Gene expression studies of the dikaryotic mycelium and primordium of Lentinula edodes by serial analysis of gene expression

Mycological Research

Volumn 112, Issue 8, 2008, Pages 950-964

  Chum, Winnie Wing Yan ^a   Ng, Kevin Tak Pan ^a   Shih, Rita Sheung Mei ^a   Au, Chun Hang ^a   Kwan, Hoi Shan ^a  

^a CHINESE UNIVERSITY OF HONG KONG   (Hong Kong)

Author keywords

Developmental mycology; Edible mushrooms; Hydrophobins; SAGE; Shiitake

Indexed keywords

DATABASE; DEVELOPMENTAL BIOLOGY; DNA; EDIBLE SPECIES; FRUIT; GENE EXPRESSION; GENETIC ANALYSIS; HYBRIDIZATION; MUSHROOM;

ARTICLE; COMPARATIVE STUDY; DNA MICROARRAY; EXPRESSED SEQUENCE TAG; FRUITING BODY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; GROWTH, DEVELOPMENT AND AGING; LENTINUS EDODES; METABOLISM; MYCELIUM; NORTHERN BLOTTING;

BLOTTING, NORTHERN; EXPRESSED SEQUENCE TAGS; FRUITING BODIES, FUNGAL; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENE EXPRESSION REGULATION, FUNGAL; MYCELIUM; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SHIITAKE MUSHROOMS; TRANSCRIPTION, GENETIC;

BASIDIOMYCOTA; LENTINULA EDODES;

EID: 47149112357     PISSN: 09537562     EISSN: 14698102     Source Type: Journal    
DOI: 10.1016/j.mycres.2008.01.028     Document Type: Article

References (78)

1. Alberts A.W., Majerus P.W., Talamo B., and Vagelos P.R. Acyl-carrier protein. II. Intermediary reactions of fatty acid synthesis. Biochemistry 3 (1964) 1563-1571
2. Altschul S.F., Madden T.L., Schäffer A.A., Zhang J., Zhang Z., Miller W., and Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research 25 (1997) 3389-3402 [Review]
3. Bradley D.J., Kjellbom P., and Lamb C.J. Elicitor and wound induced oxidative cross-linking of a proline rich plant cell-wall protein: a novel, rapid defense response. Cell 70 (1992) 21-30
4. Brownleader M.D., Ahmed N., Trevan M., Chaplin M.F., and Dey P.M. Purification and partial characterization of tomato extensin peroxidase. Plant Physiology 109 (1995) 1115-1123
5. Bishop W.R., and Bell R.M. Assembly of phospholipids into cellular membranes: biosynthesis, transmembrane movement and intracellular translocation. Annual Review of Cell Biology 4 (1988) 579-610
6. Carman G.M., and Henry S.A. Phospholipid biosynthesis in yeast. Annual Review of Biochemistry 58 (1989) 635-669
7. Chang F. Microtubule and actin-dependent movement of the formin cdc12p in fission yeast. Microscopy Research and Technique 49 (2000) 161-167
8. Chang F., Drubin D., and Nurse P. cdc12p, a protein required for cytokinesis in fission yeast, is a component of the cell division ring and interacts with profilin. Journal of Cell Biology 137 (1997) 169-182
9. Chang F., Woollard A., and Nurse P. Isolation and characterization of fission yeast mutants defective in the assembly and placement of the contractile actin ring. Journal of Cell Science 109 (1996) 131-142
10. Chen J., Lee S., Zhou G., and Wang S.M. High-throughput GLGI procedure for converting a large number of serial analysis of gene expression tag sequences into 3′ complementary DNAs. Genes Chromosomes & Cancer 33 (2002) 252-261
11. Chen J.J., Rowley J.D., and Wang S.M. Generation of longer cDNA fragments from serial analysis of gene expression tags for gene identification. Proceedings of the National Academy of Sciences, USA 97 (2000) 349-353
12. Chum W.W.Y., and Kwan H.S. Modification of LongSAGE for obtaining and cloning long concatemers. Biotechniques 39 (2005) 637-638 640
13. Clancey C.J., Chang S.C., and Dowhan W. Cloning of a gene (PSD1) encoding phosphatidylserine decarboxylase from Saccharomyces cerevisiae by complementation of an Escherichia coli mutant. Journal of Biological Chemistry 268 (1993) 24580-24590
14. De Groot P.W., Schaap P.J., Sonnenberg A.S., Visser J., and Van Griensven L.J. The Agaricus bisporus hypA gene encodes a hydrophobin and specifically accumulates in peel tissue of mushroom caps during fruit body development. Journal of Molecular Biology 257 (1996) 1008-1018
15. Deepak S., Shailasree S., Kini R.K., Hause B., Shetty S.H., and Mithofer A. Role of hydroxyproline-rich glycoproteins in resistance of pearl millet against downy mildew pathogen Sclerospora graminicola. Planta 226 (2007) 323-333
16. Diehl S., Umbricht C.B., Dackiw A.P., and Zeiger M.A. Modern approaches to age-old questions about thyroid tumors. Thyroid 15 (2005) 575-582
17. Dowhan W., Wickner W.T., and Kennedy E.P. Purification and properties of phosphatidylserine decarboxylase from Escherichia coli. Journal of Biological Chemistry 249 (1974) 3079-3084
18. Duggan D.J., Bittner M., Chen Y., Meltzer P., and Trent J.M. Expression profiling using cDNA microarrays. Nature Genetics 21 (1999) 10-14
19. Endo H., Kajiwara S., Tsunoka O., and Shishido K. A novel cDNA, priBc, encoding a protein with a Zn(II)2Cys6 zinc cluster DNA-binding motif, derived from the basidiomycete Lentinus edodes. Gene 139 (1994) 117-121
20. Hackam A.S., Qian J., Liu D., Gunatilaka T., Farkas R.H., Chowers I., Kageyama M., Parmigiani G., and Zack D.J. Comparative gene expression analysis of murine retina and brain. Molecular Vision 10 (2004) 637-649
21. Hawrot E., and Kennedy E.P. Biogenesis of membrane lipids: mutants of Escherichia coli with temperature-sensitive phosphatidylserine decarboxylase. Proceedings of the National Academy of Sciences, USA 72 (1975) 1112-1116
22. Hengst U., Albrecht H., Hess D., and Monard D. The phosphatidylethanolamine-binding protein is the prototype of a novel family of serine protease inhibitors. Journal of Biological Chemistry 276 (2001) 535-540
23. Hirano T., Sato T., and Enei H. Isolation of genes specifically expressed in the fruit body of the edible basidiomycete Lentinula edodes. Bioscience Biotechnology and Biochemistry 68 (2004) 468-472
24. Huang J., Miao X., Jin W., Couble P., Mita K., Zhang Y., Liu W., Zhuang L., Shen Y., Keime C., Gandrillon O., Brouilly P., Briolay J., Zhao G., and Huang Y. Serial analysis of gene expression in the silkworm, Bombyx mori. Genomics 86 (2005) 233-241
25. Ishizaki T., Yokoyama H., Kajiwara S., and Shishido K. Basidiomycete fungal gene encoding a regulatory subunit a homologue of protein phosphatase 2A. Bioscience Biotechnology and Biochemistry 64 (2000) 438-442
26. Ito Y., Oh-Hashi Y., and Okuyama H. Fatty acid synthetase as a thermoreceptor in Candida utilis. Journal of Biochemistry 99 (1986) 1713-1718
27. Kajiwara S., Yamaoka K., Hori K., Miyazawa H., Saito T., Kanno T., and Shishido K. Isolation and sequence of a developmentally regulated putative novel gene, priA, from the basidiomycete Lentinus edodes. Gene 114 (1992) 173-178
28. Kaneko S., Miyazaki Y., Yasuda T., and Shishido K. Cloning, sequence analysis and expression of the basidiomycete Lentinus edodes gene uck1, encoding UMP-CMP kinase, the homologue of Saccharomyces cerevisiae URA6 gene. Gene 211 (1998) 259-266
29. Kaneko S., and Shishido K. Cloning and sequence analysis of the basidiomycete Lentinus edodes ribonucleotide reductase small subunit cDNA and expression of a corresponding gene in L. edodes. Gene 262 (2001) 43-50
30. Kang Z., and Buchenauer H. Immunocytochemical localization of cell wall-bound thionins and hydroxyproline-rich glycoproteins in Fusarium culmorum-infected wheat spikes. Journal of Phytopathology-phytopathologische zeitschrift 151 (2003) 120-129
31. Kershaw M.J., and Talbot N.J. Hydrophobins and repellents: proteins with fundamental roles in fungal morphogenesis. Fungal Genetics and Biology 23 (1998) 18-33
32. Kondoh O., and Shishido K. Characterization of the promoter region of a cell-adhesion protein gene derived from the basidiomycete Lentinus edodes. FEMS Microbiology Letters 130 (1995) 189-192
33. Kranz C., Denecke J., Lehrman M.A., Ray S., Kienz P., Kreissel G., Sagi D., Peter-Katalinic J., Freeze H.H., Schmid T., Jackowski-Dohrmann S., Harms E., and Marquardt T. A mutation in the human MPDU1 gene causes congenital disorder of glycosylation type If (CDG-If). Journal of Clinical Investigation 108 (2001) 1613-1619
34. Kues U. Life history and developmental processes in the basidiomycete Coprinus cinereus. Microbiology and Molecular Biology Reviews 64 (2000) 316-353
35. Kues U., and Liu Y. Fruiting body production in basidiomycetes. Applied Microbiology and Biotechnology 54 (2000) 141-152
36. Larrabee A.R., McDaniel E.G., Bakerman H.A., and Vagelos P.R. Acyl carrier protein. V. Identification of 4′-phosphopantetheine bound to a mammalian fatty acid synthetase preparation. Proceedings of the National Academy of Sciences, USA 54 (1965) 267-273
37. Lee J.Y., and Lee D.H. Use of serial analysis of gene expression technology to reveal changes in gene expression in Arabidopsis pollen undergoing cold stress. Plant Physiology 132 (2003) 517-529
38. Leung G.S.W., Zhang M., Xie W.J., and Kwan H.S. Identification by RNA fingerprinting of genes differentially expressed during the development of the basidiomycete Lentinula edodes. Molecular and General Genetics 262 (2000) 977-990
39. Majerus P.W., Alberts A.W., and Vagelos P.R. The acyl carrier protein of fatty acid synthesis: purification, physical properties, and substrate binding site. Proceedings of the National Academy of Sciences, USA 51 (1964) 1231-1238
40. Margulies M., Egholm M., Altman W.E., Attiya S., Bader J.S., Bemben L.A., Berka J., Braverman M.S., Chen Y.J., Chen Z., Dewell S.B., Du L., Fierro J.M., Gomes X.V., Godwin B.C., He W., Helgesen S., Ho C.H., Irzyk G.P., Jando S.C., Alenquer M.L., Jarvie T.P., Jirage K.B., Kim J.B., Knight J.R., Lanza J.R., Leamon J.H., Lefkowitz S.M., Lei M., Li J., Lohman K.L., Lu H., Makhijani V.B., McDade K.E., McKenna M.P., Myers E.W., Nickerson E., Nobile J.R., Plant R., Puc B.P., Ronan M.T., Roth G.T., Sarkis G.J., Simons J.F., Simpson J.W., Srinivasan M., Tartaro K.R., Tomasz A., Vogt K.A., Volkmer G.A., Wang S.H., Wang Y., Weiner M.P., Yu P., Begley R.F., and Rothbergr J.M. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437 (2005) 376-380
41. Matsumura H., Nirasawa S., and Terauchi R. Technical advance: transcript profiling in rice (Oryza sativa L.) seedlings using serial analysis of gene expression (SAGE). Plant Journal 20 (1999) 719-726
42. Mir G., Domenech J., Huguet G., Guo W.J., Goldsbrough P., Atrian S., and Molinas M. A plant type 2 metallothionein (MT) from cork tissue responds to oxidative stress. Journal of Experimental Botany 55 (2004) 2483-2493
43. Miyazaki Y., Nakamura M., and Babasaki K. Molecular cloning of developmentally specific genes by representational difference analysis during the fruiting body formation in the basidiomycete Lentinula edodes. Fungal Genetics and Biology 42 (2005) 493-505
44. Moore D. Fungal Morphogenesis (1998), Cambridge University Press, New York
45. Naglik J.R., Challacombe S.J., and Hube B. Candida albicans secreted aspartyl proteinases in virulence and pathogenesis. Microbiology and Molecular Biology Reviews 67 (2003) 400-428 table of contents
46. Ng W.L., Ng T.P., and Kwan H.S. Cloning and characterization of two hydrophobin genes differentially expressed during fruit body development in Lentinula edodes. FEMS Microbiology Letters 185 (2000) 139-145
47. Oguri S., Ando A., and Nagata Y. A novel developmental stage-specific lectin of the basidiomycete Pleurotus cornucopiae. Journal of Bacteriology 178 (1996) 5692-5698
48. Overath P., and Stumpf P.K. Fat metabolism in higher plants. 23. Properties of a soluble fatty acid synthetase from Avocado mesocarp. The Journal of Biological Chemistry 239 (1964) 4103-4110
49. Penas M.M., Asgeirsdottir S.A., Lasa I., Culianez-Macia F.A., Pisabarro A.G., Wessels J.G., and Ramirez L. Identification, characterization, and in situ detection of a fruit-body-specific hydrophobin of Pleurotus ostreatus. Applied and Environmental Microbiology 64 (1998) 4028-4034
50. Raetz C.R., and Dowhan W. Biosynthesis and function of phospholipids in Escherichia coli. Journal of Biological Chemistry 265 (1990) 1235-1238
51. Regala R.P., and Rice C.D. Mycobacteria, but not mercury, induces metallothionein (MT) protein in striped bass, Morone saxitilis, phagocytes, while both stimuli induce MT in channel catfish, Ictalurus punctatus, phagocytes. Marine Environmental Research 58 (2004) 719-723
52. Rudney H., Stewart P.R., Majerus P.W., and Vagelos P.R. The biosynthesis of beta-hydroxy-beta-methylglutaryl coenzyme A in yeast. V. The role of acyl carrier protein. Journal of Biological Chemistry 241 (1966) 1226-1228
53. Sakai H., and Kajiwara S. A stearoyl-CoA-specific delta 9 fatty acid desaturase from the basidiomycete Lentinula edodes. Bioscience Biotechnology and Biochemistry 67 (2003) 2431-2437
54. Sakai H., and Kajiwara S. Cloning and functional characterization of a delta 12 fatty acid desaturase gene from the basidiomycete Lentinula edodes. Molecular Genetics and Genomics 273 (2005) 336-341
55. Satre M., and Kennedy E.P. Identification of bound pyruvate essential for activity of phosphatidylserine decarboxylase of Escherichia coli. Journal of Biological Chemistry 253 (1978) 479-483
56. Shailasree S., Kini K.R., Deepak S., Kumudini B.S., and Shetty H.S. Accumulation of hydroxyproline-rich glycoproteins in pearl millet seedlings in response to Sclerospora graminicola infection. Plant Science 167 (2004) 1227-1234
57. Sommer-Knudsen J., Bacic A., and Clarke A.E. Hydroxyproline-rich plant glycoproteins. Phytochemistry 47 (1998) 483-497
58. Southern E., Mir K., and Shchepinov M. Molecular interactions on microarrays. Nature Genetics 21 (1999) 5-9
59. Sreenivasaprasad S., Eastwood D.C., Browning N., Lewis S.M., and Burton K.S. Differential expression of a putative riboflavin-aldehyde-forming enzyme (raf) gene during development and post-harvest storage and in different tissue of the sporophore in Agaricus bisporus. Applied Microbiology and Biotechnology 70 (2006) 470-476
60. Staib F. Serum-proteins as nitrogen source for yeast-like fungi. Sabouraudia 4 (1965) 187-193
61. Steen B.R., Lian T., Zuyderduyn S., MacDonald W.K., Marra M., Jones S.J., and Kronstad J.W. Temperature-regulated transcription in the pathogenic fungus Cryptococcus neoformans. Genome Research 12 (2002) 1386-1400
62. Sun M., Zhou G., Lee S., Chen J., Shi R.Z., and Wang S.M. SAGE is far more sensitive than EST for detecting low-abundance transcripts. BMC Genomics 5 (2004) 1
63. Tachibana S., and Oka M. Occurrence of a vitamin B2-aldehyde-forming enzyme in Schizophyllum commune. Journal of Biological Chemistry 256 (1981) 6682-6685
64. Takagi Y., Katayose Y., and Shishido K. Intracellular levels of cyclic AMP and adenylate cyclase activity during mycelial development in fruiting body formation in Lentinus edodes. FEMS Microbiology Letters 55 (1988) 275-278
65. Techel D., Hafker T., Muschner S., Reimann M., Li Y., Monnerjahn C., and Rensing L. Molecular analysis of a glucose-regulated gene (grp78) of Neurospora crassa. Biochimica et Biophysica Acta-Biomembranes 1397 (1998) 21-26
66. Tuteja R., and Tuteja N. Serial analysis of gene expression (SAGE): unraveling the bioinformatics tools. Bioessays 26 (2004) 916-922
67. Varela C., Cardenas J., Melo F., and Agosin E. Quantitative analysis of wine yeast gene expression profiles under winemaking conditions. Yeast 22 (2005) 369-383
68. Velculescu V.E., Vogelstein B., and Kinzler K.W. Analysing uncharted transcriptomes with SAGE. Trends in Genetics 16 (2000) 423-425
69. Velculescu V.E., Zhang L., Vogelstein B., and Kinzler K.W. Serial analysis of gene expression. Science 270 (1995) 484-487
70. Velculescu V.E., Zhang L., Zhou W., Vogelstein J., Basrai M.A., Bassett Jr. D.E., Hieter P., Vogelstein B., and Kinzler K.W. Characterization of the yeast transcriptome. Cell 88 (1997) 243-251
71. Wakil S.J., Pugh E.L., and Sauer F. The mechanism of fatty acid synthesis. Proceedings of the National Academy of Sciences, USA 52 (1964) 106-114
72. Weeraratna A.T., Becker D., Carr K.M., Duray P.H., Rosenblatt K.P., Yang S., Chen Y., Bittner M., Strausberg R.L., Riggins G.J., Wagner U., Kallioniemi O.P., Trent J.M., Morin P.J., and Meltzer P.S. Generation and analysis of melanoma SAGE libraries: SAGE advice on the melanoma transcriptome. Oncogene 23 (2004) 2264-2274
73. Wessels J.G.H. Fruiting in the higher fungi. Advances in Microbial Physiology 34 (1993) 147-202
74. Wessels J.G.H. Development of fruit bodies in homobasidiomycetes. In: Wessels J.G.H., and Meinhardt F. (Eds). The Mycota I growth, differentiation and sexuality (1994), Springer-Verlag, Berlin 351-366
75. Wessels J., De Vries O., Asgeirsdottir S.A., and Schuren F. Hydrophobin genes involved in formation of aerial hyphae and fruit bodies in Schizophyllum. Plant Cell 3 (1991) 793-799
76. Yamamoto M., Wakatsuki T., Hada A., and Ryo A. Use of serial analysis of gene expression (SAGE) technology. Journal of immunological methods 250 (2001) 45-66
77. Zhang L., Zhou W., Velculescu V.E., Kern S.E., Hruban R.H., Hamilton S.R., Vogelstein B., and Kinzler K.W. Gene expression profiles in normal and cancer cells. Science 276 (1997) 1268-1272
78. Zhao J., and Kwan H.S. Characterization, molecular cloning, and differential expression analysis of laccase genes from the edible mushroom Lentinula edodes. Applied and Environmental Microbiology 65 (1999) 4908-4913