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University of Groningen Alpha-glucan acting enzymes in Aspergillus niger van der Kaaij, Rachel IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite from it. Please check the document version below. Document Version Publisher's PDF, also known as Version of record Publication date: 2007 Link to publication in University of Groningen/UMCG research database Citation for published version (APA): Kaaij, R. M. V. D. (2007). Alpha-glucan acting enzymes in Aspergillus niger: diversity in enzymatic activities and functions s.n. Copyright Other than for strictly personal use, it is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), unless the work is under an open content license (like Creative Commons). Take-down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. Downloaded from the University of Groningen/UMCG research database (Pure): http://www.rug.nl/research/portal. For technical reasons the number of authors shown on this cover page is limited to 10 maximum. Download date: 14-06-2017 Reference List 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12. 13. 14. 15. 16. 17. 18. 19. 20. 21. 22. 23. Altschul,S.F., Madden,T.L., Schaffer,A.A., Zhang,J., Zhang,Z., Miller,W., and Lipman,D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402. Arguelles,J.C. (2000) Physiological roles of trehalose in bacteria and yeasts: a comparative analysis. Arch Microbiol 174: 217-224. Ausubel,F.M., Brent,R.E., Kingston,D.D., Moore,J.G., Seidman,J.G., Smith,J.A., and Struhl,K. (1987) Current Protocols in molecular biology New York: John Wiley & Sons, Inc. Bahia,M.C., Vieira,R.P., Mulloy,B., Hartmann,R., and Bergter,E.B. (1997) The structures of polysaccharides and glycolipids of Aspergillus fumigatus grown in the presence of human serum. Mycopathologia 137: 17-25. Bardalaye,P.C., and Nordin,J.H. (1977) Chemical structure of the galactomannan from the cell wall of Aspergillus niger. J Biol Chem 252: 2584-2591. Barker,S.A., and Carrington,T.R. (1953) Studies of Aspergillus niger. Part II. Transglycosylation by Aspergillus niger. J Chem Soc 1953: 3588-3593. Bauer,S., Vasu,P., Persson,S., Mort,A.J., and Somerville,C.R. (2006) Development and application of a suite of polysaccharide-degrading enzymes for analyzing plant cell walls. Proc Natl Acad Sci U S A 103: 11417-11422. Beauvais,A., and Latgé,J.P. (2001) Membrane and cell wall targets in Aspergillus fumigatus. Drug Resist Updat 4: 38-49. Beauvais,A., Maubon,D., Park,S., Morelle,W., Tanguy,M., Huerre,M. et al. (2005) Two alpha(1-3) glucan synthases with different functions in Aspergillus fumigatus. Appl Environ Microbiol 71: 15311538. Bendtsen,J.D., Kiemer,L., Fausboll,A., and Brunak,S. (2005) Non-classical protein secretion in bacteria. BMC Microbiol 5: 58. Bendtsen,J.D., Nielsen,H., Von Heijne,G., and Brunak,S. (2004) Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 340: 783-795. Benen,J.A., Kester,H.C., and Visser,J. (1999) Kinetic characterization of Aspergillus niger N400 endopolygalacturonases I, II and C. Eur J Biochem 259: 577-585. Bennett,J.W., and Lasure,L.L. (1991) More gene manipulations in fungi. San Diego: Academic Press, pp. 441-447. Benson,D.A., Karsch-Mizrachi,I., Lipman,D.J., Ostell,J., and Wheeler,D.L. (2006) GenBank. Nucleic Acids Res 34: D16-D20. Birney,E., Clamp,M., and Durbin,R. (2004) GeneWise and Genomewise. Genome Res 14: 988-995. Blumenthal,H.J., and Roseman,S. (1957) Quantitative estimation of chitin in fungi. J Bacteriol 74: 222224. Bobbitt,T.F., Nordin,J.H., Roux,M., Revol,J.F., and Marchessault,R.H. (1977) Distribution and conformation of crystalline nigeran in hyphal walls of Aspergillus niger and Aspergillus awamori. J Bacteriol 132: 691-703. Boel,E., Brady,L., Brzozowski,A.M., Derewenda,Z., Dodson,G.G., Jensen,V.J. et al. (1990) Calcium binding in alpha-amylases: an X-ray diffraction study at 2.1-A resolution of two enzymes from Aspergillus. Biochemistry 29: 6244-6249. Boel,E., Hjort,I., Svensson,B., Norris,F., Norris,K.E., and Fiil,N.P. (1984) Glucoamylases G1 and G2 from Aspergillus niger are synthesized from two different but closely related mRNAs. EMBO J 3: 1097-1102. Borges-Walmsley,M.I., Chen,D., Shu,X., and Walmsley,A.R. (2002) The pathobiology of Paracoccidioides brasiliensis. Trends Microbiol 10: 80-87. Bos,C.J., Debets,A.J., Swart,K., Huybers,A., Kobus,G., and Slakhorst,S.M. (1988) Genetic analysis and the construction of master strains for assignment of genes to six linkage groups in Aspergillus niger. Curr Genet 14: 437-443. Bose,S., Mazumder,S., and Mukherjee,M. (2007) Laccase production by the white-rot fungus Termitomyces clypeatus. J Basic Microbiol 47: 127-131. Bowman,S.M., and Free,S.J. (2006) The structure and synthesis of the fungal cell wall. Bioessays 28: 799-808. 133 Alpha-glucan acting enzymes in Aspergillus niger 24. Bowman,S.M., Piwowar,A., Al,D.M., Vierula,J., and Free,S.J. (2006) Mutational analysis of the Glycosylphosphatidylinositol (GPI) anchor pathway demonstrates that GPI-anchored proteins are required for cell wall biogenesis and normal hyphal growth in Neurospora crassa. Eukaryot Cell 5: 587-600. 25. Brul,S., King,A., van der Vaart,J.M., Chapman,J., Klis,F., and Verrips,C.T. (1997) The incorporation of mannoproteins in the cell wall of S. cerevisiae and filamentous Ascomycetes. Antonie Van Leeuwenhoek 72: 229-237. 26. Brzozowski,A.M., Lawson,D.M., Turkenburg,J.P., Bisgaard-Frantzen,H., Svendsen,A., Borchert,T.V. et al. (2000) Structural analysis of a chimeric bacterial alpha-amylase. High-resolution analysis of native and ligand complexes. Biochemistry 39: 9099-9107. 27. Cabib,E., and Kang,M.S. (1987) Fungal 1,3-beta-glucan synthase. Methods Enzymol 138: 637-642. 28. Carlile,M.J., and Watkinson,S.C. (1994) The Fungi London: Academic Press Limited. 29. Caro,L.H., Tettelin,H., Vossen,J.H., Ram,A.F., Van Den,E.H., and Klis,F.M. (1997) In silicio identification of glycosyl-phosphatidylinositol-anchored plasma-membrane and cell wall proteins of Saccharomyces cerevisiae. Yeast 13: 1477-1489. 30. Chang,C.T., Lo,H.F., Chi,M.C., Yao,C.Y., Hsu,W.H., and Lin,L.L. (2003) Identification of essential histidine residues in a recombinant alpha-amylase of thermophilic and alkaliphilic Bacillus sp. strain TS-23. Extremophiles 7: 505-509. 31. Costachel,C., Coddeville,B., Latge,J.P., and Fontaine,T. (2005) Glycosylphosphatidylinositol-anchored fungal polysaccharide in Aspergillus fumigatus. J Biol Chem 280: 39835-39842. 32. Coutinho,P.M., Deleury,E., Davies,G.J., and Henrissat,B. (2003) An evolving hierarchical family classification for glycosyltransferases. J Mol Biol 328: 307-317. 33. Coutinho,P.M., and Henrissat,B. (1999) Carbohydrate-active enzymes: an integrated database approach. In Recent Advances in Carbohydrate Bioengineering. Gilbert,H.J., Davies,G.J., Henrissat,B., and Svensson,B. (eds). Cambridge: The Royal Society of Chemistry, pp. 3-12. 34. Crooks,G.E., Hon,G., Chandonia,J.M., and Brenner,S.E. (2004) WebLogo: a sequence logo generator. Genome Res 14: 1188-90. 35. Da Lage,J.L., Feller,G., and Janecek,S. (2004) Horizontal gene transfer from Eukarya to bacteria and domain shuffling: the alpha-amylase model. Cell Mol Life Sci 61: 97-109. 36. Damveld,R.A., Arentshorst,M., Vankuyk,P.A., Klis,F.M., van den Hondel,C.A., and Ram,A.F. (2005a) Characterisation of CwpA, a putative glycosylphosphatidylinositol-anchored cell wall mannoprotein in the filamentous fungus Aspergillus niger. Fungal Genet Biol 42: 873-885. 37. Damveld,R.A., Vankuyk,P.A., Arentshorst,M., Klis,F.M., van den Hondel,C.A., and Ram,A.F. (2005b) Expression of agsA, one of five 1,3-alpha-d-glucan synthase-encoding genes in Aspergillus niger, is induced in response to cell wall stress. Fungal Genet Biol 42: 165-177. 38. Davies,G.J., Brzozowski,A.M., Dauter,Z., Rasmussen,M.D., Borchert,T.V., and Wilson,K.S. (2005) Structure of a Bacillus halmapalus family 13 alpha-amylase, BHA, in complex with an acarbosederived nonasaccharide at 2.1 A resolution. Acta Crystallogr D Biol Crystallogr 61: 190-193. 39. Davies,G.J., Wilson,K.S., and Henrissat,B. (1997) Nomenclature for sugar-binding subsites in glycosyl hydrolases. Biochem J 321: 557-559. 40. De Bernardis,F., Muhlschlegel,F.A., Cassone,A., and Fonzi,W.A. (1998) The pH of the host niche controls gene expression in and virulence of Candida albicans. Infect Immun 66: 3317-3325. 41. De Groot,P.W., Hellingwerf,K.J., and Klis,F.M. (2003) Genome-wide identification of fungal GPI proteins. Yeast 20: 781-796. 42. De Groot,P.W., Ram,A.F., and Klis,F.M. (2005) Features and functions of covalently linked proteins in fungal cell walls. Fungal Genet Biol 42: 657-675. 43. De Groot,P.W., Yin,Q.Y., Weig,M., Sosinska,G.J., Klis,F.M., and de Koster,C.G. (2007) Mass spectrometric identification of covalently bound cell wall proteins from the fission yeast Schizosaccharomyces pombe. Yeast 24: 267-78. 44. de Ruiter-Jacobs,Y.M., Broekhuijsen,M., Unkles,S.E., Campbell,E.I., Kinghorn,J.R., Contreras,R. et al. (1989) A gene transfer system based on the homologous pyrG gene and efficient expression of bacterial genes in Aspergillus oryzae. Curr Genet 16: 159-163. 45. De Vries,R.P., and Visser,J. (2001) Aspergillus enzymes involved in degradation of plant cell wall polysaccharides. Microbiol Mol Biol Rev 65: 497-522. 46. den Herder,I.F., Rosell,A.M., van Zuilen,C.M., Punt,P.J., and van den Hondel,C.A. (1992) Cloning and expression of a member of the Aspergillus niger gene family encoding alpha-galactosidase. Mol Gen Genet 233: 404-410. 134 Reference list 47. Dey,G., Palit,S., Banerjee,R., and Maiti,B.R. (2002) Purification and characterization of maltooligosaccharide-forming amylase from Bacillus circulans GRS 313. J Ind Microbiol Biotechnol 28: 193-200. 48. Dowzer,C.E., and Kelly,J.M. (1991) Analysis of the creA gene, a regulator of carbon catabolite repression in Aspergillus nidulans. Mol Cell Biol 11: 5701-5709. 49. Duarte,J.C., and Costa-Ferreira,M. (1994) Aspergilli and lignocellulosics: enzymology and biotechnological applications. FEMS Microbiol Rev 13: 377-386. 50. Durbin,R., and Eddy,S. (1998) Biological Sequence analysis: Probabilistic Models of Proteins and Nucleic acids. A tutorial introduction to hidden Markov models and other probabilistic modelling approaches in computational sequence analysis. Cambridge: Cambridge University Press. 51. Eisenhaber,B., Schneider,G., Wildpaner,M., and Eisenhaber,F. (2004) A sensitive predictor for potential GPI lipid modification sites in fungal protein sequences and its application to genome-wide studies for Aspergillus nidulans, Candida albicans, Neurospora crassa, Saccharomyces cerevisiae and Schizosaccharomyces pombe. J Mol Biol 337: 243-253. 52. Fontaine,T., Magnin,T., Melhert,A., Lamont,D., Latgé,J.P., and Ferguson,M.A. (2003) Structures of the glycosylphosphatidylinositol membrane anchors from Aspergillus fumigatus membrane proteins. Glycobiology 13: 169-177. 53. Fontaine,T., Simenel,C., Dubreucq,G., Adam,O., Delepierre,M., Lemoine,J. et al. (2000) Molecular organization of the alkali-insoluble fraction of Aspergillus fumigatus cell wall. J Biol Chem 275: 41528. 54. Fowler,T., Berka,R.M., and Ward,M. (1990) Regulation of the glaA gene of Aspergillus niger. Curr Genet 18: 537-545. 55. Francois,J., and Parrou,J.L. (2001) Reserve carbohydrates metabolism in the yeast Saccharomyces cerevisiae. FEMS Microbiol Rev 25: 125-145. 56. Frieman,M.B., and Cormack,B.P. (2003) The omega-site sequence of glycosylphosphatidylinositolanchored proteins in Saccharomyces cerevisiae can determine distribution between the membrane and the cell wall. Mol Microbiol 50: 883-896. 57. Frieman,M.B., and Cormack,B.P. (2004) Multiple sequence signals determine the distribution of glycosylphosphatidylinositol proteins between the plasma membrane and cell wall in Saccharomyces cerevisiae. Microbiology 150: 3105-3114. 58. Galagan,J.E., Calvo,S.E., Cuomo,C., Ma,L.J., Wortman,J.R., Batzoglou,S. et al. (2005) Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae. Nature 438: 11051115. 59. Garcia,I., Tajadura,V., Martin,V., Toda,T., and Sanchez,Y. (2006) Synthesis of alpha-glucans in fission yeast spores is carried out by three alpha-glucan synthase paralogues, Mok12p, Mok13p and Mok14p. Mol Microbiol 59: 836-853. 60. Geber,A., Williamson,P.R., Rex,J.H., Sweeney,E.C., and Bennett,J.E. (1992) Cloning and characterization of a Candida albicans maltase gene involved in sucrose utilization. J Bacteriol 174: 6992-6996. 61. Geysens,S., Pakula,T., Uusitalo,J., Dewerte,I., Penttila,M., and Contreras,R. (2005) Cloning and characterization of the glucosidase II alpha subunit gene of Trichoderma reesei: a frameshift mutation results in the aberrant glycosylation profile of the hypercellulolytic strain Rut-C30. Appl Environ Microbiol 71: 2910-2924. 62. Gomi,K., Akeno,T., Minetoki,T., Ozeki,K., Kumagai,C., Okazaki,N., and Iimura,Y. (2000) Molecular cloning and characterization of a transcriptional activator gene, amyR, involved in the amylolytic gene expression in Aspergillus oryzae. Biosci Biotechnol Biochem 64: 816-827. 63. Goosen,C., Yuan,X.L., van Munster,J.M., Ram,A.F., van der Maarel,M.J., and Dijkhuizen,L. (2007) Molecular and biochemical characterization of a novel intracellular invertase from Aspergillus niger with transfructosylating activity. Eukaryot Cell 6: 674-681. 64. Grün,C.H., Hochstenbach,F., Humbel,B.M., Verkleij,A.J., Sietsma,J.H., Klis,F.M. et al. (2005) The structure of cell wall alpha-glucan from fission yeast. Glycobiology 15: 245-257. 65. Guzman-Maldonado,H., and Paredes-Lopez,O. (1995) Amylolytic enzymes and products derived from starch: a review. Crit Rev Food Sci Nutr 35: 373-403. 66. Hartland,R.P., Emerson,G.W., and Sullivan,P.A. (1991) A secreted beta-glucan-branching enzyme from Candida albicans. Proc Biol Sci 246: 155-160. 67. Hemker,M., Stratmann,A., Goeke,K., Schroder,W., Lenz,J., Piepersberg,W., and Pape,H. (2001) Identification, cloning, expression, and characterization of the extracellular acarbose-modifying glycosyltransferase, AcbD, from Actinoplanes sp. strain SE50. J Bacteriol 183: 4484-4492. 135 Alpha-glucan acting enzymes in Aspergillus niger 68. Henrissat,B. (1991) A classification of glycosyl hydrolases based on amino acid sequence similarities. Biochem J 280: 309-316. 69. Henrissat,B., and Bairoch,A. (1993) New families in the classification of glycosyl hydrolases based on amino acid sequence similarities. Biochemistry Journal 293: 781-788. 70. Henrissat,B., and Bairoch,A. (1996) Updating the sequence-based classification of glycosyl hydrolases. Biochem J 316: 695-696. 71. Hesseltine,C.W. (1983) Microbiology of oriental fermented foods. Annu Rev Microbiol 37: 575-601. 72. Hochstenbach,F., Klis,F.M., Van Den,E.H., van,D.E., Peters,P.J., and Klausner,R.D. (1998) Identification of a putative alpha-glucan synthase essential for cell wall construction and morphogenesis in fission yeast. Proc Natl Acad Sci U S A 95: 9161-9166. 73. Hogan,L.H., and Klein,B.S. (1994) Altered expression of surface alpha-1,3-glucan in genetically related strains of Blastomyces dermatitidis that differ in virulence. Infect Immun 62: 3543-3546. 74. Honegger,R. (2001) The symbiotic phenotype of lichen-forming Ascomycetes. In Fungal Associations. Hock,B. (ed). Berlin: Springer-Verlag, pp. 165-188. 75. Horisberger,M., Lewis,B.A., and Smith,F. (1972) Structure of a (1, 3)-α-D-glucan (pseudonigeran) of Aspergillus niger NNRL 326 cell wall. Carbohydr Res 23: 183-188. 76. Hoshiko,S., Makabe,O., Nojiri,C., Katsumata,K., Satoh,E., and Nagaoka,K. (1987) Molecular cloning and characterization of the Streptomyces hygroscopicus alpha-amylase gene. J Bacteriol 169: 10291036. 77. Hull,E.P., Green,P.M., Arst,H.N., Jr., and Scazzocchio,C. (1989) Cloning and physical characterization of the L-proline catabolism gene cluster of Aspergillus nidulans. Mol Microbiol 3: 553-559. 78. Iefuji,H., Chino,M., Kato,M., and Iimura,Y. (1996) Raw-starch-digesting and thermostable alphaamylase from the yeast Cryptococcus sp. S-2: purification, characterization, cloning and sequencing. Biochem J 318: 989-996. 79. Inoue,H., Nojima,H., and Okayama,H. (1990) High efficiency transformation of Escherichia coli with plasmids. Gene 96: 23-28. 80. Ito,T., Tani,S., Itoh,T., Tsukagoshi,N., Kato,M., and Kobayashi,T. (2004) Mode of AmyR binding to the CGGN8AGG sequence in the Aspergillus oryzae taaG2 promoter. Biosci Biotechnol Biochem 68: 1906-1911. 81. Iwaki,T., Morita,T., Tanaka,N., Giga-Hama,Y., and Takegawa,K. (2007) Loss of a GPI-anchored membrane protein Aah3p causes a defect in vacuolar protein sorting in Schizosaccharomyces pombe. Biosci Biotechnol Biochem 71: 623-626. 82. James,T.Y., Kauff,F., Schoch,C.L., Matheny,P.B., Hofstetter,V., Cox,C.J. et al. (2006) Reconstructing the early evolution of Fungi using a six-gene phylogeny. Nature 443: 818-822. 83. Janecek,S. (1994) Sequence similarities and evolutionary relationships of microbial, plant and animal alpha-amylases. Eur J Biochem 224: 519-524. 84. Janecek,S. (1997) Alpha-Amylase family: molecular biology and evolution. Prog Biophys Mol Biol 67: 67-97. 85. Janecek,S. (2002) How many conserved sequence regions are there in the α-amylase family? Biologia 57 (Suppl. 11): 29-41. 86. Janecek,S., Leveque,E., Belarbi,A., and Haye,B. (1999) Close evolutionary relatedness of alphaamylases from Archaea and plants. J Mol Evol 48: 421-426. 87. Janecek,S., Svensson,B., and Henrissat,B. (1997) Domain evolution in the alpha-amylase family. J Mol Evol 45: 322-331. 88. Jeang,C.L., Chen,L.S., Chen,M.Y., and Shiau,R.J. (2002) Cloning of a gene encoding raw-starchdigesting amylase from a Cytophaga sp. and its expression in Escherichia coli. Appl Environ Microbiol 68: 3651-3654. 89. Jeanmougin,F., Thompson,J.D., Gouy,M., Higgins,D.G., and Gibson,T.J. (1998) Multiple sequence alignment with Clustal X. Trends Biochem Sci 23: 403-405. 90. Jespersen,H.M., MacGregor,E.A., Sierks,M.R., and Svensson,B. (1991) Comparison of the domain-level organization of starch hydrolases and related enzymes. Biochem J 280: 51-55. 91. Johnston,I.R. (1965) The composition of the cell wall of Aspergillus niger. Biochem J 96: 651-658. 92. Juge,N., Rodenburg,K.W., Guo,X.J., Chaix,J.C., and Svensson,B. (1995) Isozyme hybrids within the protruding third loop domain of the barley alpha-amylase (beta/alpha)8-barrel. Implication for BASI sensitivity and substrate affinity. FEBS Lett 363: 299-303. 93. Kanai,R., Haga,K., Akiba,T., Yamane,K., and Harata,K. (2004) Biochemical and crystallographic analyses of maltohexaose-producing amylase from alkalophilic Bacillus sp. 707. Biochemistry 43: 14047-14056. 136 Reference list 94. Kang,H.K., Lee,J.H., Kim,D., Day,D.F., Robyt,J.F., Park,K.H., and Moon,T.W. (2004) Cloning and expression of Lipomyces starkeyi alpha-amylase in Escherichia coli and determination of some of its properties. FEMS Microbiol Lett 233: 53-64. 95. Kaper,T., Leemhuis,H., Uitdehaag,J.C., Veen,B.A., Dijkstra,B.W., Maarel,M.J., and Dijkhuizen,L. (2007) Identification of acceptor substrate binding subsites +2 and +3 in the amylomaltase from Thermus thermophilus HB8. Biochemistry 46: 5261-5269. 96. Kaper,T., Talik,B., Ettema,T.J., Bos,H., van der Maarel,M.J., and Dijkhuizen,L. (2005) Amylomaltase of Pyrobaculum aerophilum IM2 produces thermoreversible starch gels. Appl Environ Microbiol 71: 5098-5106. 97. Kaper,T., van der Maarel,M.J., Euverink,G.J., and Dijkhuizen,L. (2004) Exploring and exploiting starchmodifying amylomaltases from thermophiles. Biochem Soc Trans 32: 279-282. 98. Kapteyn,J.C., Van Egmond,P., Sievi,E., Van Den Ende,H., Makarow,M., and Klis,F.M. (1999) The contribution of the O-glycosylated protein Pir2p/Hsp150 to the construction of the yeast cell wall in wild-type cells and beta 1,6-glucan-deficient mutants. Mol Microbiol 31: 1835-1844. 99. Kato,N., Murakoshi,Y., Kato,M., Kobayashi,T., and Tsukagoshi,N. (2002a) Isomaltose formed by alphaglucosidases triggers amylase induction in Aspergillus nidulans. Curr Genet 42: 43-50. 100. Kato,N., Suyama,S., Shirokane,M., Kato,M., Kobayashi,T., and Tsukagoshi,N. (2002b) Novel alphaglucosidase from Aspergillus nidulans with strong transglycosylation activity. Appl Environ Microbiol 68: 1250-1256. 101. Keller,N.P., and Hohn,T.M. (1997) Metabolic pathway gene clusters in filamentous fungi. Fungal Genet Biol 21: 17-29. 102. Kelly,J.M., and Hynes,M.J. (1985) Transformation of Aspergillus niger by the amdS gene of Aspergillus nidulans. EMBO J 4: 475-479. 103. Khoo,S.L., Amirul,A.A., Kamaruzaman,M., Nazalan,N., and Azizan,M.N. (1994) Purification and characterization of alpha-amylase from Aspergillus flavus. Folia Microbiol (Praha) 39: 392-398. 104. Kim,M.J., Lee,S.B., Lee,H.S., Lee,S.Y., Baek,J.S., Kim,D. et al. (1999) Comparative study of the inhibition of alpha-glucosidase, alpha-amylase, and cyclomaltodextrin glucanosyltransferase by acarbose, isoacarbose, and acarviosine-glucose. Arch Biochem Biophys 371: 277-283. 105. Kim,T.J., Park,C.S., Cho,H.Y., Cha,S.S., Kim,J.S., Lee,S.B. et al. (2000) Role of the glutamate 332 residue in the transglycosylation activity of Thermus maltogenic amylase. Biochemistry 39: 67736780. 106. Kirimura,K., Yusa,S., Rugsaseel,S., Nakagawa,H., Osumi,M., and Usami,S. (1999) Amylose-like polysaccharide accumulation and hyphal cell-surface structure in relation to citric acid production by Aspergillus niger in shake culture. Appl Microbiol Biotechnol 52: 421-428. 107. Kitamoto,H.K., Ohmomo,S., and Iimura,Y. (1998) Isolation and nucleotide sequence of the gene encoding phosphoenolpyruvate carboxykinase from Kluyveromyces lactis. Yeast 14: 963-967. 108. Klein,C., Hollender,J., Bender,H., and Schulz,G.E. (1992) Catalytic center of cyclodextrin glycosyltransferase derived from X-ray structure analysis combined with site-directed mutagenesis. Biochemistry 31: 8740-8746. 109. Klis,F.M., de Groot,P., and Hellingwerf,K. (2001) Molecular organization of the cell wall of Candida albicans. Med Mycol 39 Suppl 1: 1-8. 110. Klis,F.M., Mol,P., Hellingwerf,K., and Brul,S. (2002) Dynamics of cell wall structure in Saccharomyces cerevisiae. FEMS Microbiol Rev 26: 239-256. 111. Knegtel,R.M., Strokopytov,B., Penninga,D., Faber,O.G., Rozeboom,H.J., Kalk,K.H. et al. (1995) Crystallographic studies of the interaction of cyclodextrin glycosyltransferase from Bacillus circulans strain 251 with natural substrates and products. J Biol Chem 270: 29256-29264. 112. Kolar,M., Punt,P.J., van den Hondel,C.A., and Schwab,H. (1988) Transformation of Penicillium chrysogenum using dominant selection markers and expression of an Escherichia coli lacZ fusion gene. Gene 62: 127-134. 113. Korman,D.R., Bayliss,F.T., Barnett,C.C., Carmona,C.L., Kodama,K.H., Royer,T.J. et al. (1990) Cloning, characterization, and expression of two alpha-amylase genes from Aspergillus niger var. awamori. Curr Genet 17: 203-212. 114. Kralj,S., van Geel-Schutten,G.H., Dondorff,M.M., Kirsanovs,S., van der Maarel,M.J., and Dijkhuizen,L. (2004a) Glucan synthesis in the genus Lactobacillus: isolation and characterization of glucansucrase genes, enzymes and glucan products from six different strains. Microbiology 150: 3681-3690. 115. Kralj,S., van Geel-Schutten,G.H., van der Maarel,M.J., and Dijkhuizen,L. (2004b) Biochemical and molecular characterization of Lactobacillus reuteri 121 reuteransucrase. Microbiology 150: 20992112. 137 Alpha-glucan acting enzymes in Aspergillus niger 116. Kumar,S., Tamura,K., and Nei,M. (1993) MEGA: Molecular Evolutionary Analysis, version 1.01. The Pennsylvania State University. 117. Kupfer,D.M., Drabenstot,S.D., Buchanan,K.L., Lai,H., Zhu,H., Dyer,D.W. et al. (2004) Introns and splicing elements of five diverse fungi. Eukaryot Cell 3: 1088-1100. 118. Kuriki,T., and Imanaka,T. (1999) The concept of the alpha-amylase family: structural similarity and common catalytic mechanism. J Biosci Bioeng 87: 557-565. 119. Laemmli,U.K. (1970) Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227: 680-685. 120. Lasure,L.L., and Magnuson,J.K. (2004) Organic acid production by filamentous fungi. In Advances in Fungal Biotechnology for Industry, Agriculture and Medicine. Tkacz,J.S., and Lange,L. (eds). New York: Kluwer Academic & Plenum Publishers, pp. 307-340. 121. Lawson,C.L., van Montfort,R., Strokopytov,B., Rozeboom,H.J., Kalk,K.H., de Vries,G.E. et al. (1994) Nucleotide sequence and X-ray structure of cyclodextrin glycosyltransferase from Bacillus circulans strain 251 in a maltose-dependent crystal form. J Mol Biol 236: 590-600. 122. Le Gal-Coeffet,M.F., Jacks,A.J., Sorimachi,K., Williamson,M.P., Williamson,G., and Archer,D.B. (1995) Expression in Aspergillus niger of the starch-binding domain of glucoamylase. Comparison with the proteolytically produced starch-binding domain. Eur J Biochem 233: 561-567. 123. Leandro,M.J., Goncalves,P., and Spencer-Martins,I. (2006) Two glucose/xylose transporter genes from the yeast Candida intermedia: first molecular characterization of a yeast xylose-H+ symporter. Biochem J 395: 543-549. 124. Leemhuis,H., Dijkstra,B.W., and Dijkhuizen,L. (2003) Thermoanaerobacterium thermosulfurigenes cyclodextrin glycosyltransferase. Eur J Biochem 270: 155-162. 125. Leemhuis,H., Uitdehaag,J.C., Rozeboom,H.J., Dijkstra,B.W., and Dijkhuizen,L. (2002) The remote substrate binding subsite -6 in cyclodextrin-glycosyltransferase controls the transferase activity of the enzyme via an induced-fit mechanism. J Biol Chem 277: 1113-1119. 126. Leemhuis,H., Wehmeier,U.F., and Dijkhuizen,L. (2004) Single amino acid mutations interchange the reaction specificities of Cyclodextrin Glycosyltransferase and the acarbose-modifying enzyme Acarviosyl Transferase. Biochemistry 43: 13204-13213. 127. Lesage,G., and Bussey,H. (2006) Cell wall assembly in Saccharomyces cerevisiae. Microbiol Mol Biol Rev 70: 317-343. 128. Liebl,W., Feil,R., Gabelsberger,J., Kellermann,J., and Schleifer,K.H. (1992) Purification and characterization of a novel thermostable 4-alpha-glucanotransferase of Thermotoga maritima cloned in Escherichia coli. Eur J Biochem 207: 81-88. 129. Loftus,B.J., Fung,E., Roncaglia,P., Rowley,D., Amedeo,P., Bruno,D. et al. (2005) The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans. Science 307: 1321-1324. 130. Lomako,J., Lomako,W.M., and Whelan,W.J. (2004) Glycogenin: the primer for mammalian and yeast glycogen synthesis. Biochim Biophys Acta 1673: 45-55. 131. MacGregor,E.A., Janecek,S., and Svensson,B. (2001) Relationship of sequence and structure to specificity in the alpha-amylase family of enzymes. Biochim Biophys Acta 1546: 1-20. 132. MacGregor,E.A., Jespersen,H.M., and Svensson,B. (1996) A circularly permuted alpha-amylase-type alpha/beta-barrel structure in glucan-synthesizing glucosyltransferases. FEBS Lett 378: 263-266. 133. Machida,M., Asai,K., Sano,M., Tanaka,T., Kumagai,T., Terai,G. et al. (2005) Genome sequencing and analysis of Aspergillus oryzae. Nature 438: 1157-1161. 134. Machius,M., Declerck,N., Huber,R., and Wiegand,G. (1998) Activation of Bacillus licheniformis alphaamylase through a disorder-->order transition of the substrate-binding site mediated by a calciumsodium-calcium metal triad. Structure 6: 281-292. 135. Machovic,M., and Janecek,S. (2003) The invariant residues in the alpha-amylase family: just the catalytic triad. Biologia 58: 1127-1132. 136. Marchler-Bauer,A., and Bryant,S.H. (2004) CD-Search: protein domain annotations on the fly. Nucleic Acids Res 32: W327-W331. 137. Marion,C.L., Rappleye,C.A., Engle,J.T., and Goldman,W.E. (2006) An alpha-(1,4)-amylase is essential for alpha-(1,3)-glucan production and virulence in Histoplasma capsulatum. Mol Microbiol 62: 970983. 138. Martens-Uzunova,E.S., Zandleven,J.S., Benen,J.A., Awad,H., Kools,H.J., Beldman,G. et al. (2006) A new group of exo-acting family 28 glycoside hydrolases of Aspergillus niger that are involved in pectin degradation. Biochem J 400: 43-52. 139. Matsuura,Y., Kusunoki,M., Harada,W., and Kakudo,M. (1984) Structure and possible catalytic residues of Taka-amylase A. J Biochem (Tokyo) 95: 697-702. 138 Reference list 140. Mattey,M., and Allan,A. (1990) Glycogen accumulation in Aspergillus niger. Biochem Soc Trans 18: 1020-1021. 141. Mattsson,P., Battchikova,N., Sippola,K., and Korpela,T. (1995) The role of histidine residues in the catalytic act of cyclomaltodextrin glucanotransferase from Bacillus circulans var. alkalophilus. Biochim Biophys Acta 1247: 97-103. 142. Maubon,D., Park,S., Tanguy,M., Huerre,M., Schmitt,C., Prevost,M.C. et al. (2006) AGS3, an alpha(13)glucan synthase gene family member of Aspergillus fumigatus, modulates mycelium growth in the lung of experimentally infected mice. Fungal Genet Biol 43: 366-375. 143. Mazur,P., Morin,N., Baginsky,W., el Sherbeini,M., Clemas,J.A., Nielsen,J.B., and Foor,F. (1995) Differential expression and function of two homologous subunits of yeast 1,3-beta-D-glucan synthase. Mol Cell Biol 15: 5671-5681. 144. McCarter,J.D., and Withers,S.G. (1994) Mechanisms of enzymatic glycoside hydrolysis. Curr Opin Struct Biol 4: 885-892. 145. Meeuwsen,P.J., Vincken,J.P., Beldman,G., and Voragen,A.G. (2000) A universal assay for screening expression libraries for carbohydrases. J Biosci Bioeng 89: 107-109. 146. Meyer,V., Arentshorst,M., El Ghezal,A., Drews,A.C., Kooistra,R., van den Hondel,C.A., and Ram,A.F. (2007) Highly efficient gene targeting in the Aspergillus niger kusA mutant. J Biotechnol 128: 770775. 147. Micheli,P.A. (1729) Nova plantarum genera juxta Turnefortii methodum disposita. Florence. 148. Monchois,V., Willemot,R.M., and Monsan,P. (1999) Glucansucrases: mechanism of action and structure-function relationships. FEMS Microbiol Rev 23: 131-151. 149. Moreira,F.G., Lenartovicz,V., and Peralta,R.M. (2004) A thermostable maltose-tolerant alpha-amylase from Aspergillus tamarii. J Basic Microbiol 44: 29-35. 150. Morita,T., Tanaka,N., Hosomi,A., Giga-Hama,Y., and Takegawa,K. (2006) An alpha-amylase homologue, aah3, encodes a GPI-anchored membrane protein required for cell wall integrity and morphogenesis in Schizosaccharomyces pombe. Biosci Biotechnol Biochem 70: 1454-1463. 151. Morris,M.I., and Villmann,M. (2006) Echinocandins in the management of invasive fungal infections, Part 2. Am J Health Syst Pharm 63: 1813-1820. 152. Mosi,R., He,S., Uitdehaag,J., Dijkstra,B.W., and Withers,S.G. (1997) Trapping and characterization of the reaction intermediate in cyclodextrin glycosyltransferase by use of activated substrates and a mutant enzyme. Biochemistry 36: 9927-9934. 153. Mourya,S., and Jauhri,K.S. (2000) Production of citric acid from starch-hydrolysate by Aspergillus niger. Microbiol Res 155: 37-44. 154. Mouyna,I., Fontaine,T., Vai,M., Monod,M., Fonzi,W.A., Diaquin,M. et al. (2000) Glycosylphosphatidylinositol-anchored glucanosyltransferases play an active role in the biosynthesis of the fungal cell wall. J Biol Chem 19;275: 14882-14889. 155. Mouyna,I., Morelle,W., Vai,M., Monod,M., Lechenne,B., Fontaine,T. et al. (2005) Deletion of GEL2 encoding for a beta(1-3)glucanosyltransferase affects morphogenesis and virulence in Aspergillus fumigatus. Mol Microbiol 56: 1675-1688. 156. Nakajima,T., Imanaka,T., and Aiba,S. (1986) Comparison of amino acid sequences of eleven different alpha-amylases. Appl Microbiol Biotechnol 23: 355-360. 157. Nakamura,A., Haga,K., and Yamane,K. (1993) Three histidine residues in the active center of cyclodextrin glucanotransferase from alkalophilic Bacillus sp. 1011: effects of the replacement on pH dependence and transition-state stabilization. Biochemistry 32: 6624-6631. 158. Nakamura,A., Haga,K., and Yamane,K. (1994) The transglycosylation reaction of cyclodextrin glucanotransferase is operated by a Ping-Pong mechanism. FEBS Lett 337: 66-70. 159. Nakamura,A., Nishimura,I., Yokoyama,A., Lee,D.G., Hidaka,M., Masaki,H. et al. (1997) Cloning and sequencing of an alpha-glucosidase gene from Aspergillus niger and its expression in A. nidulans. J Biotechnol 53: 75-84. 160. Nakamura,T., Maeda,Y., Tanoue,N., Makita,T., Kato,M., and Kobayashi,T. (2006) Expression profile of amylolytic genes in Aspergillus nidulans. Biosci Biotechnol Biochem 70: 2363-2370. 161. Nakao,M., Nakayama,T., Kakudo,A., Inohara,M., Harada,M., Omura,F., and Shibano,Y. (1994) Structure and expression of a gene coding for thermostable alpha-glucosidase with a broad substrate specificity from Bacillus sp. SAM1606. Eur J Biochem 220: 293-300. 162. Nielsen,A.D., Fuglsang,C.C., and Westh,P. (2003) Effect of calcium ions on the irreversible denaturation of a recombinant Bacillus halmapalus alpha-amylase: a calorimetric investigation. Biochem J 373: 337-343. 139 Alpha-glucan acting enzymes in Aspergillus niger 163. Nierman,W.C., Pain,A., Anderson,M.J., Wortman,J.R., Kim,H.S., Arroyo,J. et al. (2005) Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus. Nature 438: 1151-1156. 164. Orlean,P. (1997) Biogenesis of yeast wall and surface components. In Cell Cycle and Cell Biology. Pringle,J., Broach,J.R., and Jones,E.W. (eds). New York: Cold Spring Harbor Laboratory Press, pp. 229-362. 165. Page,R.D.M. (1996) TREEVIEW: An application to display phylogenetic trees on personal computers. Computer Applications in the Biosciences 12: 357-358. 166. Paldi,T., Levy,I., and Shoseyov,O. (2003) Glucoamylase starch-binding domain of Aspergillus niger B1: molecular cloning and functional characterization. Biochem J 372: 905-910. 167. Pan,T., and Coleman,J.E. (1990) GAL4 transcription factor is not a "zinc finger" but forms a Zn(II)2Cys6 binuclear cluster. Proc Natl Acad Sci U S A 87: 2077-2081. 168. Parenicova,L., Benen,J.A., Kester,H.C., and Visser,J. (1998) pgaE encodes a fourth member of the endopolygalacturonase gene family from Aspergillus niger. Eur J Biochem 251: 72-80. 169. Pel,H.J., de Winde,J.H., Archer,D.B., Dyer,P.S., Hofmann,G., Schaap,P.J. et al. (2007) Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88. Nat Biotechnol 25: 221-231. 170. Penninga,D., van der Veen,B.A., Knegtel,R.M., van Hijum,S.A., Rozeboom,H.J., Kalk,K.H. et al. (1996) The raw starch binding domain of cyclodextrin glycosyltransferase from Bacillus circulans strain 251. J Biol Chem 271: 32777-32784. 171. Peters,D. (2006) Carbohydrates for fermentation. Biotechnol J 1: 806-814. 172. Petersen,K.L., Lehmbeck,J., and Christensen,T. (1999) A new transcriptional activator for amylase genes in Aspergillus. Mol Gen Genet 262: 668-676. 173. Popolo,L., Vai,M., Gatti,E., Porello,S., Bonfante,P., Balestrini,R., and Alberghina,L. (1993) Physiological analysis of mutants indicates involvement of the Saccharomyces cerevisiae GPIanchored protein gp115 in morphogenesis and cell separation. J Bacteriol 175: 1879-1885. 174. Preiss,J. (2004) Plant starch synthesis. In Starch in food. Eliasson,A.-C. (ed). Cambridge: Woodhead Publishing Limited, pp. 3-56. 175. Pugsley,A.P., and Dubreuil,C. (1988) Molecular characterization of malQ, the structural gene for the Escherichia coli enzyme amylomaltase. Mol Microbiol 2: 473-479. 176. Punt,P.J., and van den Hondel,C.A. (1992) Transformation of filamentous fungi based on hygromycin B and phleomycin resistance markers. Methods Enzymol 216: 447-457. 177. Ragni,E., Fontaine,T., Gissi,C., Latge,J.P., and Popolo,L. (2007) The Gas family of proteins of Saccharomyces cerevisiae: characterization and evolutionary analysis. Yeast 24: 297-308. 178. Ram,A.F., and Klis,F.M. (2006) Identification of fungal cell wall mutants using susceptibility assays based on Calcofluor white and Congo red. Nat Protoc 1: 2253-2256. 179. Rappleye,C.A., Engle,J.T., and Goldman,W.E. (2004) RNA interference in Histoplasma capsulatum demonstrates a role for alpha-(1,3)-glucan in virulence. Mol Microbiol 53: 153-165. 180. Rappleye,C.A., and Goldman,W.E. (2006) Defining virulence genes in the dimorphic fungi. Annu Rev Microbiol 60: 281-303. 181. Reese,A.J., and Doering,T.L. (2003) Cell wall alpha-1,3-glucan is required to anchor the Cryptococcus neoformans capsule. Mol Microbiol 50: 1401-1409. 182. Reese,A.J., Yoneda,A., Breger,J.A., Beauvais,A., Liu,H., Griffith,C.L. et al. (2007) Loss of cell wall alpha(1-3) glucan affects Cryptococcus neoformans from ultrastructure to virulence. Mol Microbiol 63: 1385-1398. 183. Robyt,J.F. (1998) Essentials of Carbohydrate Chemistry New York: Springer-Verlag New York Inc. 184. Rodenburg,K.W., Juge,N., Guo,X.J., Sogaard,M., Chaix,J.C., and Svensson,B. (1994) Domain B protruding at the third beta strand of the alpha/beta barrel in barley alpha-amylase confers distinct isozyme-specific properties. Eur J Biochem 221: 277-284. 185. Ruepp,A., Zollner,A., Maier,D., Albermann,K., Hani,J., Mokrejs,M. et al. (2004) The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes. Nucleic Acids Res 32: 5539-5545. 186. Saitou,N., and Nei,M. (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406-425. 187. Sambrook,J., Fritsch,E.F., and Maniatis,T. (1989) Molecular Cloning: A Laboratory Manual Cold spring Harbor, NY: Cold Spring Harbor Laboratory Press. 188. Sasangka,P., Matsuno,A., Tanaka,A., Akasaka,Y., Suyama,S., Kano,S. et al. (2002) Structural features of the glycogen branching enzyme encoding genes from Aspergilli. Microbiol Res 157: 337-344. 140 Reference list 189. Sauer,J., Sigurskjold,B.W., Christensen,U., Frandsen,T.P., Mirgorodskaya,E., Harrison,M. et al. (2000) Glucoamylase: structure/function relationships, and protein engineering. Biochim Biophys Acta 1543: 275-293. 190. Schauer,F., and Boriss,R. (2004) Biocatalysis and biotransformation. In Advances in Fungal Biotechnology for Industry, Agriculture, and Medicine. Tkacz,J.S., and Lange,L. (eds). New York: Kluwer Academic & Plenum Publishers, pp. 237-306. 191. Schuster,E., Dunn-Coleman,N., Frisvad,J.C., and van Dijck,P.W. (2002) On the safety of Aspergillus niger -a review. Appl Microbiol Biotechnol 59: 426-435. 192. Silva,A., Bacci,M., Jr., Gomes de Siqueira,C., Correa Bueno,O., Pagnocca,F.C., and Aparecida Hebling,M.J. (2003) Survival of Atta sexdens workers on different food sources. J Insect Physiol 49: 307-313. 193. Smith,S.E., and Read,D.J. (1997) Mycorrhizal Symbiosis. London: Academic Press Ltd. 194. Sogaard,M., Kadziola,A., Haser,R., and Svensson,B. (1993) Site-directed mutagenesis of histidine 93, aspartic acid 180, glutamic acid 205, histidine 290, and aspartic acid 291 at the active site and tryptophan 279 at the raw starch binding site in barley alpha-amylase 1. J Biol Chem 268: 2248022484. 195. Southall,S.M., Simpson,P.J., Gilbert,H.J., Williamson,G., and Williamson,M.P. (1999) The starchbinding domain from glucoamylase disrupts the structure of starch. FEBS Letters 447: 58-60. 196. Stagg,C.M., and Feather,M.S. (1973) The characterization of a chitin-associated D-glucan from the cell walls of Aspergillus niger. Biochim Biophys Acta 320: 64-72. 197. Stam,M.R., Danchin,E.G., Rancurel,C., Coutinho,P.M., and Henrissat,B. (2006) Dividing the large glycoside hydrolase family 13 into subfamilies: towards improved functional annotations of alphaamylase-related proteins. Protein Eng Des Sel 19: 555-562. 198. Steyn,A.J., Marmur,J., and Pretorius,I.S. (1995) Cloning, sequence analysis and expression in yeasts of a cDNA containing a Lipomyces kononenkoae alpha-amylase-encoding gene. Gene 166: 65-71. 199. Svensson,B., Larsen,K., and Gunnarsson,A. (1986) Characterization of a glucoamylase G2 from Aspergillus niger. Eur J Biochem 154: 497-502. 200. Takaha,T., Yanase,M., Okada,S., and Smith,S.M. (1993) Disproportionating enzyme (4-alphaglucanotransferase; EC 2.4.1.25) of potato. Purification, molecular cloning, and potential role in starch metabolism. J Biol Chem 268: 1391-1396. 201. Tani,S., Katsuyama,Y., Hayashi,T., Suzuki,H., Kato,M., Gomi,K. et al. (2001) Characterization of the amyR gene encoding a transcriptional activator for the amylase genes in Aspergillus nidulans. Curr Genet 39: 10-15. 202. Tao,B.Y., Reilly,P.J., and Robyt,J.F. (1989) Detection of a covalent intermediate in the mechanism of action of porcine pancreatic alpha-amylase by using 13C nuclear magnetic resonance. Biochim Biophys Acta 995: 214-220. 203. Terada,Y., Fujii,K., Takaha,T., and Okada,S. (1999) Thermus aquaticus ATCC 33923 amylomaltase gene cloning and expression and enzyme characterization: production of cycloamylose. Appl Environ Microbiol 65: 910-915. 204. Teste,M.A., Enjalbert,B., Parrou,J.L., and Francois,J.M. (2000) The Saccharomyces cerevisiae YPR184w gene encodes the glycogen debranching enzyme. FEMS Microbiol Lett 193: 105-110. 205. 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. 206. Toh-e A, Yasunaga,S., Nisogi,H., Tanaka,K., Oguchi,T., and Matsui,Y. (1993) Three yeast genes, PIR1, PIR2 and PIR3, containing internal tandem repeats, are related to each other, and PIR1 and PIR2 are required for tolerance to heat shock. Yeast 9: 481-494. 207. Tsukagoshi,N., Kobayashi,T., and Kato,M. (2001) Regulation of the amylolytic and (hemi-)cellulolytic genes in Aspergilli. J Gen Appl Microbiol 47: 1-19. 208. Tsukamoto,A., Kimura,K., Ishii,Y., Takano,T., and Yamane,K. (1988) Nucleotide sequence of the maltohexaose-producing amylase gene from an alkalophilic Bacillus sp. #707 and structural similarity to liquefying type alpha-amylases. Biochem Biophys Res Commun 151: 25-31. 209. Uitdehaag,J.C., Mosi,R., Kalk,K.H., van der Veen,B.A., Dijkhuizen,L., Withers,S.G., and Dijkstra,B.W. (1999) X-ray structures along the reaction pathway of cyclodextrin glycosyltransferase elucidate catalysis in the alpha-amylase family. Nat Struct Biol 6: 432-436. 210. van der Kaaij,R.M., Yuan,X.L., Franken,A., Ram,A.F.J., Punt,P.J., Maarel,M.J.E.C., and Dijkhuizen,L. (2007) Characterization of two novel, putatively cell wall associated and GPI-anchored, alphaglucanotransferase enzymes of Aspergillus niger. Eukaryot Cell doi:10.1128. 141 Alpha-glucan acting enzymes in Aspergillus niger 211. van der Maarel,M.J., van,d., V, Uitdehaag,J.C., Leemhuis,H., and Dijkhuizen,L. (2002) Properties and applications of starch-converting enzymes of the alpha-amylase family. J Biotechnol 94: 137-155. 212. Van der Veen,B., Uitdehaag,J.C., Dijkstra,B.W., and Dijkhuizen,L. (2000) Engineering of cyclodextrin glycosyltransferase reaction and product specificity. Biochim Biophys Acta 1543: 336-360. 213. van Dijck,P.W., Selten,G.C., and Hempenius,R.A. (2003) On the safety of a new generation of DSM Aspergillus niger enzyme production strains. Regul Toxicol Pharmacol 38: 27-35. 214. van Hartingsveldt,W., Mattern,I.E., van Zeijl,C.M., Pouwels,P.H., and van den Hondel,C.A. (1987) Development of a homologous transformation system for Aspergillus niger based on the pyrG gene. Mol Gen Genet 206: 71-75. 215. van Hijum,S.A., Kralj,S., Ozimek,L.K., Dijkhuizen,L., and van Geel-Schutten,I.G. (2006) Structurefunction relationships of glucansucrase and fructansucrase enzymes from lactic acid bacteria. Microbiol Mol Biol Rev 70: 157-176. 216. Vankuyk,P.A., Diderich,J.A., MacCabe,A.P., Hererro,O., Ruijter,G.J., and Visser,J. (2004) Aspergillus niger mstA encodes a high-affinity sugar/H+ symporter which is regulated in response to extracellular pH. Biochem J 379: 375-383. 217. Vos,A., Dekker,N., Distel,B., Leunissen,J.A., and Hochstenbach,F. (2007) Role of the SYN domain of Ags1p in cell wall alpha -glucan biosynthesis in fission yeast. J Biol Chem 282: 18969-79. 218. Vujicic-Zagar,A., and Dijkstra,B.W. (2006) Monoclinic crystal form of Aspergillus niger alpha-amylase in complex with maltose at 1.8 angstroms resolution. Acta Crystallograph Sect F Struct Biol Cryst Commun 62: 716-721. 219. Weenink,X.O., Punt,P.J., van den Hondel,C.A., and Ram,A.F. (2006) A new method for screening and isolation of hypersecretion mutants in Aspergillus niger. Appl Microbiol Biotechnol 69: 711-717. 220. Wernars,K., Goosen,T., Wennekes,L.M., Visser,J., Bos,C.J., van den Broek,H.W. et al. (1985) Gene amplification in Aspergillus nidulans by transformation with vectors containing the amdS gene. Curr Genet 9: 361-368. 221. Williamson,G., Belshaw,N.J., and Williamson,M.P. (1992) O-glycosylation in Aspergillus glucoamylase. Conformation and role in binding. Biochem J 282: 423-428. 222. Woloshuk,C.P., Yousibova,G.L., Rollins,J.A., Bhatnagar,D., and Payne,G.A. (1995) Molecular characterization of the afl-1 locus in Aspergillus flavus. Appl Environ Microbiol 61: 3019-3023. 223. Wolschek,M.F., and Kubicek,C.P. (1997) The filamentous fungus Aspergillus niger contains two "differentially regulated" trehalose-6-phosphate synthase-encoding genes, tpsA and tpsB. J Biol Chem 272: 2729-2735. 224. Woranovicz-Barreira,S.M., Gorin,P.A., Sassaki,P.L., Marcelli,M.P., and Iacomini,M. (1999) Galactomannoglucans of lichenized fungi of Cladonia spp.: significance as chemotypes. FEMS Microbiol Lett 181: 313-317. 225. Wu,C.H., Apweiler,R., Bairoch,A., Natale,D.A., Barker,W.C., Boeckmann,B. et al. (2006) The Universal Protein Resource (UniProt): an expanding universe of protein information. Nucleic Acids Res 34: D187-D191. 226. Yamazaki,H., Yamazaki,D., Takaya,N., Takagi,M., Ohta,A., and Horiuchi,H. (2007) A chitinase gene, chiB, involved in the autolytic process of Aspergillus nidulans. Curr Genet 51: 89-98. 227. Yoder,W.T., and Lehmbeck,J. (2004) Heterologous Expression and Protein Secretion. In Advances in Fungal Biotechnology for Industry, Agriculture and Medicine. Tkacz,J.S., and Lange,L. (eds). New York: Kluwer Academic & Plenum Publishers, pp. 201-219. 228. Yuan,X.L., Goosen,C., Kools,H., van der Maarel,M.J., van den Hondel,C.A., Dijkhuizen,L., and Ram,A.F. (2006) Database mining and transcriptional analysis of genes encoding inulin-modifying enzymes of Aspergillus niger. Microbiology 152: 3061-3073. 229. Yuuki,T., Nomura,T., Tezuka,H., Tsuboi,A., Yamagata,H., Tsukagoshi,N., and Udaka,S. (1985) Complete nucleotide sequence of a gene coding for heat- and pH-stable alpha-amylase of Bacillus licheniformis: comparison of the amino acid sequences of three bacterial liquefying alpha-amylases deduced from the DNA sequences. J Biochem (Tokyo) 98: 1147-1156. 142