Comparative genomics of hemiascomycete yeasts: Genes involved in DNA replication, repair, and recombination

Molecular Biology and Evolution

Volumn 22, Issue 4, 2005, Pages 1011-1023

  Richard, Guy Franck ^a   Kerrest, Alix ^a   Lafontaine, Ingrid ^a   Dujon, Bernard ^a  

^a SORBONNE UNIVERSITÉ   (France)

Author keywords

Comparative genomics; Hemiascomycete; Recombination; Repair; Replication

Indexed keywords

DNA TOPOISOMERASE; DOUBLE STRANDED DNA; HELICASE; PROTEIN MRE11P; PROTEIN RAD50P; PROTEIN SPO11P; RECOMBINANT PROTEIN; UNCLASSIFIED DRUG;

ARTICLE; ASCOMYCETES; BACTERIUM; CANDIDA GLABRATA; COMPARATIVE GENE MAPPING; DEBARYOMYCES HANSENII; DNA RECOMBINATION; DNA REPAIR; DNA REPLICATION; DNA SEQUENCE; DNA STRAND BREAKAGE; EXCISION REPAIR; GENE DUPLICATION; GENE REPLICATION; GENETIC CONSERVATION; HEMIASCOMYCETE; HOMOLOGOUS RECOMBINATION; KLUYVEROMYCES; MAMMAL; MEIOSIS; NONHUMAN; SACCHAROMYCES CEREVISIAE; TANDEM REPEAT; YARROWIA LIPOLYTICA;

AMINO ACID SEQUENCE; ASCOMYCOTA; DNA REPAIR; DNA REPLICATION; GENOME, FUNGAL; MOLECULAR SEQUENCE DATA; RECOMBINATION, GENETIC; S PHASE; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 16344385808     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/molbev/msi083     Document Type: Article

References (50)

1. Bennett, J. E., K. Izumikawa, and K. A. Marr. 2004. Mechanism of increased fluconazole resistance in Candida glabrata during prophylaxis. Antimicrob. Agents Chemother. 48:1773-1777.
2. Bergerat, A., B. de Massy, D. Gadelle, P. C. Varoutas, A. Nicolas, and P. Forterre. 1997. An atypical topoisomerase II from Archaea with implications for meiotic recombination. Nature 386:414-417.
3. Bolotin-Fukuhara, M., C. Toffano-Nioche, F. Artiguenave et al. (11 co-authors). 2000. Genomic exploration of the hemiascomycetous yeasts: 11. Kluyveromyces lactis. FEBS Lett. 487:66-70.
4. Bon, E., S. Casaregola, G. Blandin et al. (11 co-authors). 2003. Molecular evolution of eukaryotic genomes: hemiascomycetous yeast spliceosomal introns. Nucleic Acids Res. 31:1121-1135.
5. Börner, G. V., N. Kleckner, and N. Hunter. 2004. Crossover/non-crossover differentiation, synaptonemal complex formation, and regulatory surveillance at the leptotene/zygotene transition of meiosis. Cell 117:29-45.
6. Burgers, P. M., E. V. Koonin, E. Bruford et al. (21 co-authors). 2001. Eukaryotic DNA polymerases: proposal for a revised nomenclature. J. Biol. Chem. 276:43487-43490.
7. Cann, I. K. O., and Y. Ishino. 1999. Archaeal DNA replication: identifying the pieces to solve a puzzle. Genetics 152:1249-1267.
8. Carney, J. P., R. S. Maser, H. Olivares, E. M. Davis, M. Le Beau, L R. Yates III, L. Hays, W. F. Morgan, and J. H. J. Petrini. 1998. The hMre11/hRad50 protein complex and Nijmegen breakage syndrome: linkage of double-strand break repair to the cellular DNA damage response. Cell 93:477-486.
9. Casarégola, S., C. Neuveglise, A. Lepingle, E. Bon, C. Feynerol, F. Artiguenave, P. Wincker, and C. Gaillardin. 2000. Genomic exploration of the hemiascomycetous yeasts: 17. Yarrowia lipolytica. FEBS Lett. 487:95-100.
10. Castresana, J. 2000. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 17:540-552.
11. Clatworthy, A. E., M. A. Valencia, H. J. H., and M. A. Oettinger. 2003. V(D)J recombination and RAG-mediated transposition in yeast. Cell 12:489-499.
12. Dujon, B., D. Sherman, G. Fischer et al. (67 co-authors). 2004. Genome evolution in yeasts. Nature 430:35-44.
13. Esposito, M. S., and J. E. Wagstaff. 1981. Mechanisms of mitotic recombination. Pp. 341-370 in J. N. Strathem, E. W. Jones, and J. R. Broach, eds. The molecular biology of the yeast Saccharomyces-life cycle and inheritance. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory.
14. Fabre, E., H. Muller, P. Therizols, I. Lafontaine, B. Dujon, and C. Fairhead. 2005. Comparative genomics in hemiascomycete yeasts: evolution of sex, silencing and subtelomeres. Mol. Biol. Evol. (in press).
15. Frank-Vaillant, M., and S. Marcand. 2001. NHEJ regulation by mating type is exercised through a novel protein, Lif2p, essential to the Ligase IV pathway. Genes Dev. 15:3005-3012.
16. Fricke, W. M., S. A. Bastin-Shanower, and S. J. Brill. 2005. Substrate specificity of the Saccharomyces cerevisiae Mus81-Mms4 endonuclease. DNA Repair 4:243-251.
17. Gaillardin, C., V. Charoy, and H. Heslot. 1973. A study of copulation, sporulation and meiotic segregation in Candida lipolytica. Arch. Mikrobiol. 92:69-83.
18. Gangloff, S., J. P. McDonald, C. Bendixen, L. Arthur, and R. Rothstein. 1994. The yeast type I topoisomerase Top3 interacts with Sgs1, a DNA helicase homolog: a potential eukaryotic reverse gyrase. Mol. Cell. Biol. 14:8391-8398.
19. Goldman, N., and Z. Yang. 1994. A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol. Biol. Evol. 11:725-736.
20. Grawunder, U., R. B. West, and M. R. Lieber. 1998. Antigen receptor gene rearrangement. Curr. Opin. Immunol. 10: 172-180.
21. Guindon, S., and O. Gascuel. 2003. A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52:696-704.
22. Haber, J. E. 1995. In vivo biochemistry: physical monitoring of recombination induced by site-specific endonucleases. BioEssays 17:609-620.
23. -. 1998. The many interfaces of Mre11. Cell 95: 583-586.
24. Herman, A., and H. Roman. 1966. Allele specific determinants of homothallism in Saccharomyces lactis. Genetics 53: 727-740.
25. Jones, D. T., W. R. Taylor, and Thornton J.M. 1992. The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci. 8:275-282.
26. Kolodner, R. 1996. Biochemistry and genetics of eukaryotic mismatch repair. Genes Dev. 10:1433-1442.
27. Kreger-van Rij, N. J. W., and M. Veenhuis. 1975. Electron microscopy of ascus formation in the yeast Debaryomyces hansenii. J. Gen. Microbiol. 89:256-264.
28. Krejci, L., M. Macris, Y. Li, S. Van Komen, J. Villemain, T. Ellenberger, H. Klein, and P. Sung. 2004. Role of ATP hydrolysis in the anti-recombinase function of Saccharomyces cerevisiae Srs2 protein. J. Biol. Chem. 279:23193-23199.
29. Lee, C. M., J. Sedman, W. Neupert, and R. A. Stuart. 1999. The DNA helicase, Hmi1p, is transported into mitochondria by a C-terminal cleavable targeting signal. J. Biol. Chem. 274:20937-20942.
30. Lépingle, A., S. Casaregola, C. Neuveglise, E. Bon, H. Nguyen, F. Artiguenave, P. Wincker, and C. Gaillardin. 2000. Genomic exploration of the hemiascomycetous yeasts: 14. Debaryomyces hansenii var. hansenii. FEBS Lett. 487:82-86.
31. Lindahl, T., and R. D. Wood. 1999. Quality control by DNA repair. Science 286:1897-1905.
32. Lynch, M., and J. S. Conery. 2000. The evolutionary fate and consequences of duplicate genes. Science 290:1151-1155.
33. Mullen, J. R., V. Kaliraman, and S. J. Brill. 2000. Bipartite structure of the SGS1 DNA helicase in Saccharomyces cerevisiae. Genetics 154:1101-1114.
34. Notredame, C., D. Higgins, and J. Heringa. 2000. A novel method for multiple sequence alignments. J. Mol. Biol. 302: 205-217.
35. Ögrünç, M., and A. Sancar. 2003. Identification and characterization of human MUS81-MMS4 structure-specific endonuclease. J. Biol. Chem. 278:21715-21721.
36. Pâques, F., and J. E. Haber. 1999. Multiple pathways of recombination induced by double-strand breaks in Saccharomyces cerevisiae. Microbiol. Mol. Biol. Rev. 63:349-404.
37. Pochart, P., D. Woltering, and N. M. Hollings worth. 1997. Conserved properties between functionally distinct MutS homologs in yeast. J. Biol. Chem. 272:30345-30349.
38. Sedman, T., S. Kuusk, S. Kivi, and J. Sedman. 2000. A DNA helicase required for maintenance of the functional mitochondrial genome in Saccharomyces cerevisiae. Mol. Cell. Biol. 20:1816-1824.
39. Snel, B., and M. A. Huynen. 2004. Quantifying modularity in the evolution of biomolecular systems. Genome Res. 3:391-397.
40. Stahl, F. W., H. M. Foss, L. S. Young, R. H. Borts, M. F. F. Abdullah, and G. P. Copenhaver. 2004. Does crossover interference count in Saccharomyces cerevisiae? Genetics 168:35-48.
41. Thompson, J. D., D. G. Higgins, and T. J. Gibson. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
42. Tong, A. H., M. Evangelista, A. B. Parsons et al. (13 co-authors). 2001. Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science 294:2364-2368.
43. Valencia, M., M. Bentele, M. B. Vaze, G. Herrmann, E. Kraus, S.-E. Lee, P. Schär, and J. E. Haber. 2001. NEJ1 controls non-homologous end-joining in Saccharomyces cerevisiae. Nature 414:666-669.
44. Watt, P. M., E. J. Louis, R. H. Borts, and I. D. Hickson. 1995. Sgs1: a eukaryotic homolog of E. coli RecQ that interacts with topoisomerase II in vivo and is required for faithful chromosome segregation. Cell 81:253-260.
45. Wickerham, L. J., C. P. Kurtzman, and A. I. Herman. 1970. Sexual reproduction in Candida lipolytica. Science 167:1141.
46. Yang, Z. 1997. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13:555-556.
47. Zhang, H., J. M. Barcelo, B. Lee, G. Kohlhagen, D. B. Zimonjic, N. C. Popescu, and Y. Pommier. 2001. Human mitochondrial topoisomerase I. Proc. Natl. Acad. Sci. USA 98:10608-10613.
48. Zhang, H., L. H. Meng, D. B. Zimonjic, N. C. Popescu, and Y. Pommier. 2004. Thirteen-exon-motif signature for vertebrate nuclear and mitochondrial type IB topoisomerases. Nucleic Acids Res. 32:2087-2092.
49. Zhou, B.-B. S., and S. J. Elledge. 2000. The DNA damage response: putting checkpoints in perspective. Nature 408:433-439.
50. Zickler, D., and N. Kleckner. 1998. The leptotene-zygotene transition of meiosis. Pp. 619-697 in A. Campbell, W. W. Anderson, and E. W. Jones, eds. Palo Alto, CA: Annual Review of Genetics.