Deletion of IRC19 Causes Defects in DNA Double-Strand Break Repair Pathways in Saccharomyces Cerevisiae

Overview

Journal J Microbiol

Specialty Microbiology

Date 2024 Jul 12

PMID 38995433

Authors

Ju-Hee Choi

Oyungoo Bayarmagnai

Sung-Ho Bae

Affiliations

Soon will be listed here.

Abstract

DNA double-strand break (DSB) repair is a fundamental cellular process crucial for maintaining genome stability, with homologous recombination and non-homologous end joining as the primary mechanisms, and various alternative pathways such as single-strand annealing (SSA) and microhomology-mediated end joining also playing significant roles under specific conditions. IRC genes were previously identified as part of a group of genes associated with increased levels of Rad52 foci in Saccharomyces cerevisiae. In this study, we investigated the effects of IRC gene mutations on DSB repair, focusing on uncharacterized IRC10, 19, 21, 22, 23, and 24. Gene conversion (GC) assay revealed that irc10Δ, 22Δ, 23Δ, and 24Δ mutants displayed modest increases in GC frequencies, while irc19Δ and irc21Δ mutants exhibited significant reductions. Further investigation revealed that deletion mutations in URA3 were not generated in irc19Δ mutant cells following HO-induced DSBs. Additionally, irc19Δ significantly reduced frequency of SSA, and a synergistic interaction between irc19Δ and rad52Δ was observed in DSB repair via SSA. Assays to determine the choice of DSB repair pathways indicated that Irc19 is necessary for generating both GC and deletion products. Overall, these results suggest a potential role of Irc19 in DSB repair pathways, particularly in end resection process.

References

Agmon N, Pur S, Liefshitz B, Kupiec M . Analysis of repair mechanism choice during homologous recombination. Nucleic Acids Res. 2009; 37(15):5081-92. PMC: 2731894. DOI: 10.1093/nar/gkp495. View

Alvaro D, Lisby M, Rothstein R . Genome-wide analysis of Rad52 foci reveals diverse mechanisms impacting recombination. PLoS Genet. 2007; 3(12):e228. PMC: 2134942. DOI: 10.1371/journal.pgen.0030228. View

Al-Zain A, Symington L . The dark side of homology-directed repair. DNA Repair (Amst). 2021; 106:103181. DOI: 10.1016/j.dnarep.2021.103181. View

Baudin A, Denouel A, Lacroute F, Cullin C . A simple and efficient method for direct gene deletion in Saccharomyces cerevisiae. Nucleic Acids Res. 1993; 21(14):3329-30. PMC: 309783. DOI: 10.1093/nar/21.14.3329. View

Betermier M, Bertrand P, Lopez B . Is non-homologous end-joining really an inherently error-prone process?. PLoS Genet. 2014; 10(1):e1004086. PMC: 3894167. DOI: 10.1371/journal.pgen.1004086. View

Bhargava R, Onyango D, Stark J . Regulation of Single-Strand Annealing and its Role in Genome Maintenance. Trends Genet. 2016; 32(9):566-575. PMC: 4992407. DOI: 10.1016/j.tig.2016.06.007. View

Blasiak J . Single-Strand Annealing in Cancer. Int J Mol Sci. 2021; 22(4). PMC: 7926775. DOI: 10.3390/ijms22042167. View

Ceccaldi R, Rondinelli B, DAndrea A . Repair Pathway Choices and Consequences at the Double-Strand Break. Trends Cell Biol. 2015; 26(1):52-64. PMC: 4862604. DOI: 10.1016/j.tcb.2015.07.009. View

Cejka P, Symington L . DNA End Resection: Mechanism and Control. Annu Rev Genet. 2021; 55:285-307. DOI: 10.1146/annurev-genet-071719-020312. View

10.

Chang H, Pannunzio N, Adachi N, Lieber M . Non-homologous DNA end joining and alternative pathways to double-strand break repair. Nat Rev Mol Cell Biol. 2017; 18(8):495-506. PMC: 7062608. DOI: 10.1038/nrm.2017.48. View

11.

Choi D, Lee R, Kwon S, Bae S . Hrq1 functions independently of Sgs1 to preserve genome integrity in Saccharomyces cerevisiae. J Microbiol. 2013; 51(1):105-12. DOI: 10.1007/s12275-013-3048-2. View

12.

Choi J, Lim Y, Kim M, Bae S . Analyses of DNA double-strand break repair pathways in tandem arrays of HXT genes of Saccharomyces cerevisiae. J Microbiol. 2020; 58(11):957-966. DOI: 10.1007/s12275-020-0461-1. View

13.

Dang V, Valens M, Bolotin-Fukuhara M . Cloning of the ASN1 and ASN2 genes encoding asparagine synthetases in Saccharomyces cerevisiae: differential regulation by the CCAAT-box-binding factor. Mol Microbiol. 1996; 22(4):681-92. DOI: 10.1046/j.1365-2958.1996.d01-1715.x. View

14.

Ferrari E, Bruhn C, Peretti M, Cassani C, Carotenuto W, Elgendy M . PP2A Controls Genome Integrity by Integrating Nutrient-Sensing and Metabolic Pathways with the DNA Damage Response. Mol Cell. 2017; 67(2):266-281.e4. PMC: 5526790. DOI: 10.1016/j.molcel.2017.05.027. View

15.

Gaidutsik I, Sedman T, Sillamaa S, Sedman J . Irc3 is a mitochondrial DNA branch migration enzyme. Sci Rep. 2016; 6:26414. PMC: 4872236. DOI: 10.1038/srep26414. View

16.

Gallagher D, Pham N, Tsai A, Janto N, Choi J, Ira G . A Rad51-independent pathway promotes single-strand template repair in gene editing. PLoS Genet. 2020; 16(10):e1008689. PMC: 7591047. DOI: 10.1371/journal.pgen.1008689. View

17.

Ira G, Haber J . Characterization of RAD51-independent break-induced replication that acts preferentially with short homologous sequences. Mol Cell Biol. 2002; 22(18):6384-92. PMC: 135638. DOI: 10.1128/MCB.22.18.6384-6392.2002. View

18.

Jalal D, Chalissery J, Iqbal M, Hassan A . The ATPase Irc20 facilitates Rad51 chromatin enrichment during homologous recombination in yeast Saccharomyces cerevisiae. DNA Repair (Amst). 2020; 97:103019. DOI: 10.1016/j.dnarep.2020.103019. View

19.

Lee S, Moore J, Holmes A, Umezu K, Kolodner R, Haber J . Saccharomyces Ku70, mre11/rad50 and RPA proteins regulate adaptation to G2/M arrest after DNA damage. Cell. 1998; 94(3):399-409. DOI: 10.1016/s0092-8674(00)81482-8. View

20.

Lieber M . The mechanism of double-strand DNA break repair by the nonhomologous DNA end-joining pathway. Annu Rev Biochem. 2010; 79:181-211. PMC: 3079308. DOI: 10.1146/annurev.biochem.052308.093131. View