Genetic manipulation in Sulfolobus islandicus and functional analysis of DNA repair genes

Biochemical Society Transactions

Volumn 41, Issue 1, 2013, Pages 405-410

  Zhang, Changyi ^a,b,c   Tian, Bin ^a   Li, Suming ^a,b   Ao, Xiang ^a   Dalgaard, Kevin ^b   Gökce, Serkan ^b   Liang, Yunxiang ^a   She, Qunxin ^b  

^a HUAZHONG AGRICULTURAL UNIVERSITY   (China)

^b UNIVERSITY OF COPENHAGEN   (Denmark)

^c UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

Archaea; Base excision repair (BER); Genetic manipulation; Homologous recombination (HR); Nucleotide excision repair (NER); Sulfolobus islandicus

Indexed keywords

DEOXYRIBODIPYRIMIDINE PHOTOLYASE; URACIL DNA GLYCOSIDASE;

ARCHAEON; CELL GROWTH; CELL VIABILITY; CONFERENCE PAPER; DNA REPAIR; DNA REPLICATION; ENZYME INACTIVATION; EXCISION REPAIR; FLOW CYTOMETRY; GENE DELETION; GENE FUNCTION; GENETIC ANALYSIS; GENETIC COMPLEMENTATION; GENETIC MANIPULATION; HALOBACTERIALES; HYPERTHERMOPHILE; METHANOGEN; NONHUMAN; PRIORITY JOURNAL; SULFOLOBUS; SULFOLOBUS ISLANDICUS; THERMOCOCCUS KODAKARENSIS;

DNA REPAIR; GENE DELETION; GENE KNOCKOUT TECHNIQUES; GENES, ARCHAEAL; SULFOLOBUS;

EID: 84873108850     PISSN: 03005127     EISSN: 14708752     Source Type: Journal    
DOI: 10.1042/BST20120285     Document Type: Conference Paper

References (38)

1. She, Q., Singh, R. K., Confalonieri, F., Zivanovic, Y., Allard, G., Awayez, M. J., Chan-Weiher, C. C., Clausen, I. G., Curtis, B. A., De Moors, A. et al. (2001) The complete genome of the crenarchaeon Sulfolobus solfataricus P2. Proc. Natl. Acad. Sci. U. S. A. 98, 7835-7840 (Pubitemid 32642647)
2. Kawarabayasi, Y., Hino, Y., Horikawa, H., Jin-no, K., Takahashi, M., Sekine, M., Baba, S., Ankai, A., Kosugi, H., Hosoyama, A. et al. (2001) Complete genome sequence of an aerobic thermoacidophilic crenarchaeon, Sulfolobus tokodaii strain 7. DNA Res. 8, 123-140 (Pubitemid 33622676)
3. Chen, L., Brügger, K., Skovgaard, M., Redder, P., She, Q., Torarinsson, E., Greve, B., Awayez, M., Zibat, A., Klenk, H. P. and Garrett, R. A. (2005) The genome of Sulfolobus acidocaldarius, a model organism of the Crenarchaeota. J. Bacteriol. 187, 4992-4999 (Pubitemid 40962217)
4. Reno, M. L., Held, N. L., Fields, C. J., Burke, P. V. and Whitaker, R. J. (2009) Biogeography of the Sulfolobus islandicus pan-genome. Proc. Natl. Acad. Sci. U. S. A. 106, 8605-8610
5. Guo, L., Brügger, K., Liu, C., Shah, S. A., Zheng, H., Zhu, Y., Wang, S., Lillestøl, R. K., Chen, L., Frank, J. 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
6. Zillig, W., Arnold, H. P., Holz, I., Prangishvili, D., Schweier, A., Stedman, K., She, Q., Phan, H., Garrett, R. and Kristjansson, J. K. (1998) Genetic elements in the extremely thermophilic archaeon Sulfolobus. Extremophiles 2, 131-140 (Pubitemid 28407991)
7. Contursi, P., Jensen, S., Aucelli, T., Rossi, M., Bartolucci, S. and She, Q. (2006) Characterization of the Sulfolobus host-SSV2 virus interaction. Extremophiles 10, 615-627 (Pubitemid 44764319)
8. Berkner, S. and Lipps, G. (2008) Genetic tools for Sulfolobus spp.: vectors and first applications. Arch. Microbiol. 190, 217-230
9. She, Q., Deng, L., Zhu, H., Chen, Z., Dreibrøl, M., Awayez, M. and Liang, Y. X. (2008) Host-vector systems for hyperthermophilic archaeon Sulfolobus. In Microbes and the Environment: Perspective and Challenges (Liu, S.-J. and Drake, H. L., eds), pp. 151-156, Science Press, Beijing
10. Deng, L., Zhu, H., Chen, Z., Liang, Y. X. and She, Q. (2009) Unmarked gene deletion and host-vector system for the hyperthermophilic crenarchaeon Sulfolobus islandicus. Extremophiles 13, 735-746
11. Zhang, C., Guo, L., Deng, L., Wu, Y., Liang, Y., Huang, L. and She, Q. (2010) Revealing the essentiality of multiple archaeal pcna genes using a mutant propagation assay based on an improved knockout method. Microbiology 156, 3386-3397
12. Peng, N., Xia, Q., Chen, Z., Liang, Y. X. and She, Q. (2009) An upstream activation element exerting differential transcriptional activation on an archaeal promoter. Mol. Microbiol. 74, 928-939
13. Gudbergsdottir, S., Deng, L., Chen, Z., Jensen, J. V., Jensen, L. R., She, Q. and Garrett, R. A. (2011) Dynamic properties of the Sulfolobus CRISPR/Cas and CRISPR/Cmr systems when challenged with vector-borne viral and plasmid genes and protospacers. Mol. Microbiol. 79, 35-49
14. Peng, N., Deng, L., Mei, Y., Jiang, D., Hu, Y., Awayez, M., Liang, Y. and She, Q. (2012) A synthetic arabinose-inducible promoter confers high levels of recombinant protein expression in hyperthermophilic archaeon Sulfolobus islandicus. Appl. Environ. Microbiol. 78, 5630-5637
15. Snyder, J. C., Brumfield, S. K., Peng, N., She, Q. and Young, M. J. (2011) Sulfolobus turreted icosahedral virus c92 protein responsible for the formation of pyramid-like cellular lysis structures. J. Virol. 85, 6287-6292
16. Lintner, N. G., Kerou, M., Brumfield, S. K., Graham, S., Liu, H., Naismith, J. H., Sdano, M., Peng, N., She, Q., Copié, V. et al. (2011) Structural and functional characterization of an archaeal clustered regularly interspaced short palindromic repeat (CRISPR)-associated complex for antiviral defense (CASCADE). J. Biol. Chem. 286, 21643-21656
17. Mei, Y., Peng, N., Zhao, S., Hu, Y., Wang, H., Liang, Y. and She, Q. (2012) Exceptional thermal stability and organic solvent tolerance of an esterase expressed from a thermophilic host. Appl. Microbiol. Biotechnol. 93, 1965-1974
18. Zheng, T., Huang, Q., Zhang, C., Ni, J., She, Q. and Shen, Y. (2012) Development of a simvastatin selection marker for a hyperthermophilic acidophile, Sulfolobus islandicus. Appl. Environ. Microbiol. 78, 568-574
19. She, Q., Zhang, C., Deng, L., Peng, N., Chen, Z. and Liang, Y. X. (2009) Genetic analyses in the hyperthermophilic archaeon Sulfolobus islandicus. Biochem. Soc. Trans. 37, 92-96
20. Zhang, C. and Whitaker, R. J. (2012) A broadly applicable gene knockout system for the thermoacidophilic archaeon Sulfolobus islandicus based on simvastatin selection. Microbiology 158, 1513-1522
21. Liu, W., She, Q. and Liang, Y. (2009) Genetic analysis of reverse gyrase gene in Sulfolobus islandicus. J. Huazhong Agric. Univ. 28, 39-42
22. Atomi, H., Matsumi, R. and Imanaka, T. (2004) Reverse gyrase is not a prerequisite for hyperthermophilic life. J. Bacteriol. 186, 4829-4833 (Pubitemid 38891047)
23. Forterre, P. (2002) A hot story from comparative genomics: reverse gyrase is the only hyperthermophile-specific protein. Trends Genet. 18, 236-237
24. Forterre, P., Confalonieri, F., Charbonnier, F. and Duguet, M. (1995) Speculations on the origin of life and thermophily: review of available information on reverse gyrase suggests that hyperthermophilic procaryotes are not so primitive. Orig. Life Evol. Biosph. 25, 235-249
25. Wagner, M., van Wolferen, M., Wagner, A., Lassak, K., Meyer, B. H., Reimann, J. and Albers, S.-V. (2012) Versatile genetic tool box for the Crenarchaeote Sulfolobus acidocaldarius. Front Microbiol. 3, 214
26. Zhang, S., Wei, T., Hou, G., Zhang, C., Liang, P., Ni, J., Sheng, D. and Shen, Y. (2008) Archaeal DNA helicase HerA interacts with Mre11 homologue and unwinds blunt-ended double-stranded DNA and recombination intermediates. DNA Repair 7, 380-391
27. Quaiser, A., Constantinesco, F., White, M. F., Forterre, P. and Elie, C. (2008) The Mre11 protein interacts with both Rad50 and the HerA bipolar helicase and is recruited to DNA following gamma irradiation in the archaeon Sulfolobus acidocaldarius. BMC Mol. Biol. 9, 25
28. Dionne, I. and Bell, S. D. (2005) Characterization of an archaeal family 4 uracil DNA glycosylase and its interaction with PCNA and chromatin proteins. Biochem. J. 387, 859-863 (Pubitemid 40685722)
29. Fujikane, R., Ishino, S., Ishino, Y. and Forterre, P. (2010) Genetic analysis of DNA repair in the hyperthermophilic archaeon, Thermococcus kodakaraensis. Genes Genet. Syst. 85, 243-257
30. Beattie, T. R. and Bell, S. D. (2012) Coordination of multiple enzyme activities by a single PCNA in archaeal Okazaki fragment maturation. EMBO J. 31, 1556-1567
31. Li, S., Zhang, C., Peng, N., Liang, Y. and She, Q. (2012) Construction of deletion mutants and genetic analysis of xpbs genes in Sulfolobus islandicus. J. Huazhong Agric. Univ. 31, 28-33
32. Roberts, J. A. and White, M. F. (2005) An archaeal endonuclease displays key properties of both eukaryal XPF-ERCC1 and Mus81. J. Biol. Chem. 280, 5924-5928 (Pubitemid 40280076)
33. Constantinesco, F., Forterre, P., Koonin, E. V., Aravind, L. and Elie, C. (2004) A bipolar DNA helicase gene, herA, clusters with rad50, mre11 and nurA genes in thermophilic archaea. Nucleic Acids Res. 32, 1439-1447 (Pubitemid 38854744)
34. Hong, Y., Chu, M., Li, Y., Ni, J., Sheng, D., Hou, G., She, Q. and Shen, Y. (2012) Dissection of the functional domains of an archaeal Holliday junction helicase. DNA Repair 11, 102-111
35. Kish, A. and Di Ruggiero, J. (2008) Rad50 is not essential for the Mre11-dependent repair of DNA double-strand breaks in Halobacterium sp. strain NRC-1. J. Bacteriol. 190, 5210-5216
36. Delmas, S., Shunburne, L., Ngo, H. P. and Allers, T. (2009) Mre11-Rad50 promotes rapid repair of DNA damage in the polyploid archaeon Haloferax volcanii by restraining homologous recombination. PLoS Genet. 5, e1000552
37. Sakofsky, C. J., Runck, L. A. and Grogan, D. W. (2011) Sulfolobus mutants, generated via PCR products, which lack putative enzymes of UV photoproduct repair. Archaea 2011, 864015
38. Li, X., Guo, L., Deng, L., Feng, D., Ren, Y., Chu, Y., She, Q. and Huang, L. (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. Genom. 38, 253-259