A Comparative Genome-Wide Analysis of GATA Transcription Factors in Fungi |
Park, Jong-Sun
(Fungal Bioinformatics Laboratory)
Kim, Hyo-Jeong (Department of Agricultural Biotechnology) Kim, Soon-Ok (Center for Fungal Genetic Resources) Kong, Sung-Hyung (Fungal Bioinformatics Laboratory) Park, Jae-Jin (Fungal Bioinformatics Laboratory) Kim, Se-Ryun (Fungal Bioinformatics Laboratory) Han, Hyea-Young (Fungal Bioinformatics Laboratory) Park, Bong-Soo (Fungal Bioinformatics Laboratory) Jung, Kyong-Yong (Fungal Bioinformatics Laboratory) Lee, Yong-Hwan (Fungal Bioinformatics Laboratory) |
1 | James, T. Y., Kauff, F., Schoch, C. L., Matheny, P. B., Hofstetter, V. et al. (2006). Reconstructing the early evolution of Fungi using a six-gene phylogeny. Nature 443, 818-822 DOI ScienceOn |
2 | Jones, T., Federspiel, N. A., Chibana, H., Dungan, J., Kalman, S. et al. (2004). The diploid genome sequence of Candida albicans. Proc. Natl. Acad. Sci. USA. 101, 7329-7334 |
3 | Kamper, J., Kahmann, R., Bolker, M., Ma, L. J., Brefort, T. et al. (2006). Insights from the genome of the biotrophic fungal plant pathogen Ustifago maydis. Nature 444, 97-101 DOI ScienceOn |
4 | Lee, K., Loros, J. J., and Dunlap, J. C. (2000). Interconnected feedback loops in the Neurospora circadian system. Science 289, 107-110 DOI ScienceOn |
5 | Lee, K., Singh, P., Chung, W. C., Ash, J., Kim, T. S. et al. (2006). Light regulation of asexual development in the rice blast fungus, Magnaporthe oryzae. Fungal Genet. Biol. 43, 694-706 DOI ScienceOn |
6 | Machida, M., Asai, K., Sano, M., Tanaka, T, Kumagai, T. et al. (2005). Genome sequencing and analysis of Aspergiffus oryzae. Nature 438, 1157-1161 DOI ScienceOn |
7 | Martinez, D., Larrondo, L. F., Putnam, N., Gelpke, M. D., Huang, K. et al.(2004). Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78. Nat. Biotechnol. 22, 695-700 DOI ScienceOn |
8 | Maxon, M. E. and Herskowitz, I. (2001). Ash1P is a site-specific DNA-binding protein that actively represses transcription. Proc. Natl. Acad. Sci. USA. 98, 1495-1500 |
9 | McGinnis, S. and Madden, T. L.(2004). BLAST: at the core of a powerful and diverse set of sequence analysis tools. Nucleic Acids Res. 32, W20-25 DOI |
10 | Caddick, M. X., Arst, H. N Jr. (1990). Nitrogen regulation in Aspergillus: are two fingers better than one? Gene 95, 123-127 DOI ScienceOn |
11 | Canizares, J. V., Pallotti, C., Sainz-Pardo, I., Iranzo, M., and Mormeneo, S. (2002). The SRD2 gene is involved in Saccharomyces cerevisiae morphogenesis. Arch. Microbiol. 177, 352-357 DOI ScienceOn |
12 | Cheng, P., He, Q., Yang, Y., Wang, L., and Liu, Y. (2003). Functional conservation of light, oxygen, or voltage domains in light sensing. Proc. Natl. Acad. Sci. USA. 100, 5938-5943 |
13 | Cliften, P., Sudarsanam, P., Desikan, A., Fulton, L., Fulton, B. et al. (2003). Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301, 71-76 DOI ScienceOn |
14 | Feng, B. and Marzluf, G. A. (1998). Interaction between major nitrogen regulatory protein NIT2 and pathway-specific regulatory factor NIT4 is required for their synergistic activation of gene expression in Neurospora crassa. Mol. Cell Biol. 18, 3983-3990 DOI |
15 | Haas, H. (2003). Molecular genetics of fungal siderophore biosynthesis and uptake: the role of siderophores in iron uptake and storage. Appl. Microbiol. Biotechnol. 62, 316-330 DOI |
16 | Haas, H., Angermayr, K., Zadra, I., and Stoffler, G. (1997). Overexpression of nreB, a new GATA factor-encoding gene of Penicillium chrysogenum, leads to repression of the nitrate assimilatory gene cluster. J. Biol. Chem. 272, 22576-22582 DOI ScienceOn |
17 | International Rice Genome Sequencing Project. (2005). The map-based sequence of the rice genome. Nature 436, 793-800 DOI ScienceOn |
18 | Nierman, W. C., Pain, A., Anderson, M. J., Wortman, J. R., Kim, H. S. et al. (2005). Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergiffus fumigatus. Nature 438, 1151-1156 DOI ScienceOn |
19 | Reyes, J. C., Muro-Pastor, M. I., and Florencio, F. J. (2004). The GATA family of transcription factors in Arabidopsis and rice. Plant Physiol. 134, 1718-1732 DOI ScienceOn |
20 | Thompson, J. D., Higgins, D. G., and Gibson, T. J. (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 DOI |
21 | Crosson, S., Rajagopal, S. and Moffat, K. (2003). The LOV domain family: photoresponsive signaling modules coupled to diverse output domains. Biochemistry 42, 2-10 DOI ScienceOn |
22 | Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C. et al. (2001). Initial sequencing and analysis of the human genome. Nature 409, 860-921 DOI ScienceOn |
23 | Lu, Y. K., Sun, K. H., and Shen, W. C. (2005). Blue light negatively regulates the sexual filamentation via the Cwc1 and Cwc2 proteins in Cryptococcus neoformans. Mol. Microbiol. 56, 480-491 DOI ScienceOn |
24 | Sheppard, D. C., Doedt, T., Chiang, L. Y., Kim, H. S., Chen, D. et al. (2005). The Aspergillus fumigatusStuA protein governs the up-regulation of a discrete transcriptional program during the acquisition of developmental competence. Mol. Biol. Cell 16, 5866-5879 DOI ScienceOn |
25 | Kornberg, T. B. and Krasnow, M. A. (2000). The Drosophila genome sequence: implications for biology and medicine. Science 287, 2218-2220 DOI ScienceOn |
26 | Cunningham, T. S., Rai, R., and Cooper, T. G. (2000). The level of DAL80 expression down-regulates GATA factor-mediated transcription in Saccharomyces cerevisiae. J. Bacteriol. 182, 6584-6591 DOI |
27 | Dean, R. A., Talbot, N. J., Ebbole, D. J., Farman, M. L., Mitchell, T. K. et al. (2005). The genome sequence of the rice blast fungus Magnaporlhe grisea. Nature 434, 980-986 DOI ScienceOn |
28 | Greene, A. V., Keller, N., Haas, H., and Bell-Pedersen, D. (2003). A circadian oscillator in Aspergillus spp. regulates daily development and gene expression. Eukaryot. Cell 2, 231-237 DOI |
29 | Wood, V.Gwiliiam, R.Rajandream, M. A.Lyne, M.Lyne, R. et al.(2002). The genome sequence of Schizosaccharomyces pombe. Nature 415, 871-880 DOI ScienceOn |
30 | Horowitz, N. H., Charlang, G., Horn, G., and Williams, N. P. (1976). Isolation and identification of the conidial germination factor of Neurospora crassa. J. Bacteriol. 127, 135-140 |
31 | Dietrich, F. S., Voegeli, S., Brachat, S., Lerch, A., Gates, K. et al. (2004). The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome. Science 304, 304-307 DOI ScienceOn |
32 | Svetlov, V. V. and Cooper, T. G. (1998). The Saccharomyces cerevisiaeGATA factors Dal80p and Deh1p can form homo- and heterodimeric complexes. J. Bacteriol. 180, 5682-5688 |
33 | Cosma, M. P. (2004). Daughter-specific repression of Saccharomyces cerevisiae HO: Ash1 is the commander. EMBO Rep. 5, 953-957 DOI ScienceOn |
34 | Fabian, G. R., Hess, S. M., and Hopper, A. K. (1990). srd1, a Saccharomyces cerevisiae suppressor of the temperature-sensitive pre-rRNA processing defect of rrp1-1. Genetics 124, 497-504 |
35 | Matzanke, B. F., Bill, E., Trautwein, A. X., and Winkelmann, G.(1987). Role of siderophores in iron storage in spores of Neurospora crassa and Aspergiffus ochraceus. J. Bacteriol. 169, 5873-5876 DOI |
36 | Tyler, B. M., Tripathy, S., Zhang, X., Dehal, P., Jiang, R. H. et al. (2006). Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis. Science 313, 1261-1266 DOI ScienceOn |
37 | Voisard, C., Wang, J., McEvoy, J. L., Xu, P., and Leong, S. A.(1993). urbs1, a gene regulating siderophore biosynthesis in Ustilago maydis, encodes a protein similar to the erythroid transcription factor GATA-1. Mol. Cell Biol. 13, 7091-7100 DOI |
38 | C. elegans Sequencing Consortium (1998). Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 282, 2012-2018 DOI ScienceOn |
39 | Dujon, B., Sherman, D., Fischer, G., Durrens, P., Casaregola, S. et al. (2004). Genome evolution in yeasts. Nature 430, 35-44 DOI ScienceOn |
40 | Eisendle, M., Oberegger, H., Zadra, I., and Haas, H. (2003). The siderophore system is essential for viability of Aspergillus nidulans: functional analysis of two genes encoding I-ornithine N 5-monooxygenase (sidA) and a non-ribosomal peptide synthetase (sidC). Mol. Microbiol. 49, 359-375 DOI ScienceOn |
41 | Schwede, T., Kopp, J., Guex, N., and Peitsch, M. C. (2003). SWISS-MODEL: M automated protein homology-modeling server. Nucleic Acids Res. 31, 3381-3385 DOI ScienceOn |
42 | Teakle, G. R. and Gilmartin, P. M. (1998). Two forms of type IV zinc-finger motif and their kingdom-specific distribution between the flora, fauna and fungi. Trends Biochem. Sci. 23, 100-102 |
43 | Zdobnov, E. M. and Apweiler, R. (2001). InterProScan-an integration platform for the signature-recognition methods in InterPro. Bioinformatics 17, 847-848 DOI ScienceOn |
44 | Scazzocchio, C. (2000). The fungal GATA factors. Curr. Opin. Microbiol. 3, 126-131 DOI ScienceOn |
45 | Galagan, J. E., Calvo, S. E., Cuomo, C., Ma, L. J., Wortman, J. R. et al. (2005). Sequencing of Aspergillus nidulansand comparative analysis with A. fumigatus and A. oryzae. Nature 438, 1105-1115 DOI ScienceOn |
46 | Loftus, B. J., Fung, E., Roncaglia, P., Rowley, D., Amedeo, P. et al. (2005). The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans. Science 307, 1321-1324 DOI ScienceOn |
47 | Arabidopsis Genome Initiative (2000). Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408, 796-815 DOI ScienceOn |
48 | Cao, Y., Cairns, B. R., Kornberg, R. D., and Laurent, B. C. (1997). Sfh1p, a component of a novel chromatin-remodeling complex, is required for cell cycle progression. Mol. Cell Biol. 17, 3323-3334 DOI |
49 | Mo, X. and Marzluf, G. A.(2003). Cooperative action of the NIT2 and NIT4 transcription factors upon gene expression in Neurospora crassa. Curr. Genet. 42, 260-267 |
50 | Hefti, M. H., Francoijs, K. J., de Vries, S. C., Dixon, R, and Vervoort, J. (2004). The PAS fold. A redefinition of the PAS domain based upon structural prediction. Eur. J. Biochem. 271, 1198-1208 DOI ScienceOn |
51 | Klochendler-Yeivin, A. and Yaniv, M. (2001). Chromatin modifiers and tumor suppression. Biochim. Biophys. Acta. 1551, M1-10 |
52 | Lowry, J. A. and Atchley, W. R. (2000). Molecular evolution of the GATA family of transcription factors: conservation within the DNA-binding domain. J. Mol. Evol. 50, 103-115 DOI |
53 | Riechmann, J. L., Heard, J., Martin, G., Reuber, L., Jiang, C. et al.(2000). Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science 290, 2105-2110 DOI ScienceOn |
54 | Goffeau, A., Barrell, B. G., Bussey, H., Davis, R. W., Dujon, B. et al. (1996). Life with 6000 genes. Science 274, 546, 563-547 DOI ScienceOn |
55 | Haas, H., Zadra, I., Stoffler, G., and Angermayr, K. (1999). The Aspergillus nidulansGAT A factor SREA is involved in regulation of siderophore biosynthesis and control of iron uptake. J. Biol. Chem. 274, 4613-4619 DOI ScienceOn |
56 | Linden, H., Ballario, P., and Macino, G. (1997). Blue light regulation in Neurospora crassa. Fungal Genet. Biol. 22, 141-150 DOI ScienceOn |
57 | Vitale, N., Moss, J., and Vaughan, M. (1998). Molecular characterization of the GTPase-activating domain of ADP-ribosylation factor domain protein 1 (ARD1). J. Biol. Chem. 273, 2553-2560 DOI ScienceOn |
58 | Waterston, R. H.Lindblad-Toh, K.Birney, E.Rogers, J.Abril, J. F. et al.(2002). Initial sequencing and comparative analysis of the mouse genome. Nature 420, 520-562 DOI ScienceOn |
59 | Kumar, S., Tamura, K., and Nei, M. (2004). MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Brief Bioinform. 5, 150-163 DOI ScienceOn |
60 | Han, K. H., Han, K. Y., Yu, J. H., Chae, K. S., Jahng, K. Y. et al. (2001). The nsdD gene encodes a putative GATA-type transcription factor necessary for sexual development of Aspergillus nidulans. Mol. Microbiol. 41, 299-309 DOI ScienceOn |
61 | Loros, J. J., Richman, A., and Feldman, J. F. (1986). A recessive circadian clock mutation at the frq locus of Neurospora crassa. Genetics 114, 1095-1110 |
62 | Saitou, N. and Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406-425 |
63 | Morozov, I. Y., Galbis-Martinez, M., Jones, M. G., and Caddick, M. X. (2001). Characterization of nitrogen metabolite signalling in Aspergillus via the regulated degradation of areA mRNA Mol. Microbiol. 42, 269-277 DOI ScienceOn |
64 | Banerjee, N. and Zhang, M. Q. (2003). Identifying cooperativity among transcription factors controlling the cell cycle in yeast. Nucleic Acids Res. 31, 7024-7031 DOI ScienceOn |
65 | Cavailer-Smith, T. (1987). The origin of fungi and pseudofungi. Cambridge Univ. Press |
66 | Pelletier, B., Beaudoin, J., Philpott, C. C., and Labbe, S. (2003). Fep1 represses expression of the fission yeast Schizosaccharomyces pombe siderophore-iron transport system. Nucleic Acids Res. 31, 4332-4344 DOI ScienceOn |
67 | Munchow, S., Ferring, D., Kahlina, K., and Jansen, R. P. (2002). Characterization of Candida albicans ASH1 in Saccharomyces cerevisiae. Curr. Genet. 41, 73-81 DOI |
68 | Tao, Y. and Marzluf, G. A. (1999). The NIT2 nitrogen regulatory protein of Neurospora: expression and stability of nit-2 mRNA and protein. Curr. Genet. 36, 153-158 DOI |
69 | Hayama, R. and Coupland, G. (2003). Shedding light on the circadian clock and the photoperiodic control of flowering. Curr. Opin. Plant Biol. 6, 13-19 DOI ScienceOn |
70 | Inglis, D. O. and Johnson, A. D. (2002). Ash1 protein, an asymmetrically localized transcriptional regulator, controls filamentous growth and virulence of Candida albicans. Mol. Cell Biol. 22, 8669-8680 DOI |
71 | Borkovich, K. A., Alex, L. A., Yarden, O., Freitag, M., Turner, G. E. et al. (2004). Lessons from the genome sequence of Neurospora crassa: tracing the path from genomic blueprint to multicellular organism. Microbiol. Mol. Biol. Rev. 68, 1-108, table of contents DOI ScienceOn |
72 | Conlon, H., Zadra, I., Haas, H., Arst, H. N., Jr., Jones, M. G. et al. (2001). The Aspergillus nidulans GATA transcription factor gene areB encodes at least three proteins and features three classes of mutation. Mol. Microbiol. 40, 361-375 DOI ScienceOn |
73 | Lan, C. Y., Rodarte, G., Murillo, L. A., Jones, T, Davis, R. W. et al. (2004). Regulatory networks affected by iron availability in Candida albicans. Mol. Microbiol. 53, 1451-1469 DOI ScienceOn |
74 | Feng, B., Haas, H., and Marzluf, G. A. (2000). ASD4, a new GATA factor of Neurospora crassa, displays sequence-specific DNA binding and functions in ascus and ascospore development. Biochemistry 39, 11065-11073 DOI ScienceOn |
75 | Kellis, M., Patterson, N., Endrizzi, M., Birren, B., and Lander, E. S. (2003). Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423, 241-254 DOI ScienceOn |
76 | Oliveira, E. M., Martins, A. S., Carvajal, E., and Bon, E. P. (2003). The role of the GATA factors Gln3p, Nil1p, Dal80p and the Ure2p on ASP3 regulation in Saccharomyces cerevisiae. Yeast 20, 31-37 DOI ScienceOn |
77 | Tuskan, G. A., Difazio, S., Jansson, S., Bohlmann, J., Grigoriev, I. et al. (2006). The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313, 1596-1604 DOI ScienceOn |
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