Poly (ADP-ribose) polymerase in yeasts: characterization and involvement in telomere maintenance
Jazyk angličtina Země Velká Británie, Anglie Médium print
Typ dokumentu časopisecké články
Grantová podpora
APVV-23-0056
Slovak Research and Development Agency
APVV-19-0068
Slovak Research and Development Agency
APVV 22-0144
Slovak Research and Development Agency
Ministry of Education
1/0031/24
Sport of the Slovak republic
1/0234/23
Sport of the Slovak republic
1R01ES031635-01
NIH HHS - United States
Operation Program of Integrated Infrastructure
European Regional Development Fund
MEYS
CR
CEITEC institutional
CANTAR project
Az. 10.21.1.027MN
Fritz Thyssen Foundation
PubMed
40923756
PubMed Central
PMC12412787
DOI
10.1093/nar/gkaf837
PII: 8248603
Knihovny.cz E-zdroje
- MeSH
- fungální proteiny * metabolismus genetika chemie MeSH
- homeostáza telomer * MeSH
- poly(ADP-ribosa)polymerasy * metabolismus genetika chemie MeSH
- telomerasa metabolismus genetika MeSH
- telomery * metabolismus MeSH
- Yarrowia * enzymologie genetika MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- fungální proteiny * MeSH
- poly(ADP-ribosa)polymerasy * MeSH
- telomerasa MeSH
Poly (ADP-ribose) polymerases (PARPs) are enzymes catalyzing the post-translational addition of chains of ADP-ribose moieties to proteins. In most eukaryotic cells, their primary protein targets are involved in DNA recombination, repair, and chromosome maintenance. Even though this group of enzymes is quite common in both eukaryotes and prokaryotes, no PARP homologs have been described so far in ascomycetous yeasts, leaving their potential roles in this group of organisms unexplored. Here, we characterize Pyl1 protein of Yarrowia lipolytica as the first candidate of PARP in yeasts. We show that the expression of PYL1 gene is increased in mutants lacking either subunit of telomerase and identified several of its candidate protein targets in vivo. We demonstrate that Pyl1p is a functional PARP that undergoes auto-PARylation and PARylates YlKu70/80 complex. We also show that overexpression of PYL1 in Y. lipolytica cells results in dissociation of YlKu80 from telomeres in vivo, supporting the role of Pyl1p in telomere protection and maintenance. Based on our observations, we propose Pyl1p and its homologs identified in other yeast species represent a distinct class of PARPs, thus substantiating a more detailed investigation of their roles in these organisms.
Zobrazit více v PubMed
Lüscher B, Ahel I, Altmeyer M et al. ADP-ribosyltransferases, an update on function and nomenclature. Nat Commun. 2022; 289:D543–52. PubMed PMC
Burzio LO, Riquelme PT, Koide SS ADP ribosylation of rat liver nucleosomal core histones. J Biol Chem. 1979; 254:3029–37. 10.1016/S0021-9258(17)30178-3. PubMed DOI
Chaudhuri RA, Nussenzweig A The multifaceted roles of PARP1 in DNA repair and chromatin remodelling. Nat Rev Mol Cell Biol. 2017; 18:610–21. 10.1038/nrm.2017.53. PubMed DOI PMC
Gibson BA, Kraus WL New insights into the molecular and cellular functions of poly(ADP-ribose) and PARPs. Nat Rev Mol Cell Biol. 2012; 13:411–24. 10.1038/nrm3376. PubMed DOI
Durkacz BW, Omidiji O, Gray DA et al. ADP-ribose)n participates in DNA excision repair. Nature. 1980; 283:593–6. 10.1038/283593a0. PubMed DOI
Benjamin RC, Gill DM ADP-ribosylation in mammalian cell ghosts. Dependence of poly(ADP-ribose) synthesis on strand breakage in DNA. J Biol Chem. 1980; 255:10493–501. 10.1016/S0021-9258(19)70490-6. PubMed DOI
Dockery LE, Gunderson CC, Moore KN Rucaparib: the past, present, and future of a newly approved PARP inhibitor for ovarian cancer. Onco Targets Ther. 2017; 10:3029–37. 10.2147/OTT.S114714. PubMed DOI PMC
Fong PC, Boss DS, Yap TA et al. Inhibition of poly(ADP-Ribose) polymerase in tumors from BRCA mutation carriers. N Engl J Med. 2009; 361:123–34. 10.1056/NEJMoa0900212. PubMed DOI
van Beek L, McClay É, Patel S et al. PARP power: a structural perspective on PARP1, PARP2, and PARP3 in DNA damage repair and nucleosome remodelling. Int J Mol Sci. 2021; 22:5112. 10.3390/ijms22105112. PubMed DOI PMC
Langelier MF, Planck JL, Roy S et al. Structural basis for DNA damage-dependent poly(ADP-ribosyl)ation by human PARP-1. Science. 2012; 336:728–32. 10.1126/science.1216338. PubMed DOI PMC
Liu C, Vyas A, Kassab MA et al. The role of poly ADP-ribosylation in the first wave of DNA damage response. Nucleic Acids Res. 2017; 45:8129–41. 10.1093/nar/gkx565. PubMed DOI PMC
Yang G, Liu C, Chen SH et al. Super-resolution imaging identifies PARP1 and the ku complex acting as DNA double-strand break sensors. Nucleic Acids Res. 2018; 46:3446–57. 10.1093/nar/gky088. PubMed DOI PMC
Han Y, Jin F, Xie Y et al. DNAPKcs PARylation regulates DNAPK kinase activity in the DNA damage response. Mol Med Rep. 2019; 20:3609–16. PubMed PMC
Reber JM, Božić-Petković J, Lippmann M et al. PARP1 and XRCC1 exhibit a reciprocal relationship in genotoxic stress response. Cell Biol Toxicol. 2023; 39:345–64. 10.1007/s10565-022-09739-9. PubMed DOI PMC
Miwa M, Tanaka M, Matsushima T et al. Purification and properties of a glycohydrolase from calf thymus splitting ribose-ribose linkages of poly(adenosine diphosphate ribose). J Biol Chem. 1974; 249:3475–82. 10.1016/S0021-9258(19)42597-0. PubMed DOI
Beneke S, Cohausz O, Malanga M et al. Rapid regulation of telomere length is mediated by poly(ADP-ribose) polymerase-1. Nucleic Acids Res. 2008; 36:6309–17. 10.1093/nar/gkn615. PubMed DOI PMC
Gomez M, Wu J, Schreiber V et al. PARP1 Is a TRF2-associated poly(ADP-ribose)polymerase and protects eroded telomeres. Mol Biol Cell. 2006; 17:1686–96. 10.1091/mbc.e05-07-0672. PubMed DOI PMC
Di Fagagna FDA, Hande MP, Tong WM et al. Functions of poly(ADP-ribose) polymerase in controlling telomere length and chromosomal stability. Nat Genet. 1999; 23:76–80. 10.1038/12680. PubMed DOI
Chen JL, Greider CW Telomerase RNA structure and function: implications for dyskeratosis congenita. Trends Biochem Sci. 2004; 29:183–92. 10.1016/j.tibs.2004.02.003. PubMed DOI
De Lange T Shelterin-mediated telomere protection. Annu Rev Genet. 2018; 52:223–47. 10.1146/annurev-genet-032918-021921. PubMed DOI
De Lange T Shelterin: the protein complex that shapes and safeguards human telomeres. Genes Dev. 2005; 19:2100–10. 10.1101/gad.1346005. PubMed DOI
Wright JH, Zakian VA Protein-DNA interactions in soluble telosomes from PubMed DOI PMC
Greenwood J, Patel H, Cech TR et al. Fission yeast telosomes: non-canonical histone-containing chromatin structures dependent on shelterin and RNA. Nucleic Acids Res. 2018; 46:8865. 10.1093/nar/gky605. PubMed DOI PMC
Wellinger RJ, Zakian VA Everything you ever wanted to know about PubMed DOI PMC
Červenák F, Sepšiová R, Nosek J et al. Step-by-step evolution of telomeres: lessons from yeasts. Genome Biol Evol. 2020; 13:evaa268. PubMed PMC
Červenák F, Juríková K, Sepšiová R et al. Double-stranded telomeric DNA binding proteins: diversity matters. Cell Cycle. 2017; 16:1568–77. PubMed PMC
Kramara J, Willcox S, Gunisova S et al. Tay1 protein, a novel telomere binding factor from Yarrowia lipolytica. J Biol Chem. 2010; 285:38078–92. 10.1074/jbc.M110.127605. PubMed DOI PMC
Visacka K, Hofr C, Willcox S et al. Synergism of the two Myb domains of Tay1 protein results in high affinity binding to telomeres. J Biol Chem. 2012; 287:32206–15. 10.1074/jbc.M112.385591. PubMed DOI PMC
Červenák F, Juríková K, Devillers H et al. Identification of telomerase RNAs in species of the PubMed PMC
Kinsky S, Mihalikova A, Kramara J et al. Lack of the catalytic subunit of telomerase leads to growth defects accompanied by structural changes at the chromosomal ends in PubMed DOI
Lendvay TS, Morris DK, Sah J et al. Senescence mutants of PubMed DOI PMC
Nakamura TM, Morin GB, Chapman KB et al. Telomerase catalytic subunit homologs from fission yeast and human. Science. 1997; 277:955–9. 10.1126/science.277.5328.955. PubMed DOI
Stellwagen AE, Haimberger ZW, Veatch JR et al. Ku interacts with telomerase RNA to promote telomere addition at native and broken chromosome ends. Genes Dev. 2003; 17:2384–95. 10.1101/gad.1125903. PubMed DOI PMC
Baumann P, Cech TR Protection of telomeres by the Ku protein in fission yeast. Mol Biol Cell. 2000; 11:3265–75. 10.1091/mbc.11.10.3265. PubMed DOI PMC
Gravel S, Larrivée M, Labrecque P et al. Yeast Ku as a regulator of chromosomal DNA end structure. Science. 1998; 280:741–4. 10.1126/science.280.5364.741. PubMed DOI
Porter SE, Greenwell PW, Ritchie KB et al. The DNA-binding protein Hdf1p (a putative Ku homologue) is required for maintaining normal telomere length in PubMed DOI PMC
Boulton SJ, Jackson SP Identification of a PubMed DOI PMC
Chico L, Ciudad T, Hsu M et al. The PubMed DOI PMC
Valuchova S, Fulnecek J, Prokop Z et al. Protection of PubMed DOI PMC
Espejel S, Franco S, Rodríguez-Perales S et al. Mammalian Ku86 mediates chromosomal fusions and apoptosis caused by critically short telomeres. EMBO J. 2002; 21:2207–19. 10.1093/emboj/21.9.2207. PubMed DOI PMC
Bundock P, van Attikum H, Hooykaas P Increased telomere length and hypersensitivity to DNA damaging agents in an PubMed DOI PMC
Riha K, Watson JM, Parkey J et al. Telomere length deregulation and enhanced sensitivity to genotoxic stress in PubMed DOI PMC
Gallego ME, Jalut N, White CI Telomerase dependence of telomere lengthening in Ku80 mutant PubMed DOI PMC
Bai P Biology of poly(ADP-ribose) polymerases: the factotums of cell maintenance. Mol Cell. 2015; 58:947–58. 10.1016/j.molcel.2015.01.034. PubMed DOI
Smith S, Giriat I, Schmitt A et al. Tankyrase, a poly(ADP-ribose) polymerase at human telomeres. Science. 1998; 282:1484–7. 10.1126/science.282.5393.1484. PubMed DOI
Kaminker PG, Kim SH, Taylor RD et al. TANK2, a new TRF1-associated poly(ADP-ribose) polymerase, causes rapid induction of cell death upon overexpression. J Biol Chem. 2001; 276:35891–9. 10.1074/jbc.M105968200. PubMed DOI
Doksani Y, de Lange T Telomere-internal double-strand breaks are repaired by homologous recombination and PARP1/Lig3-dependent end-joining. Cell Rep. 2016; 17:1646–56. 10.1016/j.celrep.2016.10.008. PubMed DOI PMC
Hoang SM, Kaminski N, Bhargava R et al. Regulation of ALT-associated homology-directed repair by polyADP-ribosylation. Nat Struct Mol Biol. 2020; 27:1152–64. 10.1038/s41594-020-0512-7. PubMed DOI PMC
Maresca C, Dello Stritto A, D’Angelo C et al. PARP1 allows proper telomere replication through TRF1 poly (ADP-ribosyl)ation and helicase recruitment. Commun Biol. 2023; 6:234. 10.1038/s42003-023-04596-6. PubMed DOI PMC
Ghosh U, Das N, Bhattacharyya NP Inhibition of telomerase activity by reduction of poly(ADP-ribosyl)ation of TERT and TEP1/TP1 expression in HeLa cells with knocked down poly(ADP-ribose) polymerase-1 (PARP-1) gene. Mutat Res. 2007; 615:66–74. 10.1016/j.mrfmmm.2006.10.002. PubMed DOI
Citarelli M, Teotia S, Lamb RS Evolutionary history of the poly(ADP-ribose) polymerase gene family in eukaryotes. BMC Evol Biol. 2010; 10:308. 10.1186/1471-2148-10-308. PubMed DOI PMC
Semighini CP, Savoldi M, Goldman GH et al. Functional characterization of the putative PubMed DOI PMC
Kothe GO, Kitamura M, Masutani M et al. PARP is involved in replicative aging in PubMed DOI PMC
Kretzschmar A, Otto C, Holz M et al. Increased homologous integration frequency in PubMed DOI
Laemmli UK Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature. 1970; 227:680–5. 10.1038/227680a0. PubMed DOI
Nosek J, Tomáška Ľ Laboratory Protocols in Molecular and Cell Biology of Yeasts. 2013; Charleston, SC, USA: Create Space Independent Publishing Platform Create Space Independent Publishing Platform.
Stejskal K, Potěšil D, Zdráhal Z Suppression of peptide sample losses in autosampler vials. J Proteome Res. 2013; 12:3057–62. 10.1021/pr400183v. PubMed DOI
Bateman A, Martin MJ, Orchard S et al. UniProt: the Universal Protein knowledgebase in 2023. Nucleic Acids Res. 2023; 51:D523–31. PubMed PMC
Domon B, Costello CA Systematic nomenclature for carbohydrate fragmentations in fab-ms/ms spectra of glycoconjugates. Glycoconjugate J. 1988; 5:397–409. 10.1007/BF01049915. DOI
Barth G, Gaillardin C. Wolf K. Yarrowia lipolytica. Nonconventional Yeasts in Biotechnology. 1996; Berlin, Heidelberg: Springer; 313–88. 10.1007/978-3-642-79856-6. DOI
Mender I, Shay J Telomere restriction fragment (TRF) analysis. Bio Protoc. 2015; 5:e1658. 10.21769/BioProtoc.1658. PubMed DOI PMC
Langelier MF, Planck JL, Servent KM et al. Purification of human PARP-1 and PARP-1 domains from PubMed
Misino S, Bush A, Wagner CB et al. TERRA increases at short telomeres in yeast survivors and regulates survivor associated senescence (SAS). Nucleic Acids Res. 2022; 50:12829–43. 10.1093/nar/gkac1125. PubMed DOI PMC
Altschul SF, Madden TL, Schäffer AA et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997; 25:3389–402. 10.1093/nar/25.17.3389. PubMed DOI PMC
Manni M, Berkeley MR, Seppey M et al. BUSCO: assessing genomic data quality and beyond. Curr Protoc. 2021; 1:e323. 10.1002/cpz1.323. PubMed DOI
Price MN, Dehal PS, Arkin AP FastTree 2 - approximately maximum-likelihood trees for large alignments. PLoS One. 2010; 5:e9490. 10.1371/journal.pone.0009490. PubMed DOI PMC
Yu G, Smith DK, Zhu H et al. ggtree: an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods Ecol Evol. 2017; 8:28–36. 10.1111/2041-210X.12628. DOI
Letunic I, Khedkar S, Bork P SMART: recent updates, new developments and status in 2020. Nucleic Acids Res. 2021; 49:D458–60. 10.1093/nar/gkaa937. PubMed DOI PMC
Fu H, Liu R, Jia Z et al. Poly(ADP-ribosylation) of P-TEFb by PARP1 disrupts phase separation to inhibit global transcription after DNA damage. Nat Cell Biol. 2022; 24:513–25. 10.1038/s41556-022-00872-5. PubMed DOI PMC
Kedar PS, Stefanick DF, Horton JK et al. Increased PARP-1 association with DNA in alkylation damaged, PARP-inhibited mouse fibroblasts. Mol Cancer Res. 2012; 10:360–8. 10.1158/1541-7786.MCR-11-0477. PubMed DOI PMC
La Ferla M, Mercatanti A, Rocchi G et al. Expression of human poly (ADP-ribose) polymerase 1 in PubMed
Boltz KA, Jasti M, Townley JM et al. Analysis of poly(ADP-ribose) polymerases in PubMed DOI PMC
Zhu T, Zheng JY, Huang LL et al. Human PARP1 substrates and regulators of its catalytic activity: an updated overview. Front Pharmacol. 2023; 14:1137151. 10.3389/fphar.2023.1137151. PubMed DOI PMC
Ivessa AS, Zhou JQ, Schulz VP et al. PubMed DOI PMC
Matveeva EA, Mathbout LF, Fondufe-Mittendorf YN PARP1 is a versatile factor in the regulation of mRNA stability and decay. Sci Rep. 2019; 9:3722. 10.1038/s41598-019-39969-7. PubMed DOI PMC
Matveeva EA, Al-Tinawi QMH, Rouchka EC et al. Coupling of PARP1-mediated chromatin structural changes to transcriptional RNA polymerase II elongation and cotranscriptional splicing. Epigenetics Chromatin. 2019; 12:15. 10.1186/s13072-019-0261-1. PubMed DOI PMC
Daniels CM, Ong S-E, Leung AKL Phosphoproteomic approach to characterize protein mono- and poly(ADP-ribosyl)ation sites from cells. J Proteome Res. 2014; 13:3510–22. 10.1021/pr401032q. PubMed DOI PMC
Slade D, Dunstan MS, Barkauskaite E et al. The structure and catalytic mechanism of a poly(ADP-ribose) glycohydrolase. Nature. 2011; 477:616–20. 10.1038/nature10404. PubMed DOI PMC
Trassaert M, Vandermies M, Carly F et al. New inducible promoter for gene expression and synthetic biology in PubMed DOI PMC
Campos-Góngora E, Andaluz E, Bellido A et al. The PubMed DOI
Shaw AE, Mihelich MN, Whitted JE et al. Revised mechanism of hydroxyurea-induced cell cycle arrest and an improved alternative. Proc Natl Acad Sci USA. 2024; 121:e2404470121. 10.1073/pnas.2404470121. PubMed DOI PMC
Alexander JL, Orr-Weaver TL Replication fork instability and the consequences of fork collisions from re-replication. Genes Dev. 2016; 30:2241–52. 10.1101/gad.288142.116. PubMed DOI PMC
Teixeira-Silva A, Ait Saada A, Hardy J et al. The end-joining factor Ku acts in the end-resection of double strand break-free arrested replication forks. Nat Commun. 2017; 8:1982. 10.1038/s41467-017-02144-5. PubMed DOI PMC
Mistry J, Chuguransky S, Williams L et al. Pfam: the protein families database in 2021. Nucleic Acids Res. 2021; 49:D412–9. 10.1093/nar/gkaa913. PubMed DOI PMC
Daniels CM, Ong SE, Leung AKL The promise of proteomics for the study of ADP-ribosylation. Mol Cell. 2015; 58:911–24. 10.1016/j.molcel.2015.06.012. PubMed DOI PMC
Jungmichel S, Rosenthal F, Altmeyer M et al. Proteome-wide identification of poly(ADP-ribosyl)ation targets in different genotoxic stress responses. Mol Cell. 2013; 52:272–85. 10.1016/j.molcel.2013.08.026. PubMed DOI
Muoio D, Laspata N, Fouquerel E Functions of ADP-ribose transferases in the maintenance of telomere integrity. Cell Mol Life Sci. 2022; 79:215. 10.1007/s00018-022-04235-z. PubMed DOI PMC
Hsieh MH, Chen YT, Chen YT et al. PARP1 controls KLF4-mediated telomerase expression in stem cells and cancer cells. Nucleic Acids Res. 2017; 45:10492–503. 10.1093/nar/gkx683. PubMed DOI PMC
Ye JZS, De Lange T TIN2 is a tankyrase 1 PARP modulator in the TRF1 telomere length control complex. Nat Genet. 2004; 36:618–23. 10.1038/ng1360. PubMed DOI
Fernández-Marcelo T, Frías C, Pascua I et al. Poly (ADP-ribose) polymerase 3 (PARP3), a potential repressor of telomerase activity. J Exp Clin Cancer Res. 2014; 33:19. PubMed PMC
Dantzer F, Giraud-Panis M-J, Jaco I et al. Functional interaction between poly(ADP-ribose) polymerase 2 (PARP-2) and TRF2: PARP activity negatively regulates TRF2. Mol Cell Biol. 2004; 24:1595–607. 10.1128/MCB.24.4.1595-1607.2004. PubMed DOI PMC
Nabetani A, Ishikawa F Unusual telomeric DNAs in human telomerase-negative immortalized cells. Mol Cell Biol. 2009; 29:703–13. 10.1128/MCB.00603-08. PubMed DOI PMC
Rose AM, Goncalves T, Cunniffe S et al. Induction of the alternative lengthening of telomeres pathway by trapping of proteins on DNA. Nucleic Acids Res. 2023; 51:6509–27. 10.1093/nar/gkad150. PubMed DOI PMC
Hsu HL, Gilley D, Blackburn EH et al. Ku is associated with the telomere in mammals. Proc Natl Acad Sci USA. 1999; 96:12454–8. 10.1073/pnas.96.22.12454. PubMed DOI PMC
Hsu HL, Gilley D, Galande SA et al. Ku acts in a unique way at the mammalian telomere to prevent end joining. Genes Dev. 2000; 14:2807–12. 10.1101/gad.844000. PubMed DOI PMC
Song K, Jung D, Jung Y et al. Interaction of human Ku70 with TRF2. FEBS Lett. 2000; 481:81–5. 10.1016/S0014-5793(00)01958-X. PubMed DOI
Chai W, Ford LP, Lenertz L et al. Human Ku70/80 associates physically with telomerase through interaction with hTERT. J Biol Chem. 2002; 277:47242–7. 10.1074/jbc.M208542200. PubMed DOI
Marvin ME, Griffin CD, Eyre DE et al. In PubMed DOI PMC
Wang M, Wu W, Wu W et al. PARP-1 and Ku compete for repair of DNA double strand breaks by distinct NHEJ pathways. Nucleic Acids Res. 2006; 34:6170–82. 10.1093/nar/gkl840. PubMed DOI PMC
Hamma T, Ferré-D’Amaré AR The box H/ACA ribonucleoprotein complex: interplay of RNA and protein structures in post-transcriptional RNA modification. J Biol Chem. 2010; 285:805–9. 10.1074/jbc.R109.076893. PubMed DOI PMC
Savelyev NV, Shepelev NM, Lavrik OI et al. PARP1 regulates the biogenesis and activity of telomerase complex through modification of H/ACA-proteins. Front Cell Dev Biol. 2021; 9:621134. 10.3389/fcell.2021.621134. PubMed DOI PMC
Altmeyer M, Neelsen KJ, Teloni F et al. Liquid demixing of intrinsically disordered proteins is seeded by poly(ADP-ribose). Nat Commun. 2015; 6:8088. 10.1038/ncomms9088. PubMed DOI PMC
Dukić N, Strømland Ø, Elsborg JD et al. PARP14 is a PARP with both ADP-ribosyl transferase and hydrolase activities. Sci Adv. 2023; 9:eadi2687. PubMed PMC
Perez-Riverol Y, Bai J, Bandla C et al. The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences. Nucleic Acids Res. 2022; 50:D543–52. 10.1093/nar/gkab1038. PubMed DOI PMC