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Inada T, Beckmann R. Mechanisms of Translation-coupled Quality Control. J Mol Biol 2024; 436:168496. [PMID: 38365086 DOI: 10.1016/j.jmb.2024.168496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 02/05/2024] [Accepted: 02/12/2024] [Indexed: 02/18/2024]
Abstract
Stalling of ribosomes engaged in protein synthesis can lead to significant defects in the function of newly synthesized proteins and thereby impair protein homeostasis. Consequently, partially synthesized polypeptides resulting from translation stalling are recognized and eliminated by several quality control mechanisms. First, if translation elongation reactions are halted prematurely, a quality control mechanism called ribosome-associated quality control (RQC) initiates the ubiquitination of the nascent polypeptide chain and subsequent proteasomal degradation. Additionally, when ribosomes with defective codon recognition or peptide-bond formation stall during translation, a quality control mechanism known as non-functional ribosomal RNA decay (NRD) leads to the degradation of malfunctioning ribosomes. In both of these quality control mechanisms, E3 ubiquitin ligases selectively recognize ribosomes in distinct translation-stalling states and ubiquitinate specific ribosomal proteins. Significant efforts have been devoted to characterize E3 ubiquitin ligase sensing of ribosome 'collision' or 'stalling' and subsequent ribosome is rescued. This article provides an overview of our current understanding of the molecular mechanisms and physiological functions of ribosome dynamics control and quality control of abnormal translation.
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Affiliation(s)
- Toshifumi Inada
- Division of RNA and Gene Regulation, Institute of Medical Science, The University of Tokyo, Minato-Ku, Tokyo 108-8639, Japan.
| | - Roland Beckmann
- Gene Center and Department of Biochemistry, Feodor-Lynen-Str. 25, University of Munich, 81377 Munich, Germany.
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2
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Ando R, Ishikawa Y, Kamada Y, Izawa S. Contribution of the yeast bi-chaperone system in the restoration of the RNA helicase Ded1 and translational activity under severe ethanol stress. J Biol Chem 2023; 299:105472. [PMID: 37979914 PMCID: PMC10746526 DOI: 10.1016/j.jbc.2023.105472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 10/30/2023] [Accepted: 11/03/2023] [Indexed: 11/20/2023] Open
Abstract
Preexposure to mild stress often improves cellular tolerance to subsequent severe stress. Severe ethanol stress (10% v/v) causes persistent and pronounced translation repression in Saccharomyces cerevisiae. However, it remains unclear whether preexposure to mild stress can mitigate translation repression in yeast cells under severe ethanol stress. We found that the translational activity of yeast cells pretreated with 6% (v/v) ethanol was initially significantly repressed under subsequent 10% ethanol but was then gradually restored even under severe ethanol stress. We also found that 10% ethanol caused the aggregation of Ded1, which plays a key role in translation initiation as a DEAD-box RNA helicase. Pretreatment with 6% ethanol led to the gradual disaggregation of Ded1 under subsequent 10% ethanol treatment in wild-type cells but not in fes1Δhsp104Δ cells, which are deficient in Hsp104 with significantly reduced capacity for Hsp70. Hsp104 and Hsp70 are key components of the bi-chaperone system that play a role in yeast protein quality control. fes1Δhsp104Δ cells did not restore translational activity under 10% ethanol, even after pretreatment with 6% ethanol. These results indicate that the regeneration of Ded1 through the bi-chaperone system leads to the gradual restoration of translational activity under continuous severe stress. This study provides new insights into the acquired tolerance of yeast cells to severe ethanol stress and the resilience of their translational activity.
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Affiliation(s)
- Ryoko Ando
- Graduate School of Science and Technology, Kyoto Institute of Technology, Sakyo-ku, Kyoto, Japan
| | - Yu Ishikawa
- Graduate School of Science and Technology, Kyoto Institute of Technology, Sakyo-ku, Kyoto, Japan
| | | | - Shingo Izawa
- Graduate School of Science and Technology, Kyoto Institute of Technology, Sakyo-ku, Kyoto, Japan.
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3
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Kamada Y, Ando R, Izawa S, Matsuura A. Yeast Tor complex 1 phosphorylates eIF4E-binding protein, Caf20. Genes Cells 2023; 28:789-799. [PMID: 37700444 PMCID: PMC11447835 DOI: 10.1111/gtc.13067] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/24/2023] [Accepted: 08/29/2023] [Indexed: 09/14/2023]
Abstract
Tor complex 1 (TORC1), a master regulator of cell growth, is an evolutionarily conserved protein kinase within eukaryotic organisms. To control cell growth, TORC1 governs translational processes by phosphorylating its substrate proteins in response to cellular nutritional cues. Mammalian TORC1 (mTORC1) assumes the responsibility of phosphorylating the eukaryotic translation initiation factor 4E (eIF4E)-binding protein 1 (4E-BP1) to regulate its interaction with eIF4E. The budding yeast Saccharomyces cerevisiae possesses a pair of 4E-BP genes, CAF20 and EAP1. However, the extent to which the TORC1-4E-BP axis regulates translational initiation in yeast remains uncertain. In this study, we demonstrated the influence of TORC1 on the phosphorylation status of Caf20 in vivo, as well as the direct phosphorylation of Caf20 by TORC1 in vitro. Furthermore, we found the TORC1-dependent recruitment of Caf20 to the 80S ribosome. Consequently, our study proposes a plausible involvement of yeast's 4E-BP in the efficacy of translation initiation, an aspect under the control of TORC1.
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Affiliation(s)
- Yoshiaki Kamada
- National Institute for Basic Biology, Okazaki, Japan
- Graduate University for Advanced Studies (SOKENDAI), Hayama, Kanagawa, Japan
| | - Ryoko Ando
- Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Kyoto, Japan
| | - Shingo Izawa
- Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Kyoto, Japan
| | - Akira Matsuura
- Department of Biology, Graduate School of Science, Chiba University, Chiba, Japan
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4
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Nakajima M, Koido M, Guo L, Terao C, Ikegawa S. A novel CCDC91 isoform associated with ossification of the posterior longitudinal ligament of the spine works as a non-coding RNA to regulate osteogenic genes. Am J Hum Genet 2023; 110:638-647. [PMID: 36990086 PMCID: PMC10119134 DOI: 10.1016/j.ajhg.2023.03.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 03/07/2023] [Indexed: 03/30/2023] Open
Abstract
Ossification of the posterior longitudinal ligament of the spine (OPLL) is a common intractable disease that causes spinal stenosis and myelopathy. We have previously conducted genome-wide association studies for OPLL and identified 14 significant loci, but their biological implications remain mostly unclear. Here, we examined the 12p11.22 locus and identified a variant in the 5' UTR of a novel isoform of CCDC91 that was associated with OPLL. Using machine learning prediction models, we determined that higher expression of the novel CCDC91 isoform was associated with the G allele of rs35098487. The risk allele of rs35098487 showed higher affinity in the binding of nuclear proteins and transcription activity. Knockdown and overexpression of the CCDC91 isoform in mesenchymal stem cells and MG-63 cells showed paralleled expression of osteogenic genes, including RUNX2, the master transcription factor of osteogenic differentiation. The CCDC91 isoform directly interacted with MIR890, which bound to RUNX2 and decreased RUNX2 expression. Our findings suggest that the CCDC91 isoform acts as a competitive endogenous RNA by sponging MIR890 to increase RUNX2 expression.
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Affiliation(s)
- Masahiro Nakajima
- Laboratory for Bone and Joint Diseases, Center for Integrative Medical Sciences, RIKEN, Tokyo 108-8639, Japan
| | - Masaru Koido
- Laboratory for Statistical and Translational Genetics, Center for Integrative Medical Sciences, RIKEN, Yokohama 230-0045, Japan; Laboratory of Complex Trait Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo 108-8639, Japan
| | - Long Guo
- Laboratory for Bone and Joint Diseases, Center for Integrative Medical Sciences, RIKEN, Tokyo 108-8639, Japan; Department of Laboratory Animal Science, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an 710061, China
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, Center for Integrative Medical Sciences, RIKEN, Yokohama 230-0045, Japan.
| | - Shiro Ikegawa
- Laboratory for Bone and Joint Diseases, Center for Integrative Medical Sciences, RIKEN, Tokyo 108-8639, Japan.
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5
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Nanopore Direct RNA Sequencing of Monosome- and Polysome-Bound RNA. Methods Mol Biol 2023; 2632:281-297. [PMID: 36781736 DOI: 10.1007/978-1-0716-2996-3_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Polysome fractionation makes use of density gradients and ultracentrifugation to separate transcripts based on their specific number of bound ribosomes, and can be combined with downstream analysis such as cDNA-seq (commonly known as RNA-seq), microarray analysis, RT-qPCR, or Northern blotting. Here, we describe the application of Nanopore direct RNA sequencing to quantify monosome- and polysome-bound full-length transcripts after polysome fractionation, RNA cleanup, and size selection, using the yeast glucose stress response as an example use case.
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6
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Matsuo Y, Inada T. Co-Translational Quality Control Induced by Translational Arrest. Biomolecules 2023; 13:biom13020317. [PMID: 36830686 PMCID: PMC9953336 DOI: 10.3390/biom13020317] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/19/2023] [Accepted: 02/06/2023] [Indexed: 02/11/2023] Open
Abstract
Genetic mutations, mRNA processing errors, and lack of availability of charged tRNAs sometimes slow down or completely stall translating ribosomes. Since an incomplete nascent chain derived from stalled ribosomes may function anomalously, such as by forming toxic aggregates, surveillance systems monitor every step of translation and dispose of such products to prevent their accumulation. Over the past decade, yeast models with powerful genetics and biochemical techniques have contributed to uncovering the mechanism of the co-translational quality control system, which eliminates the harmful products generated from aberrant translation. We here summarize the current knowledge of the molecular mechanism of the co-translational quality control systems in yeast, which eliminate the incomplete nascent chain, improper mRNAs, and faulty ribosomes to maintain cellular protein homeostasis.
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Rudowitz M, Cruz-Zaragoza LD, Girzalsky W, Erdmann R. Utilization of Nonstop mRNA to Assess Ribosome-Associated Nascent Polypeptide Chains in Early Topogenesis of Peroxisomal Proteins. Methods Mol Biol 2023; 2643:383-390. [PMID: 36952200 DOI: 10.1007/978-1-0716-3048-8_27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023]
Abstract
The translation of mRNAs lacking a stop codon results in a nascent polypeptide chain still attached to the translating ribosome. When containing an exposed N-terminal targeting signal, these so-called nonstop (ns) proteins have been shown to localize to their respective organellar translocation channel, resulting in stabilized translocation intermediates. Utilizing a plasmid encoding a FLAG-tagged nonstop protein with an N-terminal targeting signal early-stage ribosome-associated protein complexes can be purified by affinity chromatography. This will be exemplified by purification of protein complexes of the peroxisomal protein import machinery using different nonstop variants of the PTS2 cargo protein Fox3p from both soluble and membrane fractions.
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Affiliation(s)
- Markus Rudowitz
- Department of Systems Biochemistry, Faculty of Medicine, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Luis Daniel Cruz-Zaragoza
- Department of Systems Biochemistry, Faculty of Medicine, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Wolfgang Girzalsky
- Department of Systems Biochemistry, Faculty of Medicine, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Ralf Erdmann
- Department of Systems Biochemistry, Faculty of Medicine, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
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8
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Durmaz YT, Shatadal A, Friend K. Geneticin reduces mRNA stability. PLoS One 2022; 17:e0272058. [PMID: 35901009 PMCID: PMC9333311 DOI: 10.1371/journal.pone.0272058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 07/12/2022] [Indexed: 11/30/2022] Open
Abstract
Messenger RNA (mRNA) translation can lead to higher rates of mRNA decay, suggesting the ribosome plays a role in mRNA destruction. Furthermore, mRNA features, such as codon identities, which are directly probed by the ribosome, correlate with mRNA decay rates. Many amino acids are encoded by synonymous codons, some of which are decoded by more abundant tRNAs leading to more optimal translation and increased mRNA stability. Variable translation rates for synonymous codons can lead to ribosomal collisions as ribosomes transit regions with suboptimal codons, and ribosomal collisions can promote mRNA decay. In addition to different translation rates, the presence of certain codons can also lead to higher or lower rates of amino acid misincorporation which could potentially lead to protein misfolding if a substituted amino acid fails to make critical contacts in a structure. Here, we test whether Geneticin—G418, an aminoglycoside antibiotic known to promote amino acid misincorporation—affects mRNA stability. We observe that G418 decreases firefly luciferase mRNA stability in an in vitro translation system and also reduces mRNA stability in mouse embryonic stem cells (mESCs). G418-sensitive mRNAs are enriched for certain optimal codons that contain G or C in the wobble position, arguing that G418 blunts the stabilizing effects of codon optimality.
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Affiliation(s)
- Yavuz T. Durmaz
- Department of Chemistry and Biochemistry, Washington and Lee University, Lexington, Virginia, United States of America
| | - Alankrit Shatadal
- Department of Chemistry and Biochemistry, Washington and Lee University, Lexington, Virginia, United States of America
| | - Kyle Friend
- Department of Chemistry and Biochemistry, Washington and Lee University, Lexington, Virginia, United States of America
- * E-mail:
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9
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Ho AT, Hurst LD. Effective Population Size Predicts Local Rates but Not Local Mitigation of Read-through Errors. Mol Biol Evol 2021; 38:244-262. [PMID: 32797190 PMCID: PMC7783166 DOI: 10.1093/molbev/msaa210] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
In correctly predicting that selection efficiency is positively correlated with the effective population size (Ne), the nearly neutral theory provides a coherent understanding of between-species variation in numerous genomic parameters, including heritable error (germline mutation) rates. Does the same theory also explain variation in phenotypic error rates and in abundance of error mitigation mechanisms? Translational read-through provides a model to investigate both issues as it is common, mostly nonadaptive, and has good proxy for rate (TAA being the least leaky stop codon) and potential error mitigation via "fail-safe" 3' additional stop codons (ASCs). Prior theory of translational read-through has suggested that when population sizes are high, weak selection for local mitigation can be effective thus predicting a positive correlation between ASC enrichment and Ne. Contra to prediction, we find that ASC enrichment is not correlated with Ne. ASC enrichment, although highly phylogenetically patchy, is, however, more common both in unicellular species and in genes expressed in unicellular modes in multicellular species. By contrast, Ne does positively correlate with TAA enrichment. These results imply that local phenotypic error rates, not local mitigation rates, are consistent with a drift barrier/nearly neutral model.
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Affiliation(s)
- Alexander T Ho
- Milner Centre for Evolution, University of Bath, Bath, United Kingdom
- Corresponding author: E-mail:
| | - Laurence D Hurst
- Milner Centre for Evolution, University of Bath, Bath, United Kingdom
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10
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D'Orazio KN, Green R. Ribosome states signal RNA quality control. Mol Cell 2021; 81:1372-1383. [PMID: 33713598 PMCID: PMC8041214 DOI: 10.1016/j.molcel.2021.02.022] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 02/04/2021] [Accepted: 02/17/2021] [Indexed: 12/18/2022]
Abstract
Eukaryotic cells integrate multiple quality control (QC) responses during protein synthesis in the cytoplasm. These QC responses are signaled by slow or stalled elongating ribosomes. Depending on the nature of the delay, the signal may lead to translational repression, messenger RNA decay, ribosome rescue, and/or nascent protein degradation. Here, we discuss how the structure and composition of an elongating ribosome in a troubled state determine the downstream quality control pathway(s) that ensue. We highlight the intersecting pathways involved in RNA decay and the crosstalk that occurs between RNA decay and ribosome rescue.
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Affiliation(s)
- Karole N D'Orazio
- Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Rachel Green
- Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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11
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Influence of nascent polypeptide positive charges on translation dynamics. Biochem J 2021; 477:2921-2934. [PMID: 32797214 DOI: 10.1042/bcj20200303] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 07/17/2020] [Accepted: 07/23/2020] [Indexed: 01/05/2023]
Abstract
Protein segments with a high concentration of positively charged amino acid residues are often used in reporter constructs designed to activate ribosomal mRNA/protein decay pathways, such as those involving nonstop mRNA decay (NSD), no-go mRNA decay (NGD) and the ribosome quality control (RQC) complex. It has been proposed that the electrostatic interaction of the positively charged nascent peptide with the negatively charged ribosomal exit tunnel leads to translation arrest. When stalled long enough, the translation process is terminated with the degradation of the transcript and an incomplete protein. Although early experiments made a strong argument for this mechanism, other features associated with positively charged reporters, such as codon bias and mRNA and protein structure, have emerged as potent inducers of ribosome stalling. We carefully reviewed the published data on the protein and mRNA expression of artificial constructs with diverse compositions as assessed in different organisms. We concluded that, although polybasic sequences generally lead to lower translation efficiency, it appears that an aggravating factor, such as a nonoptimal codon composition, is necessary to cause translation termination events.
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12
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Barros GC, Requião RD, Carneiro RL, Masuda CA, Moreira MH, Rossetto S, Domitrovic T, Palhano FL. Rqc1 and other yeast proteins containing highly positively charged sequences are not targets of the RQC complex. J Biol Chem 2021; 296:100586. [PMID: 33774050 PMCID: PMC8102910 DOI: 10.1016/j.jbc.2021.100586] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 03/12/2021] [Accepted: 03/23/2021] [Indexed: 02/06/2023] Open
Abstract
Previous work has suggested that highly positively charged protein segments coded by rare codons or poly (A) stretches induce ribosome stalling and translational arrest through electrostatic interactions with the negatively charged ribosome exit tunnel, leading to inefficient elongation. This arrest leads to the activation of the Ribosome Quality Control (RQC) pathway and results in low expression of these reporter proteins. However, the only endogenous yeast proteins known to activate the RQC are Rqc1, a protein essential for RQC function, and Sdd1, a protein with unknown function, both of which contain polybasic sequences. To explore the generality of this phenomenon, we investigated whether the RQC complex controls the expression of other proteins with polybasic sequences. We showed by ribosome profiling data analysis and western blot that proteins containing polybasic sequences similar to, or even more positively charged than those of Rqc1 and Sdd1, were not targeted by the RQC complex. We also observed that the previously reported Ltn1-dependent regulation of Rqc1 is posttranslational, independent of the RQC activity. Taken together, our results suggest that RQC should not be regarded as a general regulatory pathway for the expression of highly positively charged proteins in yeast.
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Affiliation(s)
- Géssica C Barros
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Rodrigo D Requião
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Rodolfo L Carneiro
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Claudio A Masuda
- Programa de Biologia Molecular e Biotecnologia, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Mariana H Moreira
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Silvana Rossetto
- Departamento de Ciência da Computação, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Tatiana Domitrovic
- Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.
| | - Fernando L Palhano
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.
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13
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Solarte M, Cortes-Urrea C, Franco NR, Barreto G, Moreno PA. Novel mutations in breast cancer patients from southwestern Colombia. Genet Mol Biol 2020; 43:e20190359. [PMID: 33231602 PMCID: PMC7684693 DOI: 10.1590/1678-4685-gmb-2019-0359] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 08/29/2020] [Indexed: 11/29/2022] Open
Abstract
Breast cancer is the leading cause of death by cancer among women in less developed regions. In Colombia, few published studies have applied next-generation sequencing technologies to evaluate the genetic factors related to breast cancer. This study characterized the exome of three patients with breast cancer from southwestern Colombia to identify likely pathogenic or disease-related DNA sequence variants in tumor cells. For this, the exomes of three tumor tissue samples from patients with breast cancer were sequenced. The bioinformatics analysis identified two pathogenic variants in Fgfr4 and Nf1 genes, which are highly relevant for this type of cancer. Specifically, variant FGFR4-c.1162G>A predisposes individuals to a significantly accelerated progression of this pathology, while NF1-c.1915C>T negatively alters the encoded protein and should be further investigated to clarify the role of this variant in this neoplasia. Moreover, 27 novel likely pathogenic variants were found and 10 genes showed alterations of pathological interest. These results suggest that the novel variants reported here should be further studied to elucidate their role in breast cancer.
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Affiliation(s)
- Melissa Solarte
- Universidad del Valle, School of Systems and Computing Engineering, Bioinformatics and Biocomputing Laboratory, Cali, Colombia.,Universidad del Valle, Biology Department, Human molecular Genetic Laboratory, Cali, Colombia
| | - Carolina Cortes-Urrea
- Universidad del Valle, School of Systems and Computing Engineering, Bioinformatics and Biocomputing Laboratory, Cali, Colombia.,Universidad del Valle, Biology Department, Human molecular Genetic Laboratory, Cali, Colombia
| | - Nelson Rivera Franco
- Universidad del Valle, Biology Department, Human molecular Genetic Laboratory, Cali, Colombia
| | - Guillermo Barreto
- Universidad del Valle, Biology Department, Human molecular Genetic Laboratory, Cali, Colombia
| | - Pedro A Moreno
- Universidad del Valle, School of Systems and Computing Engineering, Bioinformatics and Biocomputing Laboratory, Cali, Colombia
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14
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Uemura S, Mochizuki T, Amemiya K, Kurosaka G, Yazawa M, Nakamoto K, Ishikawa Y, Izawa S, Abe F. Amino acid homeostatic control by TORC1 in Saccharomyces cerevisiae under high hydrostatic pressure. J Cell Sci 2020; 133:jcs245555. [PMID: 32801125 DOI: 10.1242/jcs.245555] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 08/05/2020] [Indexed: 12/30/2022] Open
Abstract
Mechanical stresses, including high hydrostatic pressure, elicit diverse physiological effects on organisms. Gtr1, Gtr2, Ego1 (also known as Meh1) and Ego3 (also known as Slm4), central regulators of the TOR complex 1 (TORC1) nutrient signaling pathway, are required for the growth of Saccharomyces cerevisiae cells under high pressure. Here, we showed that a pressure of 25 MPa (∼250 kg/cm2) stimulates TORC1 to promote phosphorylation of Sch9, which depends on the EGO complex (EGOC) and Pib2. Incubation of cells at this pressure aberrantly increased glutamine and alanine levels in the ego1Δ, gtr1Δ, tor1Δ and pib2Δ mutants, whereas the polysome profiles were unaffected. Moreover, we found that glutamine levels were reduced by combined deletions of EGO1, GTR1, TOR1 and PIB2 with GLN3 These results suggest that high pressure leads to the intracellular accumulation of amino acids. Subsequently, Pib2 loaded with glutamine stimulates the EGOC-TORC1 complex to inactivate Gln3, downregulating glutamine synthesis. Our findings illustrate the regulatory circuit that maintains intracellular amino acid homeostasis and suggest critical roles for the EGOC-TORC1 and Pib2-TORC1 complexes in the growth of yeast under high hydrostatic pressure.
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Affiliation(s)
- Satoshi Uemura
- Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara 252-5258, Japan
- Division of Medical Biochemistry, Faculty of Medicine, Tohoku Medical and Pharmaceutical University, 1-15-1, Fukumuro, Miyagino-ku, Sendai, Miyagi 983-8536, Japan
| | - Takahiro Mochizuki
- Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara 252-5258, Japan
| | - Kengo Amemiya
- Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara 252-5258, Japan
| | - Goyu Kurosaka
- Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara 252-5258, Japan
| | - Miho Yazawa
- Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara 252-5258, Japan
| | - Keiko Nakamoto
- Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara 252-5258, Japan
| | - Yu Ishikawa
- Laboratory of Microbial Technology, Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Kyoto 606-8585, Japan
| | - Shingo Izawa
- Laboratory of Microbial Technology, Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Kyoto 606-8585, Japan
| | - Fumiyoshi Abe
- Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara 252-5258, Japan
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15
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Abstract
Stalled protein synthesis produces defective nascent chains that can harm cells. In response, cells degrade these nascent chains via a process called ribosome-associated quality control (RQC). Here, we review the irregularities in the translation process that cause ribosomes to stall as well as how cells use RQC to detect stalled ribosomes, ubiquitylate their tethered nascent chains, and deliver the ubiquitylated nascent chains to the proteasome. We additionally summarize how cells respond to RQC failure.
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Affiliation(s)
- Cole S Sitron
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany;
| | - Onn Brandman
- Department of Biochemistry, Stanford University, Stanford, California 94305, USA;
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16
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Matsuo Y, Tesina P, Nakajima S, Mizuno M, Endo A, Buschauer R, Cheng J, Shounai O, Ikeuchi K, Saeki Y, Becker T, Beckmann R, Inada T. RQT complex dissociates ribosomes collided on endogenous RQC substrate SDD1. Nat Struct Mol Biol 2020; 27:323-332. [PMID: 32203490 DOI: 10.1038/s41594-020-0393-9] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 02/10/2020] [Indexed: 01/18/2023]
Abstract
Ribosome-associated quality control (RQC) represents a rescue pathway in eukaryotic cells that is triggered upon translational stalling. Collided ribosomes are recognized for subsequent dissociation followed by degradation of nascent peptides. However, endogenous RQC-inducing sequences and the mechanism underlying the ubiquitin-dependent ribosome dissociation remain poorly understood. Here, we identified SDD1 messenger RNA from Saccharomyces cerevisiae as an endogenous RQC substrate and reveal the mechanism of its mRNA-dependent and nascent peptide-dependent translational stalling. In vitro translation of SDD1 mRNA enabled the reconstitution of Hel2-dependent polyubiquitination of collided disomes and, preferentially, trisomes. The distinct trisome architecture, visualized using cryo-EM, provides the structural basis for the more-efficient recognition by Hel2 compared with that of disomes. Subsequently, the Slh1 helicase subunit of the RQC trigger (RQT) complex preferentially dissociates the first stalled polyubiquitinated ribosome in an ATP-dependent manner. Together, these findings provide fundamental mechanistic insights into RQC and its physiological role in maintaining cellular protein homeostasis.
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Affiliation(s)
- Yoshitaka Matsuo
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Petr Tesina
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany
| | - Shizuka Nakajima
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Masato Mizuno
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Akinori Endo
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo, Japan
| | - Robert Buschauer
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany
| | - Jingdong Cheng
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany
| | - Okuto Shounai
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Ken Ikeuchi
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Yasushi Saeki
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo, Japan
| | - Thomas Becker
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany
| | - Roland Beckmann
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany.
| | - Toshifumi Inada
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan.
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17
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Inada T. Quality controls induced by aberrant translation. Nucleic Acids Res 2020; 48:1084-1096. [PMID: 31950154 PMCID: PMC7026593 DOI: 10.1093/nar/gkz1201] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 12/01/2019] [Accepted: 12/18/2019] [Indexed: 12/31/2022] Open
Abstract
During protein synthesis, translating ribosomes encounter many challenges imposed by various types of defective mRNAs that can lead to reduced cellular fitness and, in some cases, even threaten cell viability. Aberrant translation leads to activation of one of several quality control pathways depending on the nature of the problem. These pathways promote the degradation of the problematic mRNA as well as the incomplete translation product, the nascent polypeptide chain. Many of these quality control systems feature critical roles for specialized regulatory factors that work in concert with conventional factors. This review focuses on the mechanisms used by these quality control pathways to recognize aberrant ribosome stalling and discusses the conservation of these systems.
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Affiliation(s)
- Toshifumi Inada
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan
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18
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Yoshimoto N, Kawai T, Yoshida M, Izawa S. Xylene causes oxidative stress and pronounced translation repression in Saccharomyces cerevisiae. J Biosci Bioeng 2019; 128:697-703. [DOI: 10.1016/j.jbiosc.2019.05.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/20/2019] [Accepted: 05/30/2019] [Indexed: 12/23/2022]
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19
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Fleming I, Cavalcanti ARO. Selection for tandem stop codons in ciliate species with reassigned stop codons. PLoS One 2019; 14:e0225804. [PMID: 31770405 PMCID: PMC6879139 DOI: 10.1371/journal.pone.0225804] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 11/12/2019] [Indexed: 12/11/2022] Open
Abstract
The failure of mRNA translation machinery to recognize a stop codon as a termination signal and subsequent translation of the 3' untranslated region (UTR) is referred to as stop codon readthrough, the frequency of which is related to the length, composition, and structure of mRNA sequences downstream of end-of-gene stop codons. Secondary in-frame stop codons within a few positions downstream of the primary stop codons, so-called tandem stop codons (TSCs), serve as backup termination signals, which limit the effects of readthrough: polypeptide product degradation, mislocalization, and aggregation. In this study, ciliate species with UAA and UAG stop codons reassigned to code for glutamine are found to possess statistical excesses of TSCs at the beginning of their 3' UTRs. The overrepresentation of TSCs in these species is greater than that observed in standard code organisms. Though the overall numbers of TSCs are lower in most species with alternative stop codons because they use fewer than three unique stop codons, the relatively great overrepresentation of TSCs in alternative-code ciliate species suggests that there exist stronger selective pressures to maintain TSCs in these organisms compared to standard code organisms.
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Affiliation(s)
- Ira Fleming
- Department of Molecular Biology, Pomona College, Claremont, CA, United States of America
| | - Andre R. O. Cavalcanti
- Department of Molecular Biology, Pomona College, Claremont, CA, United States of America
- * E-mail:
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20
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Hashimoto S, Nobuta R, Izawa T, Inada T. Translation arrest as a protein quality control system for aberrant translation of the 3'-UTR in mammalian cells. FEBS Lett 2019; 593:777-787. [PMID: 30883710 DOI: 10.1002/1873-3468.13362] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 02/23/2019] [Accepted: 03/11/2019] [Indexed: 01/05/2023]
Abstract
Read-through or mutations of a stop codon resulting in translation of the 3'-UTR produce potentially toxic C-terminally extended proteins. However, quality control mechanisms for such proteins are poorly understood in mammalian cells. Here, a comprehensive analysis of the 3'-UTRs of genes associated with hereditary diseases identified novel arrest-inducing sequences in the 3'-UTRs of 23 genes that can repress the levels of their protein products. In silico analysis revealed that the hydrophobicity of the polypeptides encoded in the 3'-UTRs is correlated with arrest efficiency. These results provide new insight into quality control mechanisms mediated by 3'-UTRs to prevent the production of C-terminally extended cytotoxic proteins.
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Affiliation(s)
- Satoshi Hashimoto
- Graduate School of Pharmaceutical Science, Tohoku University, Sendai, Japan
| | - Risa Nobuta
- Graduate School of Pharmaceutical Science, Tohoku University, Sendai, Japan
| | - Toshiaki Izawa
- Graduate School of Pharmaceutical Science, Tohoku University, Sendai, Japan
| | - Toshifumi Inada
- Graduate School of Pharmaceutical Science, Tohoku University, Sendai, Japan
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21
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Karamyshev AL, Karamysheva ZN. Lost in Translation: Ribosome-Associated mRNA and Protein Quality Controls. Front Genet 2018; 9:431. [PMID: 30337940 PMCID: PMC6180196 DOI: 10.3389/fgene.2018.00431] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 09/11/2018] [Indexed: 12/15/2022] Open
Abstract
Aberrant, misfolded, and mislocalized proteins are often toxic to cells and result in many human diseases. All proteins and their mRNA templates are subject to quality control. There are several distinct mechanisms that control the quality of mRNAs and proteins during translation at the ribosome. mRNA quality control systems, nonsense-mediated decay, non-stop decay, and no-go decay detect premature stop codons, the absence of a natural stop codon, and stalled ribosomes in translation, respectively, and degrade their mRNAs. Defective truncated polypeptide nascent chains generated from faulty mRNAs are degraded by ribosome-associated protein quality control pathways. Regulation of aberrant protein production, a novel pathway, senses aberrant proteins by monitoring the status of nascent chain interactions during translation and triggers degradation of their mRNA. Here, we review the current progress in understanding of the molecular mechanisms of mRNA and protein quality controls at the ribosome during translation.
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Affiliation(s)
- Andrey L Karamyshev
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX, United States
| | - Zemfira N Karamysheva
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, United States
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22
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Kato S, Yamauchi Y, Izawa S. Protein synthesis of Btn2 under pronounced translation repression during the process of alcoholic fermentation and wine-making in yeast. Appl Microbiol Biotechnol 2018; 102:9669-9677. [PMID: 30141081 DOI: 10.1007/s00253-018-9313-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 07/28/2018] [Accepted: 08/08/2018] [Indexed: 12/21/2022]
Abstract
Acute high-concentration ethanol (> 9% v/v) has adverse effects on Saccharomyces cerevisiae, including the remarkable repression of bulk mRNA translation. Therefore, increased mRNA levels do not necessarily lead to an increase in the corresponding protein levels in yeast cells under severe ethanol stress. We previously identified that synthesis of Btn2 protein was efficiently induced even under the pronounced translation repression caused by acute severe ethanol stress under laboratory conditions. However, it remains to be clarified whether the translational activity is also repressed and whether the synthesis of Btn2 protein is induced during the process of alcoholic fermentation, in which the ethanol concentration increases gradually to reach high levels. In this study, we revealed that the pronounced translation repression and the translation of BTN2 are induced by high ethanol concentrations that form gradually during alcoholic fermentation using a wine yeast strain EC1118. Furthermore, we confirmed the induced expression of non-native genes driven by the BTN2 promoter during the later stage of the wine-making process. Our findings provide new information on the translation activity in yeast cells during alcoholic fermentation and suggest the utility of the BTN2 promoter for sustaining the fermentation efficiency and quality modification of alcoholic beverages.
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Affiliation(s)
- Sae Kato
- Laboratory of Microbial Technology, Graduate School of Science and Technology, Kyoto Institute of Technology, Matsugasaki, Kyoto, 606-8585, Japan
| | - Yukina Yamauchi
- Laboratory of Microbial Technology, Graduate School of Science and Technology, Kyoto Institute of Technology, Matsugasaki, Kyoto, 606-8585, Japan
| | - Shingo Izawa
- Laboratory of Microbial Technology, Graduate School of Science and Technology, Kyoto Institute of Technology, Matsugasaki, Kyoto, 606-8585, Japan.
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23
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Heck AM, Wilusz J. The Interplay between the RNA Decay and Translation Machinery in Eukaryotes. Cold Spring Harb Perspect Biol 2018; 10:a032839. [PMID: 29311343 PMCID: PMC5932591 DOI: 10.1101/cshperspect.a032839] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
RNA decay plays a major role in regulating gene expression and is tightly networked with other aspects of gene expression to effectively coordinate post-transcriptional regulation. The goal of this work is to provide an overview of the major factors and pathways of general messenger RNA (mRNA) decay in eukaryotic cells, and then discuss the effective interplay of this cytoplasmic process with the protein synthesis machinery. Given the transcript-specific and fluid nature of mRNA stability in response to changing cellular conditions, understanding the fundamental networking between RNA decay and translation will provide a foundation for a complete mechanistic understanding of this important aspect of cell biology.
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Affiliation(s)
- Adam M Heck
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80525
- Program in Cell & Molecular Biology, Colorado State University, Fort Collins, Colorado 80525
| | - Jeffrey Wilusz
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80525
- Program in Cell & Molecular Biology, Colorado State University, Fort Collins, Colorado 80525
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24
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Arribere JA, Fire AZ. Nonsense mRNA suppression via nonstop decay. eLife 2018; 7:33292. [PMID: 29309033 PMCID: PMC5777819 DOI: 10.7554/elife.33292] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 01/05/2018] [Indexed: 11/13/2022] Open
Abstract
Nonsense-mediated mRNA decay is the process by which mRNAs bearing premature stop codons are recognized and cleared from the cell. While considerable information has accumulated regarding recognition of the premature stop codon, less is known about the ensuing mRNA suppression. During the characterization of a second, distinct translational surveillance pathway (nonstop mRNA decay), we trapped intermediates in nonsense mRNA degradation. We present data in support of a model wherein nonsense-mediated decay funnels into the nonstop decay pathway in Caenorhabditis elegans. Specifically, our results point to SKI-exosome decay and pelota-based ribosome removal as key steps facilitating suppression and clearance of prematurely-terminated translation complexes. These results suggest a model in which premature stop codons elicit nucleolytic cleavage, with the nonstop pathway disengaging ribosomes and degrading the resultant RNA fragments to suppress ongoing expression.
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Affiliation(s)
- Joshua A Arribere
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, United States
| | - Andrew Z Fire
- Departments of Pathology and Genetics, Stanford University School of Medicine, Stanford, United States
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25
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Zheng J, Yang J, Choe YJ, Hao X, Cao X, Zhao Q, Zhang Y, Franssens V, Hartl FU, Nyström T, Winderickx J, Liu B. Role of the ribosomal quality control machinery in nucleocytoplasmic translocation of polyQ-expanded huntingtin exon-1. Biochem Biophys Res Commun 2017; 493:708-717. [PMID: 28864412 DOI: 10.1016/j.bbrc.2017.08.126] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2017] [Accepted: 08/28/2017] [Indexed: 10/19/2022]
Abstract
The subcellular localization of polyQ-expanded huntingtin exon1 (Httex1) modulates polyQ toxicity in models of Huntington's disease. Using genome-wide screens in a yeast model system, we report that the ribosome quality control (RQC) machinery, recently implicated in neurodegeneration, is a key determinant for the nucleocytoplasmic distribution of Httex1-103Q. Deletion of the RQC genes, LTN1 or RQC1, caused the accumulation of Httex1-103Q in the nucleus through a process that required the CAT-tail tagging activity of Rqc2 and transport via the nuclear pore complex. We provide evidence that nuclear accumulation of Httex1-103Q enhances its cytotoxicity, suggesting that the RQC machinery plays an important role in protecting cells against the adverse effects of polyQ expansion proteins.
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Affiliation(s)
- Ju Zheng
- Department of Chemistry and Molecular Biology, University of Gothenburg, S-413 90, Göteborg, Sweden; Department of Biology, Functional Biology, KU Leuven, 3001, Heverlee, Belgium
| | - Junsheng Yang
- Department of Chemistry and Molecular Biology, University of Gothenburg, S-413 90, Göteborg, Sweden
| | - Young-Jun Choe
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried, 82152, Germany
| | - Xinxin Hao
- Department of Chemistry and Molecular Biology, University of Gothenburg, S-413 90, Göteborg, Sweden
| | - Xiuling Cao
- Department of Chemistry and Molecular Biology, University of Gothenburg, S-413 90, Göteborg, Sweden
| | - Qian Zhao
- School of Life Sciences, Shandong University of Technology, 266 New Village West Road, Zhangdian District, Zibo, Shandong, China
| | - Yuejie Zhang
- School of Life Sciences, Shandong University of Technology, 266 New Village West Road, Zhangdian District, Zibo, Shandong, China
| | - Vanessa Franssens
- Department of Biology, Functional Biology, KU Leuven, 3001, Heverlee, Belgium
| | - F Ulrich Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried, 82152, Germany
| | - Thomas Nyström
- Department of Chemistry and Molecular Biology, University of Gothenburg, S-413 90, Göteborg, Sweden
| | - Joris Winderickx
- Department of Biology, Functional Biology, KU Leuven, 3001, Heverlee, Belgium
| | - Beidong Liu
- Department of Chemistry and Molecular Biology, University of Gothenburg, S-413 90, Göteborg, Sweden.
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26
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Ubiquitination of stalled ribosome triggers ribosome-associated quality control. Nat Commun 2017; 8:159. [PMID: 28757607 PMCID: PMC5534433 DOI: 10.1038/s41467-017-00188-1] [Citation(s) in RCA: 208] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 06/08/2017] [Indexed: 11/08/2022] Open
Abstract
Translation arrest by polybasic sequences induces ribosome stalling, and the arrest product is degraded by the ribosome-mediated quality control (RQC) system. Here we report that ubiquitination of the 40S ribosomal protein uS10 by the E3 ubiquitin ligase Hel2 (or RQT1) is required for RQC. We identify a RQC-trigger (RQT) subcomplex composed of the RNA helicase-family protein Slh1/Rqt2, the ubiquitin-binding protein Cue3/Rqt3, and yKR023W/Rqt4 that is required for RQC. The defects in RQC of the RQT mutants correlate with sensitivity to anisomycin, which stalls ribosome at the rotated form. Cryo-electron microscopy analysis reveals that Hel2-bound ribosome are dominantly the rotated form with hybrid tRNAs. Ribosome profiling reveals that ribosomes stalled at the rotated state with specific pairs of codons at P-A sites serve as RQC substrates. Rqt1 specifically ubiquitinates these arrested ribosomes to target them to the RQT complex, allowing subsequent RQC reactions including dissociation of the stalled ribosome into subunits.Several protein quality control mechanisms are in place to trigger the rapid degradation of aberrant polypeptides and mRNAs. Here the authors describe a mechanism of ribosome-mediated quality control that involves the ubiquitination of ribosomal proteins by the E3 ubiquitin ligase Hel2/RQT1.
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27
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Ishida Y, Nguyen TTM, Izawa S. The yeast ADH7 promoter enables gene expression under pronounced translation repression caused by the combined stress of vanillin, furfural, and 5-hydroxymethylfurfural. J Biotechnol 2017; 252:65-72. [DOI: 10.1016/j.jbiotec.2017.04.024] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 04/03/2017] [Accepted: 04/21/2017] [Indexed: 11/30/2022]
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28
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Inada T. The Ribosome as a Platform for mRNA and Nascent Polypeptide Quality Control. Trends Biochem Sci 2017; 42:5-15. [DOI: 10.1016/j.tibs.2016.09.005] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 09/05/2016] [Accepted: 09/13/2016] [Indexed: 11/28/2022]
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29
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The Histone Deacetylase Gene Rpd3 Is Required for Starvation Stress Resistance. PLoS One 2016; 11:e0167554. [PMID: 27907135 PMCID: PMC5132236 DOI: 10.1371/journal.pone.0167554] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2016] [Accepted: 11/16/2016] [Indexed: 12/25/2022] Open
Abstract
Epigenetic regulation in starvation is important but not fully understood yet. Here we identified the Rpd3 gene, a Drosophila homolog of histone deacetylase 1, as a critical epigenetic regulator for acquiring starvation stress resistance. Immunostaining analyses of Drosophila fat body revealed that the subcellular localization and levels of Rpd3 dynamically changed responding to starvation stress. In response to starvation stress, the level of Rpd3 rapidly increased, and it accumulated in the nucleolus in what appeared to be foci. These observations suggest that Rpd3 plays a role in regulation of rRNA synthesis in the nucleolus. The RT-qPCR and ChIP-qPCR analyses clarified that Rpd3 binds to the genomic region containing the rRNA promoters and activates rRNA synthesis in response to starvation stress. Polysome analyses revealed that the amount of polysomes was decreased in Rpd3 knockdown flies under starvation stress compared with the control flies. Since the autophagy-related proteins are known to be starvation stress tolerance proteins, we examined autophagy activity, and it was reduced in Rpd3 knockdown flies. Taken together, we conclude that Rpd3 accumulates in the nucleolus in the early stage of starvation, upregulates rRNA synthesis, maintains the polysome amount for translation, and finally increases stress tolerance proteins, such as autophagy-related proteins, to acquire starvation stress resistance.
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30
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Łabno A, Tomecki R, Dziembowski A. Cytoplasmic RNA decay pathways - Enzymes and mechanisms. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1863:3125-3147. [PMID: 27713097 DOI: 10.1016/j.bbamcr.2016.09.023] [Citation(s) in RCA: 124] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 09/29/2016] [Accepted: 09/30/2016] [Indexed: 12/14/2022]
Abstract
RNA decay plays a crucial role in post-transcriptional regulation of gene expression. Work conducted over the last decades has defined the major mRNA decay pathways, as well as enzymes and their cofactors responsible for these processes. In contrast, our knowledge of the mechanisms of degradation of non-protein coding RNA species is more fragmentary. This review is focused on the cytoplasmic pathways of mRNA and ncRNA degradation in eukaryotes. The major 3' to 5' and 5' to 3' mRNA decay pathways are described with emphasis on the mechanisms of their activation by the deprotection of RNA ends. More recently discovered 3'-end modifications such as uridylation, and their relevance to cytoplasmic mRNA decay in various model organisms, are also discussed. Finally, we provide up-to-date findings concerning various pathways of non-coding RNA decay in the cytoplasm.
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Affiliation(s)
- Anna Łabno
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland; Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5A, 02-106 Warsaw, Poland
| | - Rafał Tomecki
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland; Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5A, 02-106 Warsaw, Poland.
| | - Andrzej Dziembowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland; Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5A, 02-106 Warsaw, Poland.
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31
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Different Regulations of ROM2 and LRG1 Expression by Ccr4, Pop2, and Dhh1 in the Saccharomyces cerevisiae Cell Wall Integrity Pathway. mSphere 2016; 1:mSphere00250-16. [PMID: 27704052 PMCID: PMC5040787 DOI: 10.1128/msphere.00250-16] [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: 08/23/2016] [Accepted: 09/09/2016] [Indexed: 11/25/2022] Open
Abstract
We find here that Ccr4, Pop2, and Dhh1 modulate the levels of mRNAs for specific Rho1 regulators, Rom2 and Lrg1. In budding yeast, Rho1 activity is tightly regulated both temporally and spatially. It is anticipated that Ccr4, Pop2, and Dhh1 may contribute to the precise spatiotemporal control of Rho1 activity by regulating expression of its regulators temporally and spatially. Our finding on the roles of the components of the Ccr4-Not complex in yeast would give important information for understanding the roles of the evolutionary conserved Ccr4-Not complex. Ccr4, a component of the Ccr4-Not cytoplasmic deadenylase complex, is known to be required for the cell wall integrity (CWI) pathway in the budding yeast Saccharomyces cerevisiae. However, it is not fully understood how Ccr4 and other components of the Ccr4-Not complex regulate the CWI pathway. Previously, we showed that Ccr4 functions in the CWI pathway together with Khd1 RNA binding protein. Ccr4 and Khd1 modulate a signal from Rho1 small GTPase in the CWI pathway by regulating the expression of ROM2 mRNA and LRG1 mRNA, encoding a guanine nucleotide exchange factor (GEF) and a GTPase-activating protein (GAP) for Rho1, respectively. Here we examined the possible involvement of the POP2 gene encoding a subunit of the Ccr4-Not complex and the DHH1 gene encoding a DEAD box RNA helicase that associates with the Ccr4-Not complex in the regulation of ROM2 and LRG1 expression. Neither ROM2 mRNA level nor Rom2 function was impaired by pop2Δ or dhh1Δ mutation. The LRG1 mRNA level was increased in pop2Δ and dhh1Δ mutants, as well as the ccr4Δ mutant, and the growth defects caused by pop2Δ and dhh1Δ mutations were suppressed by lrg1Δ mutation. Our results suggest that LRG1 expression is regulated by Ccr4 together with Pop2 and Dhh1 and that ROM2 expression is regulated by Khd1 and Ccr4, but not by Pop2 and Dhh1. Thus, Rho1 activity in the CWI pathway is precisely controlled by modulation of the mRNA levels for Rho1-GEF Rom2 and Rho1-GAP Lrg1. IMPORTANCE We find here that Ccr4, Pop2, and Dhh1 modulate the levels of mRNAs for specific Rho1 regulators, Rom2 and Lrg1. In budding yeast, Rho1 activity is tightly regulated both temporally and spatially. It is anticipated that Ccr4, Pop2, and Dhh1 may contribute to the precise spatiotemporal control of Rho1 activity by regulating expression of its regulators temporally and spatially. Our finding on the roles of the components of the Ccr4-Not complex in yeast would give important information for understanding the roles of the evolutionary conserved Ccr4-Not complex.
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32
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Ikeuchi K, Yazaki E, Kudo K, Inada T. Conserved functions of human Pelota in mRNA quality control of nonstop mRNA. FEBS Lett 2016; 590:3254-63. [DOI: 10.1002/1873-3468.12366] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 08/12/2016] [Accepted: 08/15/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Ken Ikeuchi
- Graduate School of Pharmaceutical Science; Tohoku University; Aoba-ku Sendai Japan
| | - Erina Yazaki
- Graduate School of Pharmaceutical Science; Tohoku University; Aoba-ku Sendai Japan
| | - Kazuhei Kudo
- Graduate School of Pharmaceutical Science; Tohoku University; Aoba-ku Sendai Japan
| | - Toshifumi Inada
- Graduate School of Pharmaceutical Science; Tohoku University; Aoba-ku Sendai Japan
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33
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Yamauchi Y, Izawa S. Prioritized Expression of BTN2 of Saccharomyces cerevisiae under Pronounced Translation Repression Induced by Severe Ethanol Stress. Front Microbiol 2016; 7:1319. [PMID: 27602028 PMCID: PMC4993754 DOI: 10.3389/fmicb.2016.01319] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 08/10/2016] [Indexed: 11/24/2022] Open
Abstract
Severe ethanol stress (>9% ethanol, v/v) as well as glucose deprivation rapidly induces a pronounced repression of overall protein synthesis in budding yeast Saccharomyces cerevisiae. Therefore, transcriptional activation in yeast cells under severe ethanol stress does not always indicate the production of expected protein levels. Messenger RNAs of genes containing heat shock elements can be intensively translated under glucose deprivation, suggesting that some mRNAs are preferentially translated even under severe ethanol stress. In the present study, we tried to identify the mRNA that can be preferentially translated under severe ethanol stress. BTN2 encodes a v-SNARE binding protein, and its null mutant shows hypersensitivity to ethanol. We found that BTN2 mRNA was efficiently translated under severe ethanol stress but not under mild ethanol stress. Moreover, the increased Btn2 protein levels caused by severe ethanol stress were smoothly decreased with the elimination of ethanol stress. These findings suggested that severe ethanol stress extensively induced BTN2 expression. Further, the BTN2 promoter induced protein synthesis of non-native genes such as CUR1, GIC2, and YUR1 in the presence of high ethanol concentrations, indicating that this promoter overcame severe ethanol stress-induced translation repression. Thus, our findings provide an important clue about yeast response to severe ethanol stress and suggest that the BTN2 promoter can be used to improve the efficiency of ethanol production and stress tolerance of yeast cells by modifying gene expression in the presence of high ethanol concentration.
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Affiliation(s)
- Yukina Yamauchi
- Laboratory of Microbial Technology, Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology Kyoto, Japan
| | - Shingo Izawa
- Laboratory of Microbial Technology, Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology Kyoto, Japan
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Arribere JA, Cenik ES, Jain N, Hess GT, Lee CH, Bassik MC, Fire AZ. Translation readthrough mitigation. Nature 2016; 534:719-23. [PMID: 27281202 PMCID: PMC5054982 DOI: 10.1038/nature18308] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 05/05/2016] [Indexed: 12/31/2022]
Abstract
A fraction of ribosomes engaged in translation will fail to terminate when reaching a stop codon, yielding nascent proteins inappropriately extended on their C termini. Although such extended proteins can interfere with normal cellular processes, known mechanisms of translational surveillance are insufficient to protect cells from potential dominant consequences. Here, through a combination of transgenics and CRISPR–Cas9 gene editing in Caenorhabditis elegans, we demonstrate a consistent ability of cells to block accumulation of C-terminal-extended proteins that result from failure to terminate at stop codons. Sequences encoded by the 3′ untranslated region (UTR) were sufficient to lower protein levels. Measurements of mRNA levels and translation suggested a co- or post-translational mechanism of action for these sequences in C. elegans. Similar mechanisms evidently operate in human cells, in which we observed a comparable tendency for translated human 3′ UTR sequences to reduce mature protein expression in tissue culture assays, including 3′ UTR sequences from the hypomorphic ‘Constant Spring’ haemoglobin stop codon variant. We suggest that 3′ UTRs may encode peptide sequences that destabilize the attached protein, providing mitigation of unwelcome and varied translation errors.
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Ribosome-associated Asc1/RACK1 is required for endonucleolytic cleavage induced by stalled ribosome at the 3' end of nonstop mRNA. Sci Rep 2016; 6:28234. [PMID: 27312062 PMCID: PMC4911565 DOI: 10.1038/srep28234] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 05/31/2016] [Indexed: 12/21/2022] Open
Abstract
Dom34-Hbs1 stimulates degradation of aberrant mRNAs lacking termination codons by dissociating ribosomes stalled at the 3′ ends, and plays crucial roles in Nonstop Decay (NSD) and No-Go Decay (NGD). In the dom34Δ mutant, nonstop mRNA is degraded by sequential endonucleolytic cleavages induced by a stalled ribosome at the 3′ end. Here, we report that ribosome-associated Asc1/RACK1 is required for the endonucleolytic cleavage of nonstop mRNA by stalled ribosome at the 3′ end of mRNA in dom34Δ mutant cells. Asc1/RACK1 facilitates degradation of truncated GFP-Rz mRNA in the absence of Dom34 and exosome-dependent decay. Asc1/RACK1 is required for the sequential endonucleolytic cleavages by the stalled ribosome in the dom34Δ mutant, depending on its ribosome-binding activity. The levels of peptidyl-tRNA derived from nonstop mRNA were elevated in dom34Δasc1Δ mutant cells, and overproduction of nonstop mRNA inhibited growth of mutant cells. E3 ubiquitin ligase Ltn1 degrades the arrest products from truncated GFP-Rz mRNA in dom34Δ and dom34Δasc1Δ mutant cells, and Asc1/RACK1 represses the levels of substrates for Ltn1-dependent degradation. These indicate that ribosome-associated Asc1/RACK1 facilitates endonucleolytic cleavage of nonstop mRNA by stalled ribosomes and represses the levels of aberrant products even in the absence of Dom34. We propose that Asc1/RACK1 acts as a fail-safe in quality control for nonstop mRNA.
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Simms CL, Thomas EN, Zaher HS. Ribosome-based quality control of mRNA and nascent peptides. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 8. [PMID: 27193249 DOI: 10.1002/wrna.1366] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 04/25/2016] [Accepted: 04/26/2016] [Indexed: 11/06/2022]
Abstract
Quality control processes are widespread and play essential roles in detecting defective molecules and removing them in order to maintain organismal fitness. Aberrant messenger RNA (mRNA) molecules, unless properly managed, pose a significant hurdle to cellular proteostasis. Often mRNAs harbor premature stop codons, possess structures that present a block to the translational machinery, or lack stop codons entirely. In eukaryotes, the three cytoplasmic mRNA-surveillance processes, nonsense-mediated decay (NMD), no-go decay (NGD), and nonstop decay (NSD), evolved to cope with these aberrant mRNAs, respectively. Nonstop mRNAs and mRNAs that inhibit translation elongation are especially problematic as they sequester valuable ribosomes from the translating ribosome pool. As a result, in addition to RNA degradation, NSD and NGD are intimately coupled to ribosome rescue in all domains of life. Furthermore, protein products produced from all three classes of defective mRNAs are more likely to malfunction. It is not surprising then that these truncated nascent protein products are subject to degradation. Over the past few years, many studies have begun to document a central role for the ribosome in initiating the RNA and protein quality control processes. The ribosome appears to be responsible for recognizing the target mRNAs as well as for recruiting the factors required to carry out the processes of ribosome rescue and nascent protein decay. WIREs RNA 2017, 8:e1366. doi: 10.1002/wrna.1366 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Carrie L Simms
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA
| | - Erica N Thomas
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA
| | - Hani S Zaher
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA
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Gratia M, Vende P, Charpilienne A, Baron HC, Laroche C, Sarot E, Pyronnet S, Duarte M, Poncet D. Challenging the Roles of NSP3 and Untranslated Regions in Rotavirus mRNA Translation. PLoS One 2016; 11:e0145998. [PMID: 26727111 PMCID: PMC4699793 DOI: 10.1371/journal.pone.0145998] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 12/01/2015] [Indexed: 12/20/2022] Open
Abstract
Rotavirus NSP3 is a translational surrogate of the PABP-poly(A) complex for rotavirus mRNAs. To further explore the effects of NSP3 and untranslated regions (UTRs) on rotavirus mRNAs translation, we used a quantitative in vivo assay with simultaneous cytoplasmic NSP3 expression (wild-type or deletion mutant) and electroporated rotavirus-like and standard synthetic mRNAs. This assay shows that the last four GACC nucleotides of viral mRNA are essential for efficient translation and that both the NSP3 eIF4G- and RNA-binding domains are required. We also show efficient translation of rotavirus-like mRNAs even with a 5’UTR as short as 5 nucleotides, while more than eleven nucleotides are required for the 3’UTR. Despite the weak requirement for a long 5’UTR, a good AUG environment remains a requirement for rotavirus mRNAs translation.
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Affiliation(s)
- Matthieu Gratia
- Institut de Biologie Integrative de la Cellule (I2BC), UMR 9198, Département de Virologie, USC INRA 1358, Gif sur Yvette, France
| | - Patrice Vende
- Institut de Biologie Integrative de la Cellule (I2BC), UMR 9198, Département de Virologie, USC INRA 1358, Gif sur Yvette, France
| | - Annie Charpilienne
- Institut de Biologie Integrative de la Cellule (I2BC), UMR 9198, Département de Virologie, USC INRA 1358, Gif sur Yvette, France
| | - Hilma Carolina Baron
- Institut de Biologie Integrative de la Cellule (I2BC), UMR 9198, Département de Virologie, USC INRA 1358, Gif sur Yvette, France
| | - Cécile Laroche
- Institut de Biologie Integrative de la Cellule (I2BC), UMR 9198, Département de Virologie, USC INRA 1358, Gif sur Yvette, France
| | - Emeline Sarot
- INSERM UMR-1037 - Université de Toulouse III-Paul Sabatier, Laboratoire d'Excellence Toulouse Cancer (TOUCAN), Equipe labellisée Ligue Contre le Cancer Toulouse, France
| | - Stéphane Pyronnet
- INSERM UMR-1037 - Université de Toulouse III-Paul Sabatier, Laboratoire d'Excellence Toulouse Cancer (TOUCAN), Equipe labellisée Ligue Contre le Cancer Toulouse, France
| | - Mariela Duarte
- Institut de Biologie Integrative de la Cellule (I2BC), UMR 9198, Département de Virologie, USC INRA 1358, Gif sur Yvette, France
- Université d’Evry Val d’Essonne, Département de Biologie, Evry, France
| | - Didier Poncet
- Institut de Biologie Integrative de la Cellule (I2BC), UMR 9198, Département de Virologie, USC INRA 1358, Gif sur Yvette, France
- * E-mail:
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Nguyen TTM, Iwaki A, Izawa S. The ADH7 Promoter of Saccharomyces cerevisiae is Vanillin-Inducible and Enables mRNA Translation Under Severe Vanillin Stress. Front Microbiol 2015; 6:1390. [PMID: 26696995 PMCID: PMC4676198 DOI: 10.3389/fmicb.2015.01390] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 11/23/2015] [Indexed: 12/24/2022] Open
Abstract
Vanillin is one of the major phenolic aldehyde compounds derived from lignocellulosic biomass and acts as a potent fermentation inhibitor to repress the growth and fermentative ability of yeast. Vanillin can be reduced to its less toxic form, vanillyl alcohol, by the yeast NADPH-dependent medium chain alcohol dehydrogenases, Adh6 and Adh7. However, there is little information available regarding the regulation of their gene expression upon severe vanillin stress, which has been shown to repress the bulk translation activity in yeast cells. Therefore, in this study, we investigated expression patterns of the ADH6 and ADH7 genes in the presence of high concentrations of vanillin. We found that although both genes were transcriptionally upregulated by vanillin stress, they showed different protein expression patterns in response to vanillin. Expression of Adh6 was constitutive and gradually decreased under vanillin stress, whereas expression of Adh7 was inducible, and, importantly, occurred under severe vanillin stress. The null mutants of ADH6 or ADH7 genes were hypersensitive to vanillin and reduced vanillin less efficiently than the wild type, confirming the importance of Adh6 and Adh7 in vanillin detoxification. Additionally, we demonstrate that the ADH7 promoter is vanillin-inducible and enables effective protein synthesis even under severe vanillin stress, and it may be useful for the improvement of vanillin-tolerance and biofuel production efficiency via modification of yeast gene expression in the presence of high concentrations of vanillin.
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Affiliation(s)
- Trinh T M Nguyen
- Laboratory of Microbial Technology, Graduate School of Science and Technology, Kyoto Institute of Technology Kyoto, Japan
| | - Aya Iwaki
- Laboratory of Microbial Technology, Graduate School of Science and Technology, Kyoto Institute of Technology Kyoto, Japan
| | - Shingo Izawa
- Laboratory of Microbial Technology, Graduate School of Science and Technology, Kyoto Institute of Technology Kyoto, Japan
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39
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Siwaszek A, Ukleja M, Dziembowski A. Proteins involved in the degradation of cytoplasmic mRNA in the major eukaryotic model systems. RNA Biol 2015; 11:1122-36. [PMID: 25483043 DOI: 10.4161/rna.34406] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The process of mRNA decay and surveillance is considered to be one of the main posttranscriptional gene expression regulation platforms in eukaryotes. The degradation of stable, protein-coding transcripts is normally initiated by removal of the poly(A) tail followed by 5'-cap hydrolysis and degradation of the remaining mRNA body by Xrn1. Alternatively, the exosome complex degrades mRNA in the 3'>5'direction. The newly discovered uridinylation-dependent pathway, which is present in many different organisms, also seems to play a role in bulk mRNA degradation. Simultaneously, to avoid the synthesis of incorrect proteins, special cellular machinery is responsible for the removal of faulty transcripts via nonsense-mediated, no-go, non-stop or non-functional 18S rRNA decay. This review is focused on the major eukaryotic cytoplasmic mRNA degradation pathways showing many similarities and pointing out main differences between the main model-species: yeast, Drosophila, plants and mammals.
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Affiliation(s)
- Aleksandra Siwaszek
- a Institute of Biochemistry and Biophysics ; Polish Academy of Sciences ; Warsaw , Poland
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40
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Crowder JJ, Geigges M, Gibson RT, Fults ES, Buchanan BW, Sachs N, Schink A, Kreft SG, Rubenstein EM. Rkr1/Ltn1 Ubiquitin Ligase-mediated Degradation of Translationally Stalled Endoplasmic Reticulum Proteins. J Biol Chem 2015; 290:18454-66. [PMID: 26055716 DOI: 10.1074/jbc.m115.663559] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Indexed: 11/06/2022] Open
Abstract
Aberrant nonstop proteins arise from translation of mRNA molecules beyond the coding sequence into the 3'-untranslated region. If a stop codon is not encountered, translation continues into the poly(A) tail, resulting in C-terminal appendage of a polylysine tract and a terminally stalled ribosome. In Saccharomyces cerevisiae, the ubiquitin ligase Rkr1/Ltn1 has been implicated in the proteasomal degradation of soluble cytosolic nonstop and translationally stalled proteins. Rkr1 is essential for cellular fitness under conditions associated with increased prevalence of nonstop proteins. Mutation of the mammalian homolog causes significant neurological pathology, suggesting broad physiological significance of ribosome-associated quality control. It is not known whether and how soluble or transmembrane nonstop and translationally stalled proteins targeted to the endoplasmic reticulum (ER) are detected and degraded. We generated and characterized model soluble and transmembrane ER-targeted nonstop and translationally stalled proteins. We found that these proteins are indeed subject to proteasomal degradation. We tested three candidate ubiquitin ligases (Rkr1 and ER-associated Doa10 and Hrd1) for roles in regulating abundance of these proteins. Our results indicate that Rkr1 plays the primary role in targeting the tested model ER-targeted nonstop and translationally stalled proteins for degradation. These data expand the catalog of Rkr1 substrates and highlight a previously unappreciated role for this ubiquitin ligase at the ER membrane.
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Affiliation(s)
- Justin J Crowder
- From the Department of Biology, Ball State University, Muncie, Indiana 47306 and
| | - Marco Geigges
- the Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Ryan T Gibson
- From the Department of Biology, Ball State University, Muncie, Indiana 47306 and
| | - Eric S Fults
- From the Department of Biology, Ball State University, Muncie, Indiana 47306 and
| | - Bryce W Buchanan
- From the Department of Biology, Ball State University, Muncie, Indiana 47306 and
| | - Nadine Sachs
- the Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Andrea Schink
- the Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Stefan G Kreft
- the Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Eric M Rubenstein
- From the Department of Biology, Ball State University, Muncie, Indiana 47306 and
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41
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Preissler S, Reuther J, Koch M, Scior A, Bruderek M, Frickey T, Deuerling E. Not4-dependent translational repression is important for cellular protein homeostasis in yeast. EMBO J 2015; 34:1905-24. [PMID: 25971775 DOI: 10.15252/embj.201490194] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 04/12/2015] [Indexed: 11/09/2022] Open
Abstract
Translation of aberrant or problematic mRNAs can cause ribosome stalling which leads to the production of truncated or defective proteins. Therefore, cells evolved cotranslational quality control mechanisms that eliminate these transcripts and target arrested nascent polypeptides for proteasomal degradation. Here we show that Not4, which is part of the multifunctional Ccr4-Not complex in yeast, associates with polysomes and contributes to the negative regulation of protein synthesis. Not4 is involved in translational repression of transcripts that cause transient ribosome stalling. The absence of Not4 affected global translational repression upon nutrient withdrawal, enhanced the expression of arrested nascent polypeptides and caused constitutive protein folding stress and aggregation. Similar defects were observed in cells with impaired mRNA decapping protein function and in cells lacking the mRNA decapping activator and translational repressor Dhh1. The results suggest a role for Not4 together with components of the decapping machinery in the regulation of protein expression on the mRNA level and emphasize the importance of translational repression for the maintenance of proteome integrity.
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Affiliation(s)
- Steffen Preissler
- Molecular Microbiology, University of Konstanz, Konstanz, Germany Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Julia Reuther
- Molecular Microbiology, University of Konstanz, Konstanz, Germany Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Miriam Koch
- Molecular Microbiology, University of Konstanz, Konstanz, Germany Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Annika Scior
- Molecular Microbiology, University of Konstanz, Konstanz, Germany Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Michael Bruderek
- Molecular Microbiology, University of Konstanz, Konstanz, Germany
| | - Tancred Frickey
- Applied Bioinformatics, University of Konstanz, Konstanz, Germany
| | - Elke Deuerling
- Molecular Microbiology, University of Konstanz, Konstanz, Germany
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42
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Tsuboi T, Yamazaki R, Nobuta R, Ikeuchi K, Makino S, Ohtaki A, Suzuki Y, Yoshihisa T, Trotta C, Inada T. The tRNA Splicing Endonuclease Complex Cleaves the Mitochondria-localized CBP1 mRNA. J Biol Chem 2015; 290:16021-30. [PMID: 25971974 DOI: 10.1074/jbc.m114.634592] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Indexed: 12/14/2022] Open
Abstract
The tRNA splicing endonuclease (Sen) complex is located on the mitochondrial outer membrane and splices precursor tRNAs in Saccharomyces cerevisiae. Here, we demonstrate that the Sen complex cleaves the mitochondria-localized mRNA encoding Cbp1 (cytochrome b mRNA processing 1). Endonucleolytic cleavage of this mRNA required two cis-elements: the mitochondrial targeting signal and the stem-loop 652-726-nt region. Mitochondrial localization of the Sen complex was required for cleavage of the CBP1 mRNA, and the Sen complex cleaved this mRNA directly in vitro. We propose that the Sen complex cleaves the CBP1 mRNA, which is co-translationally localized to mitochondria via its mitochondrial targeting signal.
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Affiliation(s)
- Tatsuhisa Tsuboi
- From the Graduate School of Pharmaceutical Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
| | - Reina Yamazaki
- From the Graduate School of Pharmaceutical Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
| | - Risa Nobuta
- From the Graduate School of Pharmaceutical Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
| | - Ken Ikeuchi
- From the Graduate School of Pharmaceutical Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
| | - Shiho Makino
- From the Graduate School of Pharmaceutical Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
| | - Ayumi Ohtaki
- From the Graduate School of Pharmaceutical Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
| | - Yutaka Suzuki
- the Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Tohru Yoshihisa
- the Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan, and
| | | | - Toshifumi Inada
- From the Graduate School of Pharmaceutical Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan,
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43
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Makino S, Mishima Y, Inoue K, Inada T. Roles of mRNA fate modulators Dhh1 and Pat1 in TNRC6-dependent gene silencing recapitulated in yeast. J Biol Chem 2015; 290:8331-47. [PMID: 25657010 DOI: 10.1074/jbc.m114.615088] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The CCR4-NOT complex, the major deadenylase in eukaryotes, plays crucial roles in gene expression at the levels of transcription, mRNA decay, and protein degradation. GW182/TNRC6 proteins, which are core components of the microRNA-induced silencing complex in animals, stimulate deadenylation and repress translation via recruitment of the CCR4-NOT complex. Here we report a heterologous experimental system that recapitulates the recruitment of CCR4-NOT complex by TNRC6 in S. cerevisiae. Using this system, we characterize conserved functions of the CCR4-NOT complex. The complex stimulates degradation of mRNA from the 5' end by Xrn1, in a manner independent of both translation and deadenylation. This degradation pathway is probably conserved in miRNA-mediated gene silencing in zebrafish. Furthermore, the mRNA fate modulators Dhh1 and Pat1 redundantly stimulate mRNA decay, but both factors are required for poly(A) tail-independent translation repression by tethered TNRC6A. Our tethering-based reconstitution system reveals that the conserved architecture of Not1/CNOT1 provides a binding surface for TNRC6, thereby connecting microRNA-induced silencing complex to the decapping machinery as well as the translation apparatus.
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Affiliation(s)
- Shiho Makino
- From the Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan
| | - Yuichiro Mishima
- the Institute of Molecular and Cellular Biosciences and the Department of Medical Genome Sciences, University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan, and
| | - Kunio Inoue
- the Graduate School of Science, Kobe University, Kobe 657-8501, Japan
| | - Toshifumi Inada
- From the Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan,
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44
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Kashima I, Takahashi M, Hashimoto Y, Sakota E, Nakamura Y, Inada T. A functional involvement of ABCE1, eukaryotic ribosome recycling factor, in nonstop mRNA decay in Drosophila melanogaster cells. Biochimie 2014; 106:10-6. [DOI: 10.1016/j.biochi.2014.08.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 08/02/2014] [Indexed: 11/25/2022]
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45
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Release factor eRF3 mediates premature translation termination on polylysine-stalled ribosomes in Saccharomyces cerevisiae. Mol Cell Biol 2014; 34:4062-76. [PMID: 25154418 DOI: 10.1128/mcb.00799-14] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ribosome stalling is an important incident enabling the cellular quality control machinery to detect aberrant mRNA. Saccharomyces cerevisiae Hbs1-Dom34 and Ski7 are homologs of the canonical release factor eRF3-eRF1, which recognize stalled ribosomes, promote ribosome release, and induce the decay of aberrant mRNA. Polyadenylated nonstop mRNA encodes aberrant proteins containing C-terminal polylysine segments which cause ribosome stalling due to electrostatic interaction with the ribosomal exit tunnel. Here we describe a novel mechanism, termed premature translation termination, which releases C-terminally truncated translation products from ribosomes stalled on polylysine segments. Premature termination during polylysine synthesis was abolished when ribosome stalling was prevented due to the absence of the ribosomal protein Asc1. In contrast, premature termination was enhanced, when the general rate of translation elongation was lowered. The unconventional termination event was independent of Hbs1-Dom34 and Ski7, but it was dependent on eRF3. Moreover, premature termination during polylysine synthesis was strongly increased in the absence of the ribosome-bound chaperones ribosome-associated complex (RAC) and Ssb (Ssb1 and Ssb2). On the basis of the data, we suggest a model in which eRF3-eRF1 can catalyze the release of nascent polypeptides even though the ribosomal A-site contains a sense codon when the rate of translation is abnormally low.
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46
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Gandin V, Senft D, Topisirovic I, Ronai ZA. RACK1 Function in Cell Motility and Protein Synthesis. Genes Cancer 2014; 4:369-77. [PMID: 24349634 DOI: 10.1177/1947601913486348] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The receptor for activated C kinase 1 (RACK1) serves as an adaptor for a number of proteins along the MAPK, protein kinase C, and Src signaling pathways. The abundance and near ubiquitous expression of RACK1 reflect its role in coordinating signaling molecules for many critical biological processes, from mRNA translation to cell motility to cell survival and death. Complete deficiency of Rack1 is embryonic lethal, but the recent development of genetic Rack1 hypomorphic mice has highlighted the central role that RACK1 plays in cell movement and protein synthesis. This review focuses on the importance of RACK1 in these processes and places the recent work in the larger context of understanding RACK1 function.
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Affiliation(s)
- Valentina Gandin
- Lady Davis Institute for Medical Research, Sir Mortimer B. Davis Jewish General Hospital, Montréal, QC, Canada ; Department of Oncology, McGill University, Montréal, QC, Canada
| | - Daniela Senft
- Signal Transduction Program, Cancer Center, Sanford-Burnham Medical Research Institute, La Jolla, CA, USA
| | - Ivan Topisirovic
- Lady Davis Institute for Medical Research, Sir Mortimer B. Davis Jewish General Hospital, Montréal, QC, Canada ; Department of Oncology, McGill University, Montréal, QC, Canada
| | - Ze'ev A Ronai
- Signal Transduction Program, Cancer Center, Sanford-Burnham Medical Research Institute, La Jolla, CA, USA
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47
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Adjibade P, Mazroui R. Control of mRNA turnover: implication of cytoplasmic RNA granules. Semin Cell Dev Biol 2014; 34:15-23. [PMID: 24946962 DOI: 10.1016/j.semcdb.2014.05.013] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 05/21/2014] [Indexed: 12/15/2022]
Abstract
The control of mRNA turnover is essential for the cell to rationalize its mRNA content both under physiological conditions and upon stress. Several mechanisms involved in the control of mRNA turnover have been elucidated. These include surveillance mechanisms such as nonsense-mediated decay, non-stop mediated decay and non-go-mediated decay that eliminate aberrant mRNAs, and regulatory mechanisms including AU-mediated decay, GU-mediated decay, and CDE-mediated decay that ensure mRNA plasticity. In general, the mechanisms of RNA decay rely on interactions between specific cis-acting RNA elements and selected RNA-binding proteins that either prevent the degradation of mRNA targets or induce the recruitment of decaying effectors leading to mRNA degradation. Formation of cytoplasmic RNA granules including processing bodies, stress granules, UV granules, and exosome granules have recently emerged as an additional mechanism that control mRNA turnover of selected mRNAs. Here we will review briefly review the main mechanisms that control mRNA decay and highlight possible implication of RNA granules in such mechanisms.
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Affiliation(s)
- Pauline Adjibade
- Centre de recherche du CHU de Québec, Département de biologie moléculaire, biochimie médicale et pathologie, Université Laval, Québec, PQ, Canada
| | - Rachid Mazroui
- Centre de recherche du CHU de Québec, Département de biologie moléculaire, biochimie médicale et pathologie, Université Laval, Québec, PQ, Canada.
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48
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Nguyen TTM, Kitajima S, Izawa S. Importance of glucose-6-phosphate dehydrogenase (G6PDH) for vanillin tolerance in Saccharomyces cerevisiae. J Biosci Bioeng 2014; 118:263-9. [PMID: 24725964 DOI: 10.1016/j.jbiosc.2014.02.025] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Revised: 02/18/2014] [Accepted: 02/25/2014] [Indexed: 11/29/2022]
Abstract
Vanillin is derived from lignocellulosic biomass and, as one of the major biomass conversion inhibitors, inhibits yeast growth and fermentation. Vanillin was recently shown to induce the mitochondrial fragmentation and formation of mRNP granules such as processing bodies and stress granules in Saccharomyces cerevisiae. Furfural, another major biomass conversion inhibitor, also induces oxidative stress and is reduced in an NAD(P)H-dependent manner to its less toxic alcohol derivative. Therefore, the pentose phosphate pathway (PPP), through which most NADPH is generated, plays a role in tolerance to furfural. Although vanillin also induces oxidative stress and is reduced to vanillyl alcohol in a NADPH-dependent manner, the relationship between vanillin and PPP has not yet been investigated. In the present study, we examined the importance of glucose-6-phosphate dehydrogenase (G6PDH), which catalyzes the rate-limiting NADPH-producing step in PPP, for yeast tolerance to vanillin. The growth of the null mutant of G6PDH gene (zwf1Δ) was delayed in the presence of vanillin, and vanillin was efficiently reduced in the culture of wild-type cells but not in the culture of zwf1Δ cells. Furthermore, zwf1Δ cells easily induced the activation of Yap1, an oxidative stress responsive transcription factor, mitochondrial fragmentation, and P-body formation with the vanillin treatment, which indicated that zwf1Δ cells were more susceptible to vanillin than wild type cells. These findings suggest the importance of G6PDH and PPP in the response of yeast to vanillin.
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Affiliation(s)
- Trinh Thi My Nguyen
- Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Matsugasaki, Kyoto 606-8585, Japan
| | - Sakihito Kitajima
- Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Matsugasaki, Kyoto 606-8585, Japan
| | - Shingo Izawa
- Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Matsugasaki, Kyoto 606-8585, Japan.
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Lykke-Andersen J, Bennett EJ. Protecting the proteome: Eukaryotic cotranslational quality control pathways. ACTA ACUST UNITED AC 2014; 204:467-76. [PMID: 24535822 PMCID: PMC3926952 DOI: 10.1083/jcb.201311103] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The correct decoding of messenger RNAs (mRNAs) into proteins is an essential cellular task. The translational process is monitored by several quality control (QC) mechanisms that recognize defective translation complexes in which ribosomes are stalled on substrate mRNAs. Stalled translation complexes occur when defects in the mRNA template, the translation machinery, or the nascent polypeptide arrest the ribosome during translation elongation or termination. These QC events promote the disassembly of the stalled translation complex and the recycling and/or degradation of the individual mRNA, ribosomal, and/or nascent polypeptide components, thereby clearing the cell of improper translation products and defective components of the translation machinery.
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Affiliation(s)
- Jens Lykke-Andersen
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093
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Tanaka M, Tokuoka M, Gomi K. Effects of codon optimization on the mRNA levels of heterologous genes in filamentous fungi. Appl Microbiol Biotechnol 2014; 98:3859-67. [PMID: 24682479 DOI: 10.1007/s00253-014-5609-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Revised: 02/07/2014] [Accepted: 02/10/2014] [Indexed: 10/25/2022]
Abstract
Filamentous fungi, particularly Aspergillus species, have recently attracted attention as host organisms for recombinant protein production. Because the secretory yields of heterologous proteins are generally low compared with those of homologous proteins or proteins from closely related fungal species, several strategies to produce substantial amounts of recombinant proteins have been conducted. Codon optimization is a powerful tool for improving the production levels of heterologous proteins. Although codon optimization is generally believed to improve the translation efficiency of heterologous genes without affecting their mRNA levels, several studies have indicated that codon optimization causes an increase in the steady-state mRNA levels of heterologous genes in filamentous fungi. However, the mechanism that determines the low mRNA levels when native heterologous genes are expressed was poorly understood. We recently showed that the transcripts of heterologous genes are polyadenylated prematurely within the coding region and that the heterologous gene transcripts can be stabilized significantly by codon optimization, which is probably attributable to the prevention of premature polyadenylation in Aspergillus oryzae. In this review, we describe the detailed mechanism of premature polyadenylation and the rapid degradation of mRNA transcripts derived from heterologous genes in filamentous fungi.
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Affiliation(s)
- Mizuki Tanaka
- Department of Bioindustrial Informatics and Genomics, Laboratory of Bioindustrial Genomics, Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Aoba-ku, Sendai, 981-8555, Japan,
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