Abstract
The in vivo functions of Hje and Hjc, two Holliday junction resolvases in Sulfolobus islandicus were investigated. We found that deletion of either hje or hjc had no effect on normal cell growth, while deletion of both hje and hjc is lethal. Although Hjc is the conserved resolvase in all archaea, the hje deletion rather than hjc deletion rendered cells more sensitive to DNA-damaging agents such as hydroxyurea, cisplatin, and methyl methanesulfonate than the wild type (WT). Intriguingly, the sensitivity of Δhje could not be rescued by ectopic expression of Hje from a plasmid and Hje overexpression slowed growth and large cells appeared with more than two genome equivalents. We showed that Hje was maintained at a low level in WT cells. Furthermore, transcriptomic microarray analysis revealed that the abundance of transcripts of many genes including those involved in DNA replication, repair, transcription regulation, and cell division changed drastically in the Hje-overexpressed strain. However, only limited genes were up- or downregulated in the hje deletion strain. Our findings collectively suggest that Hje is the primary resolvase involved in DNA repair and its expression must be tightly controlled in cells.
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References
Aravind L, Makarova KS, Koonin EV (2000) Survey and summary: Holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories. Nucleic Acids Res 28:3417–3432
Bond CS, Kvaratskhelia M, Richard D, White MF, Hunter WN (2001) Structure of Hjc, a Holliday junction resolvase, from Sulfolobus solfataricus. Proc Natl Acad Sci USA 98:5509–5514
Chan YW, West SC (2014) Spatial control of the GEN1 Holliday junction resolvase ensures genome stability. Nat Commun 5:4844
Deng L, Zhu H, Chen Z, Liang YX, She Q (2009) Unmarked gene deletion and host-vector system for the hyperthermophilic crenarchaeon Sulfolobus islandicus. Extremophiles 13:735–746
Dorazi R, Parker JL, White MF (2006) PCNA activates the Holliday junction endonuclease Hjc. J Mol Biol 364:243–247
Dunderdale HJ, Benson FE, Parsons CA, Sharples GJ, Lloyd RG, West SC (1991) Formation and resolution of recombination intermediates by E. coli RecA and RuvC proteins. Nature 354:506–510
Fekairi S et al (2009) Human SLX4 is a Holliday junction resolvase subunit that binds multiple DNA repair/recombination endonucleases. Cell 138:78–89
Fujikane R, Ishino S, Ishino Y, Forterre P (2010) Genetic analysis of DNA repair in the hyperthermophilic archaeon, Thermococcus kodakaraensis. Genes Genet Syst 85:243–257
Guo L et al (2011) Genome analyses of Icelandic strains of Sulfolobus islandicus, model organisms for genetic and virus–host interaction studies. J Bacteriol 193:1672–1680
Heyer WD, Ehmsen KT, Solinger JA (2003) Holliday junctions in the eukaryotic nucleus: resolution in sight? Trends Biochem Sci 28:548–557
Hong Y et al. (2011) Dissection of the functional domains of an archaeal Holliday junction helicase. DNA Repair (Amst)
Ip SC, Rass U, Blanco MG, Flynn HR, Skehel JM, West SC (2008) Identification of Holliday junction resolvases from humans and yeast. Nature 456:357–361
Komori K, Sakae S, Shinagawa H, Morikawa K, Ishino Y (1999) A Holliday junction resolvase from Pyrococcus furiosus: functional similarity to Escherichia coli RuvC provides evidence for conserved mechanism of homologous recombination in Bacteria, Eukarya, and Archaea. Proc Natl Acad Sci USA 96:8873–8878
Kvaratskhelia M, White MF (2000a) An archaeal Holliday junction resolving enzyme from Sulfolobus solfataricus exhibits unique properties. J Mol Biol 295:193–202
Kvaratskhelia M, White MF (2000b) Two Holliday junction resolving enzymes in Sulfolobus solfataricus. J Mol Biol 297:923–932
Lestini R, Duan Z, Allers T (2010) The archaeal Xpf/Mus81/FANCM homolog Hef and the Holliday junction resolvase Hjc define alternative pathways that are essential for cell viability in Haloferax volcanii. DNA Repair 9:994–1002
Li X et al (2011) Deletion of the topoisomerase III gene in the hyperthermophilic archaeon Sulfolobus islandicus results in slow growth and defects in cell cycle control. J Genet Genomics 38:253–259
Manosas M, Perumal SK, Croquette V, Benkovic SJ (2012) Direct observation of stalled fork restart via fork regression in the T4 replication system. Science 338:1217–1220
Matos J, West SC (2014) Holliday junction resolution: regulation in space and time. DNA Repair 19:176–181
Matos J, Blanco MG, Maslen S, Skehel JM, West SC (2011) Regulatory control of the resolution of DNA recombination intermediates during meiosis and mitosis. Cell 147:158–172
McGregor N et al (2005) The structure of Bacillus subtilis RecU Holliday junction resolvase and its role in substrate selection and sequence-specific cleavage. Structure 13:1341–1351
Mei Y et al (2012) Exceptional thermal stability and organic solvent tolerance of an esterase expressed from a thermophilic host. Appl Microbiol Biotechnol 93:1965–1974
Middleton CL, Parker JL, Richard DJ, White MF, Bond CS (2004) Substrate recognition and catalysis by the Holliday junction resolving enzyme Hje. Nucleic Acids Res 32:5442–5451
Nishino T, Ishino Y, Morikawa K (2006) Structure-specific DNA nucleases: structural basis for 3D-scissors. Curr Opin Struct Biol 16:60–67
Parker JL, White MF (2005) The endonuclease Hje catalyses rapid, multiple turnover resolution of Holliday junctions. J Mol Biol 350:1–6
Peng N et al (2012) A synthetic arabinose-inducible promoter confers high levels of recombinant protein expression in hyperthermophilic archaeon Sulfolobus islandicus. Appl Environ Microbiol 78:5630–5637
Schwartz EK, Heyer WD (2011) Processing of joint molecule intermediates by structure-selective endonucleases during homologous recombination in eukaryotes. Chromosoma 120:109–127
Svendsen JM, Harper JW (2010) GEN1/Yen1 and the SLX4 complex: solutions to the problem of Holliday junction resolution. Genes Dev 24:521–536
West SC (1997) Processing of recombination intermediates by the RuvABC proteins. Annu Rev Genet 31:213–244
West SC (2009) The search for a human Holliday junction resolvase. Biochem Soc Trans 37:519–526
Zhang C et al (2010) Revealing the essentiality of multiple archaeal pcna genes using a mutant propagation assay based on an improved knockout method. Microbiology 156:3386–3397
Acknowledgments
This work was supported by Grants 3093002, 31170072, and 31470184 from the National Natural Science Foundation of China (to YS) and FTP/11-106683 from the Danish Council of Independent Research (to QS).
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Communicated by L. Huang.
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Huang, Q., Li, Y., Zeng, C. et al. Genetic analysis of the Holliday junction resolvases Hje and Hjc in Sulfolobus islandicus . Extremophiles 19, 505–514 (2015). https://doi.org/10.1007/s00792-015-0734-5
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DOI: https://doi.org/10.1007/s00792-015-0734-5