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Meisel JD, Wiesenthal PP, Mootha VK, Ruvkun G. CMTR-1 RNA methyltransferase mutations activate widespread expression of a dopaminergic neuron-specific mitochondrial complex I gene. Curr Biol 2024; 34:2728-2738.e6. [PMID: 38810637 PMCID: PMC11265314 DOI: 10.1016/j.cub.2024.04.079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 03/05/2024] [Accepted: 04/30/2024] [Indexed: 05/31/2024]
Abstract
The mitochondrial proteome is comprised of approximately 1,100 proteins,1 all but 12 of which are encoded by the nuclear genome in C. elegans. The expression of nuclear-encoded mitochondrial proteins varies widely across cell lineages and metabolic states,2,3,4 but the factors that specify these programs are not known. Here, we identify mutations in two nuclear-localized mRNA processing proteins, CMTR1/CMTR-1 and SRRT/ARS2/SRRT-1, which we show act via the same mechanism to rescue the mitochondrial complex I mutant NDUFS2/gas-1(fc21). CMTR-1 is an FtsJ-family RNA methyltransferase that, in mammals, 2'-O-methylates the first nucleotide 3' to the mRNA CAP to promote RNA stability and translation5,6,7,8. The mutations isolated in cmtr-1 are dominant and lie exclusively in the regulatory G-patch domain. SRRT-1 is an RNA binding partner of the nuclear cap-binding complex and determines mRNA transcript fate.9 We show that cmtr-1 and srrt-1 mutations activate embryonic expression of NDUFS2/nduf-2.2, a paralog of NDUFS2/gas-1 normally expressed only in dopaminergic neurons, and that nduf-2.2 is necessary for the complex I rescue by the cmtr-1 G-patch mutant. Additionally, we find that loss of the cmtr-1 G-patch domain cause ectopic localization of CMTR-1 protein to processing bodies (P bodies), phase-separated organelles involved in mRNA storage and decay.10 P-body localization of the G-patch mutant CMTR-1 contributes to the rescue of the hyperoxia sensitivity of the NDUFS2/gas-1 mutant. This study suggests that mRNA methylation at P bodies may control nduf-2.2 gene expression, with broader implications for how the mitochondrial proteome is translationally remodeled in the face of tissue-specific metabolic requirements and stress.
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Affiliation(s)
- Joshua D Meisel
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Presli P Wiesenthal
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Vamsi K Mootha
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA.
| | - Gary Ruvkun
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA.
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2
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Warnhoff K, Bhattacharya S, Snoozy J, Breen PC, Ruvkun G. Hypoxia-inducible factor induces cysteine dioxygenase and promotes cysteine homeostasis in Caenorhabditis elegans. eLife 2024; 12:RP89173. [PMID: 38349720 PMCID: PMC10942545 DOI: 10.7554/elife.89173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2024] Open
Abstract
Dedicated genetic pathways regulate cysteine homeostasis. For example, high levels of cysteine activate cysteine dioxygenase, a key enzyme in cysteine catabolism in most animal and many fungal species. The mechanism by which cysteine dioxygenase is regulated is largely unknown. In an unbiased genetic screen for mutations that activate cysteine dioxygenase (cdo-1) in the nematode Caenorhabditis elegans, we isolated loss-of-function mutations in rhy-1 and egl-9, which encode proteins that negatively regulate the stability or activity of the oxygen-sensing hypoxia inducible transcription factor (hif-1). EGL-9 and HIF-1 are core members of the conserved eukaryotic hypoxia response. However, we demonstrate that the mechanism of HIF-1-mediated induction of cdo-1 is largely independent of EGL-9 prolyl hydroxylase activity and the von Hippel-Lindau E3 ubiquitin ligase, the classical hypoxia signaling pathway components. We demonstrate that C. elegans cdo-1 is transcriptionally activated by high levels of cysteine and hif-1. hif-1-dependent activation of cdo-1 occurs downstream of an H2S-sensing pathway that includes rhy-1, cysl-1, and egl-9. cdo-1 transcription is primarily activated in the hypodermis where it is also sufficient to drive sulfur amino acid metabolism. Thus, the regulation of cdo-1 by hif-1 reveals a negative feedback loop that maintains cysteine homeostasis. High levels of cysteine stimulate the production of an H2S signal. H2S then acts through the rhy-1/cysl-1/egl-9 signaling pathway to increase HIF-1-mediated transcription of cdo-1, promoting degradation of cysteine via CDO-1.
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Affiliation(s)
- Kurt Warnhoff
- Pediatrics and Rare Diseases Group, Sanford ResearchSioux FallsUnited States
- Department of Pediatrics, Sanford School of Medicine, University of South DakotaSioux FallsUnited States
| | | | - Jennifer Snoozy
- Pediatrics and Rare Diseases Group, Sanford ResearchSioux FallsUnited States
| | - Peter C Breen
- Department of Molecular Biology, Massachusetts General HospitalBostonUnited States
| | - Gary Ruvkun
- Department of Molecular Biology, Massachusetts General HospitalBostonUnited States
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3
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Meisel JD, Miranda M, Skinner OS, Wiesenthal PP, Wellner SM, Jourdain AA, Ruvkun G, Mootha VK. Hypoxia and intra-complex genetic suppressors rescue complex I mutants by a shared mechanism. Cell 2024; 187:659-675.e18. [PMID: 38215760 PMCID: PMC10919891 DOI: 10.1016/j.cell.2023.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 09/09/2023] [Accepted: 12/05/2023] [Indexed: 01/14/2024]
Abstract
The electron transport chain (ETC) of mitochondria, bacteria, and archaea couples electron flow to proton pumping and is adapted to diverse oxygen environments. Remarkably, in mice, neurological disease due to ETC complex I dysfunction is rescued by hypoxia through unknown mechanisms. Here, we show that hypoxia rescue and hyperoxia sensitivity of complex I deficiency are evolutionarily conserved to C. elegans and are specific to mutants that compromise the electron-conducting matrix arm. We show that hypoxia rescue does not involve the hypoxia-inducible factor pathway or attenuation of reactive oxygen species. To discover the mechanism, we use C. elegans genetic screens to identify suppressor mutations in the complex I accessory subunit NDUFA6/nuo-3 that phenocopy hypoxia rescue. We show that NDUFA6/nuo-3(G60D) or hypoxia directly restores complex I forward activity, with downstream rescue of ETC flux and, in some cases, complex I levels. Additional screens identify residues within the ubiquinone binding pocket as being required for the rescue by NDUFA6/nuo-3(G60D) or hypoxia. This reveals oxygen-sensitive coupling between an accessory subunit and the quinone binding pocket of complex I that can restore forward activity in the same manner as hypoxia.
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Affiliation(s)
- Joshua D Meisel
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Maria Miranda
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Owen S Skinner
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Presli P Wiesenthal
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Sandra M Wellner
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Alexis A Jourdain
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Gary Ruvkun
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA.
| | - Vamsi K Mootha
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA.
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4
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Fujii C, Wang D. Novel insights into virus-host interactions using the model organism C. elegans. Adv Virus Res 2023; 115:135-158. [PMID: 37173064 DOI: 10.1016/bs.aivir.2023.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Abstract
Viruses continue to pose a public health threat raising the need for effective management strategies. Currently existing antiviral therapeutics are often specific to only a single viral species, and resistance to the therapeutic can often arise, and therefore new therapeutics are needed. The C. elegans-Orsay virus system offers a powerful platform for studying RNA virus-host interactions that could ultimately lead to novel targets for antiviral therapy. The relative simplicity of C. elegans, the well-established experimental tools, and its extensive evolutionary conservation of genes and pathways with mammals are key features of this model. Orsay virus, a bisegmented positive sense RNA virus, is a natural pathogen of C. elegans. Orsay virus infection can be studied in a multicellular organismal context, overcoming some of the limitations inherent to tissue culture-based systems. Moreover, compared to mice, the rapid generation time of C. elegans enables robust and facile forward genetics. This review aims to summarize studies that have laid the foundation for the C. elegans-Orsay virus experimental system, experimental tools, and key examples of C. elegans host factors that impact Orsay virus infection that have evolutionarily conserved function in mammalian virus infection.
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Affiliation(s)
- Chika Fujii
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO, United States
| | - David Wang
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO, United States.
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Frankino PA, Siddiqi TF, Bolas T, Bar-Ziv R, Gildea HK, Zhang H, Higuchi-Sanabria R, Dillin A. SKN-1 regulates stress resistance downstream of amino catabolism pathways. iScience 2022; 25:104571. [PMID: 35784796 PMCID: PMC9240870 DOI: 10.1016/j.isci.2022.104571] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 05/03/2022] [Accepted: 06/03/2022] [Indexed: 11/04/2022] Open
Abstract
The deleterious potential to generate oxidative stress is a fundamental challenge to metabolism. The oxidative stress response transcription factor, SKN-1/NRF2, can sense and respond to changes in metabolic state, although the mechanism and consequences of this remain unknown. Here, we performed a genetic screen in C. elegans targeting amino acid catabolism and identified multiple metabolic pathways as regulators of SKN-1 activity. We found that knockdown of the conserved amidohydrolase T12A2.1/amdh-1 activates a unique subset of SKN-1 regulated genes. Interestingly, this transcriptional program is independent of canonical P38-MAPK signaling components but requires ELT-3, NHR-49 and MDT-15. This activation of SKN-1 is dependent on upstream histidine catabolism genes HALY-1 and Y51H4A.7/UROC-1 and may occur through accumulation of a catabolite, 4-imidazolone-5-propanoate. Activating SKN-1 results in increased oxidative stress resistance but decreased survival to heat stress. Together, our data suggest that SKN-1 acts downstream of key catabolic pathways to influence physiology and stress resistance.
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Affiliation(s)
- Phillip A. Frankino
- Howard Hughes Medical Institute University of California, Berkeley, CA 94720, USA
- California Institute for Regenerative Medicine, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Talha F. Siddiqi
- Howard Hughes Medical Institute University of California, Berkeley, CA 94720, USA
- California Institute for Regenerative Medicine, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Theodore Bolas
- Howard Hughes Medical Institute University of California, Berkeley, CA 94720, USA
- California Institute for Regenerative Medicine, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Raz Bar-Ziv
- Howard Hughes Medical Institute University of California, Berkeley, CA 94720, USA
- California Institute for Regenerative Medicine, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Holly K. Gildea
- Howard Hughes Medical Institute University of California, Berkeley, CA 94720, USA
- California Institute for Regenerative Medicine, Berkeley, CA 94720, USA
- Helen Wills Neuroscience Institute, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Hanlin Zhang
- Howard Hughes Medical Institute University of California, Berkeley, CA 94720, USA
- California Institute for Regenerative Medicine, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Ryo Higuchi-Sanabria
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Andrew Dillin
- Howard Hughes Medical Institute University of California, Berkeley, CA 94720, USA
- California Institute for Regenerative Medicine, Berkeley, CA 94720, USA
- Helen Wills Neuroscience Institute, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
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6
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Campos TL, Korhonen PK, Hofmann A, Gasser RB, Young ND. Harnessing model organism genomics to underpin the machine learning-based prediction of essential genes in eukaryotes - Biotechnological implications. Biotechnol Adv 2021; 54:107822. [PMID: 34461202 DOI: 10.1016/j.biotechadv.2021.107822] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 08/17/2021] [Accepted: 08/24/2021] [Indexed: 12/17/2022]
Abstract
The availability of high-quality genomes and advances in functional genomics have enabled large-scale studies of essential genes in model eukaryotes, including the 'elegant worm' (Caenorhabditis elegans; Nematoda) and the 'vinegar fly' (Drosophila melanogaster; Arthropoda). However, this is not the case for other, much less-studied organisms, such as socioeconomically important parasites, for which functional genomic platforms usually do not exist. Thus, there is a need to develop innovative techniques or approaches for the prediction, identification and investigation of essential genes. A key approach that could enable the prediction of such genes is machine learning (ML). Here, we undertake an historical review of experimental and computational approaches employed for the characterisation of essential genes in eukaryotes, with a particular focus on model ecdysozoans (C. elegans and D. melanogaster), and discuss the possible applicability of ML-approaches to organisms such as socioeconomically important parasites. We highlight some recent results showing that high-performance ML, combined with feature engineering, allows a reliable prediction of essential genes from extensive, publicly available 'omic data sets, with major potential to prioritise such genes (with statistical confidence) for subsequent functional genomic validation. These findings could 'open the door' to fundamental and applied research areas. Evidence of some commonality in the essential gene-complement between these two organisms indicates that an ML-engineering approach could find broader applicability to ecdysozoans such as parasitic nematodes or arthropods, provided that suitably large and informative data sets become/are available for proper feature engineering, and for the robust training and validation of algorithms. This area warrants detailed exploration to, for example, facilitate the identification and characterisation of essential molecules as novel targets for drugs and vaccines against parasitic diseases. This focus is particularly important, given the substantial impact that such diseases have worldwide, and the current challenges associated with their prevention and control and with drug resistance in parasite populations.
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Affiliation(s)
- Tulio L Campos
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia; Bioinformatics Core Facility, Instituto Aggeu Magalhães, Fundação Oswaldo Cruz (IAM-Fiocruz), Recife, Pernambuco, Brazil
| | - Pasi K Korhonen
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Andreas Hofmann
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Robin B Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Neil D Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia.
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7
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Backes C, Martinez-Martinez D, Cabreiro F. C. elegans: A biosensor for host-microbe interactions. Lab Anim (NY) 2021; 50:127-135. [PMID: 33649581 DOI: 10.1038/s41684-021-00724-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 01/27/2021] [Indexed: 01/31/2023]
Abstract
Microbes are an integral part of life on this planet. Microbes and their hosts influence each other in an endless dance that shapes how the meta-organism interacts with its environment. Although great advances have been made in microbiome research over the past 20 years, the mechanisms by which both hosts and their microbes interact with each other and the environment are still not well understood. The nematode Caenorhabditis elegans has been widely used as a model organism to study a remarkable number of human-like processes. Recent evidence shows that the worm is a powerful tool to investigate in fine detail the complexity that exists in microbe-host interactions. By combining the large array of genetic tools available for both organisms together with deep phenotyping approaches, it has been possible to uncover key effectors in the complex relationship between microbes and their hosts. In this perspective, we survey the literature for insightful discoveries in the microbiome field using the worm as a model. We discuss the latest conceptual and technological advances in the field and highlight the strengths that make C. elegans a valuable biosensor tool for the study of microbe-host interactions.
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Affiliation(s)
- Cassandra Backes
- MRC London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK
| | | | - Filipe Cabreiro
- MRC London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK. .,Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK.
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8
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Giunti S, Andersen N, Rayes D, De Rosa MJ. Drug discovery: Insights from the invertebrate Caenorhabditis elegans. Pharmacol Res Perspect 2021; 9:e00721. [PMID: 33641258 PMCID: PMC7916527 DOI: 10.1002/prp2.721] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 01/06/2021] [Indexed: 12/18/2022] Open
Abstract
Therapeutic drug development is a long, expensive, and complex process that usually takes 12-15 years. In the early phases of drug discovery, in particular, there is a growing need for animal models that ensure the reduction in both cost and time. Caenorhabditis elegans has been traditionally used to address fundamental aspects of key biological processes, such as apoptosis, aging, and gene expression regulation. During the last decade, with the advent of large-scale platforms for screenings, this invertebrate has also emerged as an essential tool in the pharmaceutical research industry to identify novel drugs and drug targets. In this review, we discuss the reasons why C. elegans has been positioned as an outstanding cost-effective option for drug discovery, highlighting both the advantages and drawbacks of this model. Particular attention is paid to the suitability of this nematode in large-scale genetic and pharmacological screenings. High-throughput screenings in C. elegans have indeed contributed to the breakthrough of a wide variety of candidate compounds involved in extensive fields including neurodegeneration, pathogen infections and metabolic disorders. The versatility of this nematode, which enables its instrumentation as a model of human diseases, is another attribute also herein underscored. As illustrative examples, we discuss the utility of C. elegans models of both human neurodegenerative diseases and parasitic nematodes in the drug discovery industry. Summing up, this review aims to demonstrate the impact of C. elegans models on the drug discovery pipeline.
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Affiliation(s)
- Sebastián Giunti
- Instituto de Investigaciones Bioquímicas de Bahía Blanca (INIBIBB) CCT UNS‐CONICETBahía BlancaArgentina
- Dpto de Biología, Bioquímica y FarmaciaUniversidad Nacional del SurBahía BlancaArgentina
| | - Natalia Andersen
- Instituto de Investigaciones Bioquímicas de Bahía Blanca (INIBIBB) CCT UNS‐CONICETBahía BlancaArgentina
- Dpto de Biología, Bioquímica y FarmaciaUniversidad Nacional del SurBahía BlancaArgentina
| | - Diego Rayes
- Instituto de Investigaciones Bioquímicas de Bahía Blanca (INIBIBB) CCT UNS‐CONICETBahía BlancaArgentina
- Dpto de Biología, Bioquímica y FarmaciaUniversidad Nacional del SurBahía BlancaArgentina
| | - María José De Rosa
- Instituto de Investigaciones Bioquímicas de Bahía Blanca (INIBIBB) CCT UNS‐CONICETBahía BlancaArgentina
- Dpto de Biología, Bioquímica y FarmaciaUniversidad Nacional del SurBahía BlancaArgentina
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9
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Guo Y, Tocchini C, Ciosk R. CLK-2/TEL2 is a conserved component of the nonsense-mediated mRNA decay pathway. PLoS One 2021; 16:e0244505. [PMID: 33444416 PMCID: PMC7808604 DOI: 10.1371/journal.pone.0244505] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 12/10/2020] [Indexed: 11/19/2022] Open
Abstract
Nonsense-mediated mRNA decay (NMD) controls eukaryotic mRNA quality, inducing the degradation of faulty transcripts. Key players in the NMD pathway were originally identified, through genetics, in Caenorhabditis elegans as smg (suppressor with morphological effect on genitalia) genes. Using forward genetics and fluorescence-based NMD reporters, we reexamined the genetic landscape underlying NMD. Employing a novel strategy for mapping sterile mutations, Het-Map, we identified clk-2, a conserved gene previously implicated in DNA damage signaling, as a player in the nematode NMD. We find that CLK-2 is expressed predominantly in the germline, highlighting the importance of auxiliary factors in tissue-specific mRNA decay. Importantly, the human counterpart of CLK-2/TEL2, TELO2, has been also implicated in the NMD, suggesting a conserved role of CLK-2/TEL2 proteins in mRNA surveillance. Recently, variants of TELO2 have been linked to an intellectual disability disorder, the You-Hoover-Fong syndrome, which could be related to its function in the NMD.
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Affiliation(s)
- Yanwu Guo
- Department of Biosciences, University of Oslo, Oslo, Norway
| | | | - Rafal Ciosk
- Department of Biosciences, University of Oslo, Oslo, Norway
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
- * E-mail:
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10
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Sharma R, Yeh K. The dual benefit of a dominant mutation in Arabidopsis IRON DEFICIENCY TOLERANT1 for iron biofortification and heavy metal phytoremediation. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:1200-1210. [PMID: 31671241 PMCID: PMC7152604 DOI: 10.1111/pbi.13285] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 10/17/2019] [Accepted: 10/22/2019] [Indexed: 05/12/2023]
Abstract
One of the goals of biofortification is to generate iron-enriched crops to combat growth and developmental defects especially iron (Fe) deficiency anaemia. Fe-fortification of food is challenging because soluble Fe is unstable and insoluble Fe is nonbioavailable. Genetic engineering is an alternative approach for Fe-biofortification, but so far strategies to increase Fe content have only encompassed a few genes with limited success. In this study, we demonstrate that the ethyl methanesulfonate (EMS) mutant, iron deficiency tolerant1 (idt1), can accumulate 4-7 times higher amounts of Fe than the wild type in roots, shoots and seeds, and exhibits the metal tolerance and iron accumulation (Metina) phenotype in Arabidopsis. Fe-regulated protein stability and nuclear localisation of the upstream transcriptional regulator bHLH34 were uncovered. The C to T transition mutation resulting in substitution of alanine to valine at amino acid position 320 of bHLH34 (designated as IDT1A320V ) in a conserved motif among mono- and dicots was found to be responsible for a dominant phenotype that possesses constitutive activation of the Fe regulatory pathway. Overexpression of IDT1A320V in Arabidopsis and tobacco led to the Metina phenotype; a phenotype that has escalated specificity towards optimising Fe homeostasis and may be useful in Fe-biofortification. Knowledge of the high tolerance and accumulation of heavy metals of this mutant can aid the development of tools for phytoremediation of contaminants.
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Affiliation(s)
- Reena Sharma
- Agricultural Biotechnology Research CenterAcademia SinicaTaipeiTaiwan
- Molecular and Biological Agricultural Sciences ProgramTaiwan International Graduate ProgramAcademia Sinica and National Chung Hsing UniversityTaipeiTaiwan
- Graduate Institute of BiotechnologyNational Chung Hsing UniversityTaichungTaiwan
| | - Kuo‐Chen Yeh
- Agricultural Biotechnology Research CenterAcademia SinicaTaipeiTaiwan
- Molecular and Biological Agricultural Sciences ProgramTaiwan International Graduate ProgramAcademia Sinica and National Chung Hsing UniversityTaipeiTaiwan
- Biotechnology CenterNational Chung Hsing UniversityTaichungTaiwan
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Abstract
Gram-negative carbapenem-resistant bacteria are a major threat to global health. The use of genome-wide screening approaches to probe for genes or mutations enabling resistance can lead to identification of molecular markers for diagnostics applications. We describe an approach called Mut-Seq that couples chemical mutagenesis and next-generation sequencing for studying resistance to imipenem in the Gram-negative bacteria Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa. The use of this approach highlighted shared and species-specific responses, and the role in resistance of a number of genes involved in membrane biogenesis, transcription, and signal transduction was functionally validated. Interestingly, some of the genes identified were previously considered promising therapeutic targets. Our genome-wide screen has the potential to be extended outside drug resistance studies and expanded to other organisms. Carbapenem-resistant Gram-negative bacteria are considered a major threat to global health. Imipenem (IMP) is used as a last line of treatment against these pathogens, but its efficacy is diminished by the emergence of resistance. We applied a whole-genome screen in Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa isolates that were submitted to chemical mutagenesis, selected for IMP resistance, and characterized by next-generation sequencing. A comparative analysis of IMP-resistant clones showed that most of the highly mutated genes shared by the three species encoded proteins involved in transcription or signal transduction. Of these, the rpoD gene was one of the most prevalent and an E. coli strain disrupted for rpoD displayed a 4-fold increase in resistance to IMP. E. coli and K. pneumoniae also specifically shared several mutated genes, most involved in membrane/cell envelope biogenesis, and the contribution in IMP susceptibility was experimentally proven for amidases, transferases, and transglycosidases. P. aeruginosa differed from the two Enterobacteriaceae isolates with two different resistance mechanisms, with one involving mutations in the oprD porin or, alternatively, in two-component systems. Our chemogenomic screen performed with the three species has highlighted shared and species-specific responses to IMP. IMPORTANCE Gram-negative carbapenem-resistant bacteria are a major threat to global health. The use of genome-wide screening approaches to probe for genes or mutations enabling resistance can lead to identification of molecular markers for diagnostics applications. We describe an approach called Mut-Seq that couples chemical mutagenesis and next-generation sequencing for studying resistance to imipenem in the Gram-negative bacteria Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa. The use of this approach highlighted shared and species-specific responses, and the role in resistance of a number of genes involved in membrane biogenesis, transcription, and signal transduction was functionally validated. Interestingly, some of the genes identified were previously considered promising therapeutic targets. Our genome-wide screen has the potential to be extended outside drug resistance studies and expanded to other organisms.
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Molybdenum cofactor transfer from bacteria to nematode mediates sulfite detoxification. Nat Chem Biol 2019; 15:480-488. [PMID: 30911177 PMCID: PMC6470025 DOI: 10.1038/s41589-019-0249-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 02/14/2019] [Indexed: 11/26/2022]
Abstract
The kingdoms of life share many small molecule cofactors and coenzymes. Molybdenum cofactor (Moco) is synthesized by many archaea, bacteria, and eukaryotes, and is essential for human viability. The genome of the animal Caenorhabditis elegans contains all of the Moco biosynthesis genes, and surprisingly these genes are not essential if animals are fed a bacterial diet that synthesizes Moco. C. elegans lacking both endogenous Moco synthesis and dietary Moco from bacteria arrest development, demonstrating interkingdom Moco transfer. Our screen of E. coli mutants identified genes necessary for synthesis of bacterial Moco or transfer to C. elegans. Moco-deficient C. elegans developmental arrest is caused by loss of sulfite oxidase, a Moco-requiring enzyme, and is suppressed by mutations in either C. elegans cystathionine gamma-lyase or cysteine dioxygenase, blocking toxic sulfite production from cystathionine. Thus, we define the genetic pathways for an interkingdom dialogue focused on sulfur homeostasis.
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Rhizobium induces DNA damage in Caenorhabditis elegans intestinal cells. Proc Natl Acad Sci U S A 2019; 116:3784-3792. [PMID: 30808764 DOI: 10.1073/pnas.1815656116] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
In their natural habitat of rotting fruit, the nematode Caenorhabditis elegans feeds on the complex bacterial communities that thrive in this rich growth medium. Hundreds of diverse bacterial strains cultured from such rotting fruit allow C. elegans growth and reproduction when tested individually. In screens for C. elegans responses to single bacterial strains associated with nematodes in fruit, we found that Rhizobium causes a genome instability phenotype; we observed abnormally long or fragmented intestinal nuclei due to aberrant nuclear division, or defective karyokinesis. The karyokinesis defects were restricted to intestinal cells and required close proximity between bacteria and the worm. A genetic screen for C. elegans mutations that cause the same intestinal karyokinesis defect followed by genome sequencing of the isolated mutant strains identified mutations that disrupt DNA damage repair pathways, suggesting that Rhizobium may cause DNA damage in C. elegans intestinal cells. We hypothesized that such DNA damage is caused by reactive oxygen species produced by Rhizobium and found that hydrogen peroxide added to benign Escherichia coli can cause the same intestinal karyokinesis defects in WT C. elegans Supporting this model, free radical scavengers suppressed the Rhizobium-induced C. elegans DNA damage. Thus, Rhizobium may signal to eukaryotic hosts via reactive oxygen species, and the host may respond with DNA damage repair pathways.
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14
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Cetinbas M, Yu S, Sadreyev RI. Whole Genome Next-Generation Sequencing Mutation Identification in Pseudomonas aeruginosa. ACTA ACUST UNITED AC 2018; 124:e69. [PMID: 30239153 DOI: 10.1002/cpmb.69] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Identification of spontaneous or chemically induced bacterial mutations is a powerful tool for investigation of molecular mechanisms, including the mechanism of action of novel antibiotics. However, a major bottleneck to this approach has been the identification of the causative mutation underlying a phenotype of interest. Until recently, this has required time-consuming genetic analysis. However, the advent of relatively inexpensive and rapid next-generation sequencing (NGS) technologies has revolutionized the correlation of bacterial phenotypes and genotypes. In this article we describe a simple bioinformatics pipeline to identify differences between sequenced bacterial genomes. We also describe the procedures involved in growing, extracting, and purifying DNA, and preparation of sequencing libraries for one bacterial species, Pseudomonas aeruginosa. Similar protocols will be applicable to other bacterial species. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Murat Cetinbas
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts.,Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | - Shen Yu
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts.,Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | - Ruslan I Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts.,Department of Pathology, Harvard Medical School, Boston, Massachusetts
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15
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16
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Sumaya NH, Gohil R, Okolo C, Addis T, Doerfler V, Ehlers RU, Molina C. Applying inbreeding, hybridization and mutagenesis to improve oxidative stress tolerance and longevity of the entomopathogenic nematode Heterorhabditis bacteriophora. J Invertebr Pathol 2017; 151:50-58. [PMID: 29108857 DOI: 10.1016/j.jip.2017.11.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 10/31/2017] [Accepted: 11/01/2017] [Indexed: 11/16/2022]
Abstract
Poor shelf-life and sensitivity to environmental stress of entomopathogenic nematodes (EPNs) are traits, which deserve attention for improvement. Recently, a strong positive correlation between oxidative stress tolerance and longevity of Heterorhabditis bacteriophora dauer juveniles (DJs) has been reported. In this study, the improvement of H. bacteriophora DJ longevity was achieved by hybridization and mutagenesis. A hybrid pool deriving from two oxidative stress tolerant and long-living parental strains was generated. This hybrid AU1 × HU2 survived 2.6 days and 18 days longer than its best parent under oxidative stress and control conditions, respectively. In addition to the natural genetic variability, an EMS-mutant pool (M-OXI) with high longevity was generated and one of the derived mutagenized inbred lines (MOX-IL6) survived 5.8 days and 28.4 days longer than its donor line (IL3) under oxidative stress and control conditions, respectively. A genetic cross between the mutagenized inbred line and its donor line (MOX-IL × IL3) still survived 2.5 days and 18.5 days longer than the donor line under oxidative stress and control conditions, respectively. Concerning virulence and reproductive potential, trade-off effects were not observed as a result of hybridization and mutagenesis. These results underline the potential of classical genetic approaches for trait improvement in the nematode H. bacteriophora.
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Affiliation(s)
- Nanette Hope Sumaya
- e-nema, GmbH, Klausdorfer Str. 28-36, 24223 Schwentinental, Germany; Faculty of Agricultural and Nutritional Sciences, Christian-Albrechts-University Kiel, Hermann-Rodewald-Str. 4, 24118 Kiel, Germany
| | - Riddhi Gohil
- Faculty of Agricultural and Nutritional Sciences, Christian-Albrechts-University Kiel, Hermann-Rodewald-Str. 4, 24118 Kiel, Germany
| | - Christopher Okolo
- Department of Biology, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Temesgen Addis
- e-nema, GmbH, Klausdorfer Str. 28-36, 24223 Schwentinental, Germany
| | - Verena Doerfler
- e-nema, GmbH, Klausdorfer Str. 28-36, 24223 Schwentinental, Germany
| | - Ralf-Udo Ehlers
- e-nema, GmbH, Klausdorfer Str. 28-36, 24223 Schwentinental, Germany; Faculty of Agricultural and Nutritional Sciences, Christian-Albrechts-University Kiel, Hermann-Rodewald-Str. 4, 24118 Kiel, Germany; Department of Biology, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium.
| | - Carlos Molina
- e-nema, GmbH, Klausdorfer Str. 28-36, 24223 Schwentinental, Germany
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17
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Du Y, Luo S, Li X, Yang J, Cui T, Li W, Yu L, Feng H, Chen Y, Mu J, Chen X, Shu Q, Guo T, Luo W, Zhou L. Identification of Substitutions and Small Insertion-Deletions Induced by Carbon-Ion Beam Irradiation in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2017; 8:1851. [PMID: 29163581 PMCID: PMC5665000 DOI: 10.3389/fpls.2017.01851] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 10/11/2017] [Indexed: 05/06/2023]
Abstract
Heavy-ion beam irradiation is one of the principal methods used to create mutants in plants. Research on mutagenic effects and molecular mechanisms of radiation is an important subject that is multi-disciplinary. Here, we re-sequenced 11 mutagenesis progeny (M3) Arabidopsis thaliana lines derived from carbon-ion beam (CIB) irradiation, and subsequently focused on substitutions and small insertion-deletion (INDELs). We found that CIB induced more substitutions (320) than INDELs (124). Meanwhile, the single base INDELs were more prevalent than those in large size (≥2 bp). In details, the detected substitutions showed an obvious bias of C > T transitions, by activating the formation of covalent linkages between neighboring pyrimidine residues in the DNA sequence. An A and T bias was observed among the single base INDELs, in which most of these were induced by replication slippage at either the homopolymer or polynucleotide repeat regions. The mutation rate of 200-Gy CIB irradiation was estimated as 3.37 × 10-7 per site. Different from previous researches which mainly focused on the phenotype, chromosome aberration, genetic polymorphism, or sequencing analysis of specific genes only, our study revealed genome-wide molecular profile and rate of mutations induced by CIB irradiation. We hope our data could provide valuable clues for explaining the potential mechanism of plant mutation breeding by CIB irradiation.
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Affiliation(s)
- Yan Du
- Biophysics Group, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - Shanwei Luo
- Biophysics Group, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xin Li
- Biophysics Group, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - Jiangyan Yang
- Biophysics Group, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - Tao Cui
- Biophysics Group, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Wenjian Li
- Biophysics Group, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - Lixia Yu
- Biophysics Group, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - Hui Feng
- Biophysics Group, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yuze Chen
- College of Life Sciences and Technology, Gansu Agricultural University, Lanzhou, China
| | - Jinhu Mu
- Biophysics Group, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xia Chen
- Biophysics Group, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Qingyao Shu
- National Key Laboratory of Rice Biology, Institute of Crop Sciences, Zhejiang University, Hangzhou, China
| | - Tao Guo
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, China
| | - Wenlong Luo
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, China
| | - Libin Zhou
- Biophysics Group, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- *Correspondence: Libin Zhou
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