls PABPC1 protein synthesis in cardiomyocytes and thereby titrates cellular translation in response to developmental and hypertrophic cues. Our findings identify PABPC1 as a direct regulator of cardiac hypertrophy and define a new paradigm of gene regulation in the heart, where controlled changes in poly(A) tail length influence mRNA translation. DOI:http://dx.doi.org/10.7554/eLife.24139.001 Hundreds of thousands of different proteins are needed to build and maintain the cells in the human body. All proteins are produced when copies of genetic information in the form of molecules of messenger RNA (mRNAs) are translated by the ribosome. The rate at which proteins are made varies widely between different tissues and at different times. In particular, the adult heart has one of the lowest rates of protein production, though this rate can increase markedly during exercise and heart disease. The mechanisms that drive this kind of dynamic change in protein production remain unclear. A better understanding of this process would tell scientists more about how and why cells regulate the translation of mRNAs in general, and might uncover new ways for treating heart disease. Molecules of mRNA are composed of smaller building blocks called nucleotides. All mature mRNAs in humans have a long stretch at one end that contains the nucleotide adenosine – commonly referred to as A for short – repeated 200 to 300 times. This sequence is called the poly(A) tail, and specific proteins can bind to this tail and determine the final fate of the mRNA, such as how efficiently it is translated. One such poly(A) binding protein, called PABPC1, is known to promote mRNA translation. Now, Chorghade, Seimetz et al. examine how PABPC1 regulates protein production in mice and human cells. The experiments reveal that, before birth, ample amounts of PABPC1 are found in the heart, but that this protein is undetectable in the hearts of adults. Further experiments showed that the levels of the mRNA for PABPC1 in the heart are the same before birth and in adulthood. So why is the mRNA for PABPC1 translated inefficiently in adult hearts? In general, mRNAs with long tails tend to be translated more efficiently compared to those with short tails, and it turns out that the mRNA for PABPC1 has a substantially shorter poly(A) tail in the adult heart. This tail shortening limits the translation of this specific mRNA, which leads to reduced protein production. Chorghade, Seimetz et al. also showed that the length of the poly(A) tail on the mRNA and the levels of the PABPC1 protein are restored in adult hearts during a condition known as hypertrophy. This state of hypertrophy can be triggered by exercise or heart disease and is marked by an increase in the size of individual heart cells and enhanced protein production. Finally, Chorghade, Seimetz et al. found that experimentally raising the levels of PABPC1 in adult hearts could, by itself, make the heart cells produce more protein and the heart grow more. Further studies will explore if other mRNAs in the heart also undergo similar changes and whether this is a general mechanism for controlling protein production. DOI:http://dx.doi.org/10.7554/eLife.24139.002
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Affiliation(s)
- Sandip Chorghade
- Department of Biochemistry, University of Illinois, Illinois, United States
| | - Joseph Seimetz
- Department of Biochemistry, University of Illinois, Illinois, United States
| | - Russell Emmons
- Department of Kinesiology and Community Health, University of Illinois, Illinois, United States
| | - Jing Yang
- Department of Comparative Biosciences, University of Illinois, Illinois, United States
| | - Stefan M Bresson
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Michael De Lisio
- Department of Kinesiology and Community Health, University of Illinois, Illinois, United States.,School of Human Kinetics, University of Ottawa, Ottawa, Canada
| | - Gianni Parise
- Department of Kinesiology, McMaster University, Hamilton, Canada
| | - Nicholas K Conrad
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Auinash Kalsotra
- Department of Biochemistry, University of Illinois, Illinois, United States.,Carl R. Woese Institute of Genomic Biology, University of Illinois, Illinois, United States
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14
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Zhao P, Liu Q, Miller WA, Goss DJ. Eukaryotic translation initiation factor 4G (eIF4G) coordinates interactions with eIF4A, eIF4B, and eIF4E in binding and translation of the barley yellow dwarf virus 3' cap-independent translation element (BTE). J Biol Chem 2017; 292:5921-5931. [PMID: 28242763 DOI: 10.1074/jbc.m116.764902] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 02/07/2017] [Indexed: 12/11/2022] Open
Abstract
Barley yellow dwarf virus RNA, lacking a 5' cap and a 3' poly(A) tail, contains a cap-independent translation element (BTE) in the 3'-untranslated region that interacts with host translation initiation factor eIF4G. To determine how eIF4G recruits the mRNA, three eIF4G deletion mutants were constructed: (i) eIF4G601-1196, containing amino acids 601-1196, including the putative BTE-binding region, and binding domains for eIF4E, eIF4A, and eIF4B; (ii) eIF4G601-1488, which contains an additional C-terminal eIF4A-binding domain; and (iii) eIF4G742-1196, which lacks the eIF4E-binding site. eIF4G601-1196 binds BTE tightly and supports efficient translation. The helicase complex, consisting of eIF4A, eIF4B, and ATP, stimulated BTE binding with eIF4G601-1196 but not eIF4G601-1488, suggesting that the eIF4A binding domains may serve a regulatory role, with the C-terminal binding site having negative effects. eIF4E binding to eIF4G601-1196 induced a conformational change, significantly increasing the binding affinity to BTE. A comparison of the binding of eIF4G deletion mutants with BTEs containing mutations showed a general correlation between binding affinity and ability to facilitate translation. In summary, these results reveal a new role for the helicase complex in 3' cap-independent translation element-mediated translation and show that the functional core domain of eIF4G plus an adjacent probable RNA-binding domain mediate translation initiation.
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Affiliation(s)
- Pei Zhao
- From the Biochemistry and Chemistry Graduate Programs, Graduate Center, and.,the Department of Chemistry and Biochemistry, Hunter College, City University of New York, New York, New York 10065 and
| | - Qiao Liu
- From the Biochemistry and Chemistry Graduate Programs, Graduate Center, and.,the Department of Chemistry and Biochemistry, Hunter College, City University of New York, New York, New York 10065 and
| | - W Allen Miller
- the Plant Pathology & Microbiology and.,Biochemistry, Biophysics & Molecular Biology Departments, Iowa State University, Ames, Iowa 50011
| | - Dixie J Goss
- From the Biochemistry and Chemistry Graduate Programs, Graduate Center, and .,the Department of Chemistry and Biochemistry, Hunter College, City University of New York, New York, New York 10065 and
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15
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Wang X, Hou J, Quedenau C, Chen W. Pervasive isoform-specific translational regulation via alternative transcription start sites in mammals. Mol Syst Biol 2016; 12:875. [PMID: 27430939 PMCID: PMC4965872 DOI: 10.15252/msb.20166941] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 06/17/2016] [Accepted: 06/21/2016] [Indexed: 12/02/2022] Open
Abstract
Transcription initiated at alternative sites can produce mRNA isoforms with different 5'UTRs, which are potentially subjected to differential translational regulation. However, the prevalence of such isoform-specific translational control across mammalian genomes is currently unknown. By combining polysome profiling with high-throughput mRNA 5' end sequencing, we directly measured the translational status of mRNA isoforms with distinct start sites. Among 9,951 genes expressed in mouse fibroblasts, we identified 4,153 showed significant initiation at multiple sites, of which 745 genes exhibited significant isoform-divergent translation. Systematic analyses of the isoform-specific translation revealed that isoforms with longer 5'UTRs tended to translate less efficiently. Further investigation of cis-elements within 5'UTRs not only provided novel insights into the regulation by known sequence features, but also led to the discovery of novel regulatory sequence motifs. Quantitative models integrating all these features explained over half of the variance in the observed isoform-divergent translation. Overall, our study demonstrated the extensive translational regulation by usage of alternative transcription start sites and offered comprehensive understanding of translational regulation by diverse sequence features embedded in 5'UTRs.
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Affiliation(s)
- Xi Wang
- Laboratory for Functional Genomics and Systems Biology, Berlin Institute for Medical Systems Biology, Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany
| | - Jingyi Hou
- Laboratory for Functional Genomics and Systems Biology, Berlin Institute for Medical Systems Biology, Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany
| | - Claudia Quedenau
- Laboratory for Functional Genomics and Systems Biology, Berlin Institute for Medical Systems Biology, Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany
| | - Wei Chen
- Laboratory for Functional Genomics and Systems Biology, Berlin Institute for Medical Systems Biology, Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany Department of Biology, South University of Science and Technology of China, Shenzhen, Guangdong, China
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16
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Rissland OS. The organization and regulation of mRNA-protein complexes. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 8. [PMID: 27324829 PMCID: PMC5213448 DOI: 10.1002/wrna.1369] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 05/11/2016] [Accepted: 05/12/2016] [Indexed: 12/21/2022]
Abstract
In a eukaryotic cell, each messenger RNA (mRNA) is bound to a variety of proteins to form an mRNA-protein complex (mRNP). Together, these proteins impact nearly every step in the life cycle of an mRNA and are critical for the proper control of gene expression. In the cytoplasm, for instance, mRNPs affect mRNA translatability and stability and provide regulation of specific transcripts as well as global, transcriptome-wide control. mRNPs are complex, diverse, and dynamic, and so they have been a challenge to understand. But the advent of high-throughput sequencing technology has heralded a new era in the study of mRNPs. Here, I will discuss general principles of cytoplasmic mRNP organization and regulation. Using microRNA-mediated repression as a case study, I will focus on common themes in mRNPs and highlight the interplay between mRNP composition and posttranscriptional regulation. mRNPs are an important control point in regulating gene expression, and while the study of these fascinating complexes presents remaining challenges, recent advances provide a critical lens for deciphering gene regulation. WIREs RNA 2017, 8:e1369. doi: 10.1002/wrna.1369 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Olivia S Rissland
- Molecular Structure and Function Program, The Hospital for Sick Children Research Institute, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
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17
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Horan L, Yasuhara JC, Kohlstaedt LA, Rio DC. Biochemical identification of new proteins involved in splicing repression at the Drosophila P-element exonic splicing silencer. Genes Dev 2016; 29:2298-311. [PMID: 26545814 PMCID: PMC4647562 DOI: 10.1101/gad.268847.115] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Splicing of the Drosophila P-element third intron (IVS3) is repressed in somatic tissues due to the function of an exonic splicing silencer (ESS) complex present on the 5' exon RNA. To comprehensively characterize the mechanisms of this alternative splicing regulation, we used biochemical fractionation and affinity purification to isolate the silencer complex assembled in vitro and identify the constituent proteins by mass spectrometry. Functional assays using splicing reporter minigenes identified the proteins hrp36 and hrp38 and the cytoplasmic poly(A)-binding protein PABPC1 as novel functional components of the splicing silencer. hrp48, PSI, and PABPC1 have high-affinity RNA-binding sites on the P-element IVS3 5' exon, whereas hrp36 and hrp38 proteins bind with low affinity to the P-element silencer RNA. RNA pull-down and immobilized protein assays showed that hrp48 protein binding to the silencer RNA can recruit hrp36 and hrp38. These studies identified additional components that function at the P-element ESS and indicated that proteins with low-affinity RNA-binding sites can be recruited in a functional manner through interactions with a protein bound to RNA at a high-affinity binding site. These studies have implications for the role of heterogeneous nuclear ribonucleoproteins (hnRNPs) in the control of alternative splicing at cis-acting regulatory sites.
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Affiliation(s)
- Lucas Horan
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720, USA
| | - Jiro C Yasuhara
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720, USA
| | - Lori A Kohlstaedt
- California Institute for Quantitative Biosciences (QB3), University of California at Berkeley, Berkeley, California 94720, USA
| | - Donald C Rio
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720, USA; California Institute for Quantitative Biosciences (QB3), University of California at Berkeley, Berkeley, California 94720, USA; Center for RNA Systems Biology, University of California at Berkeley, Berkeley, California 94720, USA
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18
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Kini HK, Silverman IM, Ji X, Gregory BD, Liebhaber SA. Cytoplasmic poly(A) binding protein-1 binds to genomically encoded sequences within mammalian mRNAs. RNA (NEW YORK, N.Y.) 2016; 22:61-74. [PMID: 26554031 PMCID: PMC4691835 DOI: 10.1261/rna.053447.115] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 10/02/2015] [Indexed: 06/05/2023]
Abstract
The functions of the major mammalian cytoplasmic poly(A) binding protein, PABPC1, have been characterized predominantly in the context of its binding to the 3' poly(A) tails of mRNAs. These interactions play important roles in post-transcriptional gene regulation by enhancing translation and mRNA stability. Here, we performed transcriptome-wide CLIP-seq analysis to identify additional PABPC1 binding sites within genomically encoded mRNA sequences that may impact on gene regulation. From this analysis, we found that PABPC1 binds directly to the canonical polyadenylation signal in thousands of mRNAs in the mouse transcriptome. PABPC1 binding also maps to translation initiation and termination sites bracketing open reading frames, exemplified most dramatically in replication-dependent histone mRNAs. Additionally, a more restricted subset of PABPC1 interaction sites comprised A-rich sequences within the 5' UTRs of mRNAs, including Pabpc1 mRNA itself. Functional analyses revealed that these PABPC1 interactions in the 5' UTR mediate both auto- and trans-regulatory translational control. In total, these findings reveal a repertoire of PABPC1 binding that is substantially broader than previously recognized with a corresponding potential to impact and coordinate post-transcriptional controls critical to a broad array of cellular functions.
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Affiliation(s)
- Hemant K Kini
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
| | - Ian M Silverman
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA Cell and Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Xinjun Ji
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
| | - Brian D Gregory
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Stephen A Liebhaber
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
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19
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Archer SK, Shirokikh NE, Hallwirth CV, Beilharz TH, Preiss T. Probing the closed-loop model of mRNA translation in living cells. RNA Biol 2015; 12:248-54. [PMID: 25826658 PMCID: PMC4615164 DOI: 10.1080/15476286.2015.1017242] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The mRNA closed-loop, formed through interactions between the cap structure, poly(A) tail, eIF4E, eIF4G and PAB, features centrally in models of eukaryotic translation initiation, although direct support for its existence in vivo is not well established. Here, we investigated the closed-loop using a combination of mRNP isolation from rapidly cross-linked cells and high-throughput qPCR. Using the interaction between these factors and the opposing ends of mRNAs as a proxy for the closed-loop, we provide evidence that it is prevalent for eIF4E/4G-bound but unexpectedly sparse for PAB1-bound mRNAs, suggesting it primarily occurs during a distinct phase of polysome assembly. We observed mRNA-specific variation in the extent of closed-loop formation, consistent with a role for polysome topology in the control of gene expression.
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Affiliation(s)
- Stuart K Archer
- a Genome Biology Department; The John Curtin School of Medical Research (JCSMR); The Australian National University ; Acton (Canberra), Australian Capital Territory , Australia
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20
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A posttranscriptional mechanism that controls Ptbp1 abundance in the Xenopus epidermis. Mol Cell Biol 2014; 35:758-68. [PMID: 25512611 DOI: 10.1128/mcb.01040-14] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The output of alternative splicing depends on the cooperative or antagonistic activities of several RNA-binding proteins (RBPs), like Ptbp1 and Esrp1 in Xenopus. Fine-tuning of the RBP abundance is therefore of prime importance to achieve tissue- or cell-specific splicing patterns. Here, we addressed the mechanisms leading to the high expression of the ptbp1 gene, which encodes Ptbp1, in Xenopus epidermis. Two splice isoforms of ptbp1 mRNA differ by the presence of an alternative exon 11, and only the isoform including exon 11 can be translated to a full-length protein. In vivo minigene assays revealed that the nonproductive isoform was predominantly produced. Knockdown experiments demonstrated that Esrp1, which is specific to the epidermis, strongly stimulated the expression of ptbp1 by favoring the productive isoform. Consequently, knocking down esrp1 phenocopied ptbp1 inactivation. Conversely, Ptbp1 repressed the expression of its own gene by favoring the nonproductive isoform. Hence, a complex posttranscriptional mechanism controls Ptbp1 abundance in Xenopus epidermis: skipping of exon 11 is the default splicing pattern, but Esrp1 stimulates ptbp1 expression by favoring the inclusion of exon 11 up to a level that is limited by Ptbp1 itself. These results decipher a posttranscriptional mechanism that achieves various abundances of the ubiquitous RBP Ptbp1 in different tissues.
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21
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Meyuhas O, Kahan T. The race to decipher the top secrets of TOP mRNAs. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1849:801-11. [PMID: 25234618 DOI: 10.1016/j.bbagrm.2014.08.015] [Citation(s) in RCA: 172] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Revised: 08/18/2014] [Accepted: 08/27/2014] [Indexed: 12/20/2022]
Abstract
Cells encountering hostile growth conditions, like those residing in the middle of a newly developing solid tumor, conserve resources and energy by downregulating protein synthesis. One mechanism in this response is the translational repression of multiple mRNAs that encode components of the translational apparatus. This coordinated translational control is carried through a common cis-regulatory element, the 5' Terminal OligoPyrimidine motif (5'TOP), after which these mRNAs are referred to as TOP mRNAs. Subsequent to the initial structural and functional characterization of members of this family, the research of TOP mRNAs has progressed in three major directions: a) delineating the landscape of the family; b) establishing the pathways that transduce stress cues into selective translational repression; and c) attempting to decipher the most proximal trans-acting factor(s) and defining its mode of action--a repressor or activator. The present chapter critically reviews the development in these three avenues of research with a special emphasis on the two "top secrets" of the TOP mRNA family: the scope of its members and the identity of the proximal cellular regulator(s). This article is part of a Special Issue entitled: Translation and Cancer.
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Affiliation(s)
- Oded Meyuhas
- Department of Biochemistry and Molecular Biology, Institute for Medical Research - Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel.
| | - Tamar Kahan
- Bioinformatics Unit, The Hebrew University, Hadassah Medical School, Jerusalem 91120, Israel
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22
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Wigington CP, Williams KR, Meers MP, Bassell GJ, Corbett AH. Poly(A) RNA-binding proteins and polyadenosine RNA: new members and novel functions. WILEY INTERDISCIPLINARY REVIEWS. RNA 2014; 5:601-22. [PMID: 24789627 PMCID: PMC4332543 DOI: 10.1002/wrna.1233] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 02/07/2014] [Accepted: 03/06/2014] [Indexed: 02/05/2023]
Abstract
Poly(A) RNA-binding proteins (Pabs) bind with high affinity and specificity to polyadenosine RNA. Textbook models show a nuclear Pab, PABPN1, and a cytoplasmic Pab, PABPC, where the nuclear PABPN1 modulates poly(A) tail length and the cytoplasmic PABPC stabilizes poly(A) RNA in the cytoplasm and also enhances translation. While these conventional roles are critically important, the Pab family has expanded recently both in number and in function. A number of novel roles have emerged for both PAPBPN1 and PABPC that contribute to the fine-tuning of gene expression. Furthermore, as the characterization of the nucleic acid binding properties of RNA-binding proteins advances, additional proteins that show high affinity and specificity for polyadenosine RNA are being discovered. With this expansion of the Pab family comes a concomitant increase in the potential for Pabs to modulate gene expression. Further complication comes from an expansion of the potential binding sites for Pab proteins as revealed by an analysis of templated polyadenosine stretches present within the transcriptome. Thus, Pabs could influence mRNA fate and function not only by binding to the nontemplated poly(A) tail but also to internal stretches of adenosine. Understanding the diverse functions of Pab proteins is not only critical to understand how gene expression is regulated but also to understand the molecular basis for tissue-specific diseases that occur when Pab proteins are altered. Here we describe both conventional and recently emerged functions for PABPN1 and PABPC and then introduce and discuss three new Pab family members, ZC3H14, hnRNP-Q1, and LARP4.
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Affiliation(s)
- Callie P. Wigington
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Kathryn R. Williams
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA
| | - Michael P. Meers
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, USA
| | - Gary J. Bassell
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA
| | - Anita H. Corbett
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
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23
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Zhao YB, Krishnan J. mRNA translation and protein synthesis: an analysis of different modelling methodologies and a new PBN based approach. BMC SYSTEMS BIOLOGY 2014; 8:25. [PMID: 24576337 PMCID: PMC4015640 DOI: 10.1186/1752-0509-8-25] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Accepted: 01/08/2014] [Indexed: 01/12/2023]
Abstract
Background mRNA translation involves simultaneous movement of multiple ribosomes on the mRNA and is also subject to regulatory mechanisms at different stages. Translation can be described by various codon-based models, including ODE, TASEP, and Petri net models. Although such models have been extensively used, the overlap and differences between these models and the implications of the assumptions of each model has not been systematically elucidated. The selection of the most appropriate modelling framework, and the most appropriate way to develop coarse-grained/fine-grained models in different contexts is not clear. Results We systematically analyze and compare how different modelling methodologies can be used to describe translation. We define various statistically equivalent codon-based simulation algorithms and analyze the importance of the update rule in determining the steady state, an aspect often neglected. Then a novel probabilistic Boolean network (PBN) model is proposed for modelling translation, which enjoys an exact numerical solution. This solution matches those of numerical simulation from other methods and acts as a complementary tool to analytical approximations and simulations. The advantages and limitations of various codon-based models are compared, and illustrated by examples with real biological complexities such as slow codons, premature termination and feedback regulation. Our studies reveal that while different models gives broadly similiar trends in many cases, important differences also arise and can be clearly seen, in the dependence of the translation rate on different parameters. Furthermore, the update rule affects the steady state solution. Conclusions The codon-based models are based on different levels of abstraction. Our analysis suggests that a multiple model approach to understanding translation allows one to ascertain which aspects of the conclusions are robust with respect to the choice of modelling methodology, and when (and why) important differences may arise. This approach also allows for an optimal use of analysis tools, which is especially important when additional complexities or regulatory mechanisms are included. This approach can provide a robust platform for dissecting translation, and results in an improved predictive framework for applications in systems and synthetic biology.
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Affiliation(s)
| | - J Krishnan
- Department of Chemical Engineering, Centre for Process Systems Engineering, Institute for Systems and Synthetic Biology, Imperial College London, South Kensington, London SW7 2AZ, UK.
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24
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Panda AC, Grammatikakis I, Yoon JH, Abdelmohsen K. Posttranscriptional regulation of insulin family ligands and receptors. Int J Mol Sci 2013; 14:19202-29. [PMID: 24051403 PMCID: PMC3794829 DOI: 10.3390/ijms140919202] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Revised: 08/17/2013] [Accepted: 09/06/2013] [Indexed: 01/02/2023] Open
Abstract
Insulin system including ligands (insulin and IGFs) and their shared receptors (IR and IGFR) are critical regulators of insulin signaling and glucose homeostasis. Altered insulin system is associated with major pathological conditions like diabetes and cancer. The mRNAs encoding for these ligands and their receptors are posttranscriptionally controlled by three major groups of regulators; (i) alternative splicing regulatory factors; (ii) turnover and translation regulator RNA-binding proteins (TTR-RBPs); and (iii) non-coding RNAs including miRNAs and long non-coding RNAs (lncRNAs). In this review, we discuss the influence of these regulators on alternative splicing, mRNA stability and translation. Due to the pathological impacts of insulin system, we also discussed the possibilities of discovering new potential regulators which will improve understanding of insulin system and associated diseases.
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Affiliation(s)
- Amaresh C Panda
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA.
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25
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Rotavirus prevents the expression of host responses by blocking the nucleocytoplasmic transport of polyadenylated mRNAs. J Virol 2013; 87:6336-45. [PMID: 23536677 DOI: 10.1128/jvi.00361-13] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Rotaviruses are the most important agent of severe gastroenteritis in young children. Early in infection, these viruses take over the host translation machinery, causing a severe shutoff of cell protein synthesis while viral proteins are efficiently synthesized. In infected cells, there is an accumulation of the cytoplasmic poly(A)-binding protein in the nucleus, induced by the viral protein NSP3. Here we found that poly(A)-containing mRNAs also accumulate and become hyperadenylated in the nuclei of infected cells. Using reporter genes bearing the untranslated regions (UTRs) of cellular or viral genes, we found that the viral UTRs do not determine the efficiency of translation of mRNAs in rotavirus-infected cells. Furthermore, we showed that while a polyadenylated reporter mRNA directly delivered into the cytoplasm of infected cells was efficiently translated, the same reporter introduced as a plasmid that needs to be transcribed and exported to the cytoplasm was poorly translated. Altogether, these results suggest that nuclear retention of poly(A)-containing mRNAs is one of the main strategies of rotavirus to control cell translation and therefore the host antiviral and stress responses.
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Kramer S, Bannerman-Chukualim B, Ellis L, Boulden EA, Kelly S, Field MC, Carrington M. Differential localization of the two T. brucei poly(A) binding proteins to the nucleus and RNP granules suggests binding to distinct mRNA pools. PLoS One 2013; 8:e54004. [PMID: 23382864 PMCID: PMC3559699 DOI: 10.1371/journal.pone.0054004] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Accepted: 12/06/2012] [Indexed: 12/30/2022] Open
Abstract
The number of paralogs of proteins involved in translation initiation is larger in trypanosomes than in yeasts or many metazoan and includes two poly(A) binding proteins, PABP1 and PABP2, and four eIF4E variants. In many cases, the paralogs are individually essential and are thus unlikely to have redundant functions although, as yet, distinct functions of different isoforms have not been determined. Here, trypanosome PABP1 and PABP2 have been further characterised. PABP1 and PABP2 diverged subsequent to the differentiation of the Kinetoplastae lineage, supporting the existence of specific aspects of translation initiation regulation. PABP1 and PABP2 exhibit major differences in intracellular localization and distribution on polysome fractionation under various conditions that interfere with mRNA metabolism. Most striking are differences in localization to the four known types of inducible RNP granules. Moreover, only PABP2 but not PABP1 can accumulate in the nucleus. Taken together, these observations indicate that PABP1 and PABP2 likely associate with distinct populations of mRNAs. The differences in localization to inducible RNP granules also apply to paralogs of components of the eIF4F complex: eIF4E1 showed similar localization pattern to PABP2, whereas the localisation of eIF4E4 and eIF4G3 resembled that of PABP1. The grouping of translation initiation as either colocalizing with PABP1 or with PABP2 can be used to complement interaction studies to further define the translation initiation complexes in kinetoplastids.
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Affiliation(s)
- Susanne Kramer
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | | | - Louise Ellis
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | | | - Steve Kelly
- Department of Plant Sciences, University of Oxford, and Oxford Centre for Integrative Systems Biology, Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Mark C. Field
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Mark Carrington
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
- * E-mail:
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Goss DJ, Kleiman FE. Poly(A) binding proteins: are they all created equal? WILEY INTERDISCIPLINARY REVIEWS-RNA 2012; 4:167-79. [PMID: 23424172 DOI: 10.1002/wrna.1151] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The PABP family of proteins were originally thought of as a simple shield for the mRNA poly(A) tail. Years of research have shown that PABPs interact not only with the poly(A) tail, but also with specific sequences in the mRNA, having a general and specific role on the metabolism of different mRNAs. The complexity of PABPs function is increased by the interactions of PABPs with factors involved in different cellular functions. PABPs participate in all the metabolic pathways of the mRNA: polyadenylation/deadenylation, mRNA export, mRNA surveillance, translation, mRNA degradation, microRNA-associated regulation, and regulation of expression during development. In this review, we update information on the roles of PABPs and emerging data on the specific interactions of PABP homologs. Specific functions of individual members of PABPC family in development and viral infection are beginning to be elucidated. However, the interactions are complex and recent evidence for exchange of nuclear and cytoplasmic forms of the proteins, as well as post-translational modifications, emphasize the possibilities for fine-tuning the PABP metabolic network.
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Affiliation(s)
- Dixie J Goss
- Chemistry Department, Hunter College CUNY, New York, NY, USA.
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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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Burgess HM, Gray NK. An integrated model for the nucleo-cytoplasmic transport of cytoplasmic poly(A)-binding proteins. Commun Integr Biol 2012; 5:243-7. [PMID: 22896784 PMCID: PMC3419106 DOI: 10.4161/cib.19347] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Cytoplasmic poly(A)-binding proteins (PABPs) regulate mRNA stability and translation. Although predominantly localized in the cytoplasm, PABP proteins also cycle through the nucleus. Recent work has established that their steady-state localization can be altered by cellular stresses such as ultraviolet (UV) radiation, and infection by several viruses, resulting in nuclear accumulation of PABPs. Here, we present further evidence that their interaction with and release from mRNA and translation complexes are important in determining their sub-cellular distribution and propose an integrated model for regulated nucleo-cytoplasmic transport of PABPs.
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30
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Eliseeva IA, Kim ER, Guryanov SG, Ovchinnikov LP, Lyabin DN. Y-box-binding protein 1 (YB-1) and its functions. BIOCHEMISTRY (MOSCOW) 2012; 76:1402-33. [PMID: 22339596 DOI: 10.1134/s0006297911130049] [Citation(s) in RCA: 249] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This review describes the structure and functions of Y-box binding protein 1 (YB-1) and its homologs. Interactions of YB-1 with DNA, mRNAs, and proteins are considered. Data on the participation of YB-1 in DNA reparation and transcription, mRNA splicing and translation are systematized. Results on interactions of YB-1 with cytoskeleton components and its possible role in mRNA localization are discussed. Data on intracellular distribution of YB-1, its redistribution between the nucleus and the cytoplasm, and its secretion and extracellular functions are summarized. The effect of YB-1 on cell differentiation, its involvement in extra- and intracellular signaling pathways, and its role in early embryogenesis are described. The mechanisms of regulation of YB-1 expression in the cell are presented. Special attention is paid to the involvement of YB-1 in oncogenic cell transformation, multiple drug resistance, and dissemination of tumors. Both the oncogenic and antioncogenic activities of YB-1 are reviewed. The potential use of YB-1 in diagnostics and therapy as an early cancer marker and a molecular target is discussed.
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Affiliation(s)
- I A Eliseeva
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
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31
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Kikuchi K, Shimizu S, Sato Y, Morishita EC, Takénaka A. Crystallization of oligonucleotides containing A-rich repeats suggests a structural contribution to the autoregulation mechanism of PABP translation. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:185-9. [PMID: 22297995 PMCID: PMC3274399 DOI: 10.1107/s1744309111052110] [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: 10/12/2011] [Accepted: 12/02/2011] [Indexed: 11/10/2022]
Abstract
Eukaryotic poly(A)-binding protein (PABP) commonly binds to the 3'-UTR poly(A) tail of every mRNA, but it also binds to the 5'-UTR of PABP mRNA for autoregulation of its expression. In the sequence of the latter binding site, the contiguous A residues are segmented discretely by the insertion of short pyrimidine oligonucleotides as linkers, so that (A)(6-8) segments are repeated six times. This differs from the poly(A)-tail sequence, which has a higher binding affinity for PABP. In order to examine whether the A-rich repeats have a functional structure, several RNA/DNA analogues were subjected to crystallization. It was found that some of them could be crystallized. Single crystals thus obtained diffracted to 4.1 Å resolution. The fact that the repeated sequences can be crystallized suggests the possibility that the autoregulatory sequence in PABP mRNA has a specific structure which impedes the binding of PABP. When PABP is excessively produced, it could bind to this sequence by releasing the structure in order to interfere with initiation-complex formation for suppression of PABP translation. Otherwise, PABP at low concentration preferentially binds to the poly(A) tail of PABP mRNA.
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Affiliation(s)
- Keita Kikuchi
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Nagatsuda, Midori-ku, Yokohama 226-8501, Japan
| | - Satoru Shimizu
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Nagatsuda, Midori-ku, Yokohama 226-8501, Japan
| | - Yoshiteru Sato
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Nagatsuda, Midori-ku, Yokohama 226-8501, Japan
| | - Ella Czarina Morishita
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Nagatsuda, Midori-ku, Yokohama 226-8501, Japan
| | - Akio Takénaka
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Nagatsuda, Midori-ku, Yokohama 226-8501, Japan
- Graduate School of Science and Engineering, Iwaki-Meisei University, Chuodai-iino, Iwaki, Fukushima 970-8551, Japan
- Faculty of Pharmacy, Iwaki-Meisei University, Chuodai-iino, Iwaki, Fukushima 970-8551, Japan
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32
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Oliveira GGS, Magalhães FB, Teixeira MCA, Pereira AM, Pinheiro CGM, Santos LR, Nascimento MB, Bedor CNG, Albuquerque AL, dos-Santos WLC, Gomes YM, Moreira ED, Brito MEF, Pontes de Carvalho LC, de Melo Neto OP. Characterization of novel Leishmania infantum recombinant proteins encoded by genes from five families with distinct capacities for serodiagnosis of canine and human visceral leishmaniasis. Am J Trop Med Hyg 2012; 85:1025-34. [PMID: 22144438 DOI: 10.4269/ajtmh.2011.11-0102] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
To expand the available panel of recombinant proteins that can be useful for identifying Leishmania-infected dogs and for diagnosing human visceral leishmaniasis (VL), we selected recombinant antigens from L. infantum, cDNA, and genomic libraries by using pools of serum samples from infected dogs and humans. The selected DNA fragments encoded homologs of a cytoplasmic heat-shock protein 70, a kinesin, a polyubiquitin, and two novel hypothetical proteins. Histidine-tagged recombinant proteins were produced after subcloning these DNA fragments and evaluated by using an enzyme-linked immunosorbent assays with panels of canine and human serum samples. The enzyme-linked immunosorbent assays with different recombinant proteins had different sensitivities (67.4-93.0% and 36.4-97.2%) and specificities (76.1-100% and 90.4-97.3%) when tested with serum samples from Leishmania-infected dogs and human patients with VL. Overall, no single recombinant antigen was sufficient to serodiagnosis all canine or human VL cases.
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Affiliation(s)
- Geraldo G S Oliveira
- Centro de Pesquisas Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Bahia, Brazil.
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Miroci H, Schob C, Kindler S, Ölschläger-Schütt J, Fehr S, Jungenitz T, Schwarzacher SW, Bagni C, Mohr E. Makorin ring zinc finger protein 1 (MKRN1), a novel poly(A)-binding protein-interacting protein, stimulates translation in nerve cells. J Biol Chem 2011; 287:1322-34. [PMID: 22128154 DOI: 10.1074/jbc.m111.315291] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The poly(A)-binding protein (PABP), a key component of different ribonucleoprotein complexes, plays a crucial role in the control of mRNA translation rates, stability, and subcellular targeting. In this study we identify RING zinc finger protein Makorin 1 (MKRN1), a bona fide RNA-binding protein, as a binding partner of PABP that interacts with PABP in an RNA-independent manner. In rat brain, a so far uncharacterized short MKRN1 isoform, MKRN1-short, predominates and is detected in forebrain nerve cells. In neuronal dendrites, MKRN1-short co-localizes with PABP in granule-like structures, which are morphological correlates of sites of mRNA metabolism. Moreover, in primary rat neurons MKRN1-short associates with dendritically localized mRNAs. When tethered to a reporter mRNA, MKRN1-short significantly enhances reporter protein synthesis. Furthermore, after induction of synaptic plasticity via electrical stimulation of the perforant path in vivo, MKRN1-short specifically accumulates in the activated dendritic lamina, the middle molecular layer of the hippocampal dentate gyrus. Collectively, these data indicate that in mammalian neurons MKRN1-short interacts with PABP to locally control the translation of dendritic mRNAs at synapses.
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Affiliation(s)
- Hatmone Miroci
- Institute of Neuroanatomy, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
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Covarrubias S, Gaglia MM, Kumar GR, Wong W, Jackson AO, Glaunsinger BA. Coordinated destruction of cellular messages in translation complexes by the gammaherpesvirus host shutoff factor and the mammalian exonuclease Xrn1. PLoS Pathog 2011; 7:e1002339. [PMID: 22046136 PMCID: PMC3203186 DOI: 10.1371/journal.ppat.1002339] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2011] [Accepted: 09/14/2011] [Indexed: 12/02/2022] Open
Abstract
Several viruses encode factors that promote host mRNA degradation to silence gene expression. It is unclear, however, whether cellular mRNA turnover pathways are engaged to assist in this process. In Kaposi's sarcoma-associated herpesvirus this phenotype is enacted by the host shutoff factor SOX. Here we show that SOX-induced mRNA turnover is a two-step process, in which mRNAs are first cleaved internally by SOX itself then degraded by the cellular exonuclease Xrn1. SOX therefore bypasses the regulatory steps of deadenylation and decapping normally required for Xrn1 activation. SOX is likely recruited to translating mRNAs, as it cosediments with translation initiation complexes and depletes polysomes. Cleaved mRNA intermediates accumulate in the 40S fraction, indicating that recognition occurs at an early stage of translation. This is the first example of a viral protein commandeering cellular mRNA turnover pathways to destroy host mRNAs, and suggests that Xrn1 is poised to deplete messages undergoing translation in mammalian cells. Viruses use a number of strategies to commandeer host machinery and create an optimal environment for their replication. One strategy employed by oncogenic gammaherpesviruses such as Kaposi's sarcoma-associated herpesvirus (KSHV) is to block cellular gene expression through extensive destruction of mRNAs. A single viral protein called SOX is sufficient to drive this phenotype, but the mechanism by which it does so has remained unclear. Here we show that host mRNA destruction is the result of the coordinated action of SOX and a cellular RNA degrading enzyme, Xrn1. By cleaving mRNAs internally, SOX recruits the activity of Xrn1 while bypassing the regulatory mechanisms that normally prevent this enzyme from prematurely degrading mRNAs. We also find that SOX co-sediments with translation complexes, and specifically targets mRNAs for cleavage at an early stage of translation. We hypothesize this allows the virus to selectively target mRNAs, thereby liberating host gene expression machinery. Collectively, these findings describe a novel interplay between the gammaherpesvirus SOX protein and cellular degradation machinery, and shed light on how a single viral component can hijack cellular machinery to efficiently destroy messages.
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Affiliation(s)
- Sergio Covarrubias
- Division of Infectious Diseases and Immunity, School of Public Health, University of California Berkeley, Berkeley, California, United States of America
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Marta M. Gaglia
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, United States of America
| | - G. Renuka Kumar
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Wesley Wong
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Andrew O. Jackson
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Britt A. Glaunsinger
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, United States of America
- * E-mail:
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Chritton JJ, Wickens M. A role for the poly(A)-binding protein Pab1p in PUF protein-mediated repression. J Biol Chem 2011; 286:33268-78. [PMID: 21768112 DOI: 10.1074/jbc.m111.264572] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
PUF proteins regulate translation and mRNA stability throughout eukaryotes. Using a cell-free translation assay, we examined the mechanisms of translational repression of PUF proteins in the budding yeast Saccharomyces cerevisiae. We demonstrate that the poly(A)-binding protein Pab1p is required for PUF-mediated translational repression for two distantly related PUF proteins: S. cerevisiae Puf5p and Caenorhabditis elegans FBF-2. Pab1p interacts with oligo(A) tracts in the HO 3'-UTR, a target of Puf5p, to dramatically enhance the efficiency of Puf5p repression. Both the Pab1p ability to activate translation and interact with eukaryotic initiation factor 4G (eIF4G) were required to observe maximal repression by Puf5p. Repression was also more efficient when Pab1p was bound in close proximity to Puf5p. Puf5p may disrupt translation initiation by interfering with the interaction between Pab1p and eIF4G. Finally, we demonstrate two separable mechanisms of translational repression employed by Puf5p: a Pab1p-dependent mechanism and a Pab1p-independent mechanism.
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Affiliation(s)
- Jacqueline J Chritton
- Department of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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36
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Romão TP, de-Melo-Neto OP, Silva-Filha MHNL. The N-terminal third of the BinB subunit from the Bacillus sphaericus binary toxin is sufficient for its interaction with midgut receptors in Culex quinquefasciatus. FEMS Microbiol Lett 2011; 321:167-74. [DOI: 10.1111/j.1574-6968.2011.02325.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Importin alpha-mediated nuclear import of cytoplasmic poly(A) binding protein occurs as a direct consequence of cytoplasmic mRNA depletion. Mol Cell Biol 2011; 31:3113-25. [PMID: 21646427 DOI: 10.1128/mcb.05402-11] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Recent studies have found the cytoplasmic poly(A) binding protein (PABPC) to have opposing effects on gene expression when concentrated in the cytoplasm versus in the nucleus. PABPC is predominantly cytoplasmic at steady state, where it enhances protein synthesis through simultaneous interactions with mRNA and translation factors. However, it accumulates dramatically within the nucleus in response to various pathogenic and nonpathogenic stresses, leading to an inhibition of mRNA export. The molecular events that trigger relocalization of PABPC and the mechanisms by which it translocates into the nucleus to block gene expression are not understood. Here, we reveal an RNA-based mechanism of retaining PABPC in the cytoplasm. Expression either of viral proteins that promote mRNA turnover or of a cytoplasmic deadenylase drives nuclear relocalization of PABPC in a manner dependent on the PABPC RNA recognition motifs (RRMs). Using multiple independent binding sites within its RRMs, PABPC interacts with importin α, a component of the classical import pathway. Finally, we demonstrate that the direct association of PABPC with importin α is antagonized by the presence of poly(A) RNA, supporting a model in which RNA binding masks nuclear import signals within the PABPC RRMs, thereby ensuring efficient cytoplasmic retention of this protein in normal cells. These findings further suggest that cells must carefully calibrate the ratio of PABPC to mRNA, as events that offset this balance can dramatically influence gene expression.
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Abstract
The regulation of translation has emerged as a major determinant of gene expression and is critical for both normal cellular function and the development of disease. Numerous studies have highlighted the diverse, and sometimes related, mechanisms which underlie the regulation of global translation rates and the translational control of specific mRNAs. In the present paper, we discuss the emerging roles of the basal translation factor PABP [poly(A)-binding protein] in mRNA-specific translational control in metazoa which suggest that PABP function is more complex than first recognized.
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da Costa Lima TD, Moura DMN, Reis CRS, Vasconcelos JRC, Ellis L, Carrington M, Figueiredo RCBQ, de Melo Neto OP. Functional characterization of three leishmania poly(a) binding protein homologues with distinct binding properties to RNA and protein partners. EUKARYOTIC CELL 2010; 9:1484-94. [PMID: 20675580 PMCID: PMC2950419 DOI: 10.1128/ec.00148-10] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2010] [Accepted: 07/19/2010] [Indexed: 11/20/2022]
Abstract
Trypanosomatid protozoans are reliant on posttranscriptional processes to control gene expression. Regulation occurs at the levels of mRNA processing, stability, and translation, events that may require the participation of the poly(A) binding protein (PABP). Here, we have undertaken a functional study of the three distinct Leishmania major PABP (LmPABP) homologues: the previously described LmPABP1; LmPABP2, orthologous to the PABP described from Trypanosoma species; and LmPABP3, unique to Leishmania. Sequence identity between the three PABPs is no greater than 40%. In assays measuring binding to A-rich sequences, LmPABP1 binding was poly(A) sensitive but heparin insensitive; LmPABP2 binding was heparin sensitive and less sensitive to poly(A), compatible with unique substitutions observed in residues implicated in poly(A) binding; and LmPABP3 displayed intermediate properties. All three homologues are simultaneously expressed as abundant cytoplasmic proteins in L. major promastigotes, but only LmPABP1 is present as multiple isoforms. Upon transcription inhibition, LmPABP2 and -3 migrated to the nucleus, while LmPABP1 remained predominantly cytoplasmic. Immunoprecipitation assays showed an association between LmPABP2 and -3. Although the three proteins bound to a Leishmania homologue of the translation initiation factor eukaryotic initiation factor 4G (eIF4G) (LmEIF4G3) in vitro, LmPABP1 was the only one to copurify with native LmEIF4G3 from cytoplasmic extracts. Functionality was tested using RNA interference (RNAi) in Trypanosoma brucei, where both orthologues to LmPABP1 and -2 are required for cellular viability. Our results indicate that these homologues have evolved divergent functions, some of which may be unique to the trypanosomatids, and reinforces a role for LmPABP1 in translation through its interaction with the eIF4G homologue.
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Affiliation(s)
- Tamara D. da Costa Lima
- Departamento de Microbiologia, Centro de Pesquisas Aggeu Magalhães/Fiocruz, Av. Moraes Rego s/n, Campus UFPE, Recife, PE 50670-420, Brazil
| | - Danielle M. N. Moura
- Departamento de Microbiologia, Centro de Pesquisas Aggeu Magalhães/Fiocruz, Av. Moraes Rego s/n, Campus UFPE, Recife, PE 50670-420, Brazil
| | - Christian R. S. Reis
- Departamento de Microbiologia, Centro de Pesquisas Aggeu Magalhães/Fiocruz, Av. Moraes Rego s/n, Campus UFPE, Recife, PE 50670-420, Brazil
| | - J. Ronnie C. Vasconcelos
- Departamento de Microbiologia, Centro de Pesquisas Aggeu Magalhães/Fiocruz, Av. Moraes Rego s/n, Campus UFPE, Recife, PE 50670-420, Brazil
| | - Louise Ellis
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - Mark Carrington
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - Regina C. B. Q. Figueiredo
- Departamento de Microbiologia, Centro de Pesquisas Aggeu Magalhães/Fiocruz, Av. Moraes Rego s/n, Campus UFPE, Recife, PE 50670-420, Brazil
| | - Osvaldo P. de Melo Neto
- Departamento de Microbiologia, Centro de Pesquisas Aggeu Magalhães/Fiocruz, Av. Moraes Rego s/n, Campus UFPE, Recife, PE 50670-420, Brazil
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Ferreira LM, Romão TP, de-Melo-Neto OP, Silva-Filha MHNL. The orthologue to the Cpm1/Cqm1 receptor in Aedes aegypti is expressed as a midgut GPI-anchored α-glucosidase, which does not bind to the insecticidal binary toxin. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2010; 40:604-610. [PMID: 20685335 DOI: 10.1016/j.ibmb.2010.05.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2010] [Revised: 05/14/2010] [Accepted: 05/27/2010] [Indexed: 05/29/2023]
Abstract
Aedes aegypti larvae are refractory to the insecticidal binary (Bin) toxin from Bacillus sphaericus, which is not able to bind to its target tissue in the larval midgut. In contrast, Culex pipiens larvae are highly susceptible to that toxin, which targets its midgut brush border membranes (BBMF) through the binding of the BinB subunit to specific receptors, the Cpm1/Cqm1 membrane-bound α-glucosidases. The identification of an Ae. aegypti gene encoding a Cpm1/Cqm1 orthologue, here named Aam1, led to the major goal of this study which was to investigate its expression. The aam1 transcript was found in larvae and adults from Ae. aegypti and a ≈73-kDa protein was recognized by an anti-Cqm1 antibody in midgut BBMF. The Aam1 protein displayed α-glucosidase activity and localized to the midgut epithelium, bound through a GPI anchor, similarly to Cpm1/Cqm1. However, no binding of native Aam1 was observed to the recombinant BinB subunit. Treatment of both proteins with endoglycosidase led to changes in the molecular weight of Aam1, but not Cqm1, implying that the former was glycosylated. The findings from this work rule out lack of receptors in larval stages, or its expression as soluble proteins, as a reason for Ae. aegypti refractoriness to Bin toxin.
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Affiliation(s)
- Lígia Maria Ferreira
- Department of Entomology, Centro de Pesquisas Aggeu Magalhães/FIOCRUZ, Av. Moraes Rego s/n, Cidade Universitária, Recife-PE 50670-420, Brazil
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41
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Betney R, de Silva E, Krishnan J, Stansfield I. Autoregulatory systems controlling translation factor expression: thermostat-like control of translational accuracy. RNA (NEW YORK, N.Y.) 2010; 16:655-63. [PMID: 20185543 PMCID: PMC2844614 DOI: 10.1261/rna.1796210] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
In both prokaryotes and eukaryotes, the expression of a large number of genes is controlled by negative feedback, in some cases operating at the level of translation of the mRNA transcript. Of particular interest are those cases where the proteins concerned have cell-wide function in recognizing a particular codon or RNA sequence. Examples include the bacterial translation termination release factor RF2, initiation factor IF3, and eukaryote poly(A) binding protein. The regulatory loops that control their synthesis establish a negative feedback control mechanism based upon that protein's RNA sequence recognition function in translation (for example, stop codon recognition) without compromising the accurate recognition of that codon, or sequence during general, cell-wide translation. Here, the bacterial release factor RF2 and initiation factor IF3 negative feedback loops are reviewed and compared with similar negative feedback loops that regulate the levels of the eukaryote release factor, eRF1, established artificially by mutation. The control properties of such negative feedback loops are discussed as well as their evolution. The role of negative feedback to control translation factor expression is considered in the context of a growing body of evidence that both IF3 and RF2 can play a role in stimulating stalled ribosomes to abandon translation in response to amino acid starvation. Here, we make the case that negative feedback control serves primarily to limit the overexpression of these translation factors, preventing the loss of fitness resulting from an unregulated increase in the frequency of ribosome drop-off.
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Affiliation(s)
- Russell Betney
- School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Aberdeen, AB25 2ZD, United Kingdom
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42
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Jackson RJ, Hellen CUT, Pestova TV. The mechanism of eukaryotic translation initiation and principles of its regulation. Nat Rev Mol Cell Biol 2010; 11:113-27. [PMID: 20094052 DOI: 10.1038/nrm2838] [Citation(s) in RCA: 1877] [Impact Index Per Article: 134.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Protein synthesis is principally regulated at the initiation stage (rather than during elongation or termination), allowing rapid, reversible and spatial control of gene expression. Progress over recent years in determining the structures and activities of initiation factors, and in mapping their interactions in ribosomal initiation complexes, have advanced our understanding of the complex translation initiation process. These developments have provided a solid foundation for studying the regulation of translation initiation by mechanisms that include the modulation of initiation factor activity (which affects almost all scanning-dependent initiation) and through sequence-specific RNA-binding proteins and microRNAs (which affect individual mRNAs).
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Affiliation(s)
- Richard J Jackson
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK.
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43
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Kong YW, Cannell IG, de Moor CH, Hill K, Garside PG, Hamilton TL, Meijer HA, Dobbyn HC, Stoneley M, Spriggs KA, Willis AE, Bushell M. The mechanism of micro-RNA-mediated translation repression is determined by the promoter of the target gene. Proc Natl Acad Sci U S A 2008; 105:8866-71. [PMID: 18579786 PMCID: PMC2449332 DOI: 10.1073/pnas.0800650105] [Citation(s) in RCA: 149] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2008] [Indexed: 12/20/2022] Open
Abstract
MicroRNAs (miRNAs) are noncoding RNAs that base pair imperfectly to homologous regions in target mRNAs and negatively influence the synthesis of the corresponding proteins. Repression is mediated by a number of mechanisms, one of which is the direct inhibition of protein synthesis. Surprisingly, previous studies have suggested that two mutually exclusive mechanisms exist, one acting at the initiation phase of protein synthesis and the other at a postinitiation event. Here, we resolve this apparent dichotomy by demonstrating that the promoter used to transcribe the mRNA influences the type of miRNA-mediated translational repression. Transcripts derived from the SV40 promoter that contain let-7 target sites in their 3' UTRs are repressed at the initiation stage of translation, whereas essentially identical mRNAs derived from the TK promoter are repressed at a postinitiation step. We also show that there is a miR-34 target site within the 3' UTR of c-myc mRNA and that promoter dependency is also true for this endogenous 3' UTR. Overall, these data establish a link between the nuclear history of an mRNA and the mechanism of miRNA-mediated translational regulation in the cytoplasm.
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Affiliation(s)
- Yi Wen Kong
- School of Pharmacy, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Ian G. Cannell
- School of Pharmacy, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Cornelia H. de Moor
- School of Pharmacy, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Kirsti Hill
- School of Pharmacy, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Paul G. Garside
- School of Pharmacy, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Tiffany L. Hamilton
- School of Pharmacy, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Hedda A. Meijer
- School of Pharmacy, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Helen C. Dobbyn
- School of Pharmacy, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Mark Stoneley
- School of Pharmacy, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Keith A. Spriggs
- School of Pharmacy, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Anne E. Willis
- School of Pharmacy, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Martin Bushell
- School of Pharmacy, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
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Patel GP, Bag J. IMP1 interacts with poly(A)-binding protein (PABP) and the autoregulatory translational control element of PABP-mRNA through the KH III-IV domain. FEBS J 2006; 273:5678-90. [PMID: 17212783 DOI: 10.1111/j.1742-4658.2006.05556.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Repression of poly(A)-binding protein (PABP) mRNA translation involves the formation of a heterotrimeric ribonucleoprotein complex by the binding of PABP, insulin-like growth factor II mRNA binding protein-1 (IMP1) and the unr gene encoded polypeptide (UNR) to the adenine-rich autoregulatory sequence (ARS) located at the 5' untranslated region of the PABP-mRNA. In this report, we have further characterized the interaction between PABP and IMP1 with the ARS at the molecular level. The dissociation constants of PABP and IMP1 for binding to the ARS RNA were determined to be 2.3 nM and 5.9 nM, respectively. Both PABP and IMP1 interact with each other, regardless of the presence of the ARS, through the conserved C-terminal PABP-C and K-homology (KH) III-IV domains, respectively. Interaction of PABP with the ARS requires at least three out of its four RNA-binding domains, whereas KH III-IV domain of IMP1 is necessary and sufficient for binding to the ARS. In addition, the strongest binding site for both PABP and IMP1 on the ARS was determined to be within the 22 nucleotide-long CCCAAAAAAAUUUACAAAAAA sequence located at the 3' end of the ARS. Results of our analysis suggest that both protein x protein and protein x RNA interactions are involved in forming a stable ribonucleoprotein complex at the ARS of PABP mRNA.
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Affiliation(s)
- Gopal P Patel
- Department of Molecular and Cellular Biology, University of Guelph, Ontario, Canada
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45
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Skabkin MA, Lyabin DN, Ovchinnikov LP. Nonspecific and specific interactions of Y-box-binding protein 1 (YB-1) with mRNA and posttranscriptional regulation of protein synthesis in animal cells. Mol Biol 2006. [DOI: 10.1134/s0026893306040078] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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46
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Romão TP, de Melo Chalegre KD, Key S, Ayres CFJ, Fontes de Oliveira CM, de-Melo-Neto OP, Silva-Filha MHNL. A second independent resistance mechanism to Bacillus sphaericus binary toxin targets its alpha-glucosidase receptor in Culex quinquefasciatus. FEBS J 2006; 273:1556-68. [PMID: 16689941 DOI: 10.1111/j.1742-4658.2006.05177.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The entomopathogen Bacillus sphaericus is an important tool for the vector control of Culex sp., and its effectiveness has been validated in field trials. The appearance of resistance to this bacterium, however, remains a threat to its use, and attempts have been made to understand the resistance mechanisms. Previous work showed that the resistance to B. sphaericus in a Culex quinquefasciatus colony is associated with the absence of the approximately 60-kDa binary toxin receptor in larvae midgut microvilli. Here, the gene encoding the C. quinquefasciatus toxin receptor, Cqm1, was cloned and sequenced from a susceptible colony. The deduced amino-acid sequence confirmed its identity as an alpha-glucosidase, and analysis of the corresponding gene sequence from resistant larvae implicated a 19-nucleotide deletion as the basis for resistance. This deletion changes the ORF and originates a premature stop codon, which prevents the synthesis of the full-length Cqm1. Expression of the truncated protein, however, was not detected when whole larvae extracts were probed with antibodies raised against an N-terminal 45-kDa recombinant fragment of Cqm1. It seems that the premature stop codon directs the mutated cqm1 to the nonsense-mediated decay pathway of mRNA degradation. In-gel assays confirmed that a single alpha-glucosidase protein is missing from the resistant colony. Further in vitro affinity assays showed that the recombinant fragment binds to the toxin, and mapped the binding site to the N-terminus of the receptor.
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Affiliation(s)
- Tatiany Patrícia Romão
- Department of Entomology, Centro de Pesquisas Aggeu Magalhães/Fundação Oswaldo Cruz, Recife-PE, Brazil
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47
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Patel GP, Ma S, Bag J. The autoregulatory translational control element of poly(A)-binding protein mRNA forms a heteromeric ribonucleoprotein complex. Nucleic Acids Res 2005; 33:7074-89. [PMID: 16356927 PMCID: PMC1316114 DOI: 10.1093/nar/gki1014] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Repression of poly(A)-binding protein (PABP) mRNA translation involves the binding of PABP to the adenine-rich autoregulatory sequence (ARS) in the 5′-untranslated region of its own mRNA. In this report, we show that the ARS forms a complex in vitro with PABP, and two additional polypeptides of 63 and 105 kDa. The 63 and 105 kDa polypeptides were identified, as IMP1, an ortholog of chicken zip-code binding polypeptide, and UNR, a PABP binding polypeptide, respectively, by mass spectrometry of the ARS RNA affinity purified samples. Using a modified ribonucleoprotein (RNP) immunoprecipitation procedure we further show that indeed, both IMP1 and UNR bind to the ARS containing reporter RNA in vivo. Although both IMP1 and UNR could bind independently to the ARS RNA in vitro, their RNA-binding ability was stimulated by PABP. Mutational analyses of the ARS show that the presence of four of the six oligo(A) regions of the ARS was sufficient to repress translation and the length of the conserved pyrimidine spacers between the oligo(A) sequences was important for ARS function. The ability of mutant ARS RNAs to form the PABP, IMP1 and UNR containing RNP complex correlates well with the translational repressor activity of the ARS. There is also a direct relationship between the length of the poly(A) RNAs and their ability to form a trimeric complex with PABP, and to repress mRNA translation. UV crosslinking studies suggest that the ARS is less efficient than a poly(A) RNA of similar length, to bind to PABP. We show here that the ARS cannot efficiently form a trimeric complex with PABP; therefore, additional interactions with IMP1 and UNR to form a heteromeric RNP complex may be required for maximal repression of PABP mRNA translation under physiological conditions.
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Affiliation(s)
| | | | - Jnanankur Bag
- To whom correspondence should be addressed. Tel: +1 519 824 4120 (Ext. 53390); Fax: +1 519 837 2075;
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48
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Ma S, Musa T, Bag J. Reduced stability of mitogen-activated protein kinase kinase-2 mRNA and phosphorylation of poly(A)-binding protein (PABP) in cells overexpressing PABP. J Biol Chem 2005; 281:3145-56. [PMID: 16332685 DOI: 10.1074/jbc.m508937200] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The poly(A)-binding protein (PABP) is an important regulator of mRNA translation and stability. The cellular level of PABP is controlled by regulating its mRNA translation by a feedback mechanism. The important aspect of this mechanism is that PABP binds to an adenosine-rich cis-element at the 5'-untranslated region of its own mRNA and inhibits its translation. To assess the importance of controlling the PABP level, we studied the effect of PABP overexpression on the transcription profile using the microarray technique. In PABP-overexpressing cells, 19 mRNAs showed a reduction in cellular levels due to reduced mRNA stability, and one showed an increase due to increased mRNA stability. Among these mRNAs, the MKK-2 mRNA encodes the protein kinase activator of ERK1/2 kinase, which is involved in the phosphorylation of eukaryotic initiation factor (eIF) 4E. As a result, mRNA translation may be regulated by the cellular level of MKK-2. In this study, we show that the abundance of the MKK-2 polypeptide is reduced in PABP-overexpressing cells. In these cells, the levels of phosphorylated PABP, eIF4E, and ERK2 are also reduced. Treatment of HeLa cells with the MKK-2 inhibitor U0126 reduced PABP phosphorylation, suggesting that the phosphorylation of PABP is mediated by the MKK-2/ERK signaling pathway. Thus, a novel signaling pathway involving MKK-2 and ERK1/2 may down-regulate the activity of PABP and eIF4E by controlling their phosphorylation and compensates for the effect of excess cellular PABP.
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Affiliation(s)
- Shuhua Ma
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
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49
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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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50
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Dhalia R, Reis CRS, Freire ER, Rocha PO, Katz R, Muniz JRC, Standart N, de Melo Neto OP. Translation initiation in Leishmania major: characterisation of multiple eIF4F subunit homologues. Mol Biochem Parasitol 2005; 140:23-41. [PMID: 15694484 DOI: 10.1016/j.molbiopara.2004.12.001] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2004] [Revised: 11/25/2004] [Accepted: 12/07/2004] [Indexed: 10/26/2022]
Abstract
In eukaryotes protein synthesis initiates with the binding of the multimeric translation initiation complex eIF4F - eIF4E, eIF4A and eIF4G - to the monomethylated cap present on the 5' end of mRNAs. eIF4E interacts directly with the cap nucleotide, while eIF4A is a highly conserved RNA helicase and eIF4G acts as a scaffold for the complex with binding sites for both eIF4E and eIF4A. eIF4F binding to the mRNA recruits the small ribosomal subunit to its 5' end. Little is known in detail of protein synthesis in the protozoan parasites belonging to the family Trypanosomatidae. However, the presence of the highly modified cap structure, cap4, and the spliced leader sequence on the 5' ends of all mRNAs suggests possible differences in mRNA recruitment by ribosomes. We identified several potential eIF4F homologues by searching Leishmania major databases: four eIF4Es (LmEIF4E1-4), two eIF4As (LmEIF4A1-2) and five eIF4Gs (LmEIF4G1-5). We report the initial characterisation of LmEIF4E1-3, LmEIF4A1-2 and LmEIF4G3. First, the expression of these proteins in L. major promastigotes was quantitated by Western blotting using isoform specific antibodies. LmEIF4A1 and LmEIF4E3 are very abundant, LmEIF4G3 is moderately abundant and LmEIF4E1/LmEIF4E2/LmEIF4A2 are rare or not detected. In cap-binding assays, only LmEIF4E1 bound to the 7-methyl-GTP-Sepharose resin. Molecular modelling confirmed that LmEIF4E1 has all the structural features of a cap-binding protein. Finally, pull-down assays were used to investigate the potential interaction between the eIF4A (LmEIF4A1/LmEIF4A2) and eIF4G (LmEIF4G1-3) homologues. Only LmEIF4G3, via the HEAT domain, bound specifically both to LmEIF4A1 as well as to human eIF4A. Therefore for each factor, one of the L. major forms seems to fulfil, in part at least, the expected characteristics of a translational initiation factor.
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Affiliation(s)
- Rafael Dhalia
- Departamento de Biologia Celular, Universidade de Brasilia, Brasilia 70910-900, D.F., Brazil
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