Polygenic molecular architecture underlying non-sexual cell aggregation in budding yeast

DNA Research

Volumn 20, Issue 1, 2013, Pages 55-66

  Li, Jiarui ^a   Wang, Lin ^a   Wu, Xiaoping ^a   Fang, Ou ^a   Wang, Luwen ^a   Lu, Chenqi ^a   Yang, Shengjie ^a   Hu, Xiaohua ^a   Luo, Zewei ^a,b  

^a FUDAN UNIVERSITY   (China)

^b UNIVERSITY OF BIRMINGHAM   (United Kingdom)

Author keywords

cell aggregation; map based cloning; QTL analysis; Saccharomyces cerevisiae

Indexed keywords

ALLELE; ARTICLE; BIOFILM; CELL AGGREGATION; CHEMICAL STRUCTURE; FLOCCULATION; GENETIC VARIABILITY; GENOME ANALYSIS; MOLECULAR MECHANICS; NONHUMAN; PHENOTYPE; QUANTITATIVE TRAIT LOCUS; SACCHAROMYCES CEREVISIAE; STRESS; YEAST;

AMINO ACID SEQUENCE; CELL AGGREGATION; CELL CYCLE PROTEINS; CHROMOSOME MAPPING; DATABASES, GENETIC; FLOCCULATION; GENE KNOCKOUT TECHNIQUES; GENES, FUNGAL; GENETIC VARIATION; GENOTYPE; GTPASE-ACTIVATING PROTEINS; MANNOSE-BINDING LECTINS; MICROSATELLITE REPEATS; MOLECULAR SEQUENCE DATA; MULTIFACTORIAL INHERITANCE; MULTIGENE FAMILY; NUCLEAR PROTEINS; PHENOTYPE; QUANTITATIVE TRAIT LOCI; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SEQUENCE ANALYSIS, DNA; TRANS-ACTIVATORS;

EID: 84874478803     PISSN: 13402838     EISSN: 17561663     Source Type: Journal    
DOI: 10.1093/dnares/dss033     Document Type: Article

References (40)

1. Smukalla, S., Caldara, M., Pochet, N., et al. 2008, FLO1 is a variable green beard gene that drives biofilm-like cooperation in budding yeast, Cell, 135, 726-37.
2. Gimeno, C.J., Ljungdahl, P.O., Styles, C.A. and Fink, G.R. 1992, Unipolar cell divisions in the yeast S. cerevisiae lead to flamentous growth: regulation by starvation and RAS, Cell, 68, 1077-90.
3. Cullen, P.J. and Sprague, G.F. 2000, Glucose depletion causes haploid invasive growth in yeast, Proc. Natl. Acad. Sci. USA, 97, 13461-3.
4. Pretorius, I.S. 2000, Tailoring wine yeast for the new millennium: novel approaches to the ancient art of winemaking, Yeast, 16, 675-729.
5. Teunissen, A.W., van den Berg, J.A. and Steensma, H.Y. 1995, Localization of the dominant flocculation genes FLO5 and FLO8 of Saccharomyces cerevisiae, Yeast, 30, 735-45.
6. Guo, B., Styles, C.A., Feng, Q.H. and Fink, G.R. 2000, A Saccharomyces gene family involved in invasive growth, cell-cell adhesion, and mating, Proc. Natl. Acad. Sci. USA, 97, 12158-63.
7. Kobayashi, O., Suda, H., Ohtani, T. and Sone, H. 1996, Molecular cloning and analysis of the dominant floccu-lation gene FLO8 from Saccharomyces cerevisiae, Mol. Gen. Genet., 251, 707-15.
8. Rupp, S., Summers, E., Lo, H.J., Madhani, H. and Fink, G. 1999, MAP kinase and cAMP filamentation signaling pathways converge on the unusually large promoter of the yeast FLO11 gene, EMBO J., 18, 1257-69.
9. Verstrepen, K.J., Reynolds, T.B. and Fink, G.R. 2004, Origins of variation in the fungal cell surface, Nat. Rev. Microbiol., 2, 533-40.
10. Verstrepen, K.J. and Klis, F.M. 2006, Flocculation, adhesion and biofilm formation in yeasts, Mol. Microbiol., 60, 5-15.
11. Mackay, T.F. 2001, The genetic architecture of quantitative traits, Annu. Rev. Genet., 35, 303-39.
12. Steinmetz, L.M., Sinha, H., Richards, D.R., et al. 2002, Dissecting the architecture of a quantitative trait locus in yeast, Nature, 416, 326-30.
13. Tabor, H.K., Risch, N.J. and Myers, R.M. 2002, Candidate-gene approaches for studying complex genetic traits: practical considerations, Nat. Rev. Genet., 3, 391-7.
14. Mehrabian, M., Allayee, H., Stockton, J., et al. 2005, Integrating genotypic and expression data in a segregating mouse population to identify 5-lipoxygenase as a susceptibility gene for obesity and bone traits, Nat. Genet., 37, 1224-33.
15. Hu, X.H., Wang, M.H., Tan, T., et al. 2007, Genetic dissection of ethanol tolerance in the budding yeast Saccharomyces cerevisiae, Genetics, 175, 1479-87.
16. Adams, A., Gottschling, D.E., Kaiser, C.A. and Stearns, T. 1998, Methods in Yeast Genetics. A Cold Spring Harbor Laboratory Course Manual. Cold Spring Harbor Laboratory Press: New York.
17. Benson, G. 1999, Tandem repeats finder: a program to analyze DNA sequences, Nucleic Acids Res., 27, 573-80.
18. Baudin, A., Ozier-Kalogeropoulos, O., Denouel, A., Lacroute, F. and Cullin, C. 1993, A simple and efficient method for direct gene deletion in Saccharomyces cerevi-siae, Nucleic Acids Res., 21, 3329-30.
19. Lorenz, M.C., Muir, R.S., Lim, E., McElver, J., Weber, S.C. and Heitman, J. 1995, Gene disruption with PCR products in Saccharomyces cerevisiae, Gene, 158, 113-7.
20. Schmitt, M.E., Brown, T.A. and Trumpower, B.L. 1990, A rapid and simple method for preparation of RNA from Saccharomyces cerevisiae, Nucleic Acids Res., 18, 3091-2.
21. Knop, M., Siegers, K., Pereira, G., et al. 1999, Epitope tagging of yeast genes using a PCR-based strategy: more tags and improved practical routines, Yeast, 15, 963-72.
22. James, P., Halladay, J. and Craig, E.A. 1996, Genomic Libraries and a host strain designed for highly efficient two-hybrid selection in yeast, Genetics, 144, 1425-36.
23. Harper, J.W., Adami, G.R., Wei, N., Keyomarsi, K. and Elledge, S.J. 1993, The p21 Cdk-interacting protein Cip1 is a potent inhibitor of G1 cyclin-dependent kinases, Cell, 75, 805-16.
24. Sorensen, D.A., Anderson, S., Gianola, D. and Korsgaard, I. 1995, Bayesian inference in threshold models using Gibbs sampling, Genet. Sel. Evol., 27, 229-49.
25. Li, J., Wang, S. and Zeng, Z.B. 2006, Multiple-interval mapping for ordinal traits, Genetics, 173, 1649-63.
26. Liu, H., Styles, C.A. and Fink, G.R. 1996, Saccharomyces cerevisiae S288C has a mutation in FLO8, a gene required for filamentous growth, Genetics, 144, 967-78.
27. Kobayashi, O., Yoshimoto, H. and Sone, H. 1999, Analysis of the genes activated by the FLO8 gene in Saccharomyces cerevisiae, Curr. Genet., 36, 256-61.
28. Wang, Y., Shirogane, T., Liu, D., Harper, J.W. and Elledge, S.J. 2003, Exit from exit: resetting the cell cycle through Amn1 inhibition of G protein signaling, Cell, 112, 697-709.
29. Wang, M., Hu, X., Li, G., et al. 2009, Robust detection and genotyping of single feature polymorphisms from gene expression data, PLoS Comput. Biol., 5, e1000317.
30. Voth, W.P., Yu, Y., Takahata, S., Kretschmann, K.L. and Lieb, J.D. 2007, Forkhead proteins control the outcome of transcription factor binding by antiactiva-tion, EMBO J., 26, 4324-34.
31. Lerner, A., Chin, T.E. and Brent, R. 2001, Yeast Cbk1 and Mob2 activate daughter specific genetic programs to induce asymmetric cell fates, Cell, 107, 739-50.
32. Caviston, J.P., Longtine, M., Pringle, J.R. and Bi, E. 2003, The role of Cdc42p GTPase-activating proteins in assembly of the septin ring in yeast, Mol. Biol. Cell, 14, 4051-66.
33. Tong, Z., Gao, X.D., Howell, A.S., Bose, I., Lew, D.J. and Bi, E. 2007, Adjacent positioning of cellular structures enabled by a Cdc42 GTPase-activating protein-mediated zone of inhibition, J. Cell Biol., 179, 1375-84.
34. Smith, G.R., Givan, S.A., Cullen, P. and Sprague, G.F. Jr. 2002, GTPase-activating proteins for Cdc42, Eukaryot. Cell, 1, 469-80.
35. Verstrepen, K.J., Jansen, A., Lewitter, F. and Fink, G.R. 2005, Intragenic tandem repeats generate functional variability, Nat. Genet., 37, 986-90.
36. Lynch, M. and Walsh, B. 1998, Genetics and Analysis of Quantitative Traits. Sunderland, MA, USA: Sinauer Associates.
37. Deutschbauer, A.M. and Davis, R.W. 2005, Quantitative trait loci mapped to single-nucleotide resolution in yeast, Nat. Genet., 37, 1333-40.
38. Brem, R.B., Yvert, G., Clinton, R. and Kruglyak, L. 2002, Genetic dissection of transcriptional regulation in budding yeast, Science, 296, 752-5.
39. Marchler-Bauer, A., Lu, S., Anderson, J.B., et al. 2011, CDD: a conserved domain database for the functional annotation of proteins, Nucleic Acids Res., 39, 225-9.
40. Saito, K., Fujimura-Kamada, K., Hanamatsu, H., et al. 2007, Transbilayer phospholipid flipping regulates Cdc42p signaling during poparized cell growth via Rga GTPase-activating proteins, Dev. Cell, 13, 743-51.