Ku80 is involved in telomere maintenance but dispensable for genomic stability in Leishmania mexicana
Jazyk angličtina Země Spojené státy americké Médium electronic-ecollection
Typ dokumentu časopisecké články
PubMed
34965251
PubMed Central
PMC8716037
DOI
10.1371/journal.pntd.0010041
PII: PNTD-D-21-01049
Knihovny.cz E-zdroje
- MeSH
- antigen Ku genetika metabolismus MeSH
- genom protozoální MeSH
- Leishmania mexicana genetika metabolismus MeSH
- leishmanióza kožní parazitologie MeSH
- lidé MeSH
- nestabilita genomu * MeSH
- protozoální proteiny genetika metabolismus MeSH
- telomery genetika metabolismus MeSH
- Trypanosoma brucei brucei genetika metabolismus MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- antigen Ku MeSH
- protozoální proteiny MeSH
BACKGROUND: Telomeres are indispensable for genome stability maintenance. They are maintained by the telomere-associated protein complex, which include Ku proteins and a telomerase among others. Here, we investigated a role of Ku80 in Leishmania mexicana. Leishmania is a genus of parasitic protists of the family Trypanosomatidae causing a vector-born disease called leishmaniasis. METHODOLOGY/PRINCIPAL FINDINGS: We used the previously established CRISPR/Cas9 system to mediate ablation of Ku80- and Ku70-encoding genes in L. mexicana. Complete knock-outs of both genes were confirmed by Southern blotting, whole-genome Illumina sequencing, and RT-qPCR. Resulting telomeric phenotypes were subsequently investigated using Southern blotting detection of terminal restriction fragments. The genome integrity in the Ku80- deficient cells was further investigated by whole-genome sequencing. Our work revealed that telomeres in the ΔKu80 L. mexicana are elongated compared to those of the wild type. This is a surprising finding considering that in another model trypanosomatid, Trypanosoma brucei, they are shortened upon ablation of the same gene. A telomere elongation phenotype has been documented in other species and associated with a presence of telomerase-independent alternative telomere lengthening pathway. Our results also showed that Ku80 appears to be not involved in genome stability maintenance in L. mexicana. CONCLUSION/SIGNIFICANCE: Ablation of the Ku proteins in L. mexicana triggers telomere elongation, but does not have an adverse impact on genome integrity.
Faculty of Biology M 5 Lomonosov Moscow State University Moscow Russia
Institute for Information Transmission Problems Russian Academy of Sciences Moscow Russia
Life Science Research Centre Faculty of Science University of Ostrava Ostrava Czech Republic
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Kostygov AY, Karnkowska A, Votýpka J, Tashyreva D, Maciszewski K, Yurchenko V, et al.. Euglenozoa: taxonomy, diversity and ecology, symbioses and viruses. Open Biol. 2021;11: 200407. doi: 10.1098/rsob.200407 PubMed DOI PMC
Maslov DA, Opperdoes FR, Kostygov AY, Hashimi H, Lukeš J, Yurchenko V. Recent advances in trypanosomatid research: genome organization, expression, metabolism, taxonomy and evolution. Parasitology. 2019;146: 1–27. doi: 10.1017/S0031182018000951 PubMed DOI
Bruschi F, Gradoni L. The leishmaniases: old neglected tropical diseases. Springer. 2018.
WHO. Leishmaniasis. 2020 (Cited November 19 2021). Available from: https://www.who.int/en/news-room/fact-sheets/detail/leishmaniasis
Stuart K, Brun R, Croft S, Fairlamb A, Gurtler RE, McKerrow J, et al.. Kinetoplastids: related protozoan pathogens, different diseases. J Clin Invest. 2008;118: 1301–1310. doi: 10.1172/JCI33945 PubMed DOI PMC
Aravind L, Koonin EV. Prokaryotic homologs of the eukaryotic DNA-end-binding protein Ku, novel domains in the Ku protein and prediction of a prokaryotic double-strand break repair system. Genome Res. 2001;11: 1365–1374. doi: 10.1101/gr.181001 PubMed DOI PMC
Chang HHY, Pannunzio NR, Adachi N, Lieber MR. Non-homologous DNA end joining and alternative pathways to double-strand break repair. Nat Rev Mol Cell Biol. 2017;18: 495–506. doi: 10.1038/nrm.2017.48 PubMed DOI PMC
Williams GJ, Hammel M, Radhakrishnan SK, Ramsden D, Lees-Miller SP, Tainer JA. Structural insights into NHEJ: building up an integrated picture of the dynamic DSB repair super complex, one component and interaction at a time. DNA Repair. 2014;17: 110–120. doi: 10.1016/j.dnarep.2014.02.009 PubMed DOI PMC
Zan H, Tat C, Qiu Z, Taylor JR, Guerrero JA, Shen T, et al.. Rad52 competes with Ku70/Ku86 for binding to S-region DSB ends to modulate antibody class-switch DNA recombination. Nat Commun. 2017;8: 14244. doi: 10.1038/ncomms14244 PubMed DOI PMC
Abbasi S, Schild-Poulter C. Mapping the Ku interactome using proximity-dependent biotin identification in human cells. J Proteome Res. 2019;18: 1064–1077. doi: 10.1021/acs.jproteome.8b00771 PubMed DOI
Fell VL, Schild-Poulter C. The Ku heterodimer: function in DNA repair and beyond. Mutat Res Rev Mutat Res. 2015;763: 15–29. doi: 10.1016/j.mrrev.2014.06.002 PubMed DOI
Nenarokova A, Záhonová K, Krasilnikova M, Gahura O, McCulloch R, Ziková A, et al.. Causes and effects of loss of classical nonhomologous end joining pathway in parasitic eukaryotes. mBio. 2019;10: e01541–01519. doi: 10.1128/mBio.01541-19 PubMed DOI PMC
Burton P, McBride DJ, Wilkes JM, Barry JD, McCulloch R. Ku heterodimer-independent end joining in Trypanosoma brucei cell extracts relies upon sequence microhomology. Eukaryot Cell. 2007;6: 1773–1781. doi: 10.1128/EC.00212-07 PubMed DOI PMC
Genois MM, Paquet ER, Laffitte MC, Maity R, Rodrigue A, Ouellette M, et al.. DNA repair pathways in trypanosomatids: from DNA repair to drug resistance. Microbiol Mol Biol Rev. 2014;78: 40–73. doi: 10.1128/MMBR.00045-13 PubMed DOI PMC
Poláková E, Záhonová K, Albanaz ATS, Butenko A, Lukeš J, Yurchenko V. Diverse telomeres in trypanosomatids. Parasitology. 2021;148: 1254–1270. doi: 10.1017/S0031182021000378 PubMed DOI PMC
Abbasi S, Parmar G, Kelly RD, Balasuriya N, Schild-Poulter C. The Ku complex: recent advances and emerging roles outside of non-homologous end-joining. Cell Mol Life Sci. 2021;78: 4589–4613. doi: 10.1007/s00018-021-03801-1 PubMed DOI PMC
Indiviglio SM, Bertuch AA. Ku’s essential role in keeping telomeres intact. Proc Natl Acad Sci U S A. 2009;106: 12217–12218. doi: 10.1073/pnas.0906427106 PubMed DOI PMC
Fisher TS, Zakian VA. Ku: a multifunctional protein involved in telomere maintenance. DNA Repair. 2005;4: 1215–1226. doi: 10.1016/j.dnarep.2005.04.021 PubMed DOI
Boulton SJ, Jackson SP. Components of the Ku-dependent non-homologous end-joining pathway are involved in telomeric length maintenance and telomeric silencing. EMBO J. 1998;17: 1819–1828. doi: 10.1093/emboj/17.6.1819 PubMed DOI PMC
Janzen CJ, Lander F, Dreesen O, Cross GA. Telomere length regulation and transcriptional silencing in Ku80-deficient Trypanosoma brucei. Nucleic Acids Res. 2004;32: 6575–6584. doi: 10.1093/nar/gkh991 PubMed DOI PMC
Chico L, Ciudad T, Hsu M, Lue NF, Larriba G. The Candida albicans Ku70 modulates telomere length and structure by regulating both telomerase and recombination. PLoS One. 2011;6: e23732. doi: 10.1371/journal.pone.0023732 PubMed DOI PMC
Riha K, Shippen DE. Ku is required for telomeric C-rich strand maintenance but not for end-to-end chromosome fusions in Arabidopsis. Proc Natl Acad Sci U S A. 2003;100: 611–615. doi: 10.1073/pnas.0236128100 PubMed DOI PMC
Espejel S, Franco S, Rodriguez-Perales S, Bouffler SD, Cigudosa JC, Blasco MA. Mammalian Ku86 mediates chromosomal fusions and apoptosis caused by critically short telomeres. EMBO J. 2002;21: 2207–2219. doi: 10.1093/emboj/21.9.2207 PubMed DOI PMC
Samper E, Goytisolo FA, Slijepcevic P, van Buul PP, Blasco MA. Mammalian Ku86 protein prevents telomeric fusions independently of the length of TTAGGG repeats and the G-strand overhang. EMBO Rep. 2000;1: 244–252. doi: 10.1093/embo-reports/kvd051 PubMed DOI PMC
Zellinger B, Akimcheva S, Puizina J, Schirato M, Riha K. Ku suppresses formation of telomeric circles and alternative telomere lengthening in Arabidopsis. Mol Cell. 2007;27: 163–169. doi: 10.1016/j.molcel.2007.05.025 PubMed DOI
Sui J, Zhang S, Chen BPC. DNA-dependent protein kinase in telomere maintenance and protection. Cell Mol Biol Lett. 2020;25: 2. doi: 10.1186/s11658-020-0199-0 PubMed DOI PMC
Olovnikov AM. A theory of marginotomy. The incomplete copying of template margin in enzymic synthesis of polynucleotides and biological significance of the phenomenon. J Theor Biol. 1973;41: 181–190. doi: 10.1016/0022-5193(73)90198-7 PubMed DOI
Greider CW. Telomere length regulation. Annu Rev Biochem. 1996;65: 337–365. doi: 10.1146/annurev.bi.65.070196.002005 PubMed DOI
Greider CW. Telomeres, telomerase and senescence. Bioessays. 1990;12: 363–369. doi: 10.1002/bies.950120803 PubMed DOI
Lundblad V. Telomere maintenance without telomerase. Oncogene. 2002;21: 522–531. doi: 10.1038/sj.onc.1205079 PubMed DOI
McEachern MJ, Blackburn EH. Cap-prevented recombination between terminal telomeric repeat arrays (telomere CPR) maintains telomeres in Kluyveromyces lactis lacking telomerase. Genes Dev. 1996;10: 1822–1834. doi: 10.1101/gad.10.14.1822 PubMed DOI
Muñoz-Jordán JL, Cross GA. Telomere shortening and cell cycle arrest in Trypanosoma brucei expressing human telomeric repeat factor TRF1. Mol Biochem Parasitol. 2001;114: 169–181. doi: 10.1016/s0166-6851(01)00259-6 PubMed DOI
Conte FF, Cano MI. Genomic organization of telomeric and subtelomeric sequences of Leishmania (Leishmania) amazonensis. Int J Parasitol. 2005;35: 1435–1443. doi: 10.1016/j.ijpara.2005.05.011 PubMed DOI
Fulnečková J, Ševčíková T, Fajkus J, Lukešová A, Lukeš M, Vlček Č, et al.. A broad phylogenetic survey unveils the diversity and evolution of telomeres in eukaryotes. Genome Biol Evol. 2013;5: 468–483. doi: 10.1093/gbe/evt019 PubMed DOI PMC
Reis H, Schwebs M, Dietz S, Janzen CJ, Butter F. TelAP1 links telomere complexes with developmental expression site silencing in African trypanosomes. Nucleic Acids Res. 2018;46: 2820–2833. doi: 10.1093/nar/gky028 PubMed DOI PMC
Ishemgulova A, Kraeva N, Hlaváčová J, Zimmer SL, Butenko A, Podešvová L, et al.. A putative ATP/GTP binding protein affects Leishmania mexicana growth in insect vectors and vertebrate hosts. PLoS Negl Trop Dis. 2017;11: e0005782. doi: 10.1371/journal.pntd.0005782 PubMed DOI PMC
Beneke T, Madden R, Makin L, Valli J, Sunter J, Gluenz E. A CRISPR Cas9 high-throughput genome editing toolkit for kinetoplastids. R Soc Open Sci. 2017;4: 170095. doi: 10.1098/rsos.170095 PubMed DOI PMC
Beneke T, Gluenz E. LeishGEdit: a method for rapid gene knockout and tagging using CRISPR-Cas9. In: Clos J, editor. Leishmania. New York, NY: Humana Press; 2019. pp. 189–210. PubMed
Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30: 2114–2120. doi: 10.1093/bioinformatics/btu170 PubMed DOI PMC
Ishemgulova A, Hlaváčová J, Majerová K, Butenko A, Lukeš J, Votýpka J, et al.. CRISPR/Cas9 in Leishmania mexicana: a case study of LmxBTN1. PLoS One. 2018;13: e0192723. doi: 10.1371/journal.pone.0192723 PubMed DOI PMC
Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9: 357–359. doi: 10.1038/nmeth.1923 PubMed DOI PMC
Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, et al.. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012;19: 455–477. doi: 10.1089/cmb.2012.0021 PubMed DOI PMC
Milne I, Bayer M, Stephen G, Cardle L, Marshall D. Tablet: visualizing next-generation sequence assemblies and mappings. Methods Mol Biol. 2016;1374: 253–268. doi: 10.1007/978-1-4939-3167-5_14 PubMed DOI
Kraeva N, Leštinová T, Ishemgulova A, Majerová K, Butenko A, Vaselek S, et al.. LmxM.22.0250-encoded dual specificity protein/lipid phosphatase impairs Leishmania mexicana virulence in vitro. Pathogens. 2019;8: 241. doi: 10.3390/pathogens8040241 PubMed DOI PMC
Záhonová K, Hadariová L, Vacula R, Yurchenko V, Eliáš M, Krajčovič J, et al.. A small portion of plastid transcripts is polyadenylated in the flagellate Euglena gracilis. FEBS Lett. 2014;588: 783–788. doi: 10.1016/j.febslet.2014.01.034 PubMed DOI
Ishemgulova A, Kraeva N, Faktorová D, Podešvová L, Lukeš J, Yurchenko V. T7 polymerase-driven transcription is downregulated in metacyclic promastigotes and amastigotes of Leishmania mexicana. Folia Parasitol. 2016;63: 016. doi: 10.14411/fp.2016.016 PubMed DOI
Kolmogorov M, Yuan J, Lin Y, Pevzner PA. Assembly of long, error-prone reads using repeat graphs. Nat Biotechnol. 2019;37: 540–546. doi: 10.1038/s41587-019-0072-8 PubMed DOI
Sádlová J, Podešvová L, Bečvář T, Bianchi C, Gerasimov ES, Saura A, et al.. Catalase impairs Leishmania mexicana development and virulence. Virulence. 2021;12: 852–867. doi: 10.1080/21505594.2021.1896830 PubMed DOI PMC
Rogers MB, Hilley JD, Dickens NJ, Wilkes J, Bates PA, Depledge DP, et al.. Chromosome and gene copy number variation allow major structural change between species and strains of Leishmania. Genome Res. 2011;21: 2129–2142. doi: 10.1101/gr.122945.111 PubMed DOI PMC
Aslett M, Aurrecoechea C, Berriman M, Brestelli J, Brunk BP, Carrington M, et al.. TriTrypDB: a functional genomic resource for the Trypanosomatidae. Nucleic Acids Res. 2010;38: D457–D462. doi: 10.1093/nar/gkp851 PubMed DOI PMC
Xu M, Guo L, Gu S, Wang O, Zhang R, Peters BA, et al.. TGS-GapCloser: a fast and accurate gap closer for large genomes with low coverage of error-prone long reads. Gigascience. 2020;9: giaa094. doi: 10.1093/gigascience/giaa094 PubMed DOI PMC
Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, et al.. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One. 2014;9: e112963. doi: 10.1371/journal.pone.0112963 PubMed DOI PMC
Alonge M, Soyk S, Ramakrishnan S, Wang X, Goodwin S, Sedlazeck FJ, et al.. RaGOO: fast and accurate reference-guided scaffolding of draft genomes. Genome Biol. 2019;20: 224. doi: 10.1186/s13059-019-1829-6 PubMed DOI PMC
Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics. 2013;29: 1072–1075. doi: 10.1093/bioinformatics/btt086 PubMed DOI PMC
Seppey M, Manni M, Zdobnov EM. BUSCO: assessing genome assembly and annotation completeness. In: Kollmar M, editor. Gene prediction: methods and protocols. New York, NY: Humana; 2019. pp. 227–245. PubMed
Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25: 1754–1760. doi: 10.1093/bioinformatics/btp324 PubMed DOI PMC
Ramirez-Gonzalez RH, Bonnal R, Caccamo M, Maclean D. Bio-SAMtools: Ruby bindings for SAMtools, a library for accessing BAM files containing high-throughput sequence alignments. Source Code Biol Med. 2012;7: 6. doi: 10.1186/1751-0473-7-6 PubMed DOI PMC
McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, et al.. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20: 1297–1303. doi: 10.1101/gr.107524.110 PubMed DOI PMC
Clark SC, Egan R, Frazier PI, Wang Z. ALE: a generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies. Bioinformatics. 2013;29: 435–443. doi: 10.1093/bioinformatics/bts723 PubMed DOI
Lyčka M, Peška V, Demko M, Spyroglou I, Kilar A, Fajkus J, et al.. WALTER: an easy way to online evaluate telomere lengths from terminal restriction fragment analysis. BMC Bioinformatics. 2021;22: 145. doi: 10.1186/s12859-021-04064-0 PubMed DOI PMC
Duncan SM, Jones NG, Mottram JC. Recent advances in Leishmania reverse genetics: manipulating a manipulative parasite. Mol Biochem Parasitol. 2017;216: 30–38. doi: 10.1016/j.molbiopara.2017.06.005 PubMed DOI
Boitz JM, Gilroy CA, Olenyik TD, Paradis D, Perdeh J, Dearman K, et al.. Arginase is essential for survival of Leishmania donovani promastigotes but not intracellular amastigotes. Infect Immun. 2017;85: e00554–00516. doi: 10.1128/IAI.00554-16 PubMed DOI PMC
Song K, Jung D, Jung Y, Lee SG, Lee I. Interaction of human Ku70 with TRF2. FEBS Lett. 2000;481: 81–85. doi: 10.1016/s0014-5793(00)01958-x PubMed DOI
Li B, Espinal A, Cross GA. Trypanosome telomeres are protected by a homologue of mammalian TRF2. Mol Cell Biol. 2005:25: 5011–5021. doi: 10.1128/MCB.25.12.5011-5021.2005 PubMed DOI PMC
O’Connor MS, Safari A, Liu D, Qin J, Songyang Z. The human Rap1 protein complex and modulation of telomere length. J Biol Chem. 2004;279: 28585–28591. doi: 10.1074/jbc.M312913200 PubMed DOI
Laffitte MN, Leprohon P, Papadopoulou B, Ouellette M. Plasticity of the Leishmania genome leading to gene copy number variations and drug resistance. F1000Res. 2016;5: 2350. doi: 10.12688/f1000research.9218.1 PubMed DOI PMC
Sinha R, MM C, Raghwan, Das S, Das S, Shadab M, et al.. Genome plasticity in cultured Leishmania donovani: comparison of early and late passages. Front Microbiol. 2018;9: 1279. doi: 10.3389/fmicb.2018.01279 PubMed DOI PMC
Rogozin IB, Charyyeva A, Sidorenko IA, Babenko VN, Yurchenko V. Frequent recombination events in Leishmania donovani: mining population data. Pathogens. 2020;9: 572. doi: 10.3390/pathogens9070572 PubMed DOI PMC
Kockler ZW, Comeron JM, Malkova A. A unified alternative telomere-lengthening pathway in yeast survivor cells. Mol Cell. 2021;81: 1816–1829. doi: 10.1016/j.molcel.2021.02.004 PubMed DOI PMC
Bussotti G, Gouzelou E, Cortes Boite M, Kherachi I, Harrat Z, Eddaikra N, et al.. Leishmania genome dynamics during environmental adaptation reveal strain-specific differences in gene copy number variation, karyotype instability, and telomeric amplification. mBio. 2018;9: e01399–01318. doi: 10.1128/mBio.01399-18 PubMed DOI PMC