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Alagar Boopathy LR, Beadle E, Garcia-Bueno Rico A, Vera M. Proteostasis regulation through ribosome quality control and no-go-decay. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1809. [PMID: 37488089 DOI: 10.1002/wrna.1809] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 06/14/2023] [Accepted: 06/30/2023] [Indexed: 07/26/2023]
Abstract
Cell functionality relies on the existing pool of proteins and their folding into functional conformations. This is achieved through the regulation of protein synthesis, which requires error-free mRNAs and ribosomes. Ribosomes are quality control hubs for mRNAs and proteins. Problems during translation elongation slow down the decoding rate, leading to ribosome halting and the eventual collision with the next ribosome. Collided ribosomes form a specific disome structure recognized and solved by ribosome quality control (RQC) mechanisms. RQC pathways orchestrate the degradation of the problematic mRNA by no-go decay and the truncated nascent peptide, the repression of translation initiation, and the recycling of the stalled ribosomes. All these events maintain protein homeostasis and return valuable ribosomes to translation. As such, cell homeostasis and function are maintained at the mRNA level by preventing the production of aberrant or unnecessary proteins. It is becoming evident that the crosstalk between RQC and the protein homeostasis network is vital for cell function, as the absence of RQC components leads to the activation of stress response and neurodegenerative diseases. Here, we review the molecular events of RQC discovered through well-designed stalling reporters. Given the impact of RQC in proteostasis, we discuss the relevance of identifying endogenous mRNA regulated by RQC and their preservation in stress conditions. This article is categorized under: RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms Translation > Regulation.
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Affiliation(s)
| | - Emma Beadle
- Department of Biochemistry, McGill University, Montreal, Canada
| | | | - Maria Vera
- Department of Biochemistry, McGill University, Montreal, Canada
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2
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Erath J, Djuranovic S. Association of the receptor for activated C-kinase 1 with ribosomes in Plasmodium falciparum. J Biol Chem 2022; 298:101954. [PMID: 35452681 PMCID: PMC9120242 DOI: 10.1016/j.jbc.2022.101954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 03/31/2022] [Accepted: 04/13/2022] [Indexed: 11/18/2022] Open
Abstract
The receptor for activated C-kinase 1 (RACK1), a highly conserved eukaryotic protein, is known to have many varying biological roles and functions. Previous work has established RACK1 as a ribosomal protein, with defined regions important for ribosome binding in eukaryotic cells. In Plasmodium falciparum, RACK1 has been shown to be required for parasite growth, however, conflicting evidence has been presented about RACK1 ribosome binding and its role in mRNA translation. Given the importance of RACK1 as a regulatory component of mRNA translation and ribosome quality control, the case could be made in parasites that RACK1 either binds or does not bind the ribosome. Here, we used bioinformatics and transcription analyses to further characterize the P. falciparum RACK1 protein. Based on homology modeling and structural analyses, we generated a model of P. falciparum RACK1. We then explored mutant and chimeric human and P. falciparum RACK1 protein binding properties to the human and P. falciparum ribosome. We found that WT, chimeric, and mutant RACK1 exhibit distinct ribosome interactions suggesting different binding characteristics for P. falciparum and human RACK1 proteins. The ribosomal binding of RACK1 variants in human and parasite cells shown here demonstrates that although RACK1 proteins have highly conserved sequences and structures across species, ribosomal binding is affected by species-specific alterations to this protein. In conclusion, we show that in the case of P. falciparum, contrary to the structural data, RACK1 is found to bind ribosomes and actively translating polysomes in parasite cells.
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Affiliation(s)
- Jessey Erath
- Department of Cell Biology and Physiology, Washington University School of Medicine, St Louis, Missouri, USA
| | - Sergej Djuranovic
- Department of Cell Biology and Physiology, Washington University School of Medicine, St Louis, Missouri, USA.
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3
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Machour FE, Abu-Zhayia ER, Awwad SW, Bidany-Mizrahi T, Meinke S, Bishara LA, Heyd F, Aqeilan RI, Ayoub N. RBM6 splicing factor promotes homologous recombination repair of double-strand breaks and modulates sensitivity to chemotherapeutic drugs. Nucleic Acids Res 2021; 49:11708-11727. [PMID: 34718714 PMCID: PMC8599755 DOI: 10.1093/nar/gkab976] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 09/26/2021] [Accepted: 10/07/2021] [Indexed: 12/13/2022] Open
Abstract
RNA-binding proteins regulate mRNA processing and translation and are often aberrantly expressed in cancer. The RNA-binding motif protein 6, RBM6, is a known alternative splicing factor that harbors tumor suppressor activity and is frequently mutated in human cancer. Here, we identify RBM6 as a novel regulator of homologous recombination (HR) repair of DNA double-strand breaks (DSBs). Mechanistically, we show that RBM6 regulates alternative splicing-coupled nonstop-decay of a positive HR regulator, Fe65/APBB1. RBM6 knockdown leads to a severe reduction in Fe65 protein levels and consequently impairs HR of DSBs. Accordingly, RBM6-deficient cancer cells are vulnerable to ATM and PARP inhibition and show remarkable sensitivity to cisplatin. Concordantly, cisplatin administration inhibits the growth of breast tumor devoid of RBM6 in mouse xenograft model. Furthermore, we observe that RBM6 protein is significantly lost in metastatic breast tumors compared with primary tumors, thus suggesting RBM6 as a potential therapeutic target of advanced breast cancer. Collectively, our results elucidate the link between the multifaceted roles of RBM6 in regulating alternative splicing and HR of DSBs that may contribute to tumorigenesis, and pave the way for new avenues of therapy for RBM6-deficient tumors.
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Affiliation(s)
- Feras E Machour
- Department of Biology, Technion - Israel Institute of Technology, Haifa 3200003, Israel
| | - Enas R Abu-Zhayia
- Department of Biology, Technion - Israel Institute of Technology, Haifa 3200003, Israel
| | - Samah W Awwad
- Department of Biology, Technion - Israel Institute of Technology, Haifa 3200003, Israel
| | - Tirza Bidany-Mizrahi
- The Concern Foundation Laboratories, The Lautenberg Center for Immunology and Cancer Research, Department of Immunology and Cancer Research-IMRIC, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Stefan Meinke
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of RNA Biochemistry, Takustrasse 6, 14195 Berlin, Germany
| | - Laila A Bishara
- Department of Biology, Technion - Israel Institute of Technology, Haifa 3200003, Israel
| | - Florian Heyd
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of RNA Biochemistry, Takustrasse 6, 14195 Berlin, Germany
| | - Rami I Aqeilan
- The Concern Foundation Laboratories, The Lautenberg Center for Immunology and Cancer Research, Department of Immunology and Cancer Research-IMRIC, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Nabieh Ayoub
- Department of Biology, Technion - Israel Institute of Technology, Haifa 3200003, Israel
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4
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Howard CJ, Frost A. Ribosome-associated quality control and CAT tailing. Crit Rev Biochem Mol Biol 2021; 56:603-620. [PMID: 34233554 DOI: 10.1080/10409238.2021.1938507] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Translation is the set of mechanisms by which ribosomes decode genetic messages as they synthesize polypeptides of a defined amino acid sequence. While the ribosome has been honed by evolution for high-fidelity translation, errors are inevitable. Aberrant mRNAs, mRNA structure, defective ribosomes, interactions between nascent proteins and the ribosomal exit tunnel, and insufficient cellular resources, including low tRNA levels, can lead to functionally irreversible stalls. Life thus depends on quality control mechanisms that detect, disassemble and recycle stalled translation intermediates. Ribosome-associated Quality Control (RQC) recognizes aberrant ribosome states and targets their potentially toxic polypeptides for degradation. Here we review recent advances in our understanding of RQC in bacteria, fungi, and metazoans. We focus in particular on an unusual modification made to the nascent chain known as a "CAT tail", or Carboxy-terminal Alanine and Threonine tail, and the mechanisms by which ancient RQC proteins catalyze CAT-tail synthesis.
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Affiliation(s)
- Conor J Howard
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | - Adam Frost
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
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5
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Terrey M, Adamson SI, Chuang JH, Ackerman SL. Defects in translation-dependent quality control pathways lead to convergent molecular and neurodevelopmental pathology. eLife 2021; 10:e66904. [PMID: 33899734 PMCID: PMC8075583 DOI: 10.7554/elife.66904] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 04/05/2021] [Indexed: 12/27/2022] Open
Abstract
Translation-dependent quality control pathways such as no-go decay (NGD), non-stop decay (NSD), and nonsense-mediated decay (NMD) govern protein synthesis and proteostasis by resolving non-translating ribosomes and preventing the production of potentially toxic peptides derived from faulty and aberrant mRNAs. However, how translation is altered and the in vivo defects that arise in the absence of these pathways are poorly understood. Here, we show that the NGD/NSD factors Pelo and Hbs1l are critical in mice for cerebellar neurogenesis but expendable for survival of these neurons after development. Analysis of mutant mouse embryonic fibroblasts revealed translational pauses, alteration of signaling pathways, and translational reprogramming. Similar effects on signaling pathways, including mTOR activation, the translatome and mouse cerebellar development were observed upon deletion of the NMD factor Upf2. Our data reveal that these quality control pathways that function to mitigate errors at distinct steps in translation can evoke similar cellular responses.
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Affiliation(s)
- Markus Terrey
- Howard Hughes Medical Institute, Department of Cellular and Molecular Medicine, Section of Neurobiology, Division of Biological Sciences, University of California San DiegoLa JollaUnited States
- Graduate School of Biomedical Sciences and Engineering, University of MaineOronoUnited States
| | - Scott I Adamson
- The Jackson Laboratory for Genomic MedicineFarmingtonUnited States
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn HealthFarmingtonUnited States
| | - Jeffrey H Chuang
- The Jackson Laboratory for Genomic MedicineFarmingtonUnited States
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn HealthFarmingtonUnited States
| | - Susan L Ackerman
- Howard Hughes Medical Institute, Department of Cellular and Molecular Medicine, Section of Neurobiology, Division of Biological Sciences, University of California San DiegoLa JollaUnited States
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6
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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: 58] [Impact Index Per Article: 14.5] [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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7
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Li XZ, Huang HJ, Zhang SN, Liu Q, Wang YM. Label-free quantitative proteomics positions the effects and mechanisms of Herba Lysimachiae on synovial diseases based on biolabel-led research pattern. J Chromatogr B Analyt Technol Biomed Life Sci 2020; 1138:121969. [DOI: 10.1016/j.jchromb.2020.121969] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 12/31/2019] [Accepted: 01/04/2020] [Indexed: 12/25/2022]
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8
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Pule MN, Glover ML, Fire AZ, Arribere JA. Ribosome clearance during RNA interference. RNA (NEW YORK, N.Y.) 2019; 25:963-974. [PMID: 31110136 PMCID: PMC6633202 DOI: 10.1261/rna.070813.119] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 05/08/2019] [Indexed: 06/09/2023]
Abstract
In the course of identifying and cleaving RNA, the RNAi machinery must encounter and contend with the megadalton-sized ribosomes that carry out translation. We investigated this interface by examining the fate of actively translated mRNAs subjected to RNAi in C. elegans Quantifying RNA levels (RNA-seq) and ongoing translation (Ribo-seq), we found there is a greater fold repression of ongoing translation than expected from loss of RNA alone, observing stronger translation repression relative to RNA repression for multiple, independent double-stranded RNA triggers, and for multiple genes. In animals that lack the RNA helicase SKI complex and the ribosome rescue factor PELOTA, ribosomes stall on the 3' edges of mRNAs at and upstream of the RNAi trigger. One model to explain these observations is that ribosomes are actively cleared from mRNAs by SKI and PELO during or following mRNA cleavage. Our results expand prior studies that show a role for the SKI RNA helicase complex in removing RNA targets following RNAi in flies and plants, illuminating the widespread role of the nonstop translation surveillance in RNA silencing during RNAi. Our results are also consistent with proposals that RNAi can attack messages during active translation.
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Affiliation(s)
- Makena N Pule
- Department of MCD Biology, UC Santa Cruz, Santa Cruz, California 95064, USA
| | - Marissa L Glover
- Department of MCD Biology, UC Santa Cruz, Santa Cruz, California 95064, USA
| | - Andrew Z Fire
- Departments of Pathology and Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Joshua A Arribere
- Department of MCD Biology, UC Santa Cruz, Santa Cruz, California 95064, USA
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9
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Li Z, Yang F, Xuan Y, Xi R, Zhao R. Pelota-interacting G protein Hbs1 is required for spermatogenesis in Drosophila. Sci Rep 2019; 9:3226. [PMID: 30824860 PMCID: PMC6397311 DOI: 10.1038/s41598-019-39530-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 01/08/2019] [Indexed: 12/31/2022] Open
Abstract
Hbs1, which is homologous to the GTPase eRF3, is a small G protein implicated in mRNA quality control. It interacts with a translation-release factor 1-like protein Dom34/Pelota to direct decay of mRNAs with ribosomal stalls. Although both proteins are evolutionarily conserved in eukaryotes, the biological function of Hbs1 in multicellular organisms is yet to be characterized. In Drosophila, pelota is essential for the progression through meiosis during spermatogenesis and germline stem cell maintenance. Here we show that homozygous Hbs1 mutant flies are viable, female-fertile, but male-sterile, which is due to defects in meiosis and spermatid individualization, phenotypes that are also observed in pelota hypomorphic mutants. In contrast, Hbs1 mutants have no obvious defects in germline stem cell maintenance. We show that Hbs1 genetically interacts with pelota during spermatid individualization. Furthermore, Pelota with a point mutation on the putative Hbs1-binding site cannot substitute the wild type protein for normal spermatogenesis. These data suggest that Pelota forms a complex with Hbs1 to regulate multiple processes during spermatogenesis. Our results reveal a specific requirement of Hbs1 in male gametogenesis in Drosophila and indicate an essential role for the RNA surveillance complex Pelota-Hbs1 in spermatogenesis, a function that could be conserved in mammals.
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Affiliation(s)
- Zhaohui Li
- School of Life Sciences, Tsinghua University, Beijing, 100084, China.,National Institute of Biological Sciences, No. 7 Science Park Road, Zhongguancun Life Science Park, Beijing, 102206, China
| | - Fu Yang
- National Institute of Biological Sciences, No. 7 Science Park Road, Zhongguancun Life Science Park, Beijing, 102206, China
| | - Yang Xuan
- National Institute of Biological Sciences, No. 7 Science Park Road, Zhongguancun Life Science Park, Beijing, 102206, China
| | - Rongwen Xi
- National Institute of Biological Sciences, No. 7 Science Park Road, Zhongguancun Life Science Park, Beijing, 102206, China. .,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China.
| | - Rui Zhao
- National Institute of Biological Sciences, No. 7 Science Park Road, Zhongguancun Life Science Park, Beijing, 102206, China. .,Genomics Institute of the Novartis Research Foundation, San Diego, California, 92121, USA.
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10
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O’Connell AE, Gerashchenko MV, O’Donohue MF, Rosen SM, Huntzinger E, Gleeson D, Galli A, Ryder E, Cao S, Murphy Q, Kazerounian S, Morton SU, Schmitz-Abe K, Gladyshev VN, Gleizes PE, Séraphin B, Agrawal PB. Mammalian Hbs1L deficiency causes congenital anomalies and developmental delay associated with Pelota depletion and 80S monosome accumulation. PLoS Genet 2019; 15:e1007917. [PMID: 30707697 PMCID: PMC6373978 DOI: 10.1371/journal.pgen.1007917] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 02/13/2019] [Accepted: 12/25/2018] [Indexed: 12/18/2022] Open
Abstract
Hbs1 has been established as a central component of the cell's translational quality control pathways in both yeast and prokaryotic models; however, the functional characteristics of its human ortholog (Hbs1L) have not been well-defined. We recently reported a novel human phenotype resulting from a mutation in the critical coding region of the HBS1L gene characterized by facial dysmorphism, severe growth restriction, axial hypotonia, global developmental delay and retinal pigmentary deposits. Here we further characterize downstream effects of the human HBS1L mutation. HBS1L has three transcripts in humans, and RT-PCR demonstrated reduced mRNA levels corresponding with transcripts V1 and V2 whereas V3 expression was unchanged. Western blot analyses revealed Hbs1L protein was absent in the patient cells. Additionally, polysome profiling revealed an abnormal aggregation of 80S monosomes in patient cells under baseline conditions. RNA and ribosomal sequencing demonstrated an increased translation efficiency of ribosomal RNA in Hbs1L-deficient fibroblasts, suggesting that there may be a compensatory increase in ribosome translation to accommodate the increased 80S monosome levels. This enhanced translation was accompanied by upregulation of mTOR and 4-EBP protein expression, suggesting an mTOR-dependent phenomenon. Furthermore, lack of Hbs1L caused depletion of Pelota protein in both patient cells and mouse tissues, while PELO mRNA levels were unaffected. Inhibition of proteasomal function partially restored Pelota expression in human Hbs1L-deficient cells. We also describe a mouse model harboring a knockdown mutation in the murine Hbs1l gene that shared several of the phenotypic elements observed in the Hbs1L-deficient human including facial dysmorphism, growth restriction and retinal deposits. The Hbs1lKO mice similarly demonstrate diminished Pelota levels that were rescued by proteasome inhibition.
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Affiliation(s)
- Amy E. O’Connell
- Division of Newborn Medicine, Boston Children’s Hospital, Boston, Massachusetts, United States of America
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Maxim V. Gerashchenko
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Marie-Francoise O’Donohue
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Samantha M. Rosen
- Division of Newborn Medicine, Boston Children’s Hospital, Boston, Massachusetts, United States of America
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, Massachusetts, United States of America
- The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, Massachusetts, United States of America
| | - Eric Huntzinger
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Université de Strasbourg, Centre National de La Recherche Scientifique UMR 7104, INSERM U964, Strasbourg, France
| | - Diane Gleeson
- Wellcome Sanger Institute, Cambridge, United Kingdom
| | | | - Edward Ryder
- Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Siqi Cao
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, Massachusetts, United States of America
- The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, Massachusetts, United States of America
| | - Quinn Murphy
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, Massachusetts, United States of America
- The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, Massachusetts, United States of America
| | - Shideh Kazerounian
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, Massachusetts, United States of America
- The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, Massachusetts, United States of America
| | - Sarah U. Morton
- Division of Newborn Medicine, Boston Children’s Hospital, Boston, Massachusetts, United States of America
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Klaus Schmitz-Abe
- Division of Newborn Medicine, Boston Children’s Hospital, Boston, Massachusetts, United States of America
- The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Vadim N. Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Pierre-Emmanuel Gleizes
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Bertrand Séraphin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Université de Strasbourg, Centre National de La Recherche Scientifique UMR 7104, INSERM U964, Strasbourg, France
| | - Pankaj B. Agrawal
- Division of Newborn Medicine, Boston Children’s Hospital, Boston, Massachusetts, United States of America
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, Massachusetts, United States of America
- The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
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11
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Ding W, Wu J, Ye J, Zheng W, Wang S, Zhu X, Zhou J, Pan Z, Zhang B, Zhu S. A Pelota-like gene regulates root development and defence responses in rice. ANNALS OF BOTANY 2018; 122:359-371. [PMID: 29771278 PMCID: PMC6110353 DOI: 10.1093/aob/mcy075] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 04/19/2018] [Indexed: 05/17/2023]
Abstract
BACKGROUND AND AIMS Pelota (Pelo) are evolutionarily conserved genes reported to be involved in ribosome rescue, cell cycle control and meiotic cell division. However, there is little known about their function in plants. The aim of this study was to elucidate the function of an ethylmethane sulphonate (EMS)-derived mutation of a Pelo-like gene in rice (named Ospelo). METHODS A dysfunctional mutant was used to characterize the function of OsPelo. Analyses of its expression and sub-cellular localization were performed. The whole-genome transcriptomic change in leaves of Ospelo was also investigated by RNA sequencing. KEY RESULTS The Ospelo mutant showed defects in root system development and spotted leaves at early seedling stages. Map-based cloning revealed that the mutation occurred in the putative Pelo gene. OsPelo was found to be expressed in various tissues throughout the plant, and the protein was located in mitochondria. Defence responses were induced in the Ospelo mutant, as shown by enhanced resistance to the bacterial pathogen Xanthomonas oryzae pv. oryzae, coupled with upregulation of three pathogenesis-related marker genes. In addition, whole-genome transcriptome analysis showed that OsPelo was significantly associated with a number of biological processes, including translation, metabolism and biotic stress response. Detailed analysis showed that activation of a number of innate immunity-related genes might be responsible for the enhanced disease resistance in the Ospelo mutant. CONCLUSIONS These results demonstrate that OsPelo positively regulates root development while its loss of function enhances pathogen resistance by pre-activation of defence responses in rice.
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Affiliation(s)
- Wona Ding
- College of Science & Technology, Ningbo University, Ningbo, PR China
| | - Jing Wu
- School of Marine Sciences, Ningbo University, Ningbo, PR China
| | - Jin Ye
- School of Marine Sciences, Ningbo University, Ningbo, PR China
| | - Wenjuan Zheng
- College of Science & Technology, Ningbo University, Ningbo, PR China
| | - Shanshan Wang
- School of Marine Sciences, Ningbo University, Ningbo, PR China
| | - Xinni Zhu
- School of Marine Sciences, Ningbo University, Ningbo, PR China
| | - Jiaqin Zhou
- College of Science & Technology, Ningbo University, Ningbo, PR China
| | - Zhichong Pan
- College of Science & Technology, Ningbo University, Ningbo, PR China
| | - Botao Zhang
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo, PR China
- For correspondence. E-mail or
| | - Shihua Zhu
- College of Science & Technology, Ningbo University, Ningbo, PR China
- For correspondence. E-mail or
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12
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Zhang XB, Feng BH, Wang HM, Xu X, Shi YF, He Y, Chen Z, Sathe AP, Shi L, Wu JL. A substitution mutation in OsPELOTA confers bacterial blight resistance by activating the salicylic acid pathway. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2018; 60:160-172. [PMID: 29193778 DOI: 10.1111/jipb.12613] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2017] [Accepted: 11/24/2017] [Indexed: 05/19/2023]
Abstract
We previously reported a spotted-leaf mutant pelota (originally termed HM47) in rice displaying arrested growth and enhanced resistance to multiple races of Xanthomonas oryzae pv. oryzae. Here, we report the map-based cloning of the causal gene OsPELOTA (originally termed splHM47 ). We identified a single base substitution from T to A at position 556 in the coding sequence of OsPELOTA, effectively mutating phenylalanine to isoleucine at position 186 in the translated protein sequence. Both functional complementation and over-expression could rescue the spotted-leaf phenotype. OsPELOTA, a paralogue to eukaryotic release factor 1 (eRF1), shows high sequence similarity to Drosophila Pelota and also localizes to the endoplasmic reticulum and plasma membrane. OsPELOTA is constitutively expressed in roots, leaves, sheaths, stems, and panicles. Elevated levels of salicylic acid and decreased level of jasmonate were detected in the pelota mutant. RNA-seq analysis confirmed that genes responding to salicylic acid were upregulated in the mutant. Our results indicate that the rice PELOTA protein is involved in bacterial leaf blight resistance by activating the salicylic acid metabolic pathway.
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Affiliation(s)
- Xiao-Bo Zhang
- State Key Laboratory of Rice Biology/Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Bao-Hua Feng
- State Key Laboratory of Rice Biology/Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Hui-Mei Wang
- State Key Laboratory of Rice Biology/Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Xia Xu
- State Key Laboratory of Rice Biology/Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Yong-Feng Shi
- State Key Laboratory of Rice Biology/Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Yan He
- State Key Laboratory of Rice Biology/Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Zheng Chen
- State Key Laboratory of Rice Biology/Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Atul Prakash Sathe
- State Key Laboratory of Rice Biology/Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Lei Shi
- State Key Laboratory of Rice Biology/Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Jian-Li Wu
- State Key Laboratory of Rice Biology/Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
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13
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Sitron CS, Park JH, Brandman O. Asc1, Hel2, and Slh1 couple translation arrest to nascent chain degradation. RNA (NEW YORK, N.Y.) 2017; 23:798-810. [PMID: 28223409 PMCID: PMC5393187 DOI: 10.1261/rna.060897.117] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 02/17/2017] [Indexed: 05/17/2023]
Abstract
Premature arrest of protein synthesis within the open reading frame elicits a protective response that degrades the incomplete nascent chain. In this response, arrested 80S ribosomes are split into their large and small subunits, allowing assembly of the ribosome quality control complex (RQC), which targets nascent chains for degradation. How the cell recognizes arrested nascent chains among the vast pool of actively translating polypeptides is poorly understood. We systematically examined translation arrest and modification of nascent chains in Saccharomyces cerevisiae to characterize the steps that couple arrest to RQC targeting. We focused our analysis on two poorly understood 80S ribosome-binding proteins previously implicated in the response to failed translation, Asc1 and Hel2, as well as a new component of the pathway, Slh1, that we identified here. We found that premature arrest at ribosome stalling sequences still occurred robustly in the absence of Asc1, Hel2, and Slh1. However, these three factors were required for the RQC to modify the nascent chain. We propose that Asc1, Hel2, and Slh1 target arresting ribosomes and that this targeting event is a precondition for the RQC to engage the incomplete nascent chain and facilitate its degradation.
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Affiliation(s)
- Cole S Sitron
- Department of Biochemistry, Stanford University, Stanford, California 94305, USA
| | - Joseph H Park
- Department of Biochemistry, Stanford University, Stanford, California 94305, USA
| | - Onn Brandman
- Department of Biochemistry, Stanford University, Stanford, California 94305, USA
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14
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Sun J, Hao Z, Luo H, He C, Mei L, Liu Y, Wang X, Niu Z, Chen H, Li JD, Feng Y. Functional analysis of a nonstop mutation in MITF gene identified in a patient with Waardenburg syndrome type 2. J Hum Genet 2017; 62:703-709. [PMID: 28356565 PMCID: PMC5489919 DOI: 10.1038/jhg.2017.30] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 01/30/2017] [Accepted: 02/07/2017] [Indexed: 11/09/2022]
Abstract
Waardenburg syndrome (WS) is an autosomal dominant inherited neurogenic disorder with the combination of various degrees of sensorineural deafness and pigmentary abnormalities affecting the skin, hair and eye. The four subtypes of WS were defined on the basis of the presence or absence of additional symptoms. Mutation of human microphthalmia-associated transcription factor (MITF) gene gives rise to WS2. Here, we identified a novel WS-associated mutation at the stop codon of MITF (p.X420Y) in a Chinese WS2 patient. This mutation resulted in an extension of extra 33 amino-acid residues in MITF. The mutant MITF appeared in both the nucleus and the cytoplasm, whereas the wild-type MITF was localized in the nucleus exclusively. The mutation led to a reduction in the transcriptional activities, whereas the DNA-binding activity was not altered. We show that the foremost mechanism was haploinsufficiency for the mild phenotypes of WS2 induced in X420Y MITF.
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Affiliation(s)
- Jie Sun
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Hunan, People's Republic of China.,Department of Otolaryngology, First Affiliated Hospital, Xinjiang Medical University, Xinjiang, People's Republic of China.,Province Key Laboratory of Otolaryngology Critical Disease, Xiangya Hospital, Central south University, Hunan, People's Republic of China
| | - Ziqi Hao
- Department of Center Laboratory, Taiyuan Central Hospital, Shanxi, People's Republic of China
| | - Hunjin Luo
- State Key Laboratory of Medical Genetics, Central South University, Hunan, People's Republic of China
| | - Chufeng He
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Hunan, People's Republic of China.,Province Key Laboratory of Otolaryngology Critical Disease, Xiangya Hospital, Central south University, Hunan, People's Republic of China
| | - Lingyun Mei
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Hunan, People's Republic of China.,Province Key Laboratory of Otolaryngology Critical Disease, Xiangya Hospital, Central south University, Hunan, People's Republic of China
| | - Yalan Liu
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Hunan, People's Republic of China.,Province Key Laboratory of Otolaryngology Critical Disease, Xiangya Hospital, Central south University, Hunan, People's Republic of China
| | - Xueping Wang
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Hunan, People's Republic of China.,The First Affiliated Hospital of Zhengzhou University, Zhengzhou, People's Republic of China
| | - Zhijie Niu
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Hunan, People's Republic of China
| | - Hongsheng Chen
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Hunan, People's Republic of China
| | - Jia-Da Li
- State Key Laboratory of Medical Genetics, Central South University, Hunan, People's Republic of China
| | - Yong Feng
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Hunan, People's Republic of China.,Province Key Laboratory of Otolaryngology Critical Disease, Xiangya Hospital, Central south University, Hunan, People's Republic of China.,Department of Center Laboratory, Taiyuan Central Hospital, Shanxi, People's Republic of China.,State Key Laboratory of Medical Genetics, Central South University, Hunan, People's Republic of China
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