Tryptophanyl-tRNA synthetase-1 (WARS-1) depletion and high tryptophan concentration lead to genomic instability in Caenorhabditis elegans.


Journal

Cell death discovery
ISSN: 2058-7716
Titre abrégé: Cell Death Discov
Pays: United States
ID NLM: 101665035

Informations de publication

Date de publication:
04 Apr 2024
Historique:
received: 21 10 2023
accepted: 14 03 2024
revised: 12 03 2024
medline: 5 4 2024
pubmed: 5 4 2024
entrez: 4 4 2024
Statut: epublish

Résumé

The fidelity of translation is ensured by a family of proteins named aminoacyl-tRNA synthetases (ARSs), making them crucial for development and survival. More recently, mutations in the tryptophanyl-tRNA synthetase 1 (WARS1) have been linked to various human diseases, from intellectual disability to various types of cancer. To understand the function of WARS1, we investigated the effect of WARS-1 depletion during the mitotic and meiotic cell cycle in the developing germline of Caenorhabditis elegans (C. elegans) and demonstrated the role of WARS-1 in genome integrity. wars-1 knockdown results in cell cycle arrest of the mitotically active germ cells. Such mitotic arrest is also associated with canonical DNA damage-induced checkpoint signaling in mitotic and meiotic germ cells. Significantly, such DNA checkpoint activation is associated with the morphological anomalies in chromatin structures that are the hallmarks of genome instability, such as the formation of chromatin bridges, micronuclei, and chromatin buds. We demonstrated that knocking down wars-1 results in an elevation of the intracellular concentration of tryptophan and its catabolites, a surprising finding emphasizing the impact of cellular amino acid availability and organismal/individual dietary uptake on genome integrity. Our result demonstrates that exposing C. elegans to a high tryptophan dosage leads to DNA damage checkpoint activation and a significant increase in the tryptophan metabolites. Targeting tryptophan catabolism, the least utilized amino acid in nature, can be important in developing new cancer therapeutic approaches. All in all, we have strong evidence that knocking down wars-1 results in defects in genomic integrity.

Identifiants

pubmed: 38575580
doi: 10.1038/s41420-024-01917-4
pii: 10.1038/s41420-024-01917-4
doi:

Types de publication

Journal Article

Langues

eng

Pagination

165

Informations de copyright

© 2024. The Author(s).

Références

Ogle JM, Ramakrishnan V. Structural insights into translational fidelity. Annu Rev Biochem. 2005;74:129–77.
pubmed: 15952884 doi: 10.1146/annurev.biochem.74.061903.155440
Parker J. Errors and alternatives in reading the universal genetic code. Microbiol Rev. 1989;53:273–98.
pubmed: 2677635 pmcid: 372737 doi: 10.1128/mr.53.3.273-298.1989
Zaher HS, Green R. Fidelity at the molecular level: lessons from protein synthesis. Cell. 2009;136:746–62.
pubmed: 19239893 pmcid: 3691815 doi: 10.1016/j.cell.2009.01.036
Song P, Yang F, Jin H, Wang X. The regulation of protein translation and its implications for cancer. Signal Transduct Target Ther. 2021;6:68.
pubmed: 33597534 pmcid: 7889628 doi: 10.1038/s41392-020-00444-9
Ruggero D Translational control in cancer etiology. Cold Spring Harb Perspect Biol. 5;2013.
Ibba M, Soll D. Aminoacyl-tRNA synthesis. Annu Rev Biochem. 2000;69:617–50.
pubmed: 10966471 doi: 10.1146/annurev.biochem.69.1.617
Mirando AC, Francklyn CS, Lounsbury KM. Regulation of angiogenesis by aminoacyl-tRNA synthetases. Int J Mol Sci. 2014;15:23725–48.
pubmed: 25535072 pmcid: 4284789 doi: 10.3390/ijms151223725
Sung Y, Yoon I, Han JM, Kim S. Functional and pathologic association of aminoacyl-tRNA synthetases with cancer. Exp. Mol. Med. 2022;54:553–66.
pubmed: 35501376 pmcid: 9166799 doi: 10.1038/s12276-022-00765-5
Nagao A, Suzuki T, Katoh T, Sakaguchi Y, Suzuki T. Biogenesis of glutaminyl-mt tRNAGln in human mitochondria. Proc. Natl Acad Sci USA. 2009;106:16209–14.
pubmed: 19805282 pmcid: 2752530 doi: 10.1073/pnas.0907602106
Pezo V, Metzgar D, Hendrickson TL, Waas WF, Hazebrouck S, Doring V, et al. Artificially ambiguous genetic code confers growth yield advantage. Proc. Natl Acad. Sci. USA. 2004;101:8593–7.
pubmed: 15163798 pmcid: 423239 doi: 10.1073/pnas.0402893101
Bacher JM, de Crecy-Lagard V, Schimmel PR. Inhibited cell growth and protein functional changes from an editing-defective tRNA synthetase. Proc. Natl Acad. Sci. USA. 2005;102:1697–701.
pubmed: 15647356 pmcid: 547871 doi: 10.1073/pnas.0409064102
Lee JW, Beebe K, Nangle LA, Jang J, Longo-Guess CM, Cook SA, et al. Editing-defective tRNA synthetase causes protein misfolding and neurodegeneration. Nature. 2006;443:50–5.
pubmed: 16906134 doi: 10.1038/nature05096
Song Y, Shi Y, Carland TM, Lian S, Sasaki T, Schork NJ, et al. p53-Dependent DNA damage response sensitive to editing-defective tRNA synthetase in zebrafish. Proc. Natl Acad. Sci. USA. 2016;113:8460–5.
pubmed: 27402763 pmcid: 4968768 doi: 10.1073/pnas.1608139113
Turvey AK, Horvath GA, Cavalcanti ARO. Aminoacyl-tRNA synthetases in human health and disease. Front Physiol. 2022;13:1029218.
pubmed: 36330207 pmcid: 9623071 doi: 10.3389/fphys.2022.1029218
Bogershausen N, Krawczyk HE, Jamra RA, Lin SJ, Yigit G, Huning I, et al. WARS1 and SARS1: Two tRNA synthetases implicated in autosomal recessive microcephaly. Hum. Mutat. 2022;43:1454–71.
pubmed: 35790048 doi: 10.1002/humu.24430
Lee KM, Hwang EH, Kang SE, Lee CH, Lee H, Oh HJ, et al. Tryptophanyl-tRNA Synthetase Sensitizes Hormone Receptor-Positive Breast Cancer to Docetaxel-Based Chemotherapy. J. Breast Cancer. 2020;23:599–609.
pubmed: 33408886 pmcid: 7779724 doi: 10.4048/jbc.2020.23.e67
Wang J, Vallee I, Dutta A, Wang Y, Mo Z, Liu Z, et al. Multi-Omics Database Analysis of Aminoacyl-tRNA Synthetases in Cancer. Genes (Basel). 2020;11:1384.
pubmed: 33266490 doi: 10.3390/genes11111384
Suzuki Y, Suda T, Furuhashi K, Suzuki M, Fujie M, Hahimoto D, et al. Increased serum kynurenine/tryptophan ratio correlates with disease progression in lung cancer. Lung Cancer. 2010;67:361–5.
pubmed: 19487045 doi: 10.1016/j.lungcan.2009.05.001
Schefold JC, Zeden JP, Fotopoulou C, von Haehling S, Pschowski R, Hasper D, et al. Increased indoleamine 2,3-dioxygenase (IDO) activity and elevated serum levels of tryptophan catabolites in patients with chronic kidney disease: a possible link between chronic inflammation and uraemic symptoms. Nephrol. Dial. Transpl. 2009;24:1901–8.
doi: 10.1093/ndt/gfn739
Schroecksnadel K, Kaser S, Ledochowski M, Neurauter G, Mur E, Herold M, et al. Increased degradation of tryptophan in blood of patients with rheumatoid arthritis. J. Rheumatol. 2003;30:1935–9.
pubmed: 12966593
Xue C, Li G, Zheng Q, Gu X, Shi Q, Su Y, et al. Tryptophan metabolism in health and disease. Cell Metab. 2023;35:1304–26.
pubmed: 37352864 doi: 10.1016/j.cmet.2023.06.004
Lin SJ, Vona B, Porter HM, Izadi M, Huang K, Lacassie Y, et al. Biallelic variants in WARS1 cause a highly variable neurodevelopmental syndrome and implicate a critical exon for normal auditory function. Hum. Mutat. 2022;43:1472–89.
pubmed: 35815345 doi: 10.1002/humu.24435
Barik S. The Uniqueness of Tryptophan in Biology: Properties, Metabolism, Interactions and Localization in Proteins. Int J. Mol. Sci. 2020;21:8776.
pubmed: 33233627 pmcid: 7699789 doi: 10.3390/ijms21228776
Perez-Castro L, Garcia R, Venkateswaran N, Barnes S, Conacci-Sorrell M. Tryptophan and its metabolites in normal physiology and cancer etiology. FEBS J. 2023;290:7–27.
pubmed: 34687129 doi: 10.1111/febs.16245
Granseth E, von Heijne G, Elofsson A. A study of the membrane-water interface region of membrane proteins. J. Mol. Biol. 2005;346:377–85.
pubmed: 15663952 doi: 10.1016/j.jmb.2004.11.036
Sanchez KM, Kang G, Wu B, Kim JE. Tryptophan-lipid interactions in membrane protein folding probed by ultraviolet resonance Raman and fluorescence spectroscopy. Biophys. J. 2011;100:2121–30.
pubmed: 21539779 pmcid: 3149241 doi: 10.1016/j.bpj.2011.03.018
Hendzel MJ, Wei Y, Mancini MA, Van Hooser A, Ranalli T, Brinkley BR, et al. Mitosis-specific phosphorylation of histone H3 initiates primarily within pericentromeric heterochromatin during G2 and spreads in an ordered fashion coincident with mitotic chromosome condensation. Chromosoma. 1997;106:348–60.
pubmed: 9362543 doi: 10.1007/s004120050256
Lee SJ, Gartner A, Hyun M, Ahn B, Koo HS. The Caenorhabditis elegans Werner syndrome protein functions upstream of ATR and ATM in response to DNA replication inhibition and double-strand DNA breaks. PLoS Genet. 2010;6:e1000801.
pubmed: 20062519 pmcid: 2791846 doi: 10.1371/journal.pgen.1000801
Ennis HL, Lubin M. Cycloheximide: Aspects of Inhibition of Protein Synthesis in Mammalian Cells. Science. 1964;146:1474–6.
pubmed: 14208575 doi: 10.1126/science.146.3650.1474
Dunbar TL, Yan Z, Balla KM, Smelkinson MG, Troemel ER. C. elegans detects pathogen-induced translational inhibition to activate immune signaling. Cell Host Microbe. 2012;11:375–86.
pubmed: 22520465 pmcid: 3334869 doi: 10.1016/j.chom.2012.02.008
Dalton HM, Curran SP. Hypodermal responses to protein synthesis inhibition induce systemic developmental arrest and AMPK-dependent survival in Caenorhabditis elegans. PLoS Genet. 2018;14:e1007520.
pubmed: 30020921 pmcid: 6066256 doi: 10.1371/journal.pgen.1007520
Moreno A, Carrington JT, Albergante L, Al Mamun M, Haagensen EJ, Komseli ES, et al. Unreplicated DNA remaining from unperturbed S phases passes through mitosis for resolution in daughter cells. Proc. Natl Acad. Sci. USA. 2016;113:E5757–64.
pubmed: 27516545 pmcid: 5047195 doi: 10.1073/pnas.1603252113
Chan KL, North PS, Hickson ID. BLM is required for faithful chromosome segregation and its localization defines a class of ultrafine anaphase bridges. EMBO J. 2007;26:3397–409.
pubmed: 17599064 pmcid: 1933408 doi: 10.1038/sj.emboj.7601777
Gartner A, MacQueen AJ, Villeneuve AM Methods for Analyzing Checkpoint Responses in Caenorhabditis elegans. In: Schönthal AH, editor. Checkpoint Controls and Cancer: Volume 1: Reviews and Model Systems. Totowa, NJ: Humana Press. 2004; 257–74.
Gartner A, Milstein S, Ahmed S, Hodgkin J, Hengartner MO. A conserved checkpoint pathway mediates DNA damage-induced apoptosis and cell cycle arrest in C. elegans. Mol. Cell. 2000;5:435–43.
pubmed: 10882129 doi: 10.1016/S1097-2765(00)80438-4
Garcia-Muse T, Boulton SJ. Distinct modes of ATR activation after replication stress and DNA double-strand breaks in Caenorhabditis elegans. EMBO J. 2005;24:4345–55.
pubmed: 16319925 pmcid: 1356337 doi: 10.1038/sj.emboj.7600896
Moser SC, von Elsner S, Bussing I, Alpi A, Schnabel R, Gartner A. Functional dissection of Caenorhabditis elegans CLK-2/TEL2 cell cycle defects during embryogenesis and germline development. PLoS Genet. 2009;5:e1000451.
pubmed: 19360121 pmcid: 2660272 doi: 10.1371/journal.pgen.1000451
Norbury C, Blow J, Nurse P. Regulatory phosphorylation of the p34cdc2 protein kinase in vertebrates. EMBO J. 1991;10:3321–9.
pubmed: 1655417 pmcid: 453058 doi: 10.1002/j.1460-2075.1991.tb04896.x
Mueller PR, Coleman TR, Kumagai A, Dunphy WG. Myt1: a membrane-associated inhibitory kinase that phosphorylates Cdc2 on both threonine-14 and tyrosine-15. Science. 1995;270:86–90.
pubmed: 7569953 doi: 10.1126/science.270.5233.86
Liu Q, Guntuku S, Cui XS, Matsuoka S, Cortez D, Tamai K, et al. Chk1 is an essential kinase that is regulated by Atr and required for the G(2)/M DNA damage checkpoint. Genes Dev. 2000;14:1448–59.
pubmed: 10859164 pmcid: 316686 doi: 10.1101/gad.14.12.1448
Zhao H, Piwnica-Worms H. ATR-mediated checkpoint pathways regulate phosphorylation and activation of human Chk1. Mol. Cell Biol. 2001;21:4129–39.
pubmed: 11390642 pmcid: 87074 doi: 10.1128/MCB.21.13.4129-4139.2001
Kalogeropoulos N, Christoforou C, Green AJ, Gill S, Ashcroft NR. chk-1 is an Essential Gene and is Required for an S-M Checkpoint During Early Embryogenesis. Cell Cycle. 2014;3:1194–8.
doi: 10.4161/cc.3.9.1116
Liu Y, Vidanes G, Lin YC, Mori S, Siede W. Characterization of a Saccharomyces cerevisiae homologue of Schizosaccharomyces pombe Chk1 involved in DNA-damage-induced M-phase arrest. Mol. Gen. Genet. 2000;262:1132–46.
pubmed: 10660074 doi: 10.1007/PL00008656
Wusiman W, Zhang Z, Ding Q, Liu M. The pathophyiological role of aminoacyl-tRNA synthetases in digestive system diseases. Front Physiol. 2022;13:935576.
pubmed: 36017335 pmcid: 9396140 doi: 10.3389/fphys.2022.935576
Zou Y, Liu Y, Wu X, Shell SM. Functions of human replication protein A (RPA): from DNA replication to DNA damage and stress responses. J. Cell Physiol. 2006;208:267–73.
pubmed: 16523492 pmcid: 3107514 doi: 10.1002/jcp.20622
McClintock B. The Stability of Broken Ends of Chromosomes in Zea Mays. Genetics. 1941;26:234–82.
pubmed: 17247004 pmcid: 1209127 doi: 10.1093/genetics/26.2.234
Mazur DJ, Perrino FW. Identification and expression of the TREX1 and TREX2 cDNA sequences encoding mammalian 3′->5′ exonucleases. J. Biol. Chem. 1999;274:19655–60.
pubmed: 10391904 doi: 10.1074/jbc.274.28.19655
Hong Y, Sonneville R, Wang B, Scheidt V, Meier B, Woglar A, et al. LEM-3 is a midbody-tethered DNA nuclease that resolves chromatin bridges during late mitosis. Nat. Commun. 2018;9:728.
pubmed: 29463814 pmcid: 5820297 doi: 10.1038/s41467-018-03135-w
Hong Y, Zhang H, Gartner A. The Last Chance Saloon. Front Cell Dev. Biol. 2021;9:671297.
pubmed: 34055803 pmcid: 8160109 doi: 10.3389/fcell.2021.671297
Shoshani O, Brunner SF, Yaeger R, Ly P, Nechemia-Arbely Y, Kim DH, et al. Chromothripsis drives the evolution of gene amplification in cancer. Nature. 2021;591:137–41.
pubmed: 33361815 doi: 10.1038/s41586-020-03064-z
Chin GM, Villeneuve AM. C. elegans mre-11 is required for meiotic recombination and DNA repair but is dispensable for the meiotic G(2) DNA damage checkpoint. Genes Dev. 2001;15:522–34.
pubmed: 11238374 pmcid: 312651 doi: 10.1101/gad.864101
Stracker TH, Petrini JH. The MRE11 complex: starting from the ends. Nat. Rev. Mol. Cell Biol. 2011;12:90–103.
pubmed: 21252998 pmcid: 3905242 doi: 10.1038/nrm3047
Cascarina SM, Ross ED. Proteome-scale relationships between local amino acid composition and protein fates and functions. PLoS Comput Biol. 2018;14:e1006256.
pubmed: 30248088 pmcid: 6171957 doi: 10.1371/journal.pcbi.1006256
Hsu YL, Hung JY, Chiang SY, Jian SF, Wu CY, Lin YS, et al. Lung cancer-derived galectin-1 contributes to cancer associated fibroblast-mediated cancer progression and immune suppression through TDO2/kynurenine axis. Oncotarget. 2016;7:27584–98.
pubmed: 27050278 pmcid: 5053673 doi: 10.18632/oncotarget.8488
D’Amato NC, Rogers TJ, Gordon MA, Greene LI, Cochrane DR, Spoelstra NS, et al. A TDO2-AhR signaling axis facilitates anoikis resistance and metastasis in triple-negative breast cancer. Cancer Res. 2015;75:4651–64.
pubmed: 26363006 pmcid: 4631670 doi: 10.1158/0008-5472.CAN-15-2011
Modoux M, Rolhion N, Mani S, Sokol H. Tryptophan Metabolism as a Pharmacological Target. Trends Pharm. Sci. 2021;42:60–73.
pubmed: 33256987 doi: 10.1016/j.tips.2020.11.006
Platten M, Nollen EAA, Rohrig UF, Fallarino F, Opitz CA. Tryptophan metabolism as a common therapeutic target in cancer, neurodegeneration and beyond. Nat. Rev. Drug Discov. 2019;18:379–401.
pubmed: 30760888 doi: 10.1038/s41573-019-0016-5
Sahm F, Oezen I, Opitz CA, Radlwimmer B, von Deimling A, Ahrendt T, et al. The endogenous tryptophan metabolite and NAD+ precursor quinolinic acid confers resistance of gliomas to oxidative stress. Cancer Res. 2013;73:3225–34.
pubmed: 23548271 doi: 10.1158/0008-5472.CAN-12-3831
Sarrouilhe D, Mesnil M. Serotonin and human cancer: A critical view. Biochimie. 2019;161:46–50.
pubmed: 29936294 doi: 10.1016/j.biochi.2018.06.016
K. Wu K. Tryptophan Metabolism and Cancer Progression. J. Anal. Oncol. 2021;10:1–11.
doi: 10.30683/1927-7229.2021.10.01
Soll C, Jang JH, Riener MO, Moritz W, Wild PJ, Graf R, et al. Serotonin promotes tumor growth in human hepatocellular cancer. Hepatology. 2010;51:1244–54.
pubmed: 20099302 doi: 10.1002/hep.23441
Leoncikas V, Wu H, Ward LT, Kierzek AM, Plant NJ. Generation of 2,000 breast cancer metabolic landscapes reveals a poor prognosis group with active serotonin production. Sci. Rep. 2016;6:19771.
pubmed: 26813959 pmcid: 4728432 doi: 10.1038/srep19771
Brenner S. The genetics of Caenorhabditis elegans. Genetics. 1974;77:71–94.
pubmed: 4366476 pmcid: 1213120 doi: 10.1093/genetics/77.1.71
Huang da W, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 2009;4:44–57.
pubmed: 19131956 doi: 10.1038/nprot.2008.211
Sherman BT, Hao M, Qiu J, Jiao X, Baseler MW, Lane HC, et al. DAVID: a web server for functional enrichment analysis and functional annotation of gene lists (2021 update). Nucleic Acids Res. 2022;50:W216–W21.
pubmed: 35325185 pmcid: 9252805 doi: 10.1093/nar/gkac194
Supek F, Bosnjak M, Skunca N, Smuc T. REVIGO summarizes and visualizes long lists of gene ontology terms. PLoS One. 2011;6:e21800.
pubmed: 21789182 pmcid: 3138752 doi: 10.1371/journal.pone.0021800
Fraser AG, Kamath RS, Zipperlen P, Martinez-Campos M, Sohrmann M, Ahringer J. Functional genomic analysis of C. elegans chromosome I by systematic RNA interference. Nature. 2000;408:325–30.
pubmed: 11099033 doi: 10.1038/35042517
Kamath RS, Fraser AG, Dong Y, Poulin G, Durbin R, Gotta M, et al. Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature. 2003;421:231–7.
pubmed: 12529635 doi: 10.1038/nature01278
Pourkarimi E, Greiss S, Gartner A. Evidence that CED-9/Bcl2 and CED-4/Apaf-1 localization is not consistent with the current model for C. elegans apoptosis induction. Cell Death Differ. 2012;19:406–15.
pubmed: 21886181 doi: 10.1038/cdd.2011.104
Schneider CA, Rasband WS, Eliceiri KW. NIH Image to ImageJ: 25 years of image analysis. Nat. Methods. 2012;9:671–5.
pubmed: 22930834 pmcid: 5554542 doi: 10.1038/nmeth.2089

Auteurs

Mahmoud Izadi (M)

Division of Genomics and Translational Medicine, College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha, 34110, Qatar.

Tayyiba Akbar Ali (TA)

Division of Genomics and Translational Medicine, College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha, 34110, Qatar.

Farah M Shurrab (FM)

Division of Genomics and Translational Medicine, College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha, 34110, Qatar.

Ebrahim Aharpour (E)

Kevlarr B.V, Nieuwegein, 3436ZZ, Netherlands.

Ehsan Pourkarimi (E)

Division of Genomics and Translational Medicine, College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha, 34110, Qatar. edaryakenari@hbku.edu.qa.

Classifications MeSH