Comparative analysis of 87,000 expressed sequence tags from the fumonisin-producing fungus Fusarium verticillioides

Fungal Genetics and Biology

Volumn 42, Issue 10, 2005, Pages 848-861

  Brown, Daren W ^a   Cheung, Foo ^b   Proctor, Robert H ^a   Butchko, Robert A E ^a   Zheng, Li ^b   Lee, Yuandan ^b   Utterback, Teresa ^c   Smith, Shannon ^c   Feldblyum, Tamara ^c   Glenn, Anthony E ^d   Plattner, Ronald D ^a   Kendra, David F ^a   Town, Christopher D ^b   Whitelaw, Catherine A ^b  

^a NATIONAL CENTER FOR AGRICULTURAL UTILIZATION RESEARCH   (United States)

^b J CRAIG VENTER INSTITUTE   (United States)

^c J Craig Venter Science Foundation Joint Technology Center   (United States)

^d AGRICULTURAL RESEARCH SERVICE   (United States)

Author keywords

Alternatively spliced isoforms; EST; Expressed sequence tag; FUM20; Fumonisin; Fusarium verticillioides; Gene cluster; Regulation; Secondary metabolite

Indexed keywords

COMPLEMENTARY DNA; FUMONISIN; FUNGAL PROTEIN;

ARTICLE; BIOSYNTHESIS; COMPARATIVE STUDY; DNA LIBRARY; EXPRESSED SEQUENCE TAG; FUNGAL GENE; FUNGAL GENETICS; FUSARIUM; FUSARIUM VERTICILLIOIDES; GENE CLUSTER; GENE CONTROL; GENE EXPRESSION; GENE FUNCTION; GENE LIBRARY; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC TRANSCRIPTION; GENOMICS; INTRON; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT; PRIORITY JOURNAL; RNA SPLICING; UNINDEXED SEQUENCE;

AMINO ACID SEQUENCE; BASE SEQUENCE; DNA, FUNGAL; EXPRESSED SEQUENCE TAGS; FUMONISINS; FUSARIUM; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, FUNGAL; GENE LIBRARY; GENES, FUNGAL; GENES, REGULATOR; INTRONS; MOLECULAR SEQUENCE DATA; RNA PROCESSING, POST-TRANSCRIPTIONAL; RNA, FUNGAL; RNA, MESSENGER; SEQUENCE ANALYSIS, DNA;

ANIMALIA; FUNGI; FUSARIUM; GIBBERELLA MONILIFORMIS; ZEA MAYS;

EID: 24944502751     PISSN: 10871845     EISSN: 10960937     Source Type: Journal    
DOI: 10.1016/j.fgb.2005.06.001     Document Type: Article

References (49)

1. S.F. Altschul, T.L. Madden, A.A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D.J. Lipman Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucleic Acids Res. 25 1997 3389 3402
2. M. Ashburner, C.A. Ball, J.A. Blake, D. Botstein, H. Butler, J.M. Cherry, A.P. Davis, K. Dolinski, S.S. Dwight, J.T. Eppig, M.A. Harris, D.P. Hill, L. Issel-Tarver, A. Kasarskis, S. Lewis, J.C. Matese, J.E. Richardson, M. Ringwald, G.M. Rubin, and G. Sherlock Gene ontology: tool for the unification of biology. The Gene Ontology Consortium Nat. Genet. 25 2000 25 29
3. D.L. Black Mechanisms of alternative pre-messenger RNA splicing Annu. Rev. Biochem. 72 2003 291 336
4. S. Boddi, C. Comparini, R. Calamassi, L. Pazzagli, G. Cappugi, and A. Scala Cerato-platanin protein is located in the cell walls of ascospores, conidia and hyphae of Ceratocystis fimbriata f. sp. platani FEMS Microbiol. Lett. 233 2004 341 346
5. E. Boel, I. Hjort, B. Svensson, F. Norris, K.E. Norris, and N.P. Fiil Glucoamylases G1 and G2 from Aspergillus niger are synthesized from two different but closely related mRNAs EMBO J. 3 1984 1097 1102
6. R.S. Bojja, R.L. Cerny, R.H. Proctor, and L. Du Determining the biosynthetic sequence in the early steps of the fumonisin pathway by use of three gene-disruption mutants of Fusarium verticillioides J. Agric. Food Chem. 52 2004 2855 2860
7. D.W. Brown, S.P. McCormick, N.J. Alexander, R.H. Proctor, and A.E. Desjardins A genetic and biochemical approach to study trichothecene diversity in Fusarium sporotrichioides and Fusarium graminearum Fungal Gen. Biol. 32 2001 121 144
8. D.W. Brown, J.-H. Yu, H.S. Kelkar, M. Fernandes, T.C. Nesbitt, N.P. Keller, T.H. Adams, and T.J. Leonard Twenty-five co-regulated transcripts define a sterigmatocystin gene cluster in Aspergillus nidulans Proc. Natl. Acad. Sci. USA 93 1996 1418 1422
9. R.A. Butchko, R.D. Plattner, and R.H. Proctor FUM9 is required for C-5 hydroxylation of fumonisins and complements the meitotically defined Fum3 locus in Gibberella moniliformis Appl. Environ. Microbiol. 69 2003 6935 6937
10. R.A. Butchko, R.D. Plattner, and R.H. Proctor FUM13 encodes a short chain dehydrogenase/reductase required for C-3 carbonyl reduction during fumonisin biosynthesis in Gibberella moniliformis J. Agric. Food Chem. 51 2003 3000 3006
11. H.H. Chou, and M.H. Holmes DNA sequence quality trimming and vector removal Bioinformatics 17 2001 1093 1104
12. N.C. Curach, V.S. Te'o, M.D. Gibbs, P.L. Bergquist, and K.M. Nevalainen Isolation, characterization and expression of the hex1 gene from Trichoderma reesei Gene 331 2004 133 140
13. A.E. Desjardins, R.D. Plattner, and R.H. Proctor Linkage among genes responsible for fumonisin biosynthesis in Gibberella fujikuroi mating population A Appl. Environ. Microbiol. 62 1996 2571 2576
14. D.J. Ebbole Hydrophobins and fungal infection of plants and animals Trends Microbiol. 5 1997 405 408
15. D.J. Ebbole, Y. Jin, M. Thon, H. Pan, E. Bhattarai, T. Thomas, and R. Dean Gene discovery and gene expression in the rice blast fungus, Magnaporthe grisea: analysis of expressed sequence tags Mol. Plant Microbe Interact. 17 2004 1337 1347
16. J.E. Flaherty, and C.P. Woloshuk Regulation of fumonisin biosynthesis in Fusarium verticillioides by a zinc binuclear cluster-type gene, ZFR1 Appl. Environ. Microbiol. 70 2004 2653 2659
17. U. Fuchs, K.J. Czymmek, and J.A. Sweigard Five hydrophobin genes in Fusarium verticillioides include two required for microconidial chain formation Fungal Gen. Biol. 41 2004 852 864
18. A.E. Glenn, S.E. Gold, and C.W. Bacon Fdb1 and Fdb2, Fusarium verticillioides loci necessary for detoxification of preformed antimicrobials from corn Mol. Plant Microbe Interact. 15 2002 91 101
19. A.E. Glenn, D.M. Hinton, I.E. Yates, and C.W. Bacon Detoxification of corn antimicrobial compounds as the basis for isolating Fusarium verticillioides and some other Fusarium species from corn Appl. Environ. Microbiol. 67 2001 2973 2981
20. T.M. Hohn, R. Krishna, and R.H. Proctor Characterization of a transcriptional activator controlling trichothecene toxin biosynthesis Fungal Genet. Biol. 26 1999 224 235
21. Howard, P.C., Eppley, R.M., Stack, M.E., Warbritton, A., Voss, K.A., Lorentzen, R.J., Kovach, R.M., Bucci, T.J., 2001. Fumonisin B1 carcinogenicity in a two-year feed study using F344 rats and B6C3F1 mice. Environ. Health Perspect. 109, 277-282.
22. X. Huang, M.D. Adams, H. Zhou, and A.R. Kerlavage A tool for analyzing and annotating genomic sequences Genomics 46 1997 37 45
23. T. Kawahara, H. Yanagi, T. Yura, and K. Mori Unconventional splicing of HAC1/ERN4 mRNA required for the unfolded protein response. Sequence-specific and non-sequential cleavage of the splice sites J. Biol. Chem. 273 1998 1802 1807
24. J. Kennedy, K. Auclair, S.G. Kendrew, C. Park, J.C. Vederas, and C.R. Hutchinson Modulation of polyketide synthase activity by accessory proteins during lovastatin biosynthesis Science 284 1999 1368 1372
25. R. Klassen, and F. Meinhardt Structural and functional analysis of the killer element pPin1-3 from Pichia inositovora Mol. Genet. Genomics 270 2003 190 199
26. L.F. Larrondo, B. Gonzalez, D. Cullen, and R. Vicuna Characterization of a multicopper oxidase gene cluster in Phanerochaete chrysosporium and evidence of altered splicing of the mco transcripts Microbiology 150 2004 2775 2783
27. P. Lodato, J. Alcaino, S. Barahona, P. Retamales, and V. Cifuentes Alternative splicing of transcripts from crtI and crtYB genes of Xanthophyllomyces dendrorhous Appl. Environ. Microbiol. 69 2003 4676 4682
28. W.F. Marasas, R.T. Riley, K.A. Hendricks, V.L. Stevens, T.W. Sadler, J. Gelineau-Van Waes, S.A. Missmer, J. Cabrera, O. Torres, W.C. Gelderblom, J. Allegood, C. Martinez, J. Maddox, J.D. Miller, L. Starr, M.C. Sullards, A.V. Roman, K.A. Voss, E. Wang, and A.H. Merrill Jr. Fumonisins disrupt sphingolipid metabolism, folate transport, and neural tube development in embryo culture and in vivo: a potential risk factor for human neural tube defects among populations consuming fumonisin-contaminated maize J. Nutr. 134 2004 711 716
29. A. Marchler-Bauer, J.B. Anderson, P.F. Cherukuri, C. DeWeese-Scott, L.Y. Geer, M. Gwadz, S. He, D.I. Hurwitz, J.D. Jackson, Z. Ke, C.J. Lanczycki, C.A. Liebert, C. Liu, F. Lu, G.H. Marchler, M. Mullokandov, B.A. Shoemaker, V. Simonyan, J.S. Song, P.A. Thiessen, R.A. Yamashita, J.J. Yin, D. Zhang, and S.H. Bryant CDD: a Conserved Domain Database for protein classification Nucleic Acids Res. 33 2005 D192 D196
30. D. McColl, C.A. Valencia, and P.J. Vierula Characterization and expression of the Neurospora crassa nmt-1 gene Curr. Genet. 44 2003 216 223
31. G.P. Munkvold, and A.E. Desjardins Fumonisins in maize. Can we reduce their occurrence? Plant Dis. 81 1997 556 565
32. G. OBrian, A.M. Fakhoury, and G.A. Payne Identification of genes differentially expressed during aflatoxin biosynthesis in Aspergillus flavus and Aspergillus parasiticus Fungal Genet. Biol. 39 2003 118 127
33. D. Parisot, M. Dufresne, C. Veneault, R. Lauge, and T. Langin clap1, a gene encoding a copper-transporting ATPase involved in the process of infection by the phytopathogenic fungus Colletotrichum lindemuthianum Mol. Genet. Genomics 268 2002 139 151
34. L. Pazzagli, G. Cappugi, G. Manao, G. Camici, A. Santini, and A. Scala Purification, characterization, and amino acid sequence of cerato-platanin, a new phytotoxic protein from Ceratocystis fimbriata f. sp. platani J. Biol. Chem. 274 1999 24959 24964
35. G. Pertea, X. Huang, F. Liang, V. Antonescu, R. Sultana, S. Karamycheva, Y. Lee, J. White, F. Cheung, B. Parvizi, J. Tsai, and J. Quackenbush TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets Bioinformatics 19 2003 651 652
36. P. Philippsen, K. Kleine, R. Pohlmann, A. Dusterhoft, K. Hamberg, J.H. Hegemann, B. Obermaier, L.A. Urrestarazu, R. Aert, K. Albermann, R. Altmann, B. Andre, V. Baladron, J.P. Ballesta, A.M. Becam, J. Beinhauer, J. Boskovic, M.J. Buitrago, F. Bussereau, F. Coster, M. Crouzet, M. D'Angelo, F. Dal Pero, A. De Antoni, and J. Hani The nucleotide sequence of Saccharomyces cerevisiae chromosome XIV and its evolutionary implications Nature 387 1997 93 98
37. R.H. Proctor, D.W. Brown, R.D. Plattner, and A.E. Desjardins Co-expression of 15 contiguous genes delineates a fumonisin biosynthetic gene cluster in Gibberella moniliformis Fungal Genet. Biol. 38 2003 237 249
38. O. Pylypenko, and I. Schlichting Structural aspects of ligand binding to and electron transfer in bacterial and fungal P450s Annu. Rev. Biochem. 73 2004 991 1018
39. J. Quackenbush, J. Cho, D. Lee, F. Liang, I. Holt, S. Karamycheva, B. Parvizi, G. Pertea, R. Sultana, and J. White The TIGR Gene Indices: analysis of gene transcript sequences in highly sampled eukaryotic species Nucleic Acids Res. 29 2001 159 164
40. J. Quackenbush, F. Liang, I. Holt, G. Pertea, and J. Upton The TIGR gene indices: reconstruction and representation of expressed gene sequences Nucleic Acids Res. 28 2000 141 145
41. M.S. Sachs, and C. Yanofsky Developmental expression of genes involved in conidiation and amino acid biosynthesis in Neurospora crassa Dev. Biol. 148 1991 117 128
42. W.B. Shim, and C.P. Woloshuk Regulation of fumonisin B(1) biosynthesis and conidiation in Fusarium verticillioides by a cyclin-like (C-type) gene, FCC1 Appl. Environ. Microbiol. 67 2001 1607 1612
43. D.J. Stekel, Y. Git, and F. Falciani The comparison of gene expression from multiple cDNA libraries Genome Res. 10 2000 2055 2061
44. F. Trail, J.R. Xu, P. San Miguel, R.G. Halgren, and H.C. Kistler Analysis of expressed sequence tags from Gibberella zeae (anamorph Fusarium graminearum) Fungal Genet. Biol. 38 2003 187 197
45. M. Viaud, A. Brunet-Simon, Y. Brygoo, J.M. Pradier, and C. Levis Cyclophilin A and calcineurin functions investigated by gene inactivation, cyclosporin A inhibition and cDNA arrays approaches in the phytopathogenic fungus Botrytis cinerea Mol. Microbiol. 50 2003 1451 1465
46. J.S. Yadav, M.B. Soellner, J.C. Loper, and P.K. Mishra Tandem cytochrome P450 monooxygenase genes and splice variants in the white rot fungus Phanerochaete chrysosporium: cloning, sequence analysis, and regulation of differential expression Fungal Genet. Biol. 38 2003 10 21
47. J. Yu, D. Bhatnagar, and T.E. Cleveland Completed sequence of aflatoxin pathway gene cluster in Aspergillus parasiticus FEBS Lett. 564 2004 126 130
48. J. Yu, C.A. Whitelaw, W.C. Nierman, D. Bhatnagar, and T.E. Cleveland Aspergillus flavus expressed sequence tags for identification of genes with putative roles in aflatoxin contamination of crops FEMS Microbiol. Lett. 237 2004 333 340
49. Z. Zhang, A.A. Schaffer, W. Miller, T.L. Madden, D.J. Lipman, E.V. Koonin, and S.F. Altschul Protein sequence similarity searches using patterns as seeds Nucleic Acids Res. 26 1998 3986 3990