1
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Mangkalaphiban K, Ganesan R, Jacobson A. Pleiotropic effects of PAB1 deletion: Extensive changes in the yeast proteome, transcriptome, and translatome. PLoS Genet 2024; 20:e1011392. [PMID: 39236083 PMCID: PMC11407637 DOI: 10.1371/journal.pgen.1011392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 09/17/2024] [Accepted: 08/11/2024] [Indexed: 09/07/2024] Open
Abstract
Cytoplasmic poly(A)-binding protein (PABPC; Pab1 in yeast) is thought to be involved in multiple steps of post-transcriptional control, including translation initiation, translation termination, and mRNA decay. To understand both the direct and indirect roles of PABPC in more detail, we have employed mass spectrometry to assess the abundance of the components of the yeast proteome, as well as RNA-Seq and Ribo-Seq to analyze changes in the abundance and translation of the yeast transcriptome, in cells lacking the PAB1 gene. We find that pab1Δ cells manifest drastic changes in the proteome and transcriptome, as well as defects in translation initiation and termination. Defects in translation initiation and the stabilization of specific classes of mRNAs in pab1Δ cells appear to be partly indirect consequences of reduced levels of specific initiation factors, decapping activators, and components of the deadenylation complex in addition to the general loss of Pab1's direct role in these processes. Cells devoid of Pab1 also manifested a nonsense codon readthrough phenotype indicative of a defect in translation termination. Collectively, our results indicate that, unlike the loss of simpler regulatory proteins, elimination of cellular Pab1 is profoundly pleiotropic and disruptive to numerous aspects of post-transcriptional regulation.
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Affiliation(s)
- Kotchaphorn Mangkalaphiban
- Department of Microbiology, UMass Chan Medical School, Worcester, Massachusetts, United States of America
| | - Robin Ganesan
- Department of Microbiology, UMass Chan Medical School, Worcester, Massachusetts, United States of America
| | - Allan Jacobson
- Department of Microbiology, UMass Chan Medical School, Worcester, Massachusetts, United States of America
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2
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Fabia B, Kim M, Lim J, Lee YS. Mathematical Modeling of mRNA Poly(A) Tail Shortening Process. Methods Mol Biol 2024; 2723:303-317. [PMID: 37824078 DOI: 10.1007/978-1-0716-3481-3_18] [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] [Indexed: 10/13/2023]
Abstract
A sequence of deadenylation events, or the shortening of the poly(A) tail, is a highly regulated process during the life cycle of mRNAs. Advances in biochemistry have enabled the study of deadenylation events at single-nucleotide resolution. Here we describe mathematical models and their applications to estimate the kinetics of a single deadenylation event in vitro. We demonstrate how this quantitative approach is used for assessing reactions with synthetic RNA with poly(A) tails and the CCR4-NOT complex. This method is also applicable to investigating the catalytic activities of other exonucleases and RNA substrates. All example data and custom software are available on GitHub: https://github.com/2yngsklab/deadenylation-kinetics .
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Affiliation(s)
- Benedict Fabia
- School of Computing, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Minju Kim
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Jongmin Lim
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Young-Suk Lee
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.
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3
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Mangkalaphiban K, Ganesan R, Jacobson A. Direct and indirect consequences of PAB1 deletion in the regulation of translation initiation, translation termination, and mRNA decay. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.31.543082. [PMID: 37398227 PMCID: PMC10312514 DOI: 10.1101/2023.05.31.543082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Cytoplasmic poly(A)-binding protein (PABPC; Pab1 in yeast) is thought to be involved in multiple steps of post-transcriptional control, including translation initiation, translation termination, and mRNA decay. To understand these roles of PABPC in more detail for endogenous mRNAs, and to distinguish its direct effects from indirect effects, we have employed RNA-Seq and Ribo-Seq to analyze changes in the abundance and translation of the yeast transcriptome, as well as mass spectrometry to assess the abundance of the components of the yeast proteome, in cells lacking the PAB1 gene. We observed drastic changes in the transcriptome and proteome, as well as defects in translation initiation and termination, in pab1Δ cells. Defects in translation initiation and the stabilization of specific classes of mRNAs in pab1Δ cells appear to be partly indirect consequences of reduced levels of specific initiation factors, decapping activators, and components of the deadenylation complex in addition to the general loss of Pab1's direct role in these processes. Cells devoid of Pab1 also manifested a nonsense codon readthrough phenotype indicative of a defect in translation termination, but this defect may be a direct effect of the loss of Pab1 as it could not be attributed to significant reductions in the levels of release factors.
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Affiliation(s)
- Kotchaphorn Mangkalaphiban
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, 368 Plantation Street, Worcester, MA 01655
| | - Robin Ganesan
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, 368 Plantation Street, Worcester, MA 01655
| | - Allan Jacobson
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, 368 Plantation Street, Worcester, MA 01655
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4
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Zhang G, Luo H, Li X, Hu Z, Wang Q. The Dynamic Poly(A) Tail Acts as a Signal Hub in mRNA Metabolism. Cells 2023; 12:572. [PMID: 36831239 PMCID: PMC9954528 DOI: 10.3390/cells12040572] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 01/19/2023] [Accepted: 02/08/2023] [Indexed: 02/12/2023] Open
Abstract
In eukaryotes, mRNA metabolism requires a sophisticated signaling system. Recent studies have suggested that polyadenylate tail may play a vital role in such a system. The poly(A) tail used to be regarded as a common modification at the 3' end of mRNA, but it is now known to be more than just that. It appears to act as a platform or hub that can be understood in two ways. On the one hand, polyadenylation and deadenylation machinery constantly regulates its dynamic activity; on the other hand, it exhibits the ability to recruit RNA-binding proteins and then interact with diverse factors to send various signals to regulate mRNA metabolism. In this paper, we outline the main complexes that regulate the dynamic activities of poly(A) tails, explain how these complexes participate polyadenylation/deadenylation process and summarize the diverse signals this hub emit. We are trying to make a point that the poly(A) tail can metaphorically act as a "flagman" who is supervised by polyadenylation and deadenylation and sends out signals to regulate the orderly functioning of mRNA metabolism.
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Affiliation(s)
- Guiying Zhang
- Guangdong Technology Research Center for Marine Algal Bioengineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Haolin Luo
- Guangdong Technology Research Center for Marine Algal Bioengineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China
| | - Xinyi Li
- Guangdong Technology Research Center for Marine Algal Bioengineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China
| | - Zhangli Hu
- Guangdong Technology Research Center for Marine Algal Bioengineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Quan Wang
- Guangdong Technology Research Center for Marine Algal Bioengineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
- School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning 437100, China
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5
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Lai WJC, Zhu M, Belinite M, Ballard G, Mathews DH, Ermolenko DN. Intrinsically Unstructured Sequences in the mRNA 3' UTR Reduce the Ability of Poly(A) Tail to Enhance Translation. J Mol Biol 2022; 434:167877. [PMID: 36368412 PMCID: PMC9750134 DOI: 10.1016/j.jmb.2022.167877] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 09/27/2022] [Accepted: 11/01/2022] [Indexed: 11/09/2022]
Abstract
The 5' cap and 3' poly(A) tail of mRNA are known to synergistically stimulate translation initiation via the formation of the cap•eIF4E•eIF4G•PABP•poly(A) complex. Most mRNA sequences have an intrinsic propensity to fold into extensive intramolecular secondary structures that result in short end-to-end distances. The inherent compactness of mRNAs might stabilize the cap•eIF4E•eIF4G•PABP•poly(A) complex and enhance cap-poly(A) translational synergy. Here, we test this hypothesis by introducing intrinsically unstructured sequences into the 5' or 3' UTRs of model mRNAs. We found that the introduction of unstructured sequences into the 3' UTR, but not the 5' UTR, decreases mRNA translation in cell-free wheat germ and yeast extracts without affecting mRNA stability. The observed reduction in protein synthesis results from the diminished ability of the poly(A) tail to stimulate translation. These results suggest that base pair formation by the 3' UTR enhances the cap-poly(A) synergy in translation initiation.
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Affiliation(s)
- Wan-Jung C Lai
- Department of Biochemistry & Biophysics and Center for RNA Biology, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, United States
| | - Mingyi Zhu
- Department of Biochemistry & Biophysics and Center for RNA Biology, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, United States
| | - Margarita Belinite
- Department of Biochemistry & Biophysics and Center for RNA Biology, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, United States
| | - Gregory Ballard
- Department of Biochemistry & Biophysics and Center for RNA Biology, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, United States
| | - David H Mathews
- Department of Biochemistry & Biophysics and Center for RNA Biology, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, United States
| | - Dmitri N Ermolenko
- Department of Biochemistry & Biophysics and Center for RNA Biology, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, United States.
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6
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Nicholson-Shaw AL, Kofman ER, Yeo GW, Pasquinelli A. Nuclear and cytoplasmic poly(A) binding proteins (PABPs) favor distinct transcripts and isoforms. Nucleic Acids Res 2022; 50:4685-4702. [PMID: 35438785 PMCID: PMC9071453 DOI: 10.1093/nar/gkac263] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/23/2022] [Accepted: 04/04/2022] [Indexed: 11/14/2022] Open
Abstract
The poly(A)-tail appended to the 3'-end of most eukaryotic transcripts plays a key role in their stability, nuclear transport, and translation. These roles are largely mediated by Poly(A) Binding Proteins (PABPs) that coat poly(A)-tails and interact with various proteins involved in the biogenesis and function of RNA. While it is well-established that the nuclear PABP (PABPN) binds newly synthesized poly(A)-tails and is replaced by the cytoplasmic PABP (PABPC) on transcripts exported to the cytoplasm, the distribution of transcripts for different genes or isoforms of the same gene on these PABPs has not been investigated on a genome-wide scale. Here, we analyzed the identity, splicing status, poly(A)-tail size, and translation status of RNAs co-immunoprecipitated with endogenous PABPN or PABPC in human cells. At steady state, many protein-coding and non-coding RNAs exhibit strong bias for association with PABPN or PABPC. While PABPN-enriched transcripts more often were incompletely spliced and harbored longer poly(A)-tails and PABPC-enriched RNAs had longer half-lives and higher translation efficiency, there are curious outliers. Overall, our study reveals the landscape of RNAs bound by PABPN and PABPC, providing new details that support and advance the current understanding of the roles these proteins play in poly(A)-tail synthesis, maintenance, and function.
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Affiliation(s)
| | - Eric R Kofman
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
- UCSD Stem Cell Program, Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
- UCSD Stem Cell Program, Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Amy E Pasquinelli
- Division of Biology, University of California, San Diego, La Jolla, CA 92093, USA
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7
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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: 197] [Impact Index Per Article: 98.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/16/2021] [Indexed: 02/06/2023]
Abstract
In eukaryotes, poly(A) tails are present on almost every mRNA. Early experiments led to the hypothesis that poly(A) tails and the cytoplasmic polyadenylate-binding protein (PABPC) promote translation and prevent mRNA degradation, but the details remained unclear. More recent data suggest that the role of poly(A) tails is much more complex: poly(A)-binding protein can stimulate poly(A) tail removal (deadenylation) and the poly(A) tails of stable, highly translated mRNAs at steady state are much shorter than expected. Furthermore, the rate of translation elongation affects deadenylation. Consequently, the interplay between poly(A) tails, PABPC, translation and mRNA decay has a major role in gene regulation. In this Review, we discuss recent work that is revolutionizing our understanding of the roles of poly(A) tails in the cytoplasm. Specifically, we discuss the roles of poly(A) tails in translation and control of mRNA stability and how poly(A) tails are removed by exonucleases (deadenylases), including CCR4-NOT and PAN2-PAN3. We also discuss how deadenylation rate is determined, the integration of deadenylation with other cellular processes and the function of PABPC. We conclude with an outlook for the future of research in this field.
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8
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Ermolenko DN, Mathews DH. Making ends meet: New functions of mRNA secondary structure. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 12:e1611. [PMID: 32597020 DOI: 10.1002/wrna.1611] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 05/19/2020] [Accepted: 05/19/2020] [Indexed: 11/10/2022]
Abstract
The 5' cap and 3' poly(A) tail of mRNA are known to synergistically regulate mRNA translation and stability. Recent computational and experimental studies revealed that both protein-coding and non-coding RNAs will fold with extensive intramolecular secondary structure, which will result in close distances between the sequence ends. This proximity of the ends is a sequence-independent, universal property of most RNAs. Only low-complexity sequences without guanosines are without secondary structure and exhibit end-to-end distances expected for RNA random coils. The innate proximity of RNA ends might have important biological implications that remain unexplored. In particular, the inherent compactness of mRNA might regulate translation initiation by facilitating the formation of protein complexes that bridge mRNA 5' and 3' ends. Additionally, the proximity of mRNA ends might mediate coupling of 3' deadenylation to 5' end mRNA decay. This article is categorized under: RNA Structure and Dynamics > RNA Structure, Dynamics, and Chemistry RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems Translation > Translation Regulation.
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Affiliation(s)
- Dmitri N Ermolenko
- Department of Biochemistry & Biophysics and Center for RNA Biology, School of Medicine and Dentistry, University of Rochester, Rochester, New York, USA
| | - David H Mathews
- Department of Biochemistry & Biophysics and Center for RNA Biology, School of Medicine and Dentistry, University of Rochester, Rochester, New York, USA
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9
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Yao X, Kojima S, Chen J. Critical role of deadenylation in regulating poly(A) rhythms and circadian gene expression. PLoS Comput Biol 2020; 16:e1007842. [PMID: 32339166 PMCID: PMC7205317 DOI: 10.1371/journal.pcbi.1007842] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 05/07/2020] [Accepted: 04/02/2020] [Indexed: 11/18/2022] Open
Abstract
The mammalian circadian clock is deeply rooted in rhythmic regulation of gene expression. Rhythmic transcriptional control mediated by the circadian transcription factors is thought to be the main driver of mammalian circadian gene expression. However, mounting evidence has demonstrated the importance of rhythmic post-transcriptional controls, and it remains unclear how the transcriptional and post-transcriptional mechanisms collectively control rhythmic gene expression. In mouse liver, hundreds of genes were found to exhibit rhythmicity in poly(A) tail length, and the poly(A) rhythms are strongly correlated with the protein expression rhythms. To understand the role of rhythmic poly(A) regulation in circadian gene expression, we constructed a parsimonious model that depicts rhythmic control imposed upon basic mRNA expression and poly(A) regulation processes, including transcription, deadenylation, polyadenylation, and degradation. The model results reveal the rhythmicity in deadenylation as the strongest contributor to the rhythmicity in poly(A) tail length and the rhythmicity in the abundance of the mRNA subpopulation with long poly(A) tails (a rough proxy for mRNA translatability). In line with this finding, the model further shows that the experimentally observed distinct peak phases in the expression of deadenylases, regardless of other rhythmic controls, can robustly cluster the rhythmic mRNAs by their peak phases in poly(A) tail length and abundance of the long-tailed subpopulation. This provides a potential mechanism to synchronize the phases of target gene expression regulated by the same deadenylases. Our findings highlight the critical role of rhythmic deadenylation in regulating poly(A) rhythms and circadian gene expression.
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Affiliation(s)
- Xiangyu Yao
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
- Genetics, Bioinformatics, and Computational Biology program, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
| | - Shihoko Kojima
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
- Fralin Life Sciences Institute, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
| | - Jing Chen
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
- Fralin Life Sciences Institute, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
- * E-mail:
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10
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Abstract
The proper regulation of mRNA processing, localization, translation, and degradation occurs on mRNPs. However, the global principles of mRNP organization are poorly understood. We utilize the limited, but existing, information available to present a speculative synthesis of mRNP organization with the following key points. First, mRNPs form a compacted structure due to the inherent folding of RNA. Second, the ribosome is the principal mechanism by which mRNA regions are partially decompacted. Third, mRNPs are 50%-80% protein by weight, consistent with proteins modulating mRNP organization, but also suggesting the majority of mRNA sequences are not directly interacting with RNA-binding proteins. Finally, the ratio of mRNA-binding proteins to mRNAs is higher in the nucleus to allow effective RNA processing and limit the potential for nuclear RNA based aggregation. This synthesis of mRNP understanding provides a model for mRNP biogenesis, structure, and regulation with multiple implications.
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Affiliation(s)
- Anthony Khong
- Department of Biochemistry and Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, Colorado 80303, USA
| | - Roy Parker
- Department of Biochemistry and Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, Colorado 80303, USA
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11
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Alekhina OM, Terenin IM, Dmitriev SE, Vassilenko KS. Functional Cyclization of Eukaryotic mRNAs. Int J Mol Sci 2020; 21:ijms21051677. [PMID: 32121426 PMCID: PMC7084953 DOI: 10.3390/ijms21051677] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 02/24/2020] [Accepted: 02/27/2020] [Indexed: 11/16/2022] Open
Abstract
The closed-loop model of eukaryotic translation states that mRNA is circularized by a chain of the cap-eIF4E-eIF4G-poly(A)-binding protein (PABP)-poly(A) interactions that brings 5' and 3' ends together. This circularization is thought to promote the engagement of terminating ribosomes to a new round of translation at the same mRNA molecule, thus enhancing protein synthesis. Despite the general acceptance and the elegance of the hypothesis, it has never been proved experimentally. Using continuous in situ monitoring of luciferase synthesis in a mammalian in vitro system, we show here that the rate of translation initiation at capped and polyadenylated reporter mRNAs increases after the time required for the first ribosomes to complete mRNA translation. Such acceleration strictly requires the presence of a poly(A)-tail and is abrogated by the addition of poly(A) RNA fragments or m7GpppG cap analog to the translation reaction. The optimal functional interaction of mRNA termini requires 5' untranslated region (UTR) and 3' UTR of moderate lengths and provides stronger acceleration, thus a longer poly(A)-tail. Besides, we revealed that the inhibitory effect of the dominant negative R362Q mutant of initiation factor eIF4A diminishes in the course of translation reaction, suggesting a relaxed requirement for ATP. Taken together, our results imply that, upon the functional looping of an mRNA, the recycled ribosomes can be recruited to the start codon of the same mRNA molecule in an eIF4A-independent fashion. This non-canonical closed-loop assisted reinitiation (CLAR) mode provides efficient translation of the functionally circularized mRNAs.
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Affiliation(s)
- Olga M. Alekhina
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, 142290 Moscow, Russia;
- Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency, 119435 Moscow, Russia
| | - Ilya M. Terenin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia;
- Sechenov First Moscow State Medical University, Institute of Molecular Medicine, 119991 Moscow, Russia
| | - Sergey E. Dmitriev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia;
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
- School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234 Moscow, Russia
- Correspondence: (S.E.D.); (K.S.V.); Tel.: +7-903-2220066 (S.E.D.); +7-496-7318232 (K.S.V.)
| | - Konstantin S. Vassilenko
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, 142290 Moscow, Russia;
- Correspondence: (S.E.D.); (K.S.V.); Tel.: +7-903-2220066 (S.E.D.); +7-496-7318232 (K.S.V.)
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12
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Bernardes WS, Menossi M. Plant 3' Regulatory Regions From mRNA-Encoding Genes and Their Uses to Modulate Expression. FRONTIERS IN PLANT SCIENCE 2020; 11:1252. [PMID: 32922424 PMCID: PMC7457121 DOI: 10.3389/fpls.2020.01252] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 07/29/2020] [Indexed: 05/08/2023]
Abstract
Molecular biotechnology has made it possible to explore the potential of plants for different purposes. The 3' regulatory regions have a great diversity of cis-regulatory elements directly involved in polyadenylation, stability, transport and mRNA translation, essential to achieve the desired levels of gene expression. A complex interaction between the cleavage and polyadenylation molecular complex and cis-elements determine the polyadenylation site, which may result in the choice of non-canonical sites, resulting in alternative polyadenylation events, involved in the regulation of more than 80% of the genes expressed in plants. In addition, after transcription, a wide array of RNA-binding proteins interacts with cis-acting elements located mainly in the 3' untranslated region, determining the fate of mRNAs in eukaryotic cells. Although a small number of 3' regulatory regions have been identified and validated so far, many studies have shown that plant 3' regulatory regions have a higher potential to regulate gene expression in plants compared to widely used 3' regulatory regions, such as NOS and OCS from Agrobacterium tumefaciens and 35S from cauliflower mosaic virus. In this review, we discuss the role of 3' regulatory regions in gene expression, and the superior potential that plant 3' regulatory regions have compared to NOS, OCS and 35S 3' regulatory regions.
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13
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Nicholson AL, Pasquinelli AE. Tales of Detailed Poly(A) Tails. Trends Cell Biol 2018; 29:191-200. [PMID: 30503240 DOI: 10.1016/j.tcb.2018.11.002] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 11/02/2018] [Accepted: 11/02/2018] [Indexed: 11/18/2022]
Abstract
Poly(A) tails are non-templated additions of adenosines at the 3' ends of most eukaryotic mRNAs. In the nucleus, these RNAs are co-transcriptionally cleaved at a poly(A) site and then polyadenylated before being exported to the cytoplasm. In the cytoplasm, poly(A) tails play pivotal roles in the translation and stability of the mRNA. One challenge in studying poly(A) tails is that they are difficult to sequence and accurately measure. However, recent advances in sequencing technology, computational algorithms, and other assays have enabled a more detailed look at poly(A) tail length genome-wide throughout many developmental stages and organisms. With the help of these advances, our understanding of poly(A) tail length has evolved over the past 5 years with the recognition that highly expressed genes can have short poly(A) tails and the elucidation of the seemingly contradictory roles for poly(A)-binding protein (PABP) in facilitating both protection and deadenylation.
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Affiliation(s)
- Angela L Nicholson
- Division of Biology, University of California, San Diego (USCD), La Jolla, CA 92093-0349, USA
| | - Amy E Pasquinelli
- Division of Biology, University of California, San Diego (USCD), La Jolla, CA 92093-0349, USA.
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14
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Brambilla M, Martani F, Bertacchi S, Vitangeli I, Branduardi P. The Saccharomyces cerevisiae
poly (A) binding protein (Pab1): Master regulator of mRNA metabolism and cell physiology. Yeast 2018; 36:23-34. [DOI: 10.1002/yea.3347] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 06/26/2018] [Accepted: 07/06/2018] [Indexed: 12/15/2022] Open
Affiliation(s)
- Marco Brambilla
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Piazza della Scienza 2 20126 Milan Italy
| | - Francesca Martani
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Piazza della Scienza 2 20126 Milan Italy
| | - Stefano Bertacchi
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Piazza della Scienza 2 20126 Milan Italy
| | - Ilaria Vitangeli
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Piazza della Scienza 2 20126 Milan Italy
| | - Paola Branduardi
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Piazza della Scienza 2 20126 Milan Italy
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15
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Abstract
Codon usage depends on mutation bias, tRNA-mediated selection, and the need for high efficiency and accuracy in translation. One codon in a synonymous codon family is often strongly over-used, especially in highly expressed genes, which often leads to a high dN/dS ratio because dS is very small. Many different codon usage indices have been proposed to measure codon usage and codon adaptation. Sense codon could be misread by release factors and stop codons misread by tRNAs, which also contribute to codon usage in rare cases. This chapter outlines the conceptual framework on codon evolution, illustrates codon-specific and gene-specific codon usage indices, and presents their applications. A new index for codon adaptation that accounts for background mutation bias (Index of Translation Elongation) is presented and contrasted with codon adaptation index (CAI) which does not consider background mutation bias. They are used to re-analyze data from a recent paper claiming that translation elongation efficiency matters little in protein production. The reanalysis disproves the claim.
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mRNA length-sensing in eukaryotic translation: reconsidering the "closed loop" and its implications for translational control. Curr Genet 2016; 63:613-620. [PMID: 28028558 DOI: 10.1007/s00294-016-0674-3] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 12/14/2016] [Accepted: 12/15/2016] [Indexed: 01/01/2023]
Abstract
Most eukaryotic mRNAs are recruited to the ribosome by recognition of a 5' m7GpppN cap. 30 years of genetic and biochemical evidence point to a role for interaction between the 5' cap-interacting factors and the 3' poly(A)-binding protein in bringing the ends of the mRNA into close proximity and promoting both translation and stability of the mRNA, in a form known as the "closed loop". However, the results of recent RNA-protein interaction studies suggest that not all mRNAs have equal access to the closed loop factors. Furthermore, association with closed loop factors appears to be highly biased towards mRNAs with short open reading frames, echoing the trend for higher translation of short mRNAs that has been observed in many eukaryotes. We recently reported that the ribosomal signaling scaffold protein RACK1 promotes the efficient translation of short mRNAs that strongly associate with the closed loop factors. Here, we discuss the implications of these observations with respect to translational control and suggest avenues through which the universality of the closed loop in eukaryotic translation could be revisited.
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Melamed D, Young DL, Miller CR, Fields S. Combining natural sequence variation with high throughput mutational data to reveal protein interaction sites. PLoS Genet 2015; 11:e1004918. [PMID: 25671604 PMCID: PMC4335499 DOI: 10.1371/journal.pgen.1004918] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 11/24/2014] [Indexed: 12/29/2022] Open
Abstract
Many protein interactions are conserved among organisms despite changes in the amino acid sequences that comprise their contact sites, a property that has been used to infer the location of these sites from protein homology. In an inter-species complementation experiment, a sequence present in a homologue is substituted into a protein and tested for its ability to support function. Therefore, substitutions that inhibit function can identify interaction sites that changed over evolution. However, most of the sequence differences within a protein family remain unexplored because of the small-scale nature of these complementation approaches. Here we use existing high throughput mutational data on the in vivo function of the RRM2 domain of the Saccharomyces cerevisiae poly(A)-binding protein, Pab1, to analyze its sites of interaction. Of 197 single amino acid differences in 52 Pab1 homologues, 17 reduce the function of Pab1 when substituted into the yeast protein. The majority of these deleterious mutations interfere with the binding of the RRM2 domain to eIF4G1 and eIF4G2, isoforms of a translation initiation factor. A large-scale mutational analysis of the RRM2 domain in a two-hybrid assay for eIF4G1 binding supports these findings and identifies peripheral residues that make a smaller contribution to eIF4G1 binding. Three single amino acid substitutions in yeast Pab1 corresponding to residues from the human orthologue are deleterious and eliminate binding to the yeast eIF4G isoforms. We create a triple mutant that carries these substitutions and other humanizing substitutions that collectively support a switch in binding specificity of RRM2 from the yeast eIF4G1 to its human orthologue. Finally, we map other deleterious substitutions in Pab1 to inter-domain (RRM2–RRM1) or protein-RNA (RRM2–poly(A)) interaction sites. Thus, the combined approach of large-scale mutational data and evolutionary conservation can be used to characterize interaction sites at single amino acid resolution. The interactions of proteins with each other are essential for almost all biological processes. Many of the sites of protein contact have evolved to maintain these interactions, but use different sets of amino acid residues. As a result, the residues at a contact site in a protein from one species might not allow a protein interaction when they are tested in a second species. This property underlies the idea of inter-species complementation assays, which test the effect of replacing protein segments from one species by their equivalents from another species. However, this approach has been highly limited in the number of changes that could be analyzed in a single study. Here, we present a novel approach that combines a high-throughput analysis of mutations in a single protein with the set of natural sequences corresponding to evolutionarily divergent variants of this protein. This integration step allows us to map at high resolution both sites of inter-protein interaction as well as intra-protein interaction. Our approach can be used with proteins that have limited functional and structural data, and it can be applied to improve the performance of computational tools that use sequence homology to predict function.
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Affiliation(s)
- Daniel Melamed
- Howard Hughes Medical Institute, University of Washington, Seattle, Washington, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
- * E-mail:
| | - David L. Young
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Christina R. Miller
- Howard Hughes Medical Institute, University of Washington, Seattle, Washington, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Stanley Fields
- Howard Hughes Medical Institute, University of Washington, Seattle, Washington, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
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Costello J, Castelli LM, Rowe W, Kershaw CJ, Talavera D, Mohammad-Qureshi SS, Sims PFG, Grant CM, Pavitt GD, Hubbard SJ, Ashe MP. Global mRNA selection mechanisms for translation initiation. Genome Biol 2015; 16:10. [PMID: 25650959 PMCID: PMC4302535 DOI: 10.1186/s13059-014-0559-z] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 12/03/2014] [Indexed: 12/20/2022] Open
Abstract
Background The selection and regulation of individual mRNAs for translation initiation from a competing pool of mRNA are poorly understood processes. The closed loop complex, comprising eIF4E, eIF4G and PABP, and its regulation by 4E-BPs are perceived to be key players. Using RIP-seq, we aimed to evaluate the role in gene regulation of the closed loop complex and 4E-BP regulation across the entire yeast transcriptome. Results We find that there are distinct populations of mRNAs with coherent properties: one mRNA pool contains many ribosomal protein mRNAs and is enriched specifically with all of the closed loop translation initiation components. This class likely represents mRNAs that rely heavily on the closed loop complex for protein synthesis. Other heavily translated mRNAs are apparently under-represented with most closed loop components except Pab1p. Combined with data showing a close correlation between Pab1p interaction and levels of translation, these data suggest that Pab1p is important for the translation of these mRNAs in a closed loop independent manner. We also identify a translational regulatory mechanism for the 4E-BPs; these appear to self-regulate by inhibiting translation initiation of their own mRNAs. Conclusions Overall, we show that mRNA selection for translation initiation is not as uniformly regimented as previously anticipated. Components of the closed loop complex are highly relevant for many mRNAs, but some heavily translated mRNAs interact poorly with this machinery. Therefore, alternative, possibly Pab1p-dependent mechanisms likely exist to load ribosomes effectively onto mRNAs. Finally, these studies identify and characterize a complex self-regulatory circuit for the yeast 4E-BPs. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0559-z) contains supplementary material, which is available to authorized users.
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Abstract
Human rhinoviruses (HRV) are the major etiological agents of the common cold and asthma exacerbations, with significant worldwide health and economic impact. Although large-scale population vaccination has proved successful in limiting or even eradicating many viruses, the more than 100 distinct serotypes mean that conventional vaccination is not a feasible strategy to combat HRV. An alternative strategy is to target conserved viral proteins such as the HRV proteases, 2A(pro) and 3C(pro), the focus of this review. Necessary for host cell shutoff, virus replication, and pathogenesis, 2A(pro) and 3C(pro) are clearly viable drug targets, and indeed, 3C(pro) has been successfully targeted for treating the common cold in experimental infection. 2A(pro) and 3C(pro) are crucial for virus replication due to their role in polyprotein processing as well as cleavage of key cellular proteins to inhibit cellular transcription and translation. Intriguingly, the action of the HRV proteases also disrupts nucleocytoplasmic trafficking, contributing to HRV cytopathic effects. Improved understanding of the protease-cell interactions should enable new therapeutic approaches to be identified for drug development.
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Affiliation(s)
- Lora M Jensen
- Faculty of Education, Science, Technology and Mathematics, Centre for Research in Therapeutic Solutions, University of Canberra, 1 Kirinari Street, Bruce, Canberra, ACT, 2601, Australia
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Melamed D, Young DL, Gamble CE, Miller CR, Fields S. Deep mutational scanning of an RRM domain of the Saccharomyces cerevisiae poly(A)-binding protein. RNA (NEW YORK, N.Y.) 2013; 19:1537-51. [PMID: 24064791 PMCID: PMC3851721 DOI: 10.1261/rna.040709.113] [Citation(s) in RCA: 145] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The RNA recognition motif (RRM) is the most common RNA-binding domain in eukaryotes. Differences in RRM sequences dictate, in part, both RNA and protein-binding specificities and affinities. We used a deep mutational scanning approach to study the sequence-function relationship of the RRM2 domain of the Saccharomyces cerevisiae poly(A)-binding protein (Pab1). By scoring the activity of more than 100,000 unique Pab1 variants, including 1246 with single amino acid substitutions, we delineated the mutational constraints on each residue. Clustering of residues with similar mutational patterns reveals three major classes, composed principally of RNA-binding residues, of hydrophobic core residues, and of the remaining residues. The first class also includes a highly conserved residue not involved in RNA binding, G150, which can be mutated to destabilize Pab1. A comparison of the mutational sensitivity of yeast Pab1 residues to their evolutionary conservation reveals that most residues tolerate more substitutions than are present in the natural sequences, although other residues that tolerate fewer substitutions may point to specialized functions in yeast. An analysis of ∼40,000 double mutants indicates a preference for a short distance between two mutations that display an epistatic interaction. As examples of interactions, the mutations N139T, N139S, and I157L suppress other mutations that interfere with RNA binding and protein stability. Overall, this study demonstrates that living cells can be subjected to a single assay to analyze hundreds of thousands of protein variants in parallel.
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Affiliation(s)
- Daniel Melamed
- Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - David L. Young
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Caitlin E. Gamble
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Christina R. Miller
- Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Stanley Fields
- Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
- Department of Medicine, University of Washington, Seattle, Washington 98195, USA
- Corresponding authorE-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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22
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Chase AJ, Semler BL. Viral subversion of host functions for picornavirus translation and RNA replication. Future Virol 2012; 7:179-191. [PMID: 23293659 DOI: 10.2217/fvl.12.2] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Picornavirus infections lead to symptoms that can have serious health and economic implications. The viruses in this family (Picornaviridae) have a small genomic RNA and must rely on host proteins for efficient viral gene expression and RNA replication. To ensure their effectiveness as pathogens, picornaviruses have evolved to utilize and/or alter host proteins for the benefit of the virus life cycle. This review discusses the host proteins that are subverted during infection to aid in virus replication. It will also describe proteins and functions that are altered during infection for the benefit of the virus.
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Affiliation(s)
- Amanda J Chase
- Department of Microbiology & Molecular Genetics, School of Medicine, University of California, Irvine, CA 92697, USA
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23
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A characterization of Tetrahymena mRNA by in vitro translation: The effects of culture growth on the recruitment of poly (A)(+) and poly (A)(-) RNA. Eur J Protistol 2011. [PMID: 23195657 DOI: 10.1016/s0932-4739(89)80058-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Messenger RNA was extracted from exponentially growing and from stationary cultures of Tetrahymena thermophila. It was separated into polyadenylated and non-polyadenylated fractions which were used as templates in a rabbit reticulocyte protein synthesizing system. The translated proteins were analysed by one and by two dimensional electrophoresis. Our experiments were intended to answer the question to which extent the abundance and the specificity of mRNA facilitates or accompanies the passage of cells through one culture growth cycle. As illustrated by the identification of 113 proteins very few differences between translated messages accompany the transition to the stationary phase, the most obvious feature being a change in the intracellular location of translation activities. These data are discussed with special reference to the prevailing occupation of Tetrahymena which is biomass production.
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Translation initiation: a regulatory role for poly(A) tracts in front of the AUG codon in Saccharomyces cerevisiae. Genetics 2011; 189:469-78. [PMID: 21840854 PMCID: PMC3189813 DOI: 10.1534/genetics.111.132068] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The 5'-UTR serves as the loading dock for ribosomes during translation initiation and is the key site for translation regulation. Many genes in the yeast Saccharomyces cerevisiae contain poly(A) tracts in their 5'-UTRs. We studied these pre-AUG poly(A) tracts in a set of 3274 recently identified 5'-UTRs in the yeast to characterize their effect on in vivo protein abundance, ribosomal density, and protein synthesis rate in the yeast. The protein abundance and the protein synthesis rate increase with the length of the poly(A), but exhibit a dramatic decrease when the poly(A) length is ≥12. The ribosomal density also reaches the lowest level when the poly(A) length is ≥12. This supports the hypothesis that a pre-AUG poly(A) tract can bind to translation initiation factors to enhance translation initiation, but a long (≥12) pre-AUG poly(A) tract will bind to Pab1p, whose binding size is 12 consecutive A residues in yeast, resulting in repression of translation. The hypothesis explains why a long pre-AUG poly(A) leads to more efficient translation initiation than a short one when PABP is absent, and why pre-AUG poly(A) is short in the early genes but long in the late genes of vaccinia virus.
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Abstract
Nearly all eukaryotic mRNAs terminate in a poly(A) tail that serves important roles in mRNA utilization. In the cytoplasm, the poly(A) tail promotes both mRNA stability and translation, and these functions are frequently regulated through changes in tail length. To identify the scope of poly(A) tail length control in a transcriptome, we developed the polyadenylation state microarray (PASTA) method. It involves the purification of mRNA based on poly(A) tail length using thermal elution from poly(U) sepharose, followed by microarray analysis of the resulting fractions. In this chapter we detail our PASTA approach and describe some methods for bulk and mRNA-specific poly(A) tail length measurements of use to monitor the procedure and independently verify the microarray data.
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Affiliation(s)
- Traude H Beilharz
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
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26
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Gouw JW, Pinkse MWH, Vos HR, Moshkin Y, Verrijzer CP, Heck AJR, Krijgsveld J. In vivo stable isotope labeling of fruit flies reveals post-transcriptional regulation in the maternal-to-zygotic transition. Mol Cell Proteomics 2009; 8:1566-78. [PMID: 19321433 DOI: 10.1074/mcp.m900114-mcp200] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
An important hallmark in embryonic development is characterized by the maternal-to-zygotic transition (MZT) where zygotic transcription is activated by a maternally controlled environment. Post-transcriptional and translational regulation is critical for this transition and has been investigated in considerable detail at the gene level. We used a proteomics approach using metabolic labeling of Drosophila to quantitatively assess changes in protein expression levels before and after the MZT. By combining stable isotope labeling of fruit flies in vivo with high accuracy quantitative mass spectrometry we could quantify 2,232 proteins of which about half changed in abundance during this process. We show that approximately 500 proteins increased in abundance, providing direct evidence of the identity of proteins as a product of embryonic translation. The group of down-regulated proteins is dominated by maternal factors involved in translational control of maternal and zygotic transcripts. Surprisingly a direct comparison of transcript and protein levels showed that the mRNA levels of down-regulated proteins remained relatively constant, indicating a translational control mechanism specifically targeting these proteins. In addition, we found evidence for post-translational processing of cysteine proteinase-1 (Cathepsin L), which became activated during the MZT as evidenced by the loss of its N-terminal propeptide. Poly(A)-binding protein was shown to be processed at its C-terminal tail, thereby losing one of its protein-interacting domains. Altogether this quantitative proteomics study provides a dynamic profile of known and novel proteins of maternal as well as embryonic origin. This provides insight into the production, stability, and modification of individual proteins, whereas discrepancies between transcriptional profiles and protein dynamics indicate novel control mechanisms in genome activation during early fly development.
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Affiliation(s)
- Joost W Gouw
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
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27
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Yamamoto A, Kormann M, Rosenecker J, Rudolph C. Current prospects for mRNA gene delivery. Eur J Pharm Biopharm 2009; 71:484-9. [DOI: 10.1016/j.ejpb.2008.09.016] [Citation(s) in RCA: 149] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2007] [Revised: 07/21/2008] [Accepted: 09/02/2008] [Indexed: 12/26/2022]
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28
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Hoenninger VM, Rouha H, Orlinger KK, Miorin L, Marcello A, Kofler RM, Mandl CW. Analysis of the effects of alterations in the tick-borne encephalitis virus 3′-noncoding region on translation and RNA replication using reporter replicons. Virology 2008; 377:419-30. [DOI: 10.1016/j.virol.2008.04.035] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2008] [Revised: 04/19/2008] [Accepted: 04/25/2008] [Indexed: 10/22/2022]
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Rifo RS, Ricci EP, Décimo D, Moncorgé O, Ohlmann T. Back to basics: the untreated rabbit reticulocyte lysate as a competitive system to recapitulate cap/poly(A) synergy and the selective advantage of IRES-driven translation. Nucleic Acids Res 2007; 35:e121. [PMID: 17881372 PMCID: PMC2094066 DOI: 10.1093/nar/gkm682] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2007] [Revised: 08/17/2007] [Accepted: 08/18/2007] [Indexed: 12/17/2022] Open
Abstract
Translation of most eukaryotic mRNAs involves the synergistic action between the 5' cap structure and the 3' poly(A) tail at the initiation step. The poly(A) tail has also been shown to stimulate translation of picornavirus internal ribosome entry sites (IRES)-directed translation. These effects have been attributed principally to interactions between eIF4G and poly(A)-binding protein (PABP) but also to the participation of PABP in other steps during translation initiation. As the rabbit reticulocyte lysate (RRL) does not recapitulate this cap/poly(A) synergy, several systems based on cellular cell-free extracts have been developed to study the effects of poly(A) tail in vitro but they generally exhibit low translational efficiency. Here, we describe that the non-nuclease-treated RRL (untreated RRL) is able to recapitulate the effects of poly(A) tail on translation in vitro. In this system, translation of a capped/polyadenylated RNA was specifically inhibited by either Paip2 or poly(rA), whereas translation directed by HCV IRES remained unaffected. Moreover, cleavage of eIF4G by FMDV L protease strongly stimulated translation directed by the EMCV IRES, thus recapitulating the competitive advantage that the proteolytic processing of eIF4G confers to IRES-driven RNAs.
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Affiliation(s)
- Ricardo Soto Rifo
- Inserm U 758, Lyon, F-69364 and Ecole Normale Supérieure de Lyon, Unité de Virologie Humaine, IFR 128, Lyon, F-69364, France
| | - Emiliano P. Ricci
- Inserm U 758, Lyon, F-69364 and Ecole Normale Supérieure de Lyon, Unité de Virologie Humaine, IFR 128, Lyon, F-69364, France
| | - Didier Décimo
- Inserm U 758, Lyon, F-69364 and Ecole Normale Supérieure de Lyon, Unité de Virologie Humaine, IFR 128, Lyon, F-69364, France
| | - Olivier Moncorgé
- Inserm U 758, Lyon, F-69364 and Ecole Normale Supérieure de Lyon, Unité de Virologie Humaine, IFR 128, Lyon, F-69364, France
| | - Théophile Ohlmann
- Inserm U 758, Lyon, F-69364 and Ecole Normale Supérieure de Lyon, Unité de Virologie Humaine, IFR 128, Lyon, F-69364, France
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30
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Affiliation(s)
- Michael Hampsey
- Department of Biochemistry, Division of Nucleic Acid Enzymology, University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, Piscataway, New Jersey 08854, USA
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31
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Derry MC, Yanagiya A, Martineau Y, Sonenberg N. Regulation of poly(A)-binding protein through PABP-interacting proteins. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2007; 71:537-43. [PMID: 17381337 DOI: 10.1101/sqb.2006.71.061] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Translation initiation requires the participation of eukaryotic translation initiation factors (eIFs). The poly(A)-binding protein (PABP) is thought to stimulate translation by promoting mRNA circularization through simultaneous interactions with eIF4G and the 3' poly(A) tail. PABP activity is regulated by the PABP-interacting proteins (Paips), a family of proteins consisting of Paip1, a translational stimulator, and Paip2A and Paip2B, two translational inhibitors. Paip2A controls PABP homeostasis via ubiquitination. When the cellular concentration of PABP is reduced, Paip2A becomes ubiquitinated and degraded, resulting in the relief of PABP repression. Paip1 interacts with eIF4A and eIF3, which promotes translation. The regulation of PABP activity by Paips represents the first known mechanism for controlling PABP, adding a new layer to the existing knowledge of PABP function.
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Affiliation(s)
- M C Derry
- Department of Biochemistry and McGill Cancer Centre, McGill University, Montréal, Québec, Canada
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32
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Komarova AV, Brocard M, Kean KM. The case for mRNA 5' and 3' end cross talk during translation in a eukaryotic cell. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 2007; 81:331-67. [PMID: 16891176 DOI: 10.1016/s0079-6603(06)81009-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Affiliation(s)
- Anastassia V Komarova
- Unité Postulante Régulation de la Traduction Eucaryote et Virale, Institut Pasteur, CNRS URA 1966, 75724 Paris cedex 15, France
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Guan Q, Zheng W, Tang S, Liu X, Zinkel RA, Tsui KW, Yandell BS, Culbertson MR. Impact of nonsense-mediated mRNA decay on the global expression profile of budding yeast. PLoS Genet 2006; 2:e203. [PMID: 17166056 PMCID: PMC1657058 DOI: 10.1371/journal.pgen.0020203] [Citation(s) in RCA: 102] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2006] [Accepted: 10/18/2006] [Indexed: 11/19/2022] Open
Abstract
Nonsense-mediated mRNA decay (NMD) is a eukaryotic mechanism of RNA surveillance that selectively eliminates aberrant transcripts coding for potentially deleterious proteins. NMD also functions in the normal repertoire of gene expression. In Saccharomyces cerevisiae, hundreds of endogenous RNA Polymerase II transcripts achieve steady-state levels that depend on NMD. For some, the decay rate is directly influenced by NMD (direct targets). For others, abundance is NMD-sensitive but without any effect on the decay rate (indirect targets). To distinguish between direct and indirect targets, total RNA from wild-type (Nmd+) and mutant (Nmd−) strains was probed with high-density arrays across a 1-h time window following transcription inhibition. Statistical models were developed to describe the kinetics of RNA decay. 45% ± 5% of RNAs targeted by NMD were predicted to be direct targets with altered decay rates in Nmd− strains. Parallel experiments using conventional methods were conducted to empirically test predictions from the global experiment. The results show that the global assay reliably distinguished direct versus indirect targets. Different types of targets were investigated, including transcripts containing adjacent, disabled open reading frames, upstream open reading frames, and those prone to out-of-frame initiation of translation. Known targeting mechanisms fail to account for all of the direct targets of NMD, suggesting that additional targeting mechanisms remain to be elucidated. 30% of the protein-coding targets of NMD fell into two broadly defined functional themes: those affecting chromosome structure and behavior and those affecting cell surface dynamics. Overall, the results provide a preview for how expression profiles in multi-cellular eukaryotes might be impacted by NMD. Furthermore, the methods for analyzing decay rates on a global scale offer a blueprint for new ways to study mRNA decay pathways in any organism where cultured cell lines are available. Genes determine the structure of proteins through transcription and translation in which an RNA copy of the gene is made (mRNA) and then translated to make the protein. Cellular protein levels reflect the relative rates of mRNA synthesis and degradation, which are subject to multiple layers of controls. Mechanisms also exist to ensure the quality of each mRNA. One quality control mechanism called nonsense-mediated mRNA decay (NMD) triggers the rapid degradation of mRNAs containing coding errors that would otherwise lead to the production of non-functional or potentially deleterious proteins. NMD occurs in yeasts, plants, flies, worms, mice, and humans. In humans, NMD affects the etiology of genetic disorders by affecting the expression of genes that carry disease-causing mutations. Besides quality assurance, NMD plays another role in gene expression by controlling the abundance of hundreds of normal mRNAs that are devoid of coding errors. In this paper, the authors used DNA arrays to monitor the relative decay rates of all mRNAs in budding yeast and found a subset where decay rates were dependent on NMD. Many of the corresponding proteins perform related functional roles affecting both the structure and behavior of chromosomes and the structure and integrity of the cell surface.
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Affiliation(s)
- Qiaoning Guan
- Laboratories of Genetics and Molecular Biology, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Wei Zheng
- Laboratories of Genetics and Molecular Biology, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Shijie Tang
- Department of Statistics, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Xiaosong Liu
- Department of Physics, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Robert A Zinkel
- Laboratories of Genetics and Molecular Biology, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Kam-Wah Tsui
- Department of Statistics, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Brian S Yandell
- Department of Statistics, University of Wisconsin, Madison, Wisconsin, United States of America
- Department of Horticulture, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Michael R Culbertson
- Laboratories of Genetics and Molecular Biology, University of Wisconsin, Madison, Wisconsin, United States of America
- * To whom correspondence should be addressed. E-mail:
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Brocard M, Paulous S, Komarova AV, Deveaux V, Kean KM. Evidence that PTB does not stimulate HCV IRES-driven translation. Virus Genes 2006; 35:5-15. [PMID: 17039407 DOI: 10.1007/s11262-006-0038-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2006] [Accepted: 08/29/2006] [Indexed: 02/05/2023]
Abstract
It is now well established that Hepatitis C Virus (HCV) translation is driven by an Internal Ribosome Entry Site (IRES) resulting in cap-independent translation. Such a mechanism usually occurs with the help of IRES Associated Factors (ITAFs). Moreover, an important translational feature is likely conserved from the model of classical mRNA circularisation (5'-3' cross-talk), involving the HCV RNA highly structured 3' extremity called the 3'X region. This could bind several cellular factors and modulate the translation efficacy, at least in Rabbit Reticulocyte Lysate (RRL). In particular, polypyrimidine-binding proteins have been proposed to be potential HCV ITAFs, such as Polypyrimidine Tract Binding protein (PTB). However, contradictions still exist as to the role of PTB: its ability to bind both the HCV IRES and the 3'X region leads to the hypothesis that it could positively modulate IRES-driven translation in the presence of the X structure. Results of translational and PTB-binding studies of X mutant sequences led us to discredit PTB as protagonist of 3'X region stimulation on HCV IRES-driven translation. Moreover, competition assays of X RNA in trans on IRES-driven translation demonstrate the involvement of at least two stimulating factors and led to the conclusion that this mechanism is more complex than initially thought. Although we did not identify these factors, it is no longer doubtful that there is effectively a stimulating functional interaction between the HCV IRES and the 3'X region in RRL.
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Affiliation(s)
- Michèle Brocard
- Unité Postulante Régulation de la Traduction Eucaryote et Virale, URA CNRS 1966, Institut Pasteur, 25 rue du Dr. Roux-75724, Paris cedex 15, France.
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Alvarez E, Castelló A, Menéndez-Arias L, Carrasco L. HIV protease cleaves poly(A)-binding protein. Biochem J 2006; 396:219-26. [PMID: 16594896 PMCID: PMC1462710 DOI: 10.1042/bj20060108] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The PABP [poly(A)-binding protein] is able to interact with the 3' poly(A) tail of eukaryotic mRNA, promoting its translation. Cleavage of PABP by viral proteases encoded by several picornaviruses and caliciviruses plays a role in the abrogation of cellular protein synthesis. We report that infection of MT-2 cells with HIV-1 leads to efficient proteolysis of PABP. Analysis of PABP integrity was carried out in BHK-21 (baby-hamster kidney) and COS-7 cells upon individual expression of the protease from several members of the Retroviridae family, e.g. MoMLV (Moloney murine leukaemia virus), MMTV (mouse mammary tumour virus), HTLV-I (human T-cell leukaemia virus type I), SIV (simian immunodeficiency virus), HIV-1 and HIV-2. Moreover, protease activity against PABP was tested in a HeLa-cell-free system. Only MMTV, HIV-1 and HIV-2 proteases were able to cleave PABP in the absence of other viral proteins. Purified HIV-1 and HIV-2 proteases cleave PABP1 directly at positions 237 and 477, separating the two first RNA-recognition motifs from the C-terminal domain of PABP. An additional cleavage site located at position 410 was detected for HIV-2 protease. These findings indicate that some retroviruses may share with picornaviruses and caliciviruses the capacity to proteolyse PABP.
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Affiliation(s)
- Enrique Alvarez
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Facultad de Ciencias, Universidad Autónoma, Cantoblanco, 28049 Madrid, Spain.
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Srinivasan V, Schnitzlein WM, Tripathy DN. Genetic manipulation of two fowlpox virus late transcriptional regulatory elements influences their ability to direct expression of foreign genes. Virus Res 2006; 116:85-90. [PMID: 16207500 DOI: 10.1016/j.virusres.2005.08.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2005] [Revised: 08/17/2005] [Accepted: 08/24/2005] [Indexed: 11/28/2022]
Abstract
Fowlpox virus (FWPV) is currently used as a vector to express foreign genes of various poultry and mammalian pathogens. However, due to limited information available about the primary structure of FWPV promoters required for an optimal transcriptional efficiency, the full potential of FWPV as an expression vector has not been completely realized. To dissect such transcriptional regulatory elements at the molecular level, we selected two FWPV promoters dictating contrasting levels of expression of acidic-type inclusion body protein gene (P190) and A15L vaccinia virus homolog of FWPV (P180) for site-directed mutagenesis studies. The transcriptional activity of mutated promoters was analyzed based on their ability to transcribe a reporter gene, lacZ, and translation of the resultant mRNA into functional protein. Replacement of the spacer sequences of P180 with those of P190 resulted in a five-fold increase in mRNA and a 17.6-fold increase in protein over those with its parental promoter, P180. Similarly, replacement of a thymidine after the start codon with guanosine resulted in a 2.3-fold increase in lacZ mRNA and a seven-fold increase in protein. Combining these substitutions in P180SG produced a maximum increase in mRNA and protein of 6.7- and 29.9-fold, respectively, over concentrations with its parental P180 promoter. The promoter activity of P180SG was comparable to that of the strongest natural promoter, P190. The amount of protein per transcript generated by the mutated promoters of P180 increased to at least three times that with the parental P180. In contrast, similar replacements in P190 resulted in a 40-50% reduction in mRNA and protein in all the mutated promoters. We discuss the significance of spacer sequence and the purine after the start codon in the context of a high level of expression.
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Affiliation(s)
- V Srinivasan
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Veterinary Medicine Basic Sciences Building, 2001 South Lincoln Avenue, University of Illinois, Urbana, 61802-6178, USA.
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Wang H, Iacoangeli A, Lin D, Williams K, Denman RB, Hellen CUT, Tiedge H. Dendritic BC1 RNA in translational control mechanisms. ACTA ACUST UNITED AC 2006; 171:811-21. [PMID: 16330711 PMCID: PMC1828541 DOI: 10.1083/jcb.200506006] [Citation(s) in RCA: 122] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Translational control at the synapse is thought to be a key determinant of neuronal plasticity. How is such control implemented? We report that small untranslated BC1 RNA is a specific effector of translational control both in vitro and in vivo. BC1 RNA, expressed in neurons and germ cells, inhibits a rate-limiting step in the assembly of translation initiation complexes. A translational repression element is contained within the unique 3' domain of BC1 RNA. Interactions of this domain with eukaryotic initiation factor 4A and poly(A) binding protein mediate repression, indicating that the 3' BC1 domain targets a functional interaction between these factors. In contrast, interactions of BC1 RNA with the fragile X mental retardation protein could not be documented. Thus, BC1 RNA modulates translation-dependent processes in neurons and germs cells by directly interacting with translation initiation factors.
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Affiliation(s)
- Huidong Wang
- Department of Physiology and Pharmacology, State University of New York, Health Science Center at Brooklyn, Brooklyn, NY 11203, USA
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Kondrashov AV, Kiefmann M, Ebnet K, Khanam T, Muddashetty RS, Brosius J. Inhibitory effect of naked neural BC1 RNA or BC200 RNA on eukaryotic in vitro translation systems is reversed by poly(A)-binding protein (PABP). J Mol Biol 2005; 353:88-103. [PMID: 16154588 DOI: 10.1016/j.jmb.2005.07.049] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2005] [Revised: 07/08/2005] [Accepted: 07/18/2005] [Indexed: 11/19/2022]
Abstract
Regulated protein biosynthesis in dendrites of neurons might be a key mechanism underlying learning and memory. Neuronal dendritic BC1 RNA and BC200 RNA and similar small untranslated RNAs inhibit protein translation in vitro systems, such as rabbit reticulocyte lysate. Likewise, co-transfection of these RNAs with reporter mRNA suppressed translation levels in HeLa cells. The oligo(A)-rich region of all active small RNAs were identified as the RNA domains chiefly responsible for the inhibitory effects. Addition of recombinant human poly(A)-binding protein (PABP) significantly compensated the inhibitory effect of the small oligo(A)-rich RNA. In vivo, all BC1 RNA appears to be complexed with PABP. Nevertheless, in the micro-environment of dendritic spines of neuronal cells, BC1 RNPs or BC200 RNPs might mediate regulatory functions by differential interactions with locally limited PABP and/or directly or indirectly, with other translation initiation factors.
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Affiliation(s)
- Alexander V Kondrashov
- Institute of Experimental Pathology, ZMBE, University of Münster, Von-Esmarch-Str. 56, D-48149 Münster, Germany
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39
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Mangus DA, Evans MC, Jacobson A. Poly(A)-binding proteins: multifunctional scaffolds for the post-transcriptional control of gene expression. Genome Biol 2003; 4:223. [PMID: 12844354 PMCID: PMC193625 DOI: 10.1186/gb-2003-4-7-223] [Citation(s) in RCA: 431] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Most eukaryotic mRNAs are subject to considerable post-transcriptional modification, including capping, splicing, and polyadenylation. The process of polyadenylation adds a 3' poly(A) tail and provides the mRNA with a binding site for a major class of regulatory factors, the poly(A)-binding proteins (PABPs). These highly conserved polypeptides are found only in eukaryotes; single-celled eukaryotes each have a single PABP, whereas humans have five and Arabidopis has eight. They typically bind poly(A) using one or more RNA-recognition motifs, globular domains common to numerous other eukaryotic RNA-binding proteins. Although they lack catalytic activity, PABPs have several roles in mediating gene expression. Nuclear PABPs are necessary for the synthesis of the poly(A) tail, regulating its ultimate length and stimulating maturation of the mRNA. Association with PABP is also a requirement for some mRNAs to be exported from the nucleus. In the cytoplasm, PABPs facilitate the formation of the 'closed loop' structure of the messenger ribonucleoprotein particle that is crucial for additional PABP activities that promote translation initiation and termination, recycling of ribosomes, and stability of the mRNA. Collectively, these sequential nuclear and cytoplasmic contributions comprise a cycle in which PABPs and the poly(A) tail first create and then eliminate a network of cis- acting interactions that control mRNA function.
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Affiliation(s)
- David A Mangus
- Department of Molecular Genetics and Microbiology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655-0122, USA
| | - Matthew C Evans
- Department of Molecular Genetics and Microbiology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655-0122, USA
| | - Allan Jacobson
- Department of Molecular Genetics and Microbiology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655-0122, USA
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Kahvejian A, Roy G, Sonenberg N. The mRNA closed-loop model: the function of PABP and PABP-interacting proteins in mRNA translation. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2003; 66:293-300. [PMID: 12762031 DOI: 10.1101/sqb.2001.66.293] [Citation(s) in RCA: 145] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- A Kahvejian
- Department of Biochemistry, McGill Cancer Center, McGill University, Montréal, Québec, Canada
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41
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Marcotrigiano J, Burley SK. Structural biology of eIF4F: mRNA recognition and preparation in eukaryotic translation initiation. ADVANCES IN PROTEIN CHEMISTRY 2003; 61:269-97. [PMID: 12461826 DOI: 10.1016/s0065-3233(02)61007-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
Affiliation(s)
- Joseph Marcotrigiano
- Laboratory of Molecular Biophysics, Rockefeller University, New York, New York 10021, USA
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42
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Srinivasan V, Schnitzlein WM, Tripathy DN. A consideration of previously uncharacterized fowl poxvirus unidirectional and bidirectional late promoters for inclusion in homologous recombinant vaccines. Avian Dis 2003; 47:286-95. [PMID: 12887188 DOI: 10.1637/0005-2086(2003)047[0286:acopuf]2.0.co;2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Because of the limited analysis of fowl poxvirus (FPV) promoters, expression of foreign proteins by recombinant FPV has usually been directed by heterologous vaccinia virus or synthetic poxvirus promoters. Thus, the impact of completely homologous recombinant virus vaccines has yet to be realized by the poultry industry. In an effort to increase the availability of such transcriptional regulatory elements, the modulation of gene expression by six previously uncharacterized FPV late promoters was examined. To simplify this comparison, each promoter region was separately coupled to the same reporter gene (lacZ) in individual plasmid constructs, and their activities in transfected, virus-infected cells were monitored. In each of the four selected unidirectional transcriptional regulatory elements as well as a 30-base pair representative of the bidirectional promoter region, the predicted temporal specificity of expressing at late stages of virus replicative cycle was verified. Stable lacZ gene transcripts arising from each plasmid varied less than threefold in quantity, whereas the amounts of beta-galactosidase product ranged within a 130-fold interval. Only the promoter that naturally regulates expression of the A type inclusion body protein gene directed production of beta-galactosidase at a level comparable with that associated with the strong vaccinia virus P11 promoter. Because one of the remaining unidirectional transcriptional regulatory elements, P174, was only 2.4-fold less efficient, both of these promoters, P174 and P190, should be satisfactory for directing the expression of poultry pathogen genes inserted into the genomes of FPV recombinant vaccines.
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Affiliation(s)
- V Srinivasan
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Veterinary Medicine Basic Sciences Building, 2001 South Lincoln Avenue, University of Illinois, Urbana, IL 61802, USA
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43
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Sànchez R, Marzluff WF. The stem-loop binding protein is required for efficient translation of histone mRNA in vivo and in vitro. Mol Cell Biol 2002; 22:7093-104. [PMID: 12242288 PMCID: PMC139811 DOI: 10.1128/mcb.22.20.7093-7104.2002] [Citation(s) in RCA: 110] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Metazoan replication-dependent histone mRNAs end in a conserved stem-loop rather than in the poly(A) tail found on all other mRNAs. The 3' end of histone mRNA binds a single class of proteins, the stem-loop binding proteins (SLBP). In Xenopus, there are two SLBPs: xSLBP1, the homologue of the mammalian SLBP, which is required for processing of histone pre-mRNA, and xSLBP2, which is expressed only during oogenesis and is bound to the stored histone mRNA in Xenopus oocytes. The stem-loop is required for efficient translation of histone mRNAs and substitutes for the poly(A) tail, which is required for efficient translation of other eucaryotic mRNAs. When a rabbit reticulocyte lysate is programmed with uncapped luciferase mRNA ending in the histone stem-loop, there is a three- to sixfold increase in translation in the presence of xSLBP1 while xSLBP2 has no effect on translation. Neither SLBP affected the translation of a luciferase mRNA ending in a mutant stem-loop that does not bind SLBP. Capped luciferase mRNAs ending in the stem-loop were injected into Xenopus oocytes after overexpression of either xSLBP1 or xSLBP2. Overexpression of xSLBP1 in the oocytes stimulated translation, while overexpression of xSLBP2 reduced translation of the luciferase mRNA ending in the histone stem-loop. A small region in the N-terminal portion of xSLBP1 is required to stimulate translation both in vivo and in vitro. An MS2-human SLBP1 fusion protein can activate translation of a reporter mRNA ending in an MS2 binding site, indicating that xSLBP1 only needs to be recruited to the 3' end of the mRNA but does not need to be directly bound to the histone stem-loop to activate translation.
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Affiliation(s)
- Ricardo Sànchez
- Program in Molecular Biology and Biotechnology, Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA
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44
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Borman AM, Michel YM, Malnou CE, Kean KM. Free poly(A) stimulates capped mRNA translation in vitro through the eIF4G-poly(A)-binding protein interaction. J Biol Chem 2002; 277:36818-24. [PMID: 12138105 DOI: 10.1074/jbc.m205065200] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The 5' cap and 3' poly(A) tail of classical eukaryotic mRNAs functionally communicate to synergistically enhance translation initiation. Synergy has been proposed to result in part from facilitated ribosome recapture on circularized mRNAs. Here, we demonstrate that this is not the case. In poly(A)-dependent, ribosome-depleted rabbit reticulocyte lysates, the addition of exogenous poly(A) chains of physiological length dramatically stimulated translation of a capped, nonpolyadenylated mRNA. When the poly(A):RNA ratio approached 1, exogenous poly(A) stimulated translation to the same extent as the presence of a poly(A) tail at the mRNA 3' end. In addition, exogenous poly(A) significantly improved translation of capped mRNAs carrying short poly(A(50)) tails. Trans stimulation of translation by poly(A) required the eIF4G-poly(A)-binding protein interaction and resulted in increased affinity of eIF4E for the mRNA cap, exactly as we recently described for cap-poly(A) synergy. These results formally demonstrate that mRNA circularization per se is not the cause of cap-poly(A) synergy at least in vitro.
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Affiliation(s)
- Andrew M Borman
- Unité Postulante de Régulation de la Traduction Eucaryote et Virale, CNRS URA 1966, Institut Pasteur, Paris, France
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45
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Valentini SR, Casolari JM, Oliveira CC, Silver PA, McBride AE. Genetic interactions of yeast eukaryotic translation initiation factor 5A (eIF5A) reveal connections to poly(A)-binding protein and protein kinase C signaling. Genetics 2002; 160:393-405. [PMID: 11861547 PMCID: PMC1461981 DOI: 10.1093/genetics/160.2.393] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The highly conserved eukaryotic translation initiation factor eIF5A has been proposed to have various roles in the cell, from translation to mRNA decay to nuclear protein export. To further our understanding of this essential protein, three temperature-sensitive alleles of the yeast TIF51A gene have been characterized. Two mutant eIF5A proteins contain mutations in a proline residue at the junction between the two eIF5A domains and the third, strongest allele encodes a protein with a single mutation in each domain, both of which are required for the growth defect. The stronger tif51A alleles cause defects in degradation of short-lived mRNAs, supporting a role for this protein in mRNA decay. A multicopy suppressor screen revealed six genes, the overexpression of which allows growth of a tif51A-1 strain at high temperature; these genes include PAB1, PKC1, and PKC1 regulators WSC1, WSC2, and WSC3. Further results suggest that eIF5A may also be involved in ribosomal synthesis and the WSC/PKC1 signaling pathway for cell wall integrity or related processes.
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Affiliation(s)
- Sandro R Valentini
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
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46
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de Moor CH, Richter JD. Translational control in vertebrate development. INTERNATIONAL REVIEW OF CYTOLOGY 2001; 203:567-608. [PMID: 11131527 DOI: 10.1016/s0074-7696(01)03017-0] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Translational control plays a large role in vertebrate oocyte maturation and contributes to the induction of the germ layers. Translational regulation is also observed in the regulation of cell proliferation and differentiation. The features of an mRNA that mediate translational control are found both in the 5' and in the 3' untranslated regions (UTRs). In the 5' UTR, secondary structure, the binding of proteins, and the presence of upstream open reading frames can interfere with the association of initiation factors with the cap, or with scanning of the initiation complex. The 3' UTR can mediate translational activation by directing cytoplasmic polyadenylation and can confer translational repression by interference with the assembly of initiation complexes. Besides mRNA-specific translational control elements, the nonspecific RNA-binding proteins contribute to the modulation of translation in development. This review discusses examples of translational control and their relevance for developmental regulation.
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Affiliation(s)
- C H de Moor
- Department of Molecular Genetics and Microbiology, University of Massachusetts Medical School, Worcester 01655, USA
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47
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Karikó K, Keller JM, Harris VA, Langer DJ, Welsh FA. In vivo protein expression from mRNA delivered into adult rat brain. J Neurosci Methods 2001; 105:77-86. [PMID: 11166368 DOI: 10.1016/s0165-0270(00)00355-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The expression of proteins after local mRNA delivery has a great potential for analysis of protein function in vivo. To explore the feasibility of such a technique within the central nervous system (CNS), we delivered luciferase-encoding mRNA into the rat brain. The tissue distribution and stability of injected mRNA were analyzed using in situ detection and Northern hybridization, while luciferase expression was measured by enzymatic assay. Following intracerebral injection of lipofectin-complexed mRNA, expression of luciferase was detectable as early as 1 h, was maximal at 2-3 h, but was below the level of detection by 24 h. The extent of luciferase expression correlated with the amount of mRNA delivered. Luciferase expression was higher when lipofectin-complexed rather than naked mRNA was injected. In addition, the luciferase expression increased significantly by adding a 50 nt-long poly(A) tail to the 3'-end of the mRNA. Delivering mRNA to the cerebral cortex or hippocampus resulted in measurable luciferase activity at the injection sites but not in adjacent areas. Accordingly, the luciferase mRNA was also localized to the injection site, and the amount of intact transcript was significantly higher at 3 h compared to 24 h after injection. These results demonstrate that in vivo mRNA delivery is a feasible technique for immediate, transient overexpression of desired proteins in the CNS and, therefore, can serve as a model system to study the neurobiological effects of specific proteins.
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Affiliation(s)
- K Karikó
- Department of Neurosurgery, University of Pennsylvania School of Medicine, Room 371 Stemmler Hall, 36th and Hamilton Walk, Philadelphia, PA 19104-6070, USA.
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48
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Timofeeva AV, Skrypina NA, Savochkina LP, Beabealashvilli RS. Size distribution of the urokinase mRNA decay intermediates in different tissues and cell lines. BIOCHIMICA ET BIOPHYSICA ACTA 2000; 1517:33-45. [PMID: 11118614 DOI: 10.1016/s0167-4781(00)00253-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Many genes, particularly those encoding the products participating in the regulation of transcription, replication and tissue remodeling, produce short-lived mRNA. It has been commonly accepted that once mRNA is disintegrated, the degradation process is so rapid that the decay intermediates cannot be detected. In the present study we verified this postulate and focused our attention on the quantification of the decay products of the urokinase-type plasminogen activator (uPA) mRNA that belongs to short-lived mRNAs. Using a previously described modified quantitative RT-PCR method, we have shown that intact uPA mRNA coexists in normal human tissues, Jurkat and 5637 cells with a great abundance of its degradation products. The uPA mRNA decay products were not detected in T24P cells. The content of intact uPA mRNA in normal tissues was as low as 5% of the total amount of its poly(A)(+) fraction. The size distribution of the mRNA decay products suggests that the mRNA is digested by exonucleases or/and non-specific endonuclease with cut sites evenly distributed along the mRNA chain. Different decay degrees were demonstrated for subpopulation of the uPA mRNA molecules with intact 3' and 5' ends.
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Affiliation(s)
- A V Timofeeva
- Russian Cardiology Research and Development Center, 3rd Cherepkovskaya str., 15a, Moscow 121552, Russia.
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49
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Gingras AC, Raught B, Sonenberg N. eIF4 initiation factors: effectors of mRNA recruitment to ribosomes and regulators of translation. Annu Rev Biochem 2000; 68:913-63. [PMID: 10872469 DOI: 10.1146/annurev.biochem.68.1.913] [Citation(s) in RCA: 1630] [Impact Index Per Article: 67.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Eukaryotic translation initiation factor 4F (eIF4F) is a protein complex that mediates recruitment of ribosomes to mRNA. This event is the rate-limiting step for translation under most circumstances and a primary target for translational control. Functions of the constituent proteins of eIF4F include recognition of the mRNA 5' cap structure (eIF4E), delivery of an RNA helicase to the 5' region (eIF4A), bridging of the mRNA and the ribosome (eIF4G), and circularization of the mRNA via interaction with poly(A)-binding protein (eIF4G). eIF4 activity is regulated by transcription, phosphorylation, inhibitory proteins, and proteolytic cleavage. Extracellular stimuli evoke changes in phosphorylation that influence eIF4F activity, especially through the phosphoinositide 3-kinase (PI3K) and Ras signaling pathways. Viral infection and cellular stresses also affect eIF4F function. The recent determination of the structure of eIF4E at atomic resolution has provided insight about how translation is initiated and regulated. Evidence suggests that eIF4F is also implicated in malignancy and apoptosis.
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Affiliation(s)
- A C Gingras
- Department of Biochemistry McGill University, Montréal, Québec, Canada.
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Paynton BV. RNA-binding proteins in mouse oocytes and embryos: expression of genes encoding Y box, DEAD box RNA helicase, and polyA binding proteins. DEVELOPMENTAL GENETICS 2000; 23:285-98. [PMID: 9883581 DOI: 10.1002/(sici)1520-6408(1998)23:4<285::aid-dvg4>3.0.co;2-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Growth and differentiation of early embryos depends almost entirely on information which is maternally inherited in the form of macromolecules accumulated by the female gamete during its growth phase. Most of the maternal mRNAs synthesized by growing oocytes are not immediately recruited onto polysomes but are stored as translationally dormant messenger ribonucleoprotein (mRNP) particles. mRNA binding proteins which have been associated with masked mRNP complexes in Xenopus oocytes fall into two main categories, those having affinity for a variety of RNA sequences (members of the Y box and DEAD box RNA helicase families) and those which interact more specifically with 3' polyA tails (the polyA binding proteins or PABPs). The objective of this study was to determine whether mouse oocytes and embryos express sequences encoding a Y box protein, (MSY1); on RNA helicase, (RCK/p54); and a universally expressed PABP and testis specific isoform (PABP1 and PABPt, respectively). RNAs were amplified by RT/PCR and the identities of targeted cDNAs were confirmed by restriction analysis and/or direct sequencing. Relative steady state levels and time courses of accumulation/decay were compared by Northern hybridization. All of the sequences are transcribed as maternal mRNAs. MSY1 transcripts accumulated during the growth phase appear to be degraded in parallel with the bulk of maternal mRNAs by the mid-late two-cell stage. RCK/p54 mRNAs are most abundant in growing oocytes; steady state levels decline in primary and secondary oocytes, and degradation appears to be complete by the mid-late two-cell stage. Zygotic transcription of MSY1 and RCK/p54 is evident in four-cell stage embryos. Most of the PABP1 message accumulated by growing oocytes decays during meiotic maturation with transcription resuming in two-cell embryos. PABPt is expressed at very low levels in oocytes and embryos. Based on the temporal patterns of expression and the reported activities of homologous sequences in other systems, we suggest that these RNA binding proteins may participate in the post-transcriptional regulation of gene expression during the period of maternal control of development in the mouse.
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Affiliation(s)
- B V Paynton
- Albert Einstein Medical Center, Philadelphia, PA 19141, USA.
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