1
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Oliveira MM, Mohamed M, Elder MK, Banegas-Morales K, Mamcarz M, Lu EH, Golhan EAN, Navrange N, Chatterjee S, Abel T, Klann E. The integrated stress response effector GADD34 is repurposed by neurons to promote stimulus-induced translation. Cell Rep 2024; 43:113670. [PMID: 38219147 PMCID: PMC10964249 DOI: 10.1016/j.celrep.2023.113670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 10/11/2023] [Accepted: 12/26/2023] [Indexed: 01/16/2024] Open
Abstract
Neuronal protein synthesis is required for long-lasting plasticity and long-term memory consolidation. Dephosphorylation of eukaryotic initiation factor 2α is one of the key translational control events that is required to increase de novo protein synthesis that underlies long-lasting plasticity and memory consolidation. Here, we interrogate the molecular pathways of translational control that are triggered by neuronal stimulation with brain-derived neurotrophic factor (BDNF), which results in eukaryotic initiation factor 2α (eIF2α) dephosphorylation and increases in de novo protein synthesis. Primary rodent neurons exposed to BDNF display elevated translation of GADD34, which facilitates eIF2α dephosphorylation and subsequent de novo protein synthesis. Furthermore, GADD34 requires G-actin generated by cofilin to dephosphorylate eIF2α and enhance protein synthesis. Finally, GADD34 is required for BDNF-induced translation of synaptic plasticity-related proteins. Overall, we provide evidence that neurons repurpose GADD34, an effector of the integrated stress response, as an orchestrator of rapid increases in eIF2-dependent translation in response to plasticity-inducing stimuli.
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Affiliation(s)
| | - Muhaned Mohamed
- Center for Neural Science, New York University, New York, NY, USA
| | - Megan K Elder
- Center for Neural Science, New York University, New York, NY, USA
| | | | - Maggie Mamcarz
- Center for Neural Science, New York University, New York, NY, USA
| | - Emily H Lu
- Center for Neural Science, New York University, New York, NY, USA
| | - Ela A N Golhan
- Center for Neural Science, New York University, New York, NY, USA
| | - Nishika Navrange
- Center for Neural Science, New York University, New York, NY, USA
| | - Snehajyoti Chatterjee
- Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Ted Abel
- Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Eric Klann
- Center for Neural Science, New York University, New York, NY, USA; NYU Neuroscience Institute, New York University School of Medicine, New York, NY, USA.
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2
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Mao Y, Qian SB. Making sense of mRNA translational "noise". Semin Cell Dev Biol 2024; 154:114-122. [PMID: 36925447 PMCID: PMC10500040 DOI: 10.1016/j.semcdb.2023.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 03/09/2023] [Accepted: 03/09/2023] [Indexed: 03/15/2023]
Abstract
The importance of translation fidelity has been apparent since the discovery of genetic code. It is commonly believed that translation deviating from the main coding region is to be avoided at all times inside cells. However, ribosome profiling and mass spectrometry have revealed pervasive noncanonical translation. Both the scope and origin of translational "noise" are just beginning to be appreciated. Although largely overlooked, those translational "noises" are associated with a wide range of cellular functions, such as producing unannotated protein products. Furthermore, the dynamic nature of translational "noise" is responsive to stress conditions, highlighting the beneficial effect of translational "noise" in stress adaptation. Mechanistic investigation of translational "noise" will provide better insight into the mechanisms of translational regulation. Ultimately, they are not "noise" at all but represent a signature of cellular activities under pathophysiological conditions. Deciphering translational "noise" holds the therapeutic and diagnostic potential in a wide spectrum of human diseases.
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Affiliation(s)
- Yuanhui Mao
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Shu-Bing Qian
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA.
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3
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Ma Q, Wang Y, Li S, Wen J, Zhu L, Yan K, Du Y, Li S, Yan L, Xie Z, Lyu Y, Shen F, Li Q. Ribosome footprint profiling enables elucidating the systemic regulation of fatty acid accumulation in Acer truncatum. BMC Biol 2023; 21:68. [PMID: 37013569 PMCID: PMC10071632 DOI: 10.1186/s12915-023-01564-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 03/14/2023] [Indexed: 04/05/2023] Open
Abstract
BACKGROUND The accumulation of fatty acids in plants covers a wide range of functions in plant physiology and thereby affects adaptations and characteristics of species. As the famous woody oilseed crop, Acer truncatum accumulates unsaturated fatty acids and could serve as the model to understand the regulation and trait formation in oil-accumulation crops. Here, we performed Ribosome footprint profiling combing with a multi-omics strategy towards vital time points during seed development, and finally constructed systematic profiling from transcription to proteomes. Additionally, we characterized the small open reading frames (ORFs) and revealed that the translational efficiencies of focused genes were highly influenced by their sequence features. RESULTS The comprehensive multi-omics analysis of lipid metabolism was conducted in A. truncatum. We applied the Ribo-seq and RNA-seq techniques, and the analyses of transcriptional and translational profiles of seeds collected at 85 and 115 DAF were compared. Key members of biosynthesis-related structural genes (LACS, FAD2, FAD3, and KCS) were characterized fully. More meaningfully, the regulators (MYB, ABI, bZIP, and Dof) were identified and revealed to affect lipid biosynthesis via post-translational regulations. The translational features results showed that translation efficiency tended to be lower for the genes with a translated uORF than for the genes with a non-translated uORF. They provide new insights into the global mechanisms underlying the developmental regulation of lipid metabolism. CONCLUSIONS We performed Ribosome footprint profiling combing with a multi-omics strategy in A. truncatum seed development, which provides an example of the use of Ribosome footprint profiling in deciphering the complex regulation network and will be useful for elucidating the metabolism of A. truncatum seed oil and the regulatory mechanisms.
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Affiliation(s)
- Qiuyue Ma
- Institute of Leisure Agriculture, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement Nanjing, Nanjing, 210014, China
| | - Yuxiao Wang
- Nanjing Forestry University, Nanjing, 210037, China
| | - Shushun Li
- Institute of Leisure Agriculture, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement Nanjing, Nanjing, 210014, China
| | - Jing Wen
- Institute of Leisure Agriculture, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement Nanjing, Nanjing, 210014, China
| | - Lu Zhu
- Institute of Leisure Agriculture, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement Nanjing, Nanjing, 210014, China
| | - Kunyuan Yan
- Institute of Leisure Agriculture, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement Nanjing, Nanjing, 210014, China
| | - Yiming Du
- Institute of Leisure Agriculture, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement Nanjing, Nanjing, 210014, China
| | - Shuxian Li
- Nanjing Forestry University, Nanjing, 210037, China
| | - Liping Yan
- Shandong Academy of Forestry Sciences, Jinan, 250014, China
| | - Zhijun Xie
- Xiangyang Forestry Science and Technology Extension Station, Xiangyang, 441000, China
| | - Yunzhou Lyu
- Jiangsu Academy of Forestry, Nanjing, 211153, China.
| | - Fei Shen
- Institute of Biology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100197, China.
| | - Qianzhong Li
- Institute of Leisure Agriculture, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement Nanjing, Nanjing, 210014, China.
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4
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Ryczek N, Łyś A, Makałowska I. The Functional Meaning of 5'UTR in Protein-Coding Genes. Int J Mol Sci 2023; 24:2976. [PMID: 36769304 PMCID: PMC9917990 DOI: 10.3390/ijms24032976] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/20/2023] [Accepted: 01/26/2023] [Indexed: 02/05/2023] Open
Abstract
As it is well known, messenger RNA has many regulatory regions along its sequence length. One of them is the 5' untranslated region (5'UTR), which itself contains many regulatory elements such as upstream ORFs (uORFs), internal ribosome entry sites (IRESs), microRNA binding sites, and structural components involved in the regulation of mRNA stability, pre-mRNA splicing, and translation initiation. Activation of the alternative, more upstream transcription start site leads to an extension of 5'UTR. One of the consequences of 5'UTRs extension may be head-to-head gene overlap. This review describes elements in 5'UTR of protein-coding transcripts and the functional significance of protein-coding genes 5' overlap with implications for transcription, translation, and disease.
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Affiliation(s)
| | | | - Izabela Makałowska
- Institute of Human Biology and Evolution, Adam Mickiewicz University in Poznań, Uniwersytetu Ponańskiego 6, 61-614 Poznań, Poland
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5
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Hiragori Y, Takahashi H, Karino T, Kaido A, Hayashi N, Sasaki S, Nakao K, Motomura T, Yamashita Y, Naito S, Onouchi H. Genome-wide identification of Arabidopsis non-AUG-initiated upstream ORFs with evolutionarily conserved regulatory sequences that control protein expression levels. PLANT MOLECULAR BIOLOGY 2023; 111:37-55. [PMID: 36044152 DOI: 10.1007/s11103-022-01309-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 08/11/2022] [Indexed: 06/15/2023]
Abstract
This study identified four novel regulatory non-AUG-initiated upstream ORFs (uORFs) with evolutionarily conserved sequences in Arabidopsis and elucidated the mechanism by which a non-AUG-initiated uORF promotes main ORF translation. Upstream open reading frames (uORFs) are short ORFs found in the 5'-untranslated regions (5'-UTRs) of eukaryotic transcripts and can influence the translation of protein-coding main ORFs (mORFs). Recent genome-wide ribosome profiling studies have revealed that hundreds or thousands of uORFs initiate translation at non-AUG start codons. However, the physiological significance of these non-AUG uORFs has so far been demonstrated for only a few of them. In this study, to identify physiologically important regulatory non-AUG uORFs in Arabidopsis, we took an approach that combined bioinformatics and experimental analysis. Since physiologically important non-AUG uORFs are likely to be conserved across species, we first searched the Arabidopsis genome for non-AUG-initiated uORFs with evolutionarily conserved sequences. Then, we examined the effects of the conserved non-AUG uORFs on the expression of the downstream mORFs using transient expression assays. As a result, three inhibitory and one promotive non-AUG uORFs were identified. Among the inhibitory non-AUG uORFs, two exerted repressive effects on mORF expression in an amino acid sequence-dependent manner. These two non-AUG uORFs are likely to encode regulatory peptides that cause ribosome stalling, thereby enhancing their repressive effects. In contrast, one of the identified regulatory non-AUG uORFs promoted mORF expression by alleviating the inhibitory effect of a downstream AUG-initiated uORF. These findings provide insights into the mechanisms that enable non-AUG uORFs to play regulatory roles despite their low translation initiation efficiencies.
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Affiliation(s)
- Yuta Hiragori
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Hiro Takahashi
- Graduate School of Medical Sciences, Kanazawa University, Kanazawa, 920-1192, Japan
- Graduate School of Horticulture, Chiba University, Matsudo, 271-8510, Japan
| | - Taihei Karino
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Atsushi Kaido
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Noriya Hayashi
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Shun Sasaki
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Kodai Nakao
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Taichiro Motomura
- Graduate School of Medical Sciences, Kanazawa University, Kanazawa, 920-1192, Japan
| | - Yui Yamashita
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
- Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Satoshi Naito
- Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
- Graduate School of Life Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Hitoshi Onouchi
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan.
- Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan.
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6
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Embree CM, Abu-Alhasan R, Singh G. Features and factors that dictate if terminating ribosomes cause or counteract nonsense-mediated mRNA decay. J Biol Chem 2022; 298:102592. [PMID: 36244451 PMCID: PMC9661723 DOI: 10.1016/j.jbc.2022.102592] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 10/07/2022] [Accepted: 10/10/2022] [Indexed: 11/13/2022] Open
Abstract
Nonsense-mediated mRNA decay (NMD) is a quality control pathway in eukaryotes that continuously monitors mRNA transcripts to ensure truncated polypeptides are not produced. The expression of many normal mRNAs that encode full-length polypeptides is also regulated by this pathway. Such transcript surveillance by NMD is intimately linked to translation termination. When a ribosome terminates translation at a normal termination codon, NMD is not activated, and mRNA can undergo repeated rounds of translation. On the other hand, when translation termination is deemed abnormal, such as that on a premature termination codon, it leads to a series of poorly understood events involving the NMD pathway, which destabilizes the transcript. In this review, we summarize our current understanding of how the NMD machinery interfaces with the translation termination factors to initiate NMD. We also discuss a variety of cis-acting sequence contexts and trans-acting factors that can cause readthrough, ribosome reinitiation, or ribosome frameshifting at stop codons predicted to induce NMD. These alternative outcomes can lead to the ribosome translating downstream of such stop codons and hence the transcript escaping NMD. NMD escape via these mechanisms can have wide-ranging implications on human health, from being exploited by viruses to hijack host cell systems to being harnessed as potential therapeutic possibilities to treat genetic diseases.
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Affiliation(s)
- Caleb M Embree
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, USA; Center for RNA Biology, The Ohio State University, Columbus, Ohio USA
| | - Rabab Abu-Alhasan
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, USA; Center for RNA Biology, The Ohio State University, Columbus, Ohio USA
| | - Guramrit Singh
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, USA; Center for RNA Biology, The Ohio State University, Columbus, Ohio USA.
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7
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Biziaev NS, Egorova TV, Alkalaeva EZ. Dynamics of Eukaryotic mRNA Structure during Translation. Mol Biol 2022. [DOI: 10.1134/s0026893322030037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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8
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Kute PM, Soukarieh O, Tjeldnes H, Trégouët DA, Valen E. Small Open Reading Frames, How to Find Them and Determine Their Function. Front Genet 2022; 12:796060. [PMID: 35154250 PMCID: PMC8831751 DOI: 10.3389/fgene.2021.796060] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 12/30/2021] [Indexed: 12/12/2022] Open
Abstract
Advances in genomics and molecular biology have revealed an abundance of small open reading frames (sORFs) across all types of transcripts. While these sORFs are often assumed to be non-functional, many have been implicated in physiological functions and a significant number of sORFs have been described in human diseases. Thus, sORFs may represent a hidden repository of functional elements that could serve as therapeutic targets. Unlike protein-coding genes, it is not necessarily the encoded peptide of an sORF that enacts its function, sometimes simply the act of translating an sORF might have a regulatory role. Indeed, the most studied sORFs are located in the 5′UTRs of coding transcripts and can have a regulatory impact on the translation of the downstream protein-coding sequence. However, sORFs have also been abundantly identified in non-coding RNAs including lncRNAs, circular RNAs and ribosomal RNAs suggesting that sORFs may be diverse in function. Of the many different experimental methods used to discover sORFs, the most commonly used are ribosome profiling and mass spectrometry. These can confirm interactions between transcripts and ribosomes and the production of a peptide, respectively. Extensions to ribosome profiling, which also capture scanning ribosomes, have further made it possible to see how sORFs impact the translation initiation of mRNAs. While high-throughput techniques have made the identification of sORFs less difficult, defining their function, if any, is typically more challenging. Together, the abundance and potential function of many of these sORFs argues for the necessity of including sORFs in gene annotations and systematically characterizing these to understand their potential functional roles. In this review, we will focus on the high-throughput methods used in the detection and characterization of sORFs and discuss techniques for validation and functional characterization.
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Affiliation(s)
- Preeti Madhav Kute
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
| | - Omar Soukarieh
- Department of Molecular Epidemiology Of Vascular and Brain Disorders, INSERM, BPH, U1219, University of Bordeaux, Bordeaux, France
| | - Håkon Tjeldnes
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - David-Alexandre Trégouët
- Department of Molecular Epidemiology Of Vascular and Brain Disorders, INSERM, BPH, U1219, University of Bordeaux, Bordeaux, France
| | - Eivind Valen
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
- *Correspondence: Eivind Valen,
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9
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Vindu A, Shin BS, Choi K, Christenson ET, Ivanov IP, Cao C, Banerjee A, Dever TE. Translational autoregulation of the S. cerevisiae high-affinity polyamine transporter Hol1. Mol Cell 2021; 81:3904-3918.e6. [PMID: 34375581 PMCID: PMC8500938 DOI: 10.1016/j.molcel.2021.07.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 06/15/2021] [Accepted: 07/13/2021] [Indexed: 12/13/2022]
Abstract
Polyamines, small organic polycations, are essential for cell viability, and their physiological levels are homeostatically maintained by post-transcriptional regulation of key biosynthetic enzymes. In addition to de novo synthesis, cells can also take up polyamines; however, identifying cellular polyamine transporters has been challenging. Here we show that the S. cerevisiae HOL1 mRNA is under translational control by polyamines, and we reveal that the encoded membrane transporter Hol1 is a high-affinity polyamine transporter and is required for yeast growth under limiting polyamine conditions. Moreover, we show that polyamine inhibition of the translation factor eIF5A impairs translation termination at a Pro-Ser-stop motif in a conserved upstream open reading frame on the HOL1 mRNA to repress Hol1 synthesis under conditions of elevated polyamines. Our findings reveal that polyamine transport, like polyamine biosynthesis, is under translational autoregulation by polyamines in yeast, highlighting the extensive control cells impose on polyamine levels.
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Affiliation(s)
- Arya Vindu
- Section on Protein Biosynthesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Byung-Sik Shin
- Section on Protein Biosynthesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kevin Choi
- Section on Structural and Chemical Biology of Membrane Proteins, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Eric T Christenson
- Section on Structural and Chemical Biology of Membrane Proteins, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ivaylo P Ivanov
- Section on Protein Biosynthesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Chune Cao
- Section on Protein Biosynthesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anirban Banerjee
- Section on Structural and Chemical Biology of Membrane Proteins, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Thomas E Dever
- Section on Protein Biosynthesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.
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10
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Takahashi H, Miyaki S, Onouchi H, Motomura T, Idesako N, Takahashi A, Murase M, Fukuyoshi S, Endo T, Satou K, Naito S, Itoh M. Exhaustive identification of conserved upstream open reading frames with potential translational regulatory functions from animal genomes. Sci Rep 2020; 10:16289. [PMID: 33004976 PMCID: PMC7530721 DOI: 10.1038/s41598-020-73307-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 09/15/2020] [Indexed: 11/17/2022] Open
Abstract
Upstream open reading frames (uORFs) are present in the 5′-untranslated regions of many eukaryotic mRNAs, and some peptides encoded by these regions play important regulatory roles in controlling main ORF (mORF) translation. We previously developed a novel pipeline, ESUCA, to comprehensively identify plant uORFs encoding functional peptides, based on genome-wide identification of uORFs with conserved peptide sequences (CPuORFs). Here, we applied ESUCA to diverse animal genomes, because animal CPuORFs have been identified only by comparing uORF sequences between a limited number of species, and how many previously identified CPuORFs encode regulatory peptides is unclear. By using ESUCA, 1517 (1373 novel and 144 known) CPuORFs were extracted from four evolutionarily divergent animal genomes. We examined the effects of 17 human CPuORFs on mORF translation using transient expression assays. Through these analyses, we identified seven novel regulatory CPuORFs that repressed mORF translation in a sequence-dependent manner, including one conserved only among Eutheria. We discovered a much higher number of animal CPuORFs than previously identified. Since most human CPuORFs identified in this study are conserved across a wide range of Eutheria or a wider taxonomic range, many CPuORFs encoding regulatory peptides are expected to be found in the identified CPuORFs.
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Affiliation(s)
- Hiro Takahashi
- Graduate School of Medical Sciences, Kanazawa University, Kanazawa, 920-1192, Japan. .,Graduate School of Horticulture, Chiba University, Matsudo, 271-8510, Japan. .,Fundamental Innovative Oncology Core Center, National Cancer Center, Tokyo, 104-0045, Japan.
| | - Shido Miyaki
- Graduate School of Horticulture, Chiba University, Matsudo, 271-8510, Japan
| | - Hitoshi Onouchi
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Taichiro Motomura
- Graduate School of Medical Sciences, Kanazawa University, Kanazawa, 920-1192, Japan
| | - Nobuo Idesako
- Graduate School of Horticulture, Chiba University, Matsudo, 271-8510, Japan
| | - Anna Takahashi
- Faculty of Information Technologies and Control, Belarusian State University of Informatics and Radio Electronics, 220013, Minsk, Belarus.,College of Bioscience and Biotechnology, Chubu University, Kasugai, 487-8501, Japan
| | - Masataka Murase
- Graduate School of Medical Sciences, Kanazawa University, Kanazawa, 920-1192, Japan
| | - Shuichi Fukuyoshi
- Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, 920-1192, Japan
| | - Toshinori Endo
- Graduate School of Information Science and Technology, Hokkaido University, Sapporo, 060-0814, Japan
| | - Kenji Satou
- Faculty of Biological Science and Technology, Institute of Science and Engineering, Kanazawa University, Kanazawa, 920-1192, Japan
| | - Satoshi Naito
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan.,Graduate School of Life Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Motoyuki Itoh
- Graduate School of Pharmaceutical Science, Chiba University, Chiba, 260-8675, Japan.
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11
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Dever TE, Ivanov IP, Sachs MS. Conserved Upstream Open Reading Frame Nascent Peptides That Control Translation. Annu Rev Genet 2020; 54:237-264. [PMID: 32870728 DOI: 10.1146/annurev-genet-112618-043822] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cells utilize transcriptional and posttranscriptional mechanisms to alter gene expression in response to environmental cues. Gene-specific controls, including changing the translation of specific messenger RNAs (mRNAs), provide a rapid means to respond precisely to different conditions. Upstream open reading frames (uORFs) are known to control the translation of mRNAs. Recent studies in bacteria and eukaryotes have revealed the functions of evolutionarily conserved uORF-encoded peptides. Some of these uORF-encoded nascent peptides enable responses to specific metabolites to modulate the translation of their mRNAs by stalling ribosomes and through ribosome stalling may also modulate the level of their mRNAs. In this review, we highlight several examples of conserved uORF nascent peptides that stall ribosomes to regulate gene expression in response to specific metabolites in bacteria, fungi, mammals, and plants.
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Affiliation(s)
- Thomas E Dever
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA; ,
| | - Ivaylo P Ivanov
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA; ,
| | - Matthew S Sachs
- Department of Biology, Texas A&M University, College Station, Texas 77843, USA;
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12
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Radío S, Garat B, Sotelo-Silveira J, Smircich P. Upstream ORFs Influence Translation Efficiency in the Parasite Trypanosoma cruzi. Front Genet 2020; 11:166. [PMID: 32180802 PMCID: PMC7059621 DOI: 10.3389/fgene.2020.00166] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 02/12/2020] [Indexed: 11/13/2022] Open
Abstract
It is generally accepted that the presence of ORFs in the 5' untranslated region of eukaryotic transcripts modulates the production of proteins by controlling the translation initiation rate of the main CDS. In trypanosomatid parasites, which almost exclusively depend on post-transcriptional mechanisms to regulate gene expression, translation has been identified as a key step. However, the mechanisms of control of translation are not fully understood. In the present work, we have annotated the 5'UTRs of the Trypanosoma cruzi genome both in epimastigotes and metacyclic trypomastigotes and, using a stringent classification approach, we identified putative regulatory uORFs in about 9% of the analyzed 5'UTRs. The translation efficiency (TE) and translational levels of transcripts containing putative repressive uORFs were found to be significantly reduced. These findings are supported by the fact that proteomic methods only identify a low number of proteins coded by transcripts containing repressive uORF. We additionally show that AUG is the main translation initiator codon of repressive uORFs in T. cruzi. Interestingly, the decrease in TE is more pronounced when the uORFs overlaps the main CDS. In conclusion, we show that the presence of the uORF and features such as initiation codon and/or location of the uORFs may be acting to fine tune translation levels in these parasites.
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Affiliation(s)
- Santiago Radío
- Department of Genomics, Instituto de Investigaciones Biológicas Clemente Estable, Ministerio de Educación y Cultura, Montevideo, Uruguay.,Laboratory of Molecular Interactions, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Beatriz Garat
- Laboratory of Molecular Interactions, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - José Sotelo-Silveira
- Department of Genomics, Instituto de Investigaciones Biológicas Clemente Estable, Ministerio de Educación y Cultura, Montevideo, Uruguay.,Department of Cell and Molecular Biology, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Pablo Smircich
- Department of Genomics, Instituto de Investigaciones Biológicas Clemente Estable, Ministerio de Educación y Cultura, Montevideo, Uruguay.,Laboratory of Molecular Interactions, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
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13
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Wang L, Romano MC, Davidson FA. Translational control of gene expression via interacting feedback loops. Phys Rev E 2019; 100:050402. [PMID: 31869996 DOI: 10.1103/physreve.100.050402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Indexed: 11/07/2022]
Abstract
Translation is a key step in the synthesis of proteins. Accordingly, cells have evolved an intricate array of control mechanisms to regulate this process. By constructing a multicomponent mathematical framework we uncover how translation may be controlled via interacting feedback loops. Our results reveal that this interplay gives rise to a remarkable range of protein synthesis dynamics, including oscillations, step change, and bistability. This suggests that cells may have recourse to a much richer set of control mechanisms than was previously understood.
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Affiliation(s)
- Liang Wang
- Division of Mathematics, School of Science and Engineering, University of Dundee, Dundee DD1 4HN, United Kingdom
| | - M Carmen Romano
- SUPA, Institute for Complex Systems and Mathematical Biology, Department of Physics, Aberdeen AB24 3UE, United Kingdom and Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB24 3FX, United Kingdom
| | - Fordyce A Davidson
- Division of Mathematics, School of Science and Engineering, University of Dundee, Dundee DD1 4HN, United Kingdom
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14
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Destabilization of Eukaryote mRNAs by 5' Proximal Stop Codons Can Occur Independently of the Nonsense-Mediated mRNA Decay Pathway. Cells 2019; 8:cells8080800. [PMID: 31370247 PMCID: PMC6721604 DOI: 10.3390/cells8080800] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 07/24/2019] [Accepted: 07/25/2019] [Indexed: 11/17/2022] Open
Abstract
In eukaryotes, the binding of poly(A) binding protein (PAB) to the poly(A) tail is central to maintaining mRNA stability. PABP interacts with the translation termination apparatus, and with eIF4G to maintain 3′–5′ mRNA interactions as part of an mRNA closed loop. It is however unclear how ribosome recycling on a closed loop mRNA is influenced by the proximity of the stop codon to the poly(A) tail, and how post-termination ribosome recycling affects mRNA stability. We show that in a yeast disabled for nonsense mediated mRNA decay (NMD), a PGK1 mRNA with an early stop codon at codon 22 of the reading frame is still highly unstable, and that this instability cannot be significantly countered even when 50% stop codon readthrough is triggered. In an NMD-deficient mutant yeast, stable reporter alleles with more 3′ proximal stop codons could not be rendered unstable through Rli1-depletion, inferring defective Rli1 ribosome recycling is insufficient in itself to trigger mRNA instability. Mathematical modelling of a translation system including the effect of ribosome recycling and poly(A) tail shortening supports the hypothesis that impaired ribosome recycling from 5′ proximal stop codons may compromise initiation processes and thus destabilize the mRNA. A model is proposed wherein ribosomes undergo a maturation process during early elongation steps, and acquire competency to re-initiate on the same mRNA as translation elongation progresses beyond the very 5′ proximal regions of the mRNA.
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15
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Ivanov A, Shuvalova E, Egorova T, Shuvalov A, Sokolova E, Bizyaev N, Shatsky I, Terenin I, Alkalaeva E. Polyadenylate-binding protein-interacting proteins PAIP1 and PAIP2 affect translation termination. J Biol Chem 2019; 294:8630-8639. [PMID: 30992367 DOI: 10.1074/jbc.ra118.006856] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Revised: 03/29/2019] [Indexed: 12/29/2022] Open
Abstract
Polyadenylate-binding protein (PABP) stimulates translation termination via interaction of its C-terminal domain with eukaryotic polypeptide chain release factor, eRF3. Additionally, two other proteins, poly(A)-binding protein-interacting proteins 1 and 2 (PAIP1 and PAIP2), bind the same domain of PABP and regulate its translation-related activity. To study the biochemistry of eRF3 and PAIP1/2 competition for PABP binding, we quantified the effects of PAIPs on translation termination in the presence or absence of PABP. Our results demonstrated that both PAIP1 and PAIP2 prevented translation termination at the premature termination codon, by controlling PABP activity. Moreover, PAIP1 and PAIP2 inhibited the activity of free PABP on translation termination in vitro However, after binding the poly(A) tail, PABP became insensitive to suppression by PAIPs and efficiently activated translation termination in the presence of eRF3a. Additionally, we revealed that PAIP1 binds eRF3 in solution, which stabilizes the post-termination complex. These results indicated that PAIP1 and PAIP2 participate in translation termination and are important regulators of readthrough at the premature termination codon.
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Affiliation(s)
- Alexandr Ivanov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia; Faculty of Bioengineering and Bioinformatics, M. V. Lomonosov Moscow State University, Moscow 119234, Russia
| | - Ekaterina Shuvalova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Tatiana Egorova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Alexey Shuvalov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Elizaveta Sokolova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Nikita Bizyaev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Ivan Shatsky
- Belozersky Institute of Physico-Chemical Biology, M. V. Lomonosov Moscow State University, Moscow 119234, Russia
| | - Ilya Terenin
- Belozersky Institute of Physico-Chemical Biology, M. V. Lomonosov Moscow State University, Moscow 119234, Russia; Sechenov First Moscow State Medical University, Institute of Molecular Medicine, Moscow 119146, Russia.
| | - Elena Alkalaeva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia.
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16
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Harvey RF, Smith TS, Mulroney T, Queiroz RML, Pizzinga M, Dezi V, Villenueva E, Ramakrishna M, Lilley KS, Willis AE. Trans-acting translational regulatory RNA binding proteins. WILEY INTERDISCIPLINARY REVIEWS. RNA 2018; 9:e1465. [PMID: 29341429 PMCID: PMC5947564 DOI: 10.1002/wrna.1465] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 10/31/2017] [Accepted: 12/04/2017] [Indexed: 12/13/2022]
Abstract
The canonical molecular machinery required for global mRNA translation and its control has been well defined, with distinct sets of proteins involved in the processes of translation initiation, elongation and termination. Additionally, noncanonical, trans-acting regulatory RNA-binding proteins (RBPs) are necessary to provide mRNA-specific translation, and these interact with 5' and 3' untranslated regions and coding regions of mRNA to regulate ribosome recruitment and transit. Recently it has also been demonstrated that trans-acting ribosomal proteins direct the translation of specific mRNAs. Importantly, it has been shown that subsets of RBPs often work in concert, forming distinct regulatory complexes upon different cellular perturbation, creating an RBP combinatorial code, which through the translation of specific subsets of mRNAs, dictate cell fate. With the development of new methodologies, a plethora of novel RNA binding proteins have recently been identified, although the function of many of these proteins within mRNA translation is unknown. In this review we will discuss these methodologies and their shortcomings when applied to the study of translation, which need to be addressed to enable a better understanding of trans-acting translational regulatory proteins. Moreover, we discuss the protein domains that are responsible for RNA binding as well as the RNA motifs to which they bind, and the role of trans-acting ribosomal proteins in directing the translation of specific mRNAs. This article is categorized under: RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes Translation > Translation Regulation Translation > Translation Mechanisms.
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Affiliation(s)
| | - Tom S. Smith
- Cambridge Centre for Proteomics, Department of BiochemistryUniversity of CambridgeCambridgeUK
| | | | - Rayner M. L. Queiroz
- Cambridge Centre for Proteomics, Department of BiochemistryUniversity of CambridgeCambridgeUK
| | | | | | - Eneko Villenueva
- Cambridge Centre for Proteomics, Department of BiochemistryUniversity of CambridgeCambridgeUK
| | | | - Kathryn S. Lilley
- Cambridge Centre for Proteomics, Department of BiochemistryUniversity of CambridgeCambridgeUK
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17
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Datta S, Seed B. Influence of multiplicative stochastic variation on translational elongation rates. PLoS One 2018; 13:e0191152. [PMID: 29351322 PMCID: PMC5774726 DOI: 10.1371/journal.pone.0191152] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 12/30/2017] [Indexed: 11/18/2022] Open
Abstract
Experimental data indicate that stochastic effects exerted at the level of translation contribute substantially to the variation in abundance of proteins expressed at moderate to high levels. This study analyzes the theoretical consequences of fluctuations in residue-specific elongation rates during translation. A simple analytical framework shows that rate variation during elongation gives rise to protein production rates that consist of sums of products of random variables. Simulations show that because the contribution to total variation of products of random variables greatly exceeds that of sums of random variables, the overall distribution exhibits approximately log-normal behavior. Empirical fits of the data can be satisfied by either sums of log-normal distributions, or sums of log-normal and log-logistic distributions. Elongation rate stochastic variation offers an accounting for a major component of biological variation. The analysis provided here highlights a probability distribution that is a natural extension of the Poisson and has broad applicability to many types of multiplicative noise processes.
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Affiliation(s)
- Sandip Datta
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, United States of America
| | - Brian Seed
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, United States of America
- * E-mail:
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18
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Dacheux E, Malys N, Meng X, Ramachandran V, Mendes P, McCarthy JEG. Translation initiation events on structured eukaryotic mRNAs generate gene expression noise. Nucleic Acids Res 2017; 45:6981-6992. [PMID: 28521011 PMCID: PMC5499741 DOI: 10.1093/nar/gkx430] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 05/10/2017] [Indexed: 11/14/2022] Open
Abstract
Gene expression stochasticity plays a major role in biology, creating non-genetic cellular individuality and influencing multiple processes, including differentiation and stress responses. We have addressed the lack of knowledge about posttranscriptional contributions to noise by determining cell-to-cell variations in the abundance of mRNA and reporter protein in yeast. Two types of structural element, a stem–loop and a poly(G) motif, not only inhibit translation initiation when inserted into an mRNA 5΄ untranslated region, but also generate noise. The noise-enhancing effect of the stem–loop structure also remains operational when combined with an upstream open reading frame. This has broad significance, since these elements are known to modulate the expression of a diversity of eukaryotic genes. Our findings suggest a mechanism for posttranscriptional noise generation that will contribute to understanding of the generally poor correlation between protein-level stochasticity and transcriptional bursting. We propose that posttranscriptional stochasticity can be linked to cycles of folding/unfolding of a stem–loop structure, or to interconversion between higher-order structural conformations of a G-rich motif, and have created a correspondingly configured computational model that generates fits to the experimental data. Stochastic events occurring during the ribosomal scanning process can therefore feature alongside transcriptional bursting as a source of noise.
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Affiliation(s)
- Estelle Dacheux
- Warwick Integrative Synthetic Biology Centre (WISB) and School of Life Sciences, University of Warwick, Gibbet Hill, Coventry CV4 7AL, UK
| | - Naglis Malys
- Warwick Integrative Synthetic Biology Centre (WISB) and School of Life Sciences, University of Warwick, Gibbet Hill, Coventry CV4 7AL, UK
| | - Xiang Meng
- Warwick Integrative Synthetic Biology Centre (WISB) and School of Life Sciences, University of Warwick, Gibbet Hill, Coventry CV4 7AL, UK
| | - Vinoy Ramachandran
- Warwick Integrative Synthetic Biology Centre (WISB) and School of Life Sciences, University of Warwick, Gibbet Hill, Coventry CV4 7AL, UK
| | - Pedro Mendes
- Center for Quantitative Medicine, UConn Health, 263 Farmington Avenue, CT 06030-6033, USA
| | - John E G McCarthy
- Warwick Integrative Synthetic Biology Centre (WISB) and School of Life Sciences, University of Warwick, Gibbet Hill, Coventry CV4 7AL, UK
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19
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Mechanism and Regulation of Protein Synthesis in Saccharomyces cerevisiae. Genetics 2017; 203:65-107. [PMID: 27183566 DOI: 10.1534/genetics.115.186221] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 02/24/2016] [Indexed: 12/18/2022] Open
Abstract
In this review, we provide an overview of protein synthesis in the yeast Saccharomyces cerevisiae The mechanism of protein synthesis is well conserved between yeast and other eukaryotes, and molecular genetic studies in budding yeast have provided critical insights into the fundamental process of translation as well as its regulation. The review focuses on the initiation and elongation phases of protein synthesis with descriptions of the roles of translation initiation and elongation factors that assist the ribosome in binding the messenger RNA (mRNA), selecting the start codon, and synthesizing the polypeptide. We also examine mechanisms of translational control highlighting the mRNA cap-binding proteins and the regulation of GCN4 and CPA1 mRNAs.
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20
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Curran JA, Weiss B. What Is the Impact of mRNA 5' TL Heterogeneity on Translational Start Site Selection and the Mammalian Cellular Phenotype? Front Genet 2016; 7:156. [PMID: 27630668 PMCID: PMC5005323 DOI: 10.3389/fgene.2016.00156] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 08/16/2016] [Indexed: 12/23/2022] Open
Abstract
A major determinant in the efficiency of ribosome loading onto mRNAs is the 5′ TL (transcript leader or 5′ UTR). In addition, elements within this region also impact on start site selection demonstrating that it can modulate the protein readout at both quantitative and qualitative levels. With the increasing wealth of data generated by the mining of the mammalian transcriptome, it has become evident that a genes 5′ TL is not homogeneous but actually exhibits significant heterogeneity. This arises due to the utilization of alternative promoters, and is further compounded by significant variability with regards to the precise transcriptional start sites of each (not to mention alternative splicing). Consequently, the transcript for a protein coding gene is not a unique mRNA, but in-fact a complexed quasi-species of variants whose composition may respond to the changing physiological environment of the cell. Here we examine the potential impact of these events with regards to the protein readout.
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Affiliation(s)
- Joseph A Curran
- Department of Microbiology and Molecular Medicine, Medical School, University of GenevaGeneva, Switzerland; Institute of Genetics and Genomics of Geneva, University of GenevaGeneva, Switzerland
| | - Benjamin Weiss
- Department of Microbiology and Molecular Medicine, Medical School, University of Geneva Geneva, Switzerland
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21
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Ivanov A, Mikhailova T, Eliseev B, Yeramala L, Sokolova E, Susorov D, Shuvalov A, Schaffitzel C, Alkalaeva E. PABP enhances release factor recruitment and stop codon recognition during translation termination. Nucleic Acids Res 2016; 44:7766-76. [PMID: 27418677 PMCID: PMC5027505 DOI: 10.1093/nar/gkw635] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 07/01/2016] [Indexed: 01/01/2023] Open
Abstract
Poly(A)-binding protein (PABP) is a major component of the messenger RNA–protein complex. PABP is able to bind the poly(A) tail of mRNA, as well as translation initiation factor 4G and eukaryotic release factor 3a (eRF3a). PABP has been found to stimulate translation initiation and to inhibit nonsense-mediated mRNA decay. Using a reconstituted mammalian in vitro translation system, we show that PABP directly stimulates translation termination. PABP increases the efficiency of translation termination by recruitment of eRF3a and eRF1 to the ribosome. PABP's function in translation termination depends on its C-terminal domain and its interaction with the N-terminus of eRF3a. Interestingly, we discover that full-length eRF3a exerts a different mode of function compared to its truncated form eRF3c, which lacks the N-terminal domain. Pre-association of eRF3a, but not of eRF3c, with pre-termination complexes (preTCs) significantly increases the efficiency of peptidyl–tRNA hydrolysis by eRF1. This implicates new, additional interactions of full-length eRF3a with the ribosomal preTC. Based on our findings, we suggest that PABP enhances the productive binding of the eRF1–eRF3 complex to the ribosome, via interactions with the N-terminal domain of eRF3a which itself has an active role in translation termination.
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Affiliation(s)
- Alexandr Ivanov
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, 119991 Moscow, Russia Faculty of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Tatyana Mikhailova
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, 119991 Moscow, Russia
| | - Boris Eliseev
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Lahari Yeramala
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Elizaveta Sokolova
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, 119991 Moscow, Russia
| | - Denis Susorov
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, 119991 Moscow, Russia Faculty of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Alexey Shuvalov
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, 119991 Moscow, Russia
| | - Christiane Schaffitzel
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38042 Grenoble, France School of Biochemistry, University of Bristol, BS8 1TD, UK
| | - Elena Alkalaeva
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, 119991 Moscow, Russia
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22
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Tzani I, Ivanov IP, Andreev DE, Dmitriev RI, Dean KA, Baranov PV, Atkins JF, Loughran G. Systematic analysis of the PTEN 5' leader identifies a major AUU initiated proteoform. Open Biol 2016; 6:rsob.150203. [PMID: 27249819 PMCID: PMC4892431 DOI: 10.1098/rsob.150203] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 04/26/2016] [Indexed: 12/22/2022] Open
Abstract
Abundant evidence for translation within the 5' leaders of many human genes is rapidly emerging, especially, because of the advent of ribosome profiling. In most cases, it is believed that the act of translation rather than the encoded peptide is important. However, the wealth of available sequencing data in recent years allows phylogenetic detection of sequences within 5' leaders that have emerged under coding constraint and therefore allow for the prediction of functional 5' leader translation. Using this approach, we previously predicted a CUG-initiated, 173 amino acid N-terminal extension to the human tumour suppressor PTEN. Here, a systematic experimental analysis of translation events in the PTEN 5' leader identifies at least two additional non-AUG-initiated PTEN proteoforms that are expressed in most human cell lines tested. The most abundant extended PTEN proteoform initiates at a conserved AUU codon and extends the canonical AUG-initiated PTEN by 146 amino acids. All N-terminally extended PTEN proteoforms tested retain the ability to downregulate the PI3K pathway. We also provide evidence for the translation of two conserved AUG-initiated upstream open reading frames within the PTEN 5' leader that control the ratio of PTEN proteoforms.
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Affiliation(s)
- Ioanna Tzani
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Ivaylo P Ivanov
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dmitri E Andreev
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia
| | - Ruslan I Dmitriev
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Kellie A Dean
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Pavel V Baranov
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - John F Atkins
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland Department of Human Genetics, University of Utah, Salt Lake City, UT 84112-5330, USA
| | - Gary Loughran
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
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23
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Gunišová S, Beznosková P, Mohammad MP, Vlčková V, Valášek LS. In-depth analysis of cis-determinants that either promote or inhibit reinitiation on GCN4 mRNA after translation of its four short uORFs. RNA (NEW YORK, N.Y.) 2016; 22:542-558. [PMID: 26822200 PMCID: PMC4793210 DOI: 10.1261/rna.055046.115] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 12/18/2015] [Indexed: 05/29/2023]
Abstract
Translational control in eukaryotes is exerted by many means, one of which involves a ribosome translating multiple cistrons per mRNA as in bacteria. It is called reinitiation (REI) and occurs on mRNAs where the main ORF is preceded by a short upstream uORF(s). Some uORFs support efficient REI on downstream cistrons, whereas some others do not. The mRNA of yeast transcriptional activator GCN4 contains four uORFs of both types that together compose an intriguing regulatory mechanism of its expression responding to nutrients' availability and various stresses. Here we subjected all GCN4 uORFs to a comprehensive analysis to identify all REI-promoting and inhibiting cis-determinants that contribute either autonomously or in synergy to the overall efficiency of REI on GCN4. We found that the 3' sequences of uORFs 1-3 contain a conserved AU1-2A/UUAU2 motif that promotes REI in position-specific, autonomous fashion such as the REI-promoting elements occurring in 5' sequences of uORF1 and uORF2. We also identified autonomous and transferable REI-inhibiting elements in the 3' sequences of uORF2 and uORF3, immediately following their AU-rich motif. Furthermore, we analyzed contributions of coding triplets and terminating stop codon tetranucleotides of GCN4 uORFs showing a negative correlation between the efficiency of reinitiation and efficiency of translation termination. Together we provide a complex overview of all cis-determinants of REI with their effects set in the context of the overall GCN4 translational control.
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Affiliation(s)
- Stanislava Gunišová
- Laboratory of Regulation of Gene Expression, Institute of Microbiology AS CR, Prague 142 20, Czech Republic
| | - Petra Beznosková
- Laboratory of Regulation of Gene Expression, Institute of Microbiology AS CR, Prague 142 20, Czech Republic
| | - Mahabub Pasha Mohammad
- Laboratory of Regulation of Gene Expression, Institute of Microbiology AS CR, Prague 142 20, Czech Republic
| | - Vladislava Vlčková
- Laboratory of Regulation of Gene Expression, Institute of Microbiology AS CR, Prague 142 20, Czech Republic
| | - Leoš Shivaya Valášek
- Laboratory of Regulation of Gene Expression, Institute of Microbiology AS CR, Prague 142 20, Czech Republic
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24
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Ebina I, Takemoto-Tsutsumi M, Watanabe S, Koyama H, Endo Y, Kimata K, Igarashi T, Murakami K, Kudo R, Ohsumi A, Noh AL, Takahashi H, Naito S, Onouchi H. Identification of novel Arabidopsis thaliana upstream open reading frames that control expression of the main coding sequences in a peptide sequence-dependent manner. Nucleic Acids Res 2015; 43:1562-76. [PMID: 25618853 PMCID: PMC4330380 DOI: 10.1093/nar/gkv018] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Upstream open reading frames (uORFs) are often found in the 5'-leader regions of eukaryotic mRNAs and can negatively modulate the translational efficiency of the downstream main ORF. Although the effects of most uORFs are thought to be independent of their encoded peptide sequences, certain uORFs control translation of the main ORF in a peptide sequence-dependent manner. For genome-wide identification of such peptide sequence-dependent regulatory uORFs, exhaustive searches for uORFs with conserved amino acid sequences have been conducted using bioinformatic analyses. However, whether the conserved uORFs identified by these bioinformatic approaches encode regulatory peptides has not been experimentally determined. Here we analyzed 16 recently identified Arabidopsis thaliana conserved uORFs for the effects of their amino acid sequences on the expression of the main ORF using a transient expression assay. We identified five novel uORFs that repress main ORF expression in a peptide sequence-dependent manner. Mutational analysis revealed that, in four of them, the C-terminal region of the uORF-encoded peptide is critical for the repression of main ORF expression. Intriguingly, we also identified one exceptional sequence-dependent regulatory uORF, in which the stop codon position is not conserved and the C-terminal region is not important for the repression of main ORF expression.
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Affiliation(s)
- Isao Ebina
- Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | | | - Shun Watanabe
- Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Hiroaki Koyama
- Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Yayoi Endo
- Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Kaori Kimata
- Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Takuya Igarashi
- Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Karin Murakami
- Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Rin Kudo
- Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Arisa Ohsumi
- Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Abdul Latif Noh
- Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Hiro Takahashi
- Graduate School of Horticulture, Chiba University, Matsudo 271-8510, Japan
| | - Satoshi Naito
- Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Hitoshi Onouchi
- Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
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Lukowski SW, Rothnagel JA, Trezise AEO. CFTR mRNA expression is regulated by an upstream open reading frame and RNA secondary structure in its 5' untranslated region. Hum Mol Genet 2014; 24:899-912. [PMID: 25274779 DOI: 10.1093/hmg/ddu501] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Post-transcriptional regulation of gene expression through 5' untranslated region (5'UTR)-encoded cis-acting elements is an important mechanism for the control of protein expression levels. Through controlling specific aspects of translation initiation, expression can be tightly regulated while remaining responsive to cellular requirements. With respect to cystic fibrosis (CF), the overexpression of cystic fibrosis transmembrane conductance regulator (CFTR) protein trafficking mutants, such as delta-F508, is of great biological and clinical interest. By understanding the post-transcriptional mechanisms that regulate CFTR expression, new procedures can be developed to enhance CFTR expression in homozygous delta-F508 CF patients. We have identified the key elements of a complex negative regulatory mechanism that is encoded within the human CFTR 5'UTR and show how these elements act in combination to restrict CFTR gene expression to a consistently low level in a transcript-specific manner. This study shows, for the first time, that endogenous human CFTR expression is post-transcriptionally regulated through a 5'UTR-mediated mechanism. We show that the very low levels of endogenous CFTR expression, compared with other low expression genes, are maintained through the co-operative inhibitory effects of an upstream open reading frame and a thermodynamically stable RNA secondary structure.
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Affiliation(s)
- Samuel W Lukowski
- School of Chemistry and Molecular Biosciences and Australian Equine Genetics Research Centre, The University of Queensland, Brisbane, QLD 4072, Australia
| | | | - Ann E O Trezise
- School of Chemistry and Molecular Biosciences and Australian Equine Genetics Research Centre, The University of Queensland, Brisbane, QLD 4072, Australia
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26
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Eliseeva IA, Lyabin DN, Ovchinnikov LP. Poly(A)-binding proteins: structure, domain organization, and activity regulation. BIOCHEMISTRY (MOSCOW) 2014; 78:1377-91. [PMID: 24490729 DOI: 10.1134/s0006297913130014] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
RNA-binding proteins are of vital importance for mRNA functioning. Among these, poly(A)-binding proteins (PABPs) are of special interest due to their participation in virtually all mRNA-dependent events that is caused by their high affinity for A-rich mRNA sequences. Apart from mRNAs, PABPs interact with many proteins, thus promoting their involvement in cellular events. In the nucleus, PABPs play a role in polyadenylation, determine the length of the poly(A) tail, and may be involved in mRNA export. In the cytoplasm, they participate in regulation of translation initiation and either protect mRNAs from decay through binding to their poly(A) tails or stimulate this decay by promoting mRNA interactions with deadenylase complex proteins. This review presents modern notions of the role of PABPs in mRNA-dependent events; peculiarities of regulation of PABP amount in the cell and activities are also discussed.
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Affiliation(s)
- I A Eliseeva
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
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27
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Hurtado S, Kim Guisbert KS, Sontheimer EJ. SPO24 is a transcriptionally dynamic, small ORF-encoding locus required for efficient sporulation in Saccharomyces cerevisiae. PLoS One 2014; 9:e105058. [PMID: 25127041 PMCID: PMC4134269 DOI: 10.1371/journal.pone.0105058] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2013] [Accepted: 07/20/2014] [Indexed: 01/22/2023] Open
Abstract
In Saccharomyces cerevisiae, meiosis and sporulation are highly regulated responses that are driven in part by changes in RNA expression. Alternative mRNA forms with extended 5′ UTRs are atypical in S. cerevisiae, and 5′ extensions with upstream open reading frames (uORFs) are even more unusual. Here we characterize the gene YPR036W-A, now renamed SPO24, which encodes a very small (67-amino-acid) protein. This gene gives rise to two mRNA forms: a shorter form throughout meiosis and a longer, 5′-extended form in mid-late meiosis. The latter form includes a uORF for a 14-amino-acid peptide (Spo24u14). Deletion of the downstream ORF (dORF) leads to sporulation defects and the appearance of pseudohyphae-like projections. Experiments with luciferase reporters indicate that the uORF does not downregulate dORF translation. The protein encoded by the dORF (Spo24d67) localizes to the prospore membrane and is differentially phosphorylated during meiosis. Transcription of the 5′-extended mRNA in mid-meiosis depends upon the presence of two middle sporulation elements (MSEs). Removal of the MSEs severely inhibits the mid-meiotic appearance of the 5′-extended mRNA and limits the ability of plasmid-borne SPO24 to rescue the sporulation defect of a spo24Δ mutant, suggesting that the 5′-extended mRNA is functionally important. These results reveal Spo24d67 as a sporulation-related factor that is encoded by a transcriptionally dynamic, uORF-containing locus.
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Affiliation(s)
- Sara Hurtado
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
| | - Karen S. Kim Guisbert
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
| | - Erik J. Sontheimer
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
- * E-mail:
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28
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Wethmar K. The regulatory potential of upstream open reading frames in eukaryotic gene expression. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 5:765-78. [DOI: 10.1002/wrna.1245] [Citation(s) in RCA: 127] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 05/09/2014] [Accepted: 05/09/2014] [Indexed: 01/04/2023]
Affiliation(s)
- Klaus Wethmar
- Max-Delbrueck-Center for Molecular Medicine; Berlin Germany
- Helios Klinikum Berlin-Buch; Berlin Germany
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29
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Retzer K, Butt H, Korbei B, Luschnig C. The far side of auxin signaling: fundamental cellular activities and their contribution to a defined growth response in plants. PROTOPLASMA 2014; 251:731-46. [PMID: 24221297 PMCID: PMC4059964 DOI: 10.1007/s00709-013-0572-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 10/15/2013] [Indexed: 05/04/2023]
Abstract
Recent years have provided us with spectacular insights into the biology of the plant hormone auxin, leaving the impression of a highly versatile molecule involved in virtually every aspect of plant development. A combination of genetics, biochemistry, and cell biology has established auxin signaling pathways, leading to the identification of two distinct modes of auxin perception and downstream regulatory cascades. Major targets of these signaling modules are components of the polar auxin transport machinery, mediating directional distribution of the phytohormone throughout the plant body, and decisively affecting plant development. Alterations in auxin transport, metabolism, or signaling that occur as a result of intrinsic as well as environmental stimuli, control adjustments in morphogenetic programs, giving rise to defined growth responses attributed to the activity of the phytohormone. Some of the results obtained from the analysis of auxin, however, do not fit coherently into a picture of highly specific signaling events, but rather suggest mutual interactions between auxin and fundamental cellular pathways, like the control of intracellular protein sorting or translation. Crosstalk between auxin and these basic determinants of cellular activity and how they might shape auxin effects in the control of morphogenesis are the subject of this review.
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Affiliation(s)
- Katarzyna Retzer
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, BOKU, Wien Muthgasse 18, 1190 Wien, Austria
| | - Haroon Butt
- Department of Biological Sciences, Forman Christian College, Ferozepur Road, Lahore, 54600 Pakistan
| | - Barbara Korbei
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, BOKU, Wien Muthgasse 18, 1190 Wien, Austria
| | - Christian Luschnig
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, BOKU, Wien Muthgasse 18, 1190 Wien, Austria
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Barbosa C, Romão L. Translation of the human erythropoietin transcript is regulated by an upstream open reading frame in response to hypoxia. RNA (NEW YORK, N.Y.) 2014; 20:594-608. [PMID: 24647661 PMCID: PMC3988562 DOI: 10.1261/rna.040915.113] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 01/10/2014] [Indexed: 05/22/2023]
Abstract
Erythropoietin (EPO) is a key mediator hormone for hypoxic induction of erythropoiesis that also plays important nonhematopoietic functions. It has been shown that EPO gene expression regulation occurs at different levels, including transcription and mRNA stabilization. In this report, we show that expression of EPO is also regulated at the translational level by an upstream open reading frame (uORF) of 14 codons. As judged by comparisons of protein and mRNA levels, the uORF acts as a cis-acting element that represses translation of the main EPO ORF in unstressed HEK293, HepG2, and HeLa cells. However, in response to hypoxia, this repression is significantly released, specifically in HeLa cells, through a mechanism that involves processive scanning of ribosomes from the 5' end of the EPO transcript and enhanced ribosome bypass of the uORF. In addition, we demonstrate that in HeLa cells, hypoxia induces the phosphorylation of eukaryotic translation initiation factor 2α (eIF2α) concomitantly with a significant increase of EPO protein synthesis. These findings provide a framework for understanding that production of high levels of EPO induced by hypoxia also involves regulation at the translational level.
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31
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Mather WH, Hasty J, Tsimring LS, Williams RJ. Translational cross talk in gene networks. Biophys J 2014; 104:2564-72. [PMID: 23746529 DOI: 10.1016/j.bpj.2013.04.049] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2012] [Revised: 04/03/2013] [Accepted: 04/11/2013] [Indexed: 01/25/2023] Open
Abstract
It has been shown experimentally that competition for limited translational resources by upstream mRNAs can lead to an anticorrelation between protein counts. Here, we investigate a stochastic model for this phenomenon, in which gene transcripts of different types compete for a finite pool of ribosomes. Throughout, we utilize concepts from the theory of multiclass queues to describe a qualitative shift in protein count statistics as the system transitions from being underloaded (ribosomes exceed transcripts in number) to being overloaded (transcripts exceed ribosomes in number). The exact analytical solution of a simplified stochastic model, in which the numbers of competing mRNAs and ribosomes are fixed, exhibits weak positive correlations between steady-state protein counts when total transcript count slightly exceeds ribosome count, whereas the solution can exhibit strong negative correlations when total transcript count significantly exceeds ribosome count. Extending this analysis, we find approximate but reasonably accurate solutions for a more realistic model, in which abundances of mRNAs and ribosomes are allowed to fluctuate randomly. Here, ribosomal fluctuations contribute positively and mRNA fluctuations contribute negatively to correlations, and when mRNA fluctuations dominate ribosomal fluctuations, a strong anticorrelation extremum reliably occurs near the transition from the underloaded to the overloaded regime.
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Affiliation(s)
- William H Mather
- Department of Physics, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
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32
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Bunnik EM, Chung DWD, Hamilton M, Ponts N, Saraf A, Prudhomme J, Florens L, Le Roch KG. Polysome profiling reveals translational control of gene expression in the human malaria parasite Plasmodium falciparum. Genome Biol 2013; 14:R128. [PMID: 24267660 PMCID: PMC4053746 DOI: 10.1186/gb-2013-14-11-r128] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Accepted: 11/22/2013] [Indexed: 12/02/2022] Open
Abstract
Background In eukaryotic organisms, gene expression is regulated at multiple levels during the processes of transcription and translation. The absence of a tight regulatory network for transcription in the human malaria parasite suggests that gene expression may largely be controlled at post-transcriptional and translational levels. Results In this study, we compare steady-state mRNA and polysome-associated mRNA levels of Plasmodium falciparum at different time points during its asexual cell cycle. For more than 30% of its genes, we observe a delay in peak transcript abundance in the polysomal fraction as compared to the steady-state mRNA fraction, suggestive of strong translational control. Our data show that key regulatory mechanisms could include inhibitory activity of upstream open reading frames and translational repression of the major virulence gene family by intronic transcripts. In addition, we observe polysomal mRNA-specific alternative splicing events and widespread transcription of non-coding transcripts. Conclusions These different layers of translational regulation are likely to contribute to a complex network that controls gene expression in this eukaryotic pathogen. Disrupting the mechanisms involved in such translational control could provide novel anti-malarial strategies.
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Deletion of creB in Aspergillus oryzae increases secreted hydrolytic enzyme activity. Appl Environ Microbiol 2013; 79:5480-7. [PMID: 23835170 DOI: 10.1128/aem.01406-13] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Aspergillus oryzae has been used in the food and beverage industry for centuries, and industrial strains have been produced by multiple rounds of selection. Targeted gene deletion technology is particularly useful for strain improvement in such strains, particularly when they do not have a well-characterized meiotic cycle. Phenotypes of an Aspergillus nidulans strain null for the CreB deubiquitinating enzyme include effects on growth and repression, including increased activity levels of various enzymes. We show that Aspergillus oryzae contains a functional homologue of the CreB deubiquitinating enzyme and that a null strain shows increased activity levels of industrially important secreted enzymes, including cellulases, xylanases, amylases, and proteases, as well as alleviated inhibition of spore germination on glucose medium. Reverse transcription-quantitative PCR (RT-qPCR) analysis showed that the increased levels of enzyme activity in both Aspergillus nidulans and Aspergillus oryzae are mirrored at the transcript level, indicating transcriptional regulation. We report that Aspergillus oryzae DAR3699, originally isolated from soy fermentation, has a similar phenotype to that of a creB deletion mutant of the RIB40 strain, and it contains a mutation in the creB gene. Collectively, the results for Aspergillus oryzae, Aspergillus nidulans, Trichoderma reesei, and Penicillium decumbens show that deletion of creB may be broadly useful in diverse fungi for increasing production of a variety of enzymes.
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34
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Valásek LS. 'Ribozoomin'--translation initiation from the perspective of the ribosome-bound eukaryotic initiation factors (eIFs). Curr Protein Pept Sci 2013; 13:305-30. [PMID: 22708493 PMCID: PMC3434475 DOI: 10.2174/138920312801619385] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2011] [Revised: 01/16/2012] [Accepted: 02/16/2012] [Indexed: 02/05/2023]
Abstract
Protein synthesis is a fundamental biological mechanism bringing the DNA-encoded genetic information into
life by its translation into molecular effectors - proteins. The initiation phase of translation is one of the key points of gene
regulation in eukaryotes, playing a role in processes from neuronal function to development. Indeed, the importance of the
study of protein synthesis is increasing with the growing list of genetic diseases caused by mutations that affect mRNA
translation. To grasp how this regulation is achieved or altered in the latter case, we must first understand the molecular
details of all underlying processes of the translational cycle with the main focus put on its initiation. In this review I discuss
recent advances in our comprehension of the molecular basis of particular initiation reactions set into the context of
how and where individual eIFs bind to the small ribosomal subunit in the pre-initiation complex. I also summarize our
current knowledge on how eukaryotic initiation factor eIF3 controls gene expression in the gene-specific manner via reinitiation.
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Affiliation(s)
- Leos Shivaya Valásek
- Laboratory of Eukaryotic Gene Regulation, Institute of Microbiology AS CR, Prague, Czech Republic.
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35
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Loughran G, Sachs MS, Atkins JF, Ivanov IP. Stringency of start codon selection modulates autoregulation of translation initiation factor eIF5. Nucleic Acids Res 2012; 40:2898-906. [PMID: 22156057 PMCID: PMC3326321 DOI: 10.1093/nar/gkr1192] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2011] [Revised: 11/14/2011] [Accepted: 11/15/2011] [Indexed: 12/26/2022] Open
Abstract
An AUG in an optimal nucleotide context is the preferred translation initiation site in eukaryotic cells. Interactions among translation initiation factors, including eIF1 and eIF5, govern start codon selection. Experiments described here showed that high intracellular eIF5 levels reduced the stringency of start codon selection in human cells. In contrast, high intracellular eIF1 levels increased stringency. High levels of eIF5 induced translation of inhibitory upstream open reading frames (uORFs) in eIF5 mRNA that initiate with AUG codons in conserved poor contexts. This resulted in reduced translation from the downstream eIF5 start codon, indicating that eIF5 autoregulates its own synthesis. As with eIF1, which is also autoregulated through translation initiation, features contributing to eIF5 autoregulation show deep evolutionary conservation. The results obtained provide the basis for a model in which auto- and cross-regulation of eIF5 and eIF1 translation establish a regulatory feedback loop that would stabilize the stringency of start codon selection.
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Affiliation(s)
- Gary Loughran
- BioSciences Institute, University College Cork, Ireland, Department of Biology, Texas A&M University, College Station, TX 77843 and Department of Human Genetics, University of Utah, Salt Lake City, UT 84112-5330, USA
| | - Matthew S. Sachs
- BioSciences Institute, University College Cork, Ireland, Department of Biology, Texas A&M University, College Station, TX 77843 and Department of Human Genetics, University of Utah, Salt Lake City, UT 84112-5330, USA
| | - John F. Atkins
- BioSciences Institute, University College Cork, Ireland, Department of Biology, Texas A&M University, College Station, TX 77843 and Department of Human Genetics, University of Utah, Salt Lake City, UT 84112-5330, USA
| | - Ivaylo P. Ivanov
- BioSciences Institute, University College Cork, Ireland, Department of Biology, Texas A&M University, College Station, TX 77843 and Department of Human Genetics, University of Utah, Salt Lake City, UT 84112-5330, USA
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36
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Alternative splicing within the elk-1 5' untranslated region serves to modulate initiation events downstream of the highly conserved upstream open reading frame 2. Mol Cell Biol 2012; 32:1745-56. [PMID: 22354998 DOI: 10.1128/mcb.06751-11] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The 5' untranslated region (UTR) plays a central role in the regulation of mammalian translation initiation. Key components include RNA structure, upstream AUGs (uAUGs), upstream open reading frames (uORFs), and internal ribosome entry site elements that can interact to modulate the readout. We previously reported the characterization of two alternatively spliced 5' UTR isoforms of the human elk-1 gene. Both contain two uAUGs and a stable RNA stem-loop, but the long form (5' UTR(L)) was more repressive than the short form (5' UTR(S)) for initiation at the ELK-1 AUG. We now demonstrate that ELK-1 expression arises by a combination of leaky scanning and reinitiation, with the latter mediated by the small uORF2 conserved in both spliced isoforms. In HEK293T cells, a considerable fraction of ribosomes scans beyond the ELK-1 AUG in a reinitiation mode. These are sequestered by a series of out-of-frame AUG codons that serve to prevent access to a second in-frame AUG start site used to express short ELK-1 (sELK-1), an N-terminally truncated form of ELK-1 that has been observed only in neuronal cells. We present evidence that all these events are fine-tuned by the nature of the 5' UTR and the activity of the α subunit of eukaryotic initiation factor 2 and provide insights into the neuronal specificity of sELK-1 expression.
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Ivanov IP, Firth AE, Michel AM, Atkins JF, Baranov PV. Identification of evolutionarily conserved non-AUG-initiated N-terminal extensions in human coding sequences. Nucleic Acids Res 2011; 39:4220-34. [PMID: 21266472 PMCID: PMC3105428 DOI: 10.1093/nar/gkr007] [Citation(s) in RCA: 173] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
In eukaryotes, it is generally assumed that translation initiation occurs at the AUG codon closest to the messenger RNA 5' cap. However, in certain cases, initiation can occur at codons differing from AUG by a single nucleotide, especially the codons CUG, UUG, GUG, ACG, AUA and AUU. While non-AUG initiation has been experimentally verified for a handful of human genes, the full extent to which this phenomenon is utilized--both for increased coding capacity and potentially also for novel regulatory mechanisms--remains unclear. To address this issue, and hence to improve the quality of existing coding sequence annotations, we developed a methodology based on phylogenetic analysis of predicted 5' untranslated regions from orthologous genes. We use evolutionary signatures of protein-coding sequences as an indicator of translation initiation upstream of annotated coding sequences. Our search identified novel conserved potential non-AUG-initiated N-terminal extensions in 42 human genes including VANGL2, FGFR1, KCNN4, TRPV6, HDGF, CITED2, EIF4G3 and NTF3, and also affirmed the conservation of known non-AUG-initiated extensions in 17 other genes. In several instances, we have been able to obtain independent experimental evidence of the expression of non-AUG-initiated products from the previously published literature and ribosome profiling data.
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Affiliation(s)
- Ivaylo P Ivanov
- BioSciences Institute, University College Cork, Cork, Ireland.
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Abstract
Conserved upstream open reading frames (uORFs) are found within many eukaryotic transcripts and are known to regulate protein translation. Evidence from genetic and bioinformatic studies implicates disturbed uORF-mediated translational control in the etiology of human diseases. A genetic mouse model has recently provided proof-of-principle support for the physiological relevance of uORF-mediated translational control in mammals. The targeted disruption of the uORF initiation codon within the transcription factor CCAAT/enhancer binding protein β (C/EBPβ) gene resulted in deregulated C/EBPβ protein isoform expression, associated with defective liver regeneration and impaired osteoclast differentiation. The high prevalence of uORFs in the human transcriptome suggests that intensified search for mutations within 5' RNA leader regions may reveal a multitude of alterations affecting uORFs, causing pathogenic deregulation of protein expression.
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Affiliation(s)
- Klaus Wethmar
- Max Delbrueck Center for Molecular MedicineBerlin, Germany
- Charité, University Medicine BerlinGermany
| | - Jeske J Smink
- Max Delbrueck Center for Molecular MedicineBerlin, Germany
| | - Achim Leutz
- Max Delbrueck Center for Molecular MedicineBerlin, Germany
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Zhou F, Roy B, von Arnim AG. Translation reinitiation and development are compromised in similar ways by mutations in translation initiation factor eIF3h and the ribosomal protein RPL24. BMC PLANT BIOLOGY 2010; 10:193. [PMID: 20799971 PMCID: PMC3020687 DOI: 10.1186/1471-2229-10-193] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2010] [Accepted: 08/27/2010] [Indexed: 05/19/2023]
Abstract
BACKGROUND Within the scanning model of translation initiation, reinitiation is a non-canonical mechanism that operates on mRNAs harboring upstream open reading frames. The h subunit of eukaryotic initiation factor 3 (eIF3) boosts translation reinitiation on the uORF-containing mRNA coding for the Arabidopsis bZip transcription factor, AtbZip11, among others. The RPL24B protein of the large ribosomal subunit, which is encoded by SHORT VALVE1, likewise fosters translation of uORF-containing mRNAs, for example mRNAs for auxin response transcription factors (ARFs). RESULTS Here we tested the hypothesis that RPL24B and eIF3h affect translation reinitiation in a similar fashion. First, like eif3h mutants, rpl24b mutants under-translate the AtbZip11 mRNA, and the detailed spectrum of translational defects in rpl24b is remarkably similar to that of eif3h. Second, eif3h mutants display defects in auxin mediated organogenesis and gene expression, similar to rpl24b. Like AtbZip11, the uORF-containing ARF mRNAs are indeed undertranslated in eif3h mutant seedlings. CONCLUSION We conclude that, similar to eIF3h, RPL24B bolsters the reinitiation competence of uORF-translating ribosomes. Coordination between eIF3 and the large ribosomal subunit helps to fine-tune translation of uORF-containing mRNAs and, in turn, to orchestrate plant development.
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Affiliation(s)
- Fujun Zhou
- Genome Science and Technology Program, The University of Tennessee, Knoxville, TN 37996, USA
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
| | - Bijoyita Roy
- Department of Biochemistry, Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN 37996, USA
| | - Albrecht G von Arnim
- Department of Biochemistry, Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN 37996, USA
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40
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Ribosome recycling step in yeast cytoplasmic protein synthesis is catalyzed by eEF3 and ATP. Proc Natl Acad Sci U S A 2010; 107:10854-9. [PMID: 20534490 DOI: 10.1073/pnas.1006247107] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
After each round of protein biosynthesis, the posttermination complex (PoTC) consisting of a ribosome, mRNA, and tRNA must be disassembled into its components for a new round of translation. Here, we show that a Saccharomyces cerevisiae model PoTC was disassembled by ATP and eukaryotic elongation factor 3 (eEF3). GTP or ITP functioned with less efficiency and adenosine 5gamma'-(beta,gamma-imido)triphosphate did not function at all. The k(cat) of eEF3 was 1.12 min(-1), which is comparable to that of the in vitro initiation step. The disassembly reaction was inhibited by aminoglycosides and cycloheximide. The subunits formed from the yeast model PoTC remained separated under ionic conditions close to those existing in vivo, suggesting that they are ready to enter the initiation process. Based on our experimental techniques used in this paper, the release of mRNA and tRNA and ribosome dissociation took place simultaneously. No 40S*mRNA complex was observed, indicating that eEF3 action promotes ribosome recycling, not reinitiation.
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41
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Roy B, Vaughn JN, Kim BH, Zhou F, Gilchrist MA, Von Arnim AG. The h subunit of eIF3 promotes reinitiation competence during translation of mRNAs harboring upstream open reading frames. RNA (NEW YORK, N.Y.) 2010; 16:748-61. [PMID: 20179149 PMCID: PMC2844622 DOI: 10.1261/rna.2056010] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Upstream open reading frames (uORFs) are protein coding elements in the 5' leader of messenger RNAs. uORFs generally inhibit translation of the main ORF because ribosomes that perform translation elongation suffer either permanent or conditional loss of reinitiation competence. After conditional loss, reinitiation competence may be regained by, at the minimum, reacquisition of a fresh methionyl-tRNA. The conserved h subunit of Arabidopsis eukaryotic initiation factor 3 (eIF3) mitigates the inhibitory effects of certain uORFs. Here, we define more precisely how this occurs, by combining gene expression data from mutated 5' leaders of Arabidopsis AtbZip11 (At4g34590) and yeast GCN4 with a computational model of translation initiation in wild-type and eif3h mutant plants. Of the four phylogenetically conserved uORFs in AtbZip11, three are inhibitory to translation, while one is anti-inhibitory. The mutation in eIF3h has no major effect on uORF start codon recognition. Instead, eIF3h supports efficient reinitiation after uORF translation. Modeling suggested that the permanent loss of reinitiation competence during uORF translation occurs at a faster rate in the mutant than in the wild type. Thus, eIF3h ensures that a fraction of uORF-translating ribosomes retain their competence to resume scanning. Experiments using the yeast GCN4 leader provided no evidence that eIF3h fosters tRNA reaquisition. Together, these results attribute a specific molecular function in translation initiation to an individual eIF3 subunit in a multicellular eukaryote.
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Affiliation(s)
- Bijoyita Roy
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee, Knoxville, Tennessee 37996, USA
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Hood HM, Neafsey DE, Galagan J, Sachs MS. Evolutionary roles of upstream open reading frames in mediating gene regulation in fungi. Annu Rev Microbiol 2009; 63:385-409. [PMID: 19514854 DOI: 10.1146/annurev.micro.62.081307.162835] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Upstream open reading frames (uORFs) are frequently present in the 5'-leader regions of fungal mRNAs. They can affect translation by controlling the ability of ribosomes that scan from the mRNA 5' end to reach the downstream genic reading frame. The translation of uORFs can also affect mRNA stability. For several genes, including Saccharomyces cerevisiae GCN4, S. cerevisiae CPA1, and Neurospora crassa arg-2, regulation by uORFs controls expression in response to specific physiological signals. The roles of many uORFs that are identified by genome-level approaches, as have been initiated for Saccharomyces, Aspergillus, and Cryptococcus species, remain to be determined. Some uORFs may have regulatory roles, while others may exist to insulate the genic reading frame from the negative impacts of upstream translation start sites in the mRNA 5' leader.
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Affiliation(s)
- Heather M Hood
- Department of Science and Engineering, Oregon Health & Science University, Beaverton, Oregon 97006, USA
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Romano MC, Thiel M, Stansfield I, Grebogi C. Queueing phase transition: theory of translation. PHYSICAL REVIEW LETTERS 2009; 102:198104. [PMID: 19519001 PMCID: PMC3639427 DOI: 10.1103/physrevlett.102.198104] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2009] [Indexed: 05/27/2023]
Abstract
We study the current of particles on a lattice, where to each site a different hopping probability has been associated and the particles can move only in one direction. We show that the queueing of the particles behind a slow site can lead to a first-order phase transition, and derive analytical expressions for the configuration of slow sites for this to happen. We apply this stochastic model to describe the translation of mRNAs. We show that the first-order phase transition, uncovered in this work, is the process responsible for the classification of the proteins having different biological functions.
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Affiliation(s)
- M Carmen Romano
- Institute for Complex Systems and Mathematical Biology, University of Aberdeen, Aberdeen, AB24 3UE, United Kingdom
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Lawless C, Pearson RD, Selley JN, Smirnova JB, Grant CM, Ashe MP, Pavitt GD, Hubbard SJ. Upstream sequence elements direct post-transcriptional regulation of gene expression under stress conditions in yeast. BMC Genomics 2009; 10:7. [PMID: 19128476 PMCID: PMC2649001 DOI: 10.1186/1471-2164-10-7] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2008] [Accepted: 01/07/2009] [Indexed: 01/01/2023] Open
Abstract
Background The control of gene expression in eukaryotic cells occurs both transcriptionally and post-transcriptionally. Although many genes are now known to be regulated at the translational level, in general, the mechanisms are poorly understood. We have previously presented polysomal gradient and array-based evidence that translational control is widespread in a significant number of genes when yeast cells are exposed to a range of stresses. Here we have re-examined these gene sets, considering the role of UTR sequences in the translational responses of these genes using recent large-scale datasets which define 5' and 3' transcriptional ends for many yeast genes. In particular, we highlight the potential role of 5' UTRs and upstream open reading frames (uORFs). Results We show a highly significant enrichment in specific GO functional classes for genes that are translationally up- and down-regulated under given stresses (e.g. carbohydrate metabolism is up-regulated under amino acid starvation). Cross-referencing these data with the stress response data we show that translationally upregulated genes have longer 5' UTRs, consistent with their role in translational regulation. In the first genome-wide study of uORFs in a set of mapped 5' UTRs, we show that uORFs are rare, being statistically under-represented in UTR sequences. However, they have distinct compositional biases consistent with their putative role in translational control and are more common in genes which are apparently translationally up-regulated. Conclusion These results demonstrate a central regulatory role for UTR sequences, and 5' UTRs in particular, highlighting the significant role of uORFs in post-transcriptional control in yeast. Yeast uORFs are more highly conserved than has been suggested, lending further weight to their significance as functional elements involved in gene regulation. It also suggests a more complex and novel mechanism of control, whereby uORFs permit genes to escape from a more general attenuation of translation under conditions of stress. However, since uORFs are relatively rare (only ~13% of yeast genes have them) there remain many unanswered questions as to how UTR elements can direct translational control of many hundreds of genes under stress.
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Affiliation(s)
- Craig Lawless
- Michael Smith Building, Faculty of Life Sciences, University of Manchester, Manchester, UK.
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An upstream open reading frame controls translation of var2csa, a gene implicated in placental malaria. PLoS Pathog 2009; 5:e1000256. [PMID: 19119419 PMCID: PMC2603286 DOI: 10.1371/journal.ppat.1000256] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2008] [Accepted: 12/05/2008] [Indexed: 01/06/2023] Open
Abstract
Malaria, caused by the parasite Plasmodium falciparum, is responsible for substantial morbidity, mortality and economic losses in tropical regions of the world. Pregnant women are exceptionally vulnerable to severe consequences of the infection, due to the specific adhesion of parasite-infected erythrocytes in the placenta. This adhesion is mediated by a unique variant of PfEMP1, a parasite encoded, hyper-variable antigen placed on the surface of infected cells. This variant, called VAR2CSA, binds to chondroitin sulfate A on syncytiotrophoblasts in the intervillous space of placentas. VAR2CSA appears to only be expressed in the presence of a placenta, suggesting that its expression is actively repressed in men, children or non-pregnant women; however, the mechanism of repression is not understood. Using cultured parasite lines and reporter gene constructs, we show that the gene encoding VAR2CSA contains a small upstream open reading frame that acts to repress translation of the resulting mRNA, revealing a novel form of gene regulation in malaria parasites. The mechanism underlying this translational repression is reversible, allowing high levels of protein translation upon selection, thus potentially enabling parasites to upregulate expression of this variant antigen in the presence of the appropriate host tissue. Infection by the protozoan parasite Plasmodium falciparum results in the most severe form of human malaria and is responsible for significant morbidity and mortality in the developing world. This disease can be particularly severe in pregnant women due to the specific adhesion of parasite-infected red blood cells within the placenta. Expression of a single gene called var2csa has been linked to targeting of the placenta, and thus this gene represents a key element in the virulence of P. falciparum infections. It was previously shown that var2csa is predominantly expressed by parasites in pregnant women, suggesting that parasites might have the ability to down regulate this gene when no placenta is available. Here we describe an upstream open reading frame (uORF)–mediated mechanism used by parasites to repress translation of var2csa mRNA, thus providing a mechanism for controlling gene expression at the level of protein translation. This mechanism has not previously been observed in malaria parasites, and may represent a form of regulation used to control expression of other genes within the genome.
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Szamecz B, Rutkai E, Cuchalová L, Munzarová V, Herrmannová A, Nielsen KH, Burela L, Hinnebusch AG, Valásek L. eIF3a cooperates with sequences 5' of uORF1 to promote resumption of scanning by post-termination ribosomes for reinitiation on GCN4 mRNA. Genes Dev 2008; 22:2414-25. [PMID: 18765792 DOI: 10.1101/gad.480508] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Yeast initiation factor eIF3 (eukaryotic initiation factor 3) has been implicated in multiple steps of translation initiation. Previously, we showed that the N-terminal domain (NTD) of eIF3a interacts with the small ribosomal protein RPS0A located near the mRNA exit channel, where eIF3 is proposed to reside. Here, we demonstrate that a partial deletion of the RPS0A-binding domain of eIF3a impairs translation initiation and reduces binding of eIF3 and associated eIFs to native preinitiation complexes in vivo. Strikingly, it also severely blocks the induction of GCN4 translation that occurs via reinitiation. Detailed examination unveiled a novel reinitiation defect resulting from an inability of 40S ribosomes to resume scanning after terminating at the first upstream ORF (uORF1). Genetic analysis reveals a functional interaction between the eIF3a-NTD and sequences 5' of uORF1 that is critically required to enhance reinitiation. We further demonstrate that these stimulatory sequences must be positioned precisely relative to the uORF1 stop codon and that reinitiation efficiency after uORF1 declines with its increasing length. Together, our results suggest that eIF3 is retained on ribosomes throughout uORF1 translation and, upon termination, interacts with its 5' enhancer at the mRNA exit channel to stabilize mRNA association with post-termination 40S subunits and enable resumption of scanning for reinitiation downstream.
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Affiliation(s)
- Béla Szamecz
- Laboratory of Regulation of Gene Expression, Institute of Microbiology AVCR, Prague, Videnska 1083, 142 20, The Czech Republic
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Vopálenský V, Masek T, Horváth O, Vicenová B, Mokrejs M, Pospísek M. Firefly luciferase gene contains a cryptic promoter. RNA (NEW YORK, N.Y.) 2008; 14:1720-9. [PMID: 18697919 PMCID: PMC2525954 DOI: 10.1261/rna.831808] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
A firefly luciferase (FLuc) counts among the most popular reporters of present-day molecular and cellular biology. In this study, we report a cryptic promoter activity in the luc+ gene, which is the most frequently used version of the firefly luciferase. The FLuc coding region displays cryptic promoter activity both in mammalian and yeast cells. In human CCL13 and Huh7 cells, cryptic transcription from the luc+ gene is 10-16 times weaker in comparison to the strong immediate-early cytomegalovirus promoter. Additionally, we discuss a possible impact of the FLuc gene cryptic promoter on experimental results especially in some fields of the RNA-oriented research, for example, in analysis of translation initiation or analysis of miRNA/siRNA function. Specifically, we propose how this newly described cryptic promoter activity within the FLuc gene might contribute to the previous determination of the strength of the cryptic promoter found in the cDNA corresponding to the hepatitis C virus internal ribosome entry site. Our findings should appeal to the researchers to be more careful when designing firefly luciferase-based assays as well as open the possibility of performing some experiments with the hepatitis C virus internal ribosome entry site, which could not be considered until now.
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Affiliation(s)
- Václav Vopálenský
- Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Vinicna 5, 128 44 Prague, Czech Republic
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Kim BH, Cai X, Vaughn JN, von Arnim AG. On the functions of the h subunit of eukaryotic initiation factor 3 in late stages of translation initiation. Genome Biol 2007; 8:R60. [PMID: 17439654 PMCID: PMC1896003 DOI: 10.1186/gb-2007-8-4-r60] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2006] [Revised: 01/15/2007] [Accepted: 04/17/2007] [Indexed: 12/29/2022] Open
Abstract
Reporter transgene assays and comparative polysome-microarray analysis reveal that the intact h subunit of Arabidopsis eIF3 contributes to efficient translation initiation on mRNA leader sequences harbouring multiple uORFs. Background The eukaryotic translation initiation factor 3 (eIF3) has multiple roles during the initiation of translation of cytoplasmic mRNAs. How individual subunits of eIF3 contribute to the translation of specific mRNAs remains poorly understood, however. This is true in particular for those subunits that are not conserved in budding yeast, such as eIF3h. Results Working with stable reporter transgenes in Arabidopsis thaliana mutants, it was demonstrated that the h subunit of eIF3 contributes to the efficient translation initiation of mRNAs harboring upstream open reading frames (uORFs) in their 5' leader sequence. uORFs, which can function as devices for translational regulation, are present in over 30% of Arabidopsis mRNAs, and are enriched among mRNAs for transcriptional regulators and protein modifying enzymes. Microarray comparisons of polysome loading in wild-type and eif3h mutant seedlings revealed that eIF3h generally helps to maintain efficient polysome loading of mRNAs harboring multiple uORFs. In addition, however, eIF3h also boosted the polysome loading of mRNAs with long leaders or coding sequences. Moreover, the relative polysome loading of certain functional groups of mRNAs, including ribosomal proteins, was actually increased in the eif3h mutant, suggesting that regulons of translational control can be revealed by mutations in generic translation initiation factors. Conclusion The intact eIF3h protein contributes to efficient translation initiation on 5' leader sequences harboring multiple uORFs, although mRNA features independent of uORFs are also implicated.
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Affiliation(s)
- Byung-Hoon Kim
- Department of Biochemistry, Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN 37996-0840, USA
| | - Xue Cai
- Department of Biochemistry, Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN 37996-0840, USA
- Department of Cell Biology, The University of Oklahoma Health Sciences Center, Stanton L Young Blvd, Oklahoma City, OK 73104, USA
| | - Justin N Vaughn
- Department of Biochemistry, Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN 37996-0840, USA
| | - Albrecht G von Arnim
- Department of Biochemistry, Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN 37996-0840, USA
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Masek T, Vopalensky V, Horvath O, Vortelova L, Feketova Z, Pospisek M. Hepatitis C virus internal ribosome entry site initiates protein synthesis at the authentic initiation codon in yeast. J Gen Virol 2007; 88:1992-2002. [PMID: 17554033 DOI: 10.1099/vir.0.82782-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Hepatitis C virus (HCV) is an important pathogen causing both acute and chronic infections in humans. The HCV polyprotein is synthesized by cap-independent translation initiation after ribosome binding to the highly structured internal ribosome entry site (IRES). The HCV IRES has been shown to have a low requirement for translation initiation factors and the ability to bind directly to the 40S ribosomal subunit. A novel yeast bicistronic reporter system, suitable for sensitive and accurate analysis of IRES activity, has been developed. It employs signal amplification based on the Gal4p transcription factor-mediated activation of a variety of secondary reporter genes. The system has a broad dynamic range and, depending on the nature of the particular secondary reporter, can be used both for precise measurements of IRES activity and for selection and screening for novel IRES variants and IRES trans-acting factors. By using this novel bicistronic system, it was shown that the HCV IRES is functional in yeast cells. Mutational analysis of the IRES loop IV and the adjacent region revealed that, in yeast, as in mammalian cells, translation initiates preferentially at the authentic (342)AUG codon and that disruption of the HCV IRES loop IV abrogates its function, whilst minor positional changes or substitutions of the initiation codon within loop IV are largely tolerated. These findings bring more general insights to translation initiation, but also open the door for utilization of yeast and its sophisticated genetics for searching for new antiviral drugs and HCV IRES trans-acting proteins.
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Affiliation(s)
- Tomas Masek
- Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Vinicna 5, 128 44 Prague, Czech Republic
| | - Vaclav Vopalensky
- Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Vinicna 5, 128 44 Prague, Czech Republic
| | - Ondrej Horvath
- Institute of Molecular Genetics, Laboratory of Leukocyte Antigens, AS CR, Videnska 1083, 140 00 Prague, Czech Republic
| | - Lucie Vortelova
- Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Vinicna 5, 128 44 Prague, Czech Republic
| | - Zuzana Feketova
- Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Vinicna 5, 128 44 Prague, Czech Republic
| | - Martin Pospisek
- Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Vinicna 5, 128 44 Prague, Czech Republic
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Haar TVD, Jossé LJ, Byrne LJ. 8 Reporter Genes and Their Uses in Studying Yeast Gene Expression. J Microbiol Methods 2007. [DOI: 10.1016/s0580-9517(06)36008-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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