Gene discovery for the bark beetle-vectored fungal tree pathogen Grosmannia clavigera

BMC Genomics

Volumn 11, Issue 1, 2010, Pages

  Hesse Orce, Uljana ^a   DiGuistini, Scott ^a   Keeling, Christopher I ^b   Wang, Ye ^a   Li, Maria ^b   Henderson, Hannah ^b   Docking, T Roderick ^c   Liao, Nancy Y ^c   Robertson, Gordon ^c   Holt, Robert A ^c   Jones, Steven J M ^c   Bohlmann, Jörg ^b   Breuil, Colette ^a  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^b UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^c BRITISH COLUMBIA CANCER AGENCY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; MESSENGER RNA; PLANT EXTRACT;

ARTICLE; BEETLE; CONIFER; CONTROLLED STUDY; CULTURE MEDIUM; DNA LIBRARY; EXPRESSED SEQUENCE TAG; FUNGAL SPORE GERMINATION; FUNGUS CULTURE; FUNGUS ISOLATION; GENE CONSTRUCT; GENE EXPRESSION; GENE IDENTIFICATION; GENE SEQUENCE; GROSMANNIA CLAVIGERA; MYCELIUM; NONHUMAN; OPHIOSTOMA; PHLOEM; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; UPREGULATION; ANIMAL; BARK; CHEMISTRY; DISEASE CARRIER; DRUG EFFECT; FUNGAL GENE; FUNGUS SPORE; GENE EXPRESSION REGULATION; GENE LIBRARY; GENETIC DATABASE; GENETICS; ISOLATION AND PURIFICATION; METABOLISM; MICROBIOLOGY; OPHIOSTOMATALES; PINE; TREE;

CLAVIGERA; COLEOPTERA; FUNGI; PINUS CONTORTA; SCOLYTINAE;

ANIMALS; BEETLES; DATABASES, GENETIC; EXPRESSED SEQUENCE TAGS; GENE EXPRESSION REGULATION, FUNGAL; GENE LIBRARY; GENES, FUNGAL; INSECT VECTORS; METABOLIC NETWORKS AND PATHWAYS; MYCELIUM; OPHIOSTOMATALES; PHLOEM; PINUS; PLANT BARK; PLANT EXTRACTS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, MESSENGER; SPORES, FUNGAL; TREES;

EID: 77957255772     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-11-536     Document Type: Article

References (49)

1. Reid RW, Whitney HS, Watson JA. Reactions of lodgepole pine to attack by Dendroctonus ponderosae Hopkins and blue stain fungi. Can J Bot 1967, 45:1115-1126.
2. Zipfel RD, de Beer ZW, Jacobs K, Wingfield BD, Wingfield MJ. Multi-gene phylogenies define Ceratocystiopsis and Grosmannia distinct from Ophiostoma. Stud Mycol 2006, 55:75-97. 10.3114/sim.55.1.75, 2104718, 18490973.
3. Yamaoka Y, Hiratsuka Y, Maruyama PJ. The ability of Ophiostoma clavigerum to kill mature lodgepole pine trees. Eur J For Pathol 1995, 25:401-404.
4. Lee S, Kim JJ, Breuil C. Pathogenicity of Leptographium longiclavatum associated with Dendroctonus ponderosae to Pinus contorta. Can J For Res 2006, 36:2864-2872.
5. Six DL. A comparison of mycangial and phoretic fungi of individual mountain pine beetles. Can J For Res 2003, 33:1331-1334.
6. Paine TD, Raffa KF, Harrington TC. Interactions among scolytid bark beetles, their associated fungi and live host conifers. Annu Rev Entomol 1997, 42:179-206. 10.1146/annurev.ento.42.1.179, 15012312.
7. Krokene P, Nagy NE, Krekling T. Traumatic resin ducts and polyphenolic parenchyma cells in conifers. Induced plant resistance to herbivory 2008, 147-169. Springer, Dordrecht, Schaller A.
8. Keeling CI, Bohlmann J. Genes, enzymes and chemicals of terpenoid diversity in the constitutive and induced defense of conifers against insects and pathogens. New Phytol 2006, 170:657-675. 10.1111/j.1469-8137.2006.01716.x, 16684230.
9. Keeling CI, Bohlmann J. Diterpene resin acids in conifers. Phytochem 2006, 67:2415-2423.
10. Blanchette RA, Farrell RL, Burnes TA, Wendler PA, Zimmerman W, Brush TS, Snyder RA. Biological control of pitch in pulp and paper production by Ophiostoma piliferum. TAPPI J 1992, 75:102-106.
11. Brush TS, Farrell RL, Ho C. Biodetoxification of wood extractives from southern yellow pine by Ophiostoma piliferum. TAPPI J 1994, 77:155-159.
12. Wang Z, Chen T, Gao Y, Breuil C, Hiratsuka Y. Biological degradation of resin acids in wood chips by wood-inhabiting fungi. Appl Environ Microbiol 1995, 61:222-225. 167276, 7887603.
13. DiGuistini S, Ralph SG, Lim YW, Holt R, Jones S, Bohlmann J, Breuil C. Generation and annotation of lodgepole pine and oleoresin-induced expressed sequences from the blue-stain fungus Ophiostoma clavigerum, a mountain pine beetle-associated pathogen. FEMS Microbiol Lett 2007, 267:151-158. 10.1111/j.1574-6968.2006.00565.x, 17328114.
14. Hergert HL. The flavonoids of lodgepole pine bark. J Org Chem 1956, 21:534-53.
15. Vercruysse SAR, Delcour JA, Dondeyne P. Isolation of quercetin, myricetin, and their respective dihydro-compounds by Sephadex LH-20 chromatography. J Chrom 1985, 324:495-497.
16. Matthews S, Mila I, Scalbert A, Pollet B, Lapierre C, Herve' du Penhoat CLM, Rolando C, Donnelly DMXL. Method for estimation of proanthocyanidins based on their acid depolymerization in the presence of nucleophiles. J Agric Food Chem 1997, 45:1195-1201.
17. Stolter C, Niemela P, Ball JP, Julkunen-Tiitto R, Vanhatalo A, Danell K, Varvikko T, Ganzhorn JU. Comparison of plant secondary metabolites and digestibility of three different boreal coniferous trees. Basic Appl Ecol 2009, 10:19-26.
18. Witzell J, Martin JA. Phenolic metabolites in the resistance of northern forest trees to pathogens - past experiences and future prospects. Can J For Res 2008, 38:2711-2727.
19. Kocabas DS, Bakir U, Phillips SE, Mcpherson MJ, Ogel ZB. Purification, characterization and identification of a novel bifunctional catalase-phenol oxidase from Scytalidium thermophilum. New Biotechnol 2009, 25:S92-93.
20. Band L, Ciofi-Baffoni S, Tien M. Lignin and Mn-peroxidase-catalyzed oxidation of phenolic lignin oligomers. Biochem 1999, 38:3205-3210.
21. Hammer E, Schoefer L, Schäfer A, Hundt K, Schauer F. Formation of glucoside conjugates during biotransformation of dibenzofuran by penicillium canescens SBUG-M 1139. Appl Microbiol Biotechnol 2001, 57:390-394. 10.1007/s002530100768, 11759691.
22. McCue P, Shetty K. Role of carbohydrate-cleaving enzymes in antioxidant mobilization from whole soybean fermented with Rhizopus oligosporus. Food Biotechnol 2003, 17:27-37.
23. Nicholson RL, Hipskind J, Hanau RM. Protection against phenol toxicity by the spore mucilage of Colletotrichum graminicola, an aid to secondary spread. Physiol Mol Plant Pathol 1989, 35:243-252.
24. DiGuistini S, Liao NY, Platt D, Robertson G, Seidel M, Chan SK, Birol I, Holt RA, Hirst M, Mardis E, Marra MA, Hamelin RC, Bohlmann J, Breuil C, Jones SJM. De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data. Genome Biol 2009, 10:R94. 10.1186/gb-2009-10-9-r94, 2768983, 19747388.
25. Nagaraj SH, Deshpande N, Gasser RB, Ranganathan S. ESTExplorer: an expressed sequence tag (EST) assembly and annotation platform. Nucleic Acids Res 2007, 35:W143-147. 10.1093/nar/gkm378, 1933243, 17545197.
26. Tang Z, Choi JH, Hemmerich C, Sarangi A, Colbourne JK, Dong Q. ESTPiper - a web-based analysis pipeline for expressed sequence tags. BMC Genomics 2009, 10:174. 10.1186/1471-2164-10-174, 2676306, 19383159.
27. Makalowska I, Lin CF, Makalowski W. Overlapping genes in vertebrate genomes. Comput Biol Chem 2005, 29:1-12. 10.1016/j.compbiolchem.2004.12.006, 15680581.
28. Smith CA, Robertson D, Yates B, Nielsen DM, Brown D, Dean RA, Payne GA. The effect of temperature on Natural Antisense Transcript (NAT) expression in Aspergillus flavus. Curr Genet 2008, 54:241-69. 10.1007/s00294-008-0215-9, 18813928.
29. Oh YT, Ahna CS, Kima JG, Roa HS, Lee CW, Kim JW. Proteomic analysis of early phase of conidia germination in Aspergillus nidulans. Fungal Genet Biol 2010, 47:246-253. 10.1016/j.fgb.2009.11.002, 19919853.
30. Taubitz A, Bauer B, Heesemann J, Ebel F. Role of respiration in the germination process of the pathogenic mold Aspergillus fumigatus. Curr Microbiol 2007, 54:354-360. 10.1007/s00284-006-0413-y, 17486408.
31. Takatsume Y, Maeta K, Izawa S, Inoue Y. Enrichment of yeast thioredoxin by green tea extract through activation of Yap1 transcription factor in Saccharomyces cerevisiae. J Agric Food Chem 2005, 53:332-337. 10.1021/jf048818h, 15656669.
32. Kim JH, Campbell BC, Mahoney N, Chan KL, May GS. Targeting antioxidative signal transduction and stress response system: control of pathogenic Aspergillus with phenolics that inhibit mitochondrial function. J Appl Microbiol 2005, 101:181-189.
33. Chary P, Dillon D, Schroeder AL, Natvig DO. Superoxide dismutase (sod-1) null mutants of Neurospora crassa: oxidative stress sensitivity, spontaneous mutation rate and response to mutagens. Genetics 1994, 137:723-730. 1206032, 8088518.
34. Moore S, De Vries OMH, Tudzynski P. The major Cu,Zn SOD of the phytopathogen Claviceps purpurea is not essential for pathogenicity. Molec Plant Pathol 2002, 3:9-22.
35. Xia Z, Yoshida T, Funaoka M. Enzymatic degradation of highly phenolic lignin-based polymers (lignophenols). Eur Polym J 2003, 39:909-914.
36. Bryant C, McElroy WD. Nitroreductases. Chemistry and Biochemistry of Flavoenzymes 1991, II:291-304. CRC Press: Boca Raton, FL, Muller F.
37. Dai R, Chen J, Lin J, Xiao S, Chen S, Deng Y. Reduction of nitro phenols using nitroreductase from E. coli in the presence of NADH. J Hazard Mater 2009, 170:141-143. 10.1016/j.jhazmat.2009.04.122, 19481342.
38. Peterson FJ, Mason RP, Hovespian J, Holtzman JL. Oxygen-sensitive and -insensitive nitroreduction by Escherichia coli and rat hepatic microsomes. J Biol Chem 1979, 254:4009-4014.
39. Angermaier L, Simon H. On nitroaryl reductase activities in several clostridia. H-S Z Physiol Chem 1983, 364:1653-1663.
40. de Oliveira IM, Henriques JA, Bonatto D. In silico identification of a new group of specific bacterial and fungal nitroreductases-like proteins. Biochem Biophys Res Commun 2007, 355:919-925. 10.1016/j.bbrc.2007.02.049, 17331467.
41. de Oliveira IM, Zanotto-Filho A, Fonseca Moreira JC, Bonatto D, Pegas Henriques JA. The role of two putative nitroreductases, Frm2p and Hbn1p, in the oxidative stress response in Saccharomyces cerevisia. Yeast 2010, 27:89-102.
42. Nierman WC, Pain A, Anderson MJ, Wortman JR, Kim HS, Arroyo J, Berriman B, Abe K, Archer DB, Bermejo C, et al. Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus. Nature 2005, 438:1151-1156. 10.1038/nature04332, 16372009.
43. Kämper J, Kahmann R, Bölker M, Ma LJ, Brefort T, Saville BJ, Banuett F, Kronstad JW, Gold SE, Müller O, et al. Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis. Nature 2006, 444:97-101. 10.1038/nature05248, 17080091.
44. Matthews DE, VanEtten HD. Detoxification of the phytoalexin pisatin by a fungal cytochrome P-450. Arch Biochem Biophys 1983, 224:494-505. 10.1016/0003-9861(83)90237-0, 6870275.
45. Kelly DE, Krasevec N, Mullins J, Nelson DR. The CYPome (Cytochrome P450 complement) of Aspergillus nidulans. Fungal Genet Biol 2009, 46:S53-61. 10.1016/j.fgb.2008.08.010, 18824241.
46. Ewing B, Green P. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 1998, 8:186-194.
47. Huang X, Madan A. CAP3: a DNA sequence assembly program. Genome Res 1999, 9:868-877. 10.1101/gr.9.9.868, 310812, 10508846.
48. Kent WJ. BLAT--the BLAST-like alignment tool. Genome Res 2002, 12:656-664. 187518, 11932250.
49. Moriya Y, Itoh M, Okuda S, Yoshizawa A, Kanehisa M. KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res 2007, 35:W182-185. 10.1093/nar/gkm321, 1933193, 17526522.