Comparative EST analysis provides insights into the basal aquatic fungus Blastocladiella emersonii

BMC Genomics

Volumn 7, Issue , 2006, Pages

  Ribichich, Karina F ^a   Georg, Raphaela C ^a   Gomes, Suely L ^a  

^a UNIVERSITY OF SÃO PAULO   (Brazil)

Author keywords

[No Author keywords available]

Indexed keywords

COBAMAMIDE; COMPLEMENTARY DNA; FUNGAL PROTEIN; PROPIONYL COENZYME A;

AMINO ACID SEQUENCE; AQUATIC FAUNA; ARTICLE; BLASTOCLADIELLA; BLASTOCLADIELLA EMERSONII; CHYTRIDIOMYCETES; COMPARATIVE STUDY; DATA BASE; DNA SEQUENCE; EXPRESSED SEQUENCE TAG; GENE EXPRESSION REGULATION; GENE IDENTIFICATION; GENETIC CONSERVATION; GENETIC VARIABILITY; NEUROSPORA CRASSA; NONHUMAN; NORTHERN BLOTTING; NUCLEOTIDE SEQUENCE; ORTHOLOGY; PLESIOMORPHY; PROTEIN DATABASE; SEQUENCE ANALYSIS; UNINDEXED SEQUENCE; USTILAGO MAYDIS; VALIDATION PROCESS;

ANIMALS; BLASTOCLADIELLA; CONSERVED SEQUENCE; DATABASES, GENETIC; DNA, FUNGAL; DNA, PLANT; EXPRESSED SEQUENCE TAGS; GENETIC SPECIATION; HUMANS; METHYLMALONYL-COA DECARBOXYLASE; MICE; NEUROSPORA CRASSA; PHYLOGENY; RATS; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, NUCLEIC ACID; SPECIES SPECIFICITY; USTILAGO; VITAMIN B 12;

ANIMALIA; BLASTOCLADIELLA EMERSONII; FUNGI; NEUROSPORA CRASSA; USTILAGO MAYDIS;

EID: 33747335894     PISSN: 14712164     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-7-177     Document Type: Article

References (65)

1. Goffeau A, Barrell BG, Bussey H, Davis RW, Dujon B, Feldmann H, Galibert F, Hoheisel JD, Jacq C, Johnston M, Louis EJ, Mewes HW, Murakami Y, Philippsen P, Tettelin H, Oliver SG: Life With 6000 genes. Science 1996, 274:546, 563-7.
2. Wood V, Gwilliam R, Rajandream MA, Lyne M, Lyne R, Stewart A, Sgouros J, Peat N, Hayles J, Baker S, Basham D, Bowman S, Brooks K, Brown D, Brown S, Chillingworth T, Churcher C, Collins M, Connor R, Cronin A, Davis P, Feltwell T, Fraser A, Gentles S, Goble A, Hamlin N, Harris D, Hidalgo J, Hodgson G, Holroyd S, Hornsby T, Howarth S, Huckle EJ, Hunt S, Jagels K, James K, Jones L, Jones M, Leather S, McDonald S, McLean J, Mooney P, Moule S, Mungall K, Murphy L, Niblett D, Odell C, Oliver K, O'Neil S, Pearson D, Quail MA, Rabbinowitsch E, Rutherford K, Rutter S, Saunders D, Seeger K, Sharp S, Skelton J, Simmonds M, Squares R, Squares S, Stevens K, Taylor K, Taylor RG, Tivey A, Walsh S, Warren T, Whitehead S, Woodward J, Volckaert G, Aert R, Robben J, Grymonprez B, Weitjens I, Vanstreels E, Rieger M, Schafer M, Muller-Auer S, Gabel C, Fuchs M, Dusterhoft A, Fritzc C, Holzer E, Moestl D, Hilbert H, Borzym K, Langer I, Beck A, Lehrach H, Reinhardt R, Pohl TM, Eger P, Zimmermann W, Wedler H, Wambutt R, Purnelle B, Goffeau A, Cadieu E, Dreano S, et al., The genome sequence of Schizosaccharomyces pombe. Nature 2002, 415:871-880.
3. Galagan JE, Calvo SE, Borkovich KA, Selker EU, Read ND, Jaffe D, FitzHugh W, Ma LJ, Smirnov S, Purcell S, Rehman B, Elkins T, Engels R, Wang S, Nielsen CB, Butler J, Endrizzi M, Qui D, Ianakiev P, Bell-Pedersen D, Nelson MA, Werner-Washburne M, Selitrennikoff CP, Kinsey JA, Braun EL, Zelter A, Schulte U, Kothe GO, Jedd G, Mewes W, Staben C, Marcotte E, Greenberg D, Roy A, Foley K, Naylor J, Stange-Thomann N, Barrett R, Gnerre S, Kamal M, Kamvysselis M, Mauceli E, Bielke C, Rudd S, Frishman D, Krystofova S, Rasmussen C, Metzenberg RL, Perkins DD, Kroken S, Cogoni C, Macino G, Catcheside D, Li W, Pratt RJ, Osmani SA, DeSouza CP, Glass L, Orbach MJ, Berglund JA, Voelker R, Yarden O, Plamann M, Seiler S, Dunlap J, Radford A, Aramayo R, Natvig DO, Alex LA, Mannhaupt G, Ebbole DJ, Freitag M, Paulsen I, Sachs MS, Lander ES, Nusbaum C, Birren B: The genome sequence of the filamentous fungus Neurospora crassa. Nature 2003, 422:859-868.
4. Martinez D, Larrondo LF, Putnam N, Gelpke MD, Huang K, Chapman J, Helfenbein KG, Ramaiya P, Detter JC, Larimer F, Coutinho PM, Henrissat B, Berka R, Cullen D, Rokhsar D: Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78. Nat Biotechnol 2004, 22:695-700.
5. Loftus BJ, Fung E, Roncaglia P, Rowley D, Amedeo P, Bruno D, Vamathevan J, Miranda M, Anderson IJ, Fraser JA, Allen JE, Bosdet IE, Brent MR, Chiu R, Doering TL, Donlin MJ, D'Souza CA, Fox DS, Grinberg V, Fu J, Fukushima M, Haas BJ, Huang JC, Janbon G, Jones SJ, Koo HL, Krzywinsiki MI, Kwon-Chung JK, Lengeler KB, Maiti R, Marra MA, Marra RE, Mathewson CA, Mitchell TG, Pertea M, Riggs FR, Salzberg SL, Schein JE, Shvartsbeyn A, Shin H, Shumway M, Specht CA, Suh BB, Tenney A, Utterback TR, Wickes BL, Wortman JR, Wye NH, Kronstad JW, Lodge JK, Heitman J, Davis RW, Fraser CM, Hyman RW: The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans. Science 2005, 307:1321-1324.
6. Galagan JE, Henn MR, Ma LJ, Cuomo CA, Birren B: Genomics of the fungal kingdom: insights into eukaryotic biology Genome. Genome Res 2005, 15:1620-1631.
7. Diener SE, Chellappan MK, Mitchell TK, Dunn-Coleman N, Ward M, Dean RA: Insight into Trichoderma reesei's genome content, organization and evolution revealed through BAC library characterization. Fungal Genet Biol 2004, 41:1077-1087.
8. Braun EL, Halpern AL, Nelson MA, Natvig DO: Large-scale comparison of fungal sequence information: mechanisms of innovation in Neurospora crassa and gene loss in Saccharomyces cerevisiae. Genome Res 2000, 10:416-430.
9. Zhu H, Nowrousian M, Kupfer D, Colot HV, Berrocal-Tito G, Lai H, Bell-Pedersen D, Roe BA, Loros JJ, Dunlap JC: Analysis of expressed sequence tags from two starvation, time-of-day-specific libraries of Neurospora crassa reveals novel clock-controlled genes. Genetics 2001, 157:1057-1065.
10. Soanes DM, Talbot NJ: Comparative genomic analysis of phytopathogenic fungi using expressed sequence tag (EST) collections. Molecular Plant Pathology 2006, 7:61-70.
11. Austin R, Provart NJ, Sacadura NT, Nugent KG, Babu M, Saville BJ: A comparative genomic analysis of ESTs from Ustilago maydis. Funct Integr Genomics 2004, 4:207-218.
12. Sims AH, Gent ME, Robson GD, Dunn-Coleman NS, Oliver SG: Combining transcriptome data with genomic and cDNA sequence alignments to make confident functional assignments for Aspergillus nidulans genes. Mycol Res 2004, 108:853-857.
13. Ebbole DJ, Jin Y, Thon M, Pan H, Bhattarai E, Thomas T, Dean R. Gene discovery and gene expression in the rice blast fungus, Magnaporthe grisea: analysis of expressed sequence tags. Mol Plant Microbe Interact 2004, 17:1337-1347.
14. Ribichich KF, Salem-Izacc SM, Georg RC, Vencio RZ, Navarro LD, Gomes SL: Gene discovery and expression profile analysis through sequencing of expressed sequence tags from different developmental stages of the chytridiomycete Blastocladiella emersonii. Eukaryot Cell 2005, 4:455-464.
15. Steenkamp ET, Wright J, Baldauf SL: The protistan origins of animals and fungi. Mol Biol Evol 2006, 23:93-106.
16. Baldauf SL: The deep roots of eukaryotes. Science 2003, 300:1703-1706.
17. Bobik TA, Rasche ME: Identification of the human methylmalonyl-CoA racemase gene based on the analysis of prokaryotic gene arrangements. Implications for decoding the human genome. J Biol Chem 2001, 276:37194-37198.
18. Ledley FD, Crane AM, Klish KT, May GS: Is there methylmalonyl CoA mutase in Aspergillus nidulans? Biochem Biophys Res Commun 1991, 177:1076-1081.
19. Lubkowitz MA, Hauser L, Breslav M, Naider F, Becker JM: An oligopeptide transport gene from Candida albicans. Microbiology 1997, 143 (Pt 2):387-396.
20. Lubkowitz MA, Barnes D, Breslav M, Burchfield A, Naider F, Becker JM: Schizosaccharomyces pombe isp4 encodes a transporter representing a novel family of oligopeptide transporters. Mol Microbiol 1998, 28:729-741.
21. Hauser M, Donhardt AM, Barnes D, Naider F, Becker JM: Enkephalins are transported by a novel eukaryotic peptide uptake system. J Biol Chem 2000, 275:3037-3041.
22. Koh S, Wiles AM, Sharp JS, Naider FR, Becker JM, Stacey G: An oilgopeptide transporter gene family in Arabidopsis. Plant Physiol 2002, 128:21-29.
23. Sanderfoot AA, Kovaleva V, Bassham DC, Raikhel NV: Interactions between syntaxins identify at least five SNARE complexes within the Golgil/ prevacuolar system of the Arabidopsis cell. Mol Biol Cell 2001, 12:3733-3743.
24. Sanderfoot AA, Assaad FF, Raikhel NV: The Arabidopsis genome. An abundance of soluble N-ethylmaleimide-sensitive factor adaptor protein receptors. Plant Physiol 2000, 124:1558-1569.
25. Tabor H, Mehler AH, Hayaishi O, White J: Urocanic acid as an intermediate in the enzymatic conversion of histidine to glutamic and formic acids. J Biol Chem 1952, 196:121-128.
26. Retey J: The urocanase story: a novel role of NAD+ as electrophile. Arch Biochem Biophys 1994, 314:1-16.
27. Hellio C, Veron B, Le Gal Y: Amino acid utilization by Chlamydomonas reinhardtii: specific study of histidine. Plant Physiol Biochem 2004, 42:257-264.
28. Polkinghorne MA, Hynes MJ: L-histidine utilization in Aspergillus nidulans. J Bacteriol 1982, 149:931-940.
29. Rogers M, Keeling PJ: Lateral transfer and recompartmentalization of Calvin cycle enzymes of plants and algae. J Mol Evol 2004, 58:367-375.
30. Weidenhaupt M, Bruckert F, Louwagie M, Garin J, Satre M: Functional and molecular identification of novel members of the ubiquitous membrane fusion proteins alpha- and gamma-SNAP (soluble N-ethylmaleimide-sensitive factor-attachment proteins) families in Dictyostelium discoideum. Eur J Biochem 2000, 267:2062-2070.
31. Nepomuceno-Silva JL, de Melo LD, Mendonca SM, Paixao JC, Lopes UG: RJLs: a new family of Ras-related GTP-binding proteins. Gene 2004, 327:221-232.
32. Bendtsen JD, Nielsen H, von Heijne G, Brunak S: Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 2004, 340:783-795.
33. Nielsen H, Krogh A. Prediction of signal peptides and signal anchors by a hidden Markov model. Proc Int Conf Intell Syst Mol Biol 1998, 6:122-130.
34. Keeling PJ, Inagaki Y: A class of eukaryotic GTPase with a punctate distribution suggesting multiple functional replacements of translation elongation factor 1 alpha. Proc Natl Acad Sci U S A 2004, 101:15380-15385.
35. Bof M, Brandolin G, Satre M, Klein G: The mitochondrial adenine nucleotide translocator from Dictyostelium discoideum. Functional characterization and DNA sequencing. Eur J Biochem 1999, 259:795-800.
36. Muraki T, Taki M, Hasegawa Y, Iwaki H, Lau PC: Prokaryotic homologs of the eukaryotic 3-hydroxyanthranilate 3,4-dioxygenase and 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase in the 2-nitrobenzoate degradation pathway of Pseudomonas fluorescens strain KU-7. Appl Environ Microbiol 2003, 69:1564-1572.
37. Brock M, Fischer R, Linder D, Buckel W: Methylcitrate synthase from Aspergillus nidulans: implications for propionate as an antifungal agent. Mol Microbiol 2000, 35:961-973.
38. Bobik TA, Rasche ME: Purification and partial characterization of the Pyrococcus horikoshii methylmalonyl-CoA epimerase. Appl Microbiol Biotechnol 2004, 63:682-685.
39. Brock M, Buckel W: On the mechanism of action of the antifungal agent propionate. Eur J Biochem 2004, 271:3227-3241.
40. Conklin DS, McMaster JA, Culbertson MR, Kung C: COTI, a gene involved in cobalt accumulation in Saccharomyces cerevisiae. Mol Cell Biol 1992, 12:3678-3688.
41. Uemura T, Ueda T, Ohniwa RL, Nakano A, Takeyasu K, Sato MH: Systematic analysis of SNARE molecules in Arabidopsis: dissection of the post-Golgi network in plant cells. Cell Struct Funct 2004, 29:49-65.
42. Lovett JS: Growth and differentiation of the water mold Blastocladiella emersonii: cytodifferentiation and the role of ribonucleic acid and protein synthesis. Bacteriol Rev 1975, 39:345-404.
43. database. B: Blastocladiella emersonii database. [http://blasto.iq.usp.br].
44. Machlis L: Effect of certain organic acidson the utilization of mannose and fructose by the filamentous watermold, Allomyces macrogynus. J Bacteriol 1957, 73:627-631.
45. Marsh JJ, Lebherz HG: Fructose-bisphosphate aldolases: an evolutionary history. Trends Biochem Sci 1992, 17:110-113.
46. Gross W, Lenze D, Nowitzki U, Weiske J, Schnarrenberger C: Characterization, cloning, and evolutionary history of the chloroplast and cytosolic class I aldolases of the red alga Galdieria sulphuraria. Gene 1999, 230:7-14.
47. Plaumann M, Pelzer-Reith B, Martin WF, Schnarrenberger C: Multiple recruitment of class-I aldolase to chloroplasts and eubacterial origin of eukaryotic class-II aldolases revealed by cDNAs from Euglena gracilis. Curr Genet 1997, 31:430-438.
48. Kuba M, Yatsuki H, Kusakabe T, Takasaki Y, Nikoh N, Miyata T, Yamaguchi T, Hori K: Molecular evolution of amphioxus fructose-1,6-bisphosphate aldolase. Arch Biochem Biophys 1997, 348:329-336.
49. Canete-Soler R, Reddy KS, Tolan DR, Zhai J: Aldolases a and C are ribonucleolytic components of a neuronal complex that regulates the stability of the light-neurofilament mRNA. J Neurosci 2005, 25:4353-4364.
50. Chen D, Xu W, He P, Medrano EE, Whiteheart SW: Gaf-I, a gamma -SNAP-binding protein associated with the mitochondria. J Biol Chem 2001, 276:13127-13135.
51. Bock JB, Matern HT, Peden AA, Scheller RH: A genomic perspective on membrane compartment organization. Nature 2001, 409:839-841.
52. National Center for Biotechnology Information. EST database.: National Center for Biotechnology Information. EST database. [http://www.ncbi.nlm.nih.gov/dbEST/].
53. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25:3389-3402.
54. database. JGIIMR:JGI. Integrated Microbial Resource database. [http://img.igi.doe.gov/pub/main.cgi/].
55. Broad Institute. Fungal Genome Initiative Web site: Broad Institute. Fungal Genome Initiative Web site. http://www.broad.mit.edu/annotation/ fgi/].
56. University of Oklahoma. Advanced Center for Genome Technology.: University of Oklahoma. Advanced Center for Genome Technology. [ftp://ftp.genome.ou.edu/pub/].
57. Entrez NCBI: NCBI Entrez. http://www.ncbi.nlm.nih.gov/entrez/ query.fcgi?db=genomeprj].
58. NCBI. Basic Local Alignment Search Tool.: NCBI. Basic Local Alignment Search Tool. [http://www.ncbi.nlm.nih.gov/blast/].
59. NCBI. BLAST file transfer protocol (ftp) site: NCBI. BLAST file transfer protocol (ftp) site. [ftp://ncbi.nlm.nih.gov/blast/].
60. Consortium GO: Gene Onthollogy Consortium. [http://www.geneontology.org].
61. Swiss Institute of Bioinformatics. Expert Protein Analysis System.: Swiss Institute of Bioinformatics. Expert Protein Analysis System. [http://www.expasy.org].
62. InterPro. EBI: European Bioinformatics Institute. InterPro. [http://www.ebi.ac.uk/interpro].
63. Munich Information Center for Protein Sequences.: Munich Information Center for Protein Sequences. [http://mips.gsf.de].
64. Consortium. FAM: Functional Annotation of Mouse-3 Consortium. [http://fantom3.gsc.riken.jp/].
65. U.S. National Institutes of Health and the British Medical Research Council. A Database of the, (FlyBase). DG: U.S. National Institutes of Health and the British Medical Research Council. A Database of the Drosophila Genome (FlyBase). http://flybase.bio.indiana.edu/].