Regulation of Plant Biomass Utilization in Aspergillus

Advances in Applied Microbiology

Volumn 88, Issue , 2014, Pages 31-56

  Kowalczyk, Joanna E ^a   Benoit, Isabelle ^a   De Vries, Ronald P ^a  

^a CBS KNAW FUNGAL BIODIVERSITY CENTRE   (Netherlands)

Author keywords

Aspergillus; Biomass utilization; Gene regulation; Plant polysaccharides; Transcriptional regulators

Indexed keywords

AMYR PROTEIN; ARAR PROTEIN; CARBON; CLBR PROTEIN; CREA PROTEIN; FUNGAL PROTEIN; GALR PROTEIN; GALX PROTEIN; INUR PROTEIN; MALR PROTEIN; MANR PROTEIN; POLYSACCHARIDE; REGULATOR PROTEIN; RHAR PROTEIN; UNCLASSIFIED DRUG; XLNR PROTEIN;

ARTICLE; ASPERGILLUS; BIOMASS; BIOMASS PRODUCTION; BIOTOPE; CARBON SOURCE; CHEMICAL COMPOSITION; DEGRADATION; FUNGAL BIOMASS; FUNGAL GENOME; NONHUMAN; PLANT BIOMASS; TRANSCRIPTION REGULATION;

ASPERGILLUS; BIOMASS UTILIZATION; GENE REGULATION; PLANT POLYSACCHARIDES; TRANSCRIPTIONAL REGULATORS;

ASPERGILLUS; BIOMASS; CARBON; FUNGAL PROTEINS; GENE EXPRESSION REGULATION, ENZYMOLOGIC; PLANTS; TRANS-ACTIVATORS;

EID: 84899140731     PISSN: 00652164     EISSN: None     Source Type: Book Series    
DOI: 10.1016/B978-0-12-800260-5.00002-4     Document Type: Chapter

References (92)

1. Abarca M.L., Accensi F., Cano J., Cabanes F.J. Taxonomy and significance of black Aspergilli. Antonie van Leeuwenhoek 2004, 86:33-49.
2. Abe K., Gomi K., Hasegawa F., Machida M. Impact of Aspergillus oryzae genomics on industrial production of metabolites. Mycopathologia 2006, 162:143-153.
3. Archer D.B. Filamentous fungi as microbial cell factories for food use. Current Opinion in Biotechnology 2000, 11:478-483.
4. Aro N., Pakula T., Penttilä M. Transcriptional regulation of plant cell wall degradation by filamentous fungi. FEMS Microbiology Review 2005, 29:719-739.
5. Aro N., Saloheimo M., Ilmén M., Penttilä M. ACEII, a novel transcriptional activator involved in regulation of cellulase and xylanase genes of Trichoderma reesei. Journal of Biological Chemistry 2001, 276:24309-24314.
6. Aro N., Saloheimo M., Ilmén M., Penttilä M. ACEI, of Trichoderma reesei is a repressor of cellulase and xylanase expression. Applied and Environmental Microbiology 2003, 69:56-65.
7. Barclay T., Ginic-Markovic M., Cooper P., Petrovsky N. Inulin-A versatile polysaccharide with multiple pharmaceutical and food chemical uses. Journal of Excipients and Food Chemicals 2010, 1(3):27-50.
8. Battaglia E., Visser L., Nijssen A., van Veluw J., Wösten H.A.B., de Vries R.P. Analysis of regulation of pentose utilisation in Aspergillus niger reveals evolutionary adaptations in the Eurotiales. Studies in Mycology 2011, 69:31-38.
9. Bennett J. An overview of the genus Aspergillus. Aspergillus molecular biology and genomics 2010, Caister Academic Press, Portland, OR. M. Machida, K. Gomi (Eds.).
10. Benoit I., Coutinho P.M., Schols H.A., Gerlach J.P., Henrissat B., de Vries R.P. Degradation of different pectins by fungi: Correlations and contrasts between the pectinolytic enzyme sets identified in genomes and the growth on pectins of different origin. BMC Genomics 2012, 13:321.
11. Benoit I., Danchin E.G., Bleichrodt R.J., de Vries R.P. Biotechnological applications and potential of fungal feruloyl esterases based on prevalence, classification and biochemical diversity. Biotechnology Letters 2008, 30:387-396.
12. Benoit I., de Vries R.P., Baker S.E., Karagiosis S.A. Aspergilli and biomass-degrading fungi 2013, Wiley, Hoboken, NJ.
13. Benoit I., Malavazi I., Goldman G., Baker S.E., de Vries R.P. Aspergillus-Genomics of a cosmopolitan fungus 2013, Springer, Heidelberg.
14. Brakhage A.A. Regulation of fungal secondary metabolism. Nature Reviews. Microbiology 2013, 11:21-32.
15. Brun S., Malagnac F., Bidard F., Lalucque H., Silar P. Functions and regulation of the Nox family in the filamentous fungus Podospora anserina: A new role in cellulose degradation. Molecular Microbiology 2009, 74:480-496.
16. Caffall K.H., Mohnen D. The structure, function, and biosynthesis of plant cell wall pectic polysaccharides. Carbohydrate Research 2009, 344:1879-1900.
17. Carlsen M., Nielsen J. Influence of carbon source on alpha-amylase production by Aspergillus oryzae. Applied Microbiology and Biotechnology 2001, 57:346-349.
18. Cerqueira G.C., Arnaud M.B., Inglis D.O., Skrzypek M.S., Binkley G., Simison M., et al. The Aspergillus Genome Database (AspGD): Multispecies curation and incorporation of RNA-Seq data to improve structural gene annotations. Nucleic Acids Research 2013, 42(database issue):D705-D710.
19. Christensen U., Gruben B.S., Madrid S., Mulder H., Nikolaev I., de Vries R.P. Unique regulatory mechanism for d-galactose utilization in Aspergillus nidulans. Applied and Environmental Microbiology 2011, 77:7084-7087.
20. Coradetti S.T., Craig J.P., Xiong Y., Shock T., Tian C., Glass N.L. Conserved and essential transcription factors for cellulase gene expression in ascomycete fungi. Proceedings of the National Academy of Sciences of the United States of America 2012, 109:7397-7402.
21. Coradetti S.T., Xiong Y., Glass N.L. Analysis of conserved cellulose transcriptional regulator reveals inducer-independent production of cellulolytic enzymes in Neurospora crassa. MicrobiologyOpen 2013, 2(4):595-609.
22. Culleton H., McKie V., de Vries R.P. Physiological and molecular aspects of degradation of plant polysaccharides by fungi: What have we learned from Aspergillus?. Biotechnology Journal 2013, 8(8):884-894.
23. de Groot M.J.L., van de Vondervoort P.J.I., de Vries R.P., vanKuyk P.A., Ruijter G.J.G., Visser J. Isolation and characterization of two specific regulatory Aspergillus niger mutants shows antagonistic regulation of arabinan and xylan metabolism. Microbiology 2003, 149:1183-1191.
24. Delmas S., Pullan S.T., Gaddipati S., Kokolski M., Malla S., Blythe M.J., et al. Uncovering the genome-wide transcriptional responses of the filamentous fungus Aspergillus niger to lignocellulose using RNA sequencing. PLoS Genetics 2012, 8:e1002875.
25. de Vries R.P. Regulation of Aspergillus genes encoding plant cell wall polysaccharide degrading enzymes; relevance for industrial production. Applied Microbiology and Biotechnology 2003, 61:10-20.
26. de Vries R.P., Faulds C.B., Visser J. The faeA gene from Aspergillus niger encoding a feruloyl esterase with activity on xylan and pectin is subject to a complex system of regulation. Journal of the Science of Food and Agriculture 1999, 79:443-446.
27. de Vries R.P., Jansen J., Aguilar G., Parenicová L., Benen J.A.E., Joosten V., et al. Expression profiling of pectinolytic genes from Aspergillus niger. FEBS Letters 2002, 530:41-47.
28. de Vries R.P., Kester H.C.M., vanKuyk P.A., Visser J. The Aspergillus niger faeB gene encodes a second feruloyl esterase involved in pectin and xylan degradation, and is specifically induced on aromatic compounds. Biochemical Journal 2002, 363:377-386.
29. de Vries R.P., Nayak V., van den Brink J., Vivas Duarte A.D., Stalbrand H. Fungal degradation of plant oligo- and polysaccharides. Carbohydrate modifying biocatalysts 2012, 693-759. Pan Stanford Publishing Pte Ltd., Singapore. P. Grunwald (Ed.).
30. de Vries R.P., van de Vondervoort P.J.I., Hendriks L., van de Belt M., Visser J. Regulation of the a-glucuronidase encoding gene (aguA) from Aspergillus niger. Molecular and General Genetics 2002, 268:96-102.
31. de Vries R.P., van den Broeck H.C., Dekkers E., Manzanares P., de Graaff L.H., Visser J. Differential expression of three a-galactosidase genes and a single b-galactosidase gene from Aspergillus niger. Applied and Environmental Microbiology 1999, 65:2453-2460.
32. de Vries R.P., Visser J. Regulation of the feruloyl esterase (faeA) gene from Aspergillus niger. Applied and Environmental Microbiology 1999, 65:5500-5503.
33. de Vries R.P., Visser J. Aspergillus enzymes involved in degradation of plant cell wall polysaccharides. Microbiology and Molecular Biology Reviews 2001, 65:497-522.
34. Dowzer C.E., Kelly J.M. Cloning of the creA gene from Aspergillus nidulans: A gene involved in carbon catabolite repression. Current Genetics 1989, 15:457-459.
35. Dowzer C.E.A., Kelly J.M. Analysis of the creA gene, a regulator of carbon catabolite repression in Aspergillus nidulans. Molecular and Cellular Biology 1991, 11:5701-5709.
36. Espagne E., Lespinet O., Malagnac F., Da Silva C., Jaillon O., Porcel B.M., et al. The genome sequence of the model ascomycete fungus Podospora anserina. Genome Biology 2008, 9:R77.
37. Fedorova N.D., Khaldi N., Joardar V.S., Maiti R., Amedeo P., Anderson M.J., et al. Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatus. PLoS Genetics 2008, 4:e1000046.
38. Flipphi M.J.A., Visser J., van der Veen P., de Graaff L.H. Arabinase gene expression in Aspergillus niger: Indications for co-ordinated gene expression. Microbiology 1994, 140:2673-2682.
39. Futagami T., Mori K., Yamashita A., Wada S., Kajiwara Y., Takashita H., et al. Genome sequence of the white koji mold Aspergillus kawachii IFO 4308, used for brewing the Japanese distilled spirit shochu. Eukaryotic Cell 2011, 10:1586-1587.
40. Galagan J.E., Calvo S.E., Cuomo C., Ma L.J., Wortman J.R., Batzoglou S., et al. Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae. Nature 2005, 438:1105-1115.
41. Gibbons J.G., Rokas A. The function and evolution of the Aspergillus genome. Trends in Microbiology 2013, 21(1):14-22.
42. Gielkens M.M., Dekkers E., Visser J., de Graaff L.H. Two cellobiohydrolase-encoding genes from Aspergillus niger require d-xylose and the xylanolytic transcriptional activator XlnR for their expression. Applied and Environmental Microbiology 1999, 65:4340-4345.
43. Goldman G.H., Kafer E. Aspergillus nidulans as a model system to characterize the DNA damage response in eukaryotes. Fungal Genetics and Biology 2004, 41:428-442.
44. Gomi K., Akeno T., Minetoki T., Ozeki K., Kumagai C., Okazaki N., et al. Molecular cloning and characterization of a transcriptional activator gene, amyR, involved in the amylolytic gene expression in Aspergillus oryzae. Bioscience, Biotechnology, and Biochemistry 2000, 64:816-827.
45. Gruben B.S., Zhou M., de Vries R.P. GalX regulates the d-galactose oxido-reductive pathway in Aspergillus niger. FEBS Letters 2012, 586(22):3980-3985.
46. Gruben B.S., Zhou M., Wiebenga A., Ballering J., Overkamp K.M., Punt P.J., et al. Aspergillus niger RhaR, a regulator involved in L-rhamnose release and catabolism. Applied Microbiology and Biotechnology 2014, 10.1007/s00253-014-5607-9.
47. Hasegawa S., Takizawa M., Suyama H., Shintani T., Gomi K. Characterization and expression analysis of a maltose-utilizing (MAL) cluster in Aspergillus oryzae. Fungal Genetics and Biology 2010, 47:1-9.
48. Hasper A.A., Dekkers E., van Mil M., van de Vondervoort P.J., de Graaff L.H. EglC, a new endoglucanase from Aspergillus niger with major activity towards xyloglucan. Applied and Environmental Microbiology 2002, 68:1556-1560.
49. Hasper A.A., Trindade L.M., van der Veen D., van Ooyen A.J., de Graaff L.H. Functional analysis of the transcriptional activator XlnR from Aspergillus niger. Microbiology 2004, 150:1367-1375.
50. Hedayati M.T., Pasqualotto A.C., Warn P.A., Bowyer P., Denning W.D. Aspergillus flavus: Human pathogen, allergen and mycotoxin producer. Microbiology 2007, 153:1677-1692.
51. Keller N.P., Turner G., Bennett J.W. Fungal secondary metabolism-From biochemistry to genomics. Nature Reviews. Microbiology 2005, 3(12):937-947.
52. Klich M.A. Aspergillus flavus: The major producer of aflatoxin. Molecular Plant Pathology 2007, 8(6):713-722.
53. Kobayashi T., Kato M. Transcriptional regulation in Aspergillus. Aspergillus molecular biology and genomics 2012, 85-114. Caister Academic Press, Norfolk, UK. M. Machida, K. Gomi (Eds.).
54. Kunitake E., Tani S., Sumitani J. A novel transcriptional regulator, ClbR, controls the cellobiose- and cellulose-responsive induction of cellulase and xylanase genes regulated by two distinct signaling pathways in Aspergillus aculeatus. Applied Microbiology and Biotechnology 2012, 97:2017-2028.
55. Lombard V., Ramulu H.G., Drula E., Coutinho P.M., Henrissat B. The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Research 2014, 42:D490-D495.
56. Lubertozzi D., Keasling J.D. Developing Aspergillus as a host for heterologous expression. Biotechnology Advances 2009, 27:53-75.
57. Machida M., Asai K., Sano M., Tanaka T., Kumagai T., Terai G., et al. Genome sequencing and analysis of Aspergillus oryzae. Nature 2005, 438:1157-1161.
58. Makita T., Katsuyama Y., Tani S., Suzuki H., Kato N., Todd R.B., et al. Inducer-dependent nuclear localization of a Zn(II)(2)Cys(6) transcriptional activator, AmyR, in Aspergillus nidulans. Bioscience, Biotechnology, and Biochemistry 2009, 73:391-399.
59. Malagnac F., Bidard F., Lalucque H., Brun S., Lambou K., Lebrun M.H., et al. Convergent evolution of morphogenetic processes in fungi. Communicative and Integrative Biology 2008, 1(2):180-181.
60. Marui J., Kitamoto N., Kato M., Kobayashi T., Tsukagoshi N. Transcriptional activator, AoXlnR, mediates cellulose-inductive expression of the xylanolytic and cellulolytic genes in Aspergillus oryzae. FEBS Letters 2002, 528:279-282.
61. Moreira L.R., Filho E.X. An overview of mannan structure and mannan-degrading enzyme systems. Applied Microbiology and Biotechnology 2008, 79:165-178.
62. Nierman W.C., Pain A., Anderson M.J., Wortman J.R., Kim H.S., Arroyo J., et al. Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus. Nature 2005, 438:1151-1156.
63. Noguchi Y., Tanaka H., Kanamaru K., Kato M., Kobayashi T. Xylose triggers reversible phosphorylation of XlnR, the fungal transcriptional activator of xylanolytic and cellulolytic genes in Aspergillus oryzae. Bioscience, Biotechnology, and Biochemistry 2011, 75:953-959.
64. Ogawa M., Kobayashi T., Koyama Y. ManR, a novel Zn(II)(2)Cys(6) transcriptional activator, controls the beta-mannan utilization system in Aspergillus oryzae. Fungal Genetics and Biology 2012, 49(12):987-995.
65. Ogawa M., Kobayashi T., Koyama Y. ManR, a transcriptional regulator of the β-mannan utilization system, controls the cellulose utilization system in Aspergillus oryzae. Bioscience, Biotechnology, and Biochemistry 2013, 77:426-429.
66. Park S., Baker J.O., Himmel M.E., Parilla P.A., Johnson D.K. Cellulose crystallinity index: Measurement techniques and their impact on interpreting cellulose performance. Biotechnology for Biofuels 2010, 3(10):1-10.
67. Payne G.A., Nierman W.C., Wortman J.R., Pritchard B.L., Brown D., Dean R.A., et al. Whole genome comparison of Aspergillus flavus and Aspergillus oryzae. Medical Mycology 2006, 44(S1):9-11.
68. Pel H.J., de Winde J.H., Archer D.B., Dyer P.S., Hofmann G., Schaap P.J., et al. Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88. Nature Biotechnology 2007, 25:221-231.
69. Petersen K.L., Lehmbeck J., Christensen T. A new transcriptional activator for amylase genes in Aspergillus. Molecular and General Genetics 1999, 262:668-676.
70. Roy P., Lockington R.A., Kelly J.M. CreA-mediated repression in Aspergillus nidulans does not require transcriptional auto-regulation, regulated intracellular localisation or degradation of CreA. Fungal Genetics and Biology 2008, 45:657-670.
71. Ruijter G.J.G., Visser J. Carbon repression in Aspergilli. FEMS Microbiology Letters 1997, 151:103-114.
72. Sato A., Oshima K., Noguchi H., Ogawa M., Takahashi T., Oguma T., et al. Draft genome sequencing and comparative analysis of Aspergillus sojae NBRC4239. DNA Research 2011, 18:165-176.
73. Scheller H.V., Ulvskov P. Hemicelluloses. Annual Review of Plant Biology 2010, 61:263-289.
74. Strauss J., Horvath H.K., Abdallah B.M., Kindermann J., Mach R.L., Kubicek C.P. The function of CreA, the carbon catabolite repressor of Aspergillus nidulans, is regulated at the transcriptional and post-transcriptional level. Molecular Microbiology 1999, 32:169-178.
75. Stricker A.R., Grosstessner-Hain K., Wurleitner E., Mach R.L. Xyr1 (xylanase regulator 1) regulates both the hydrolytic enzyme system and d-xylose metabolism in Hypocrea jecorina. Eukaryotic Cell 2006, 5:2128-2137.
76. Stricker A.R., Mach R.L., de Graaff L.H. Regulation of transcription of cellulases- and hemicellulases-encoding genes in Aspergillus niger and Hypocrea jecorina (Trichoderma reesei). Applied Microbiology and Biotechnology 2008, 78:211-220.
77. Tamayo-Ramos J.A., Flipphi M., Pardo E., Manzanares P., Orejas M. l-rhamnose induction of Aspergillus nidulans alpha-l-rhamnosidase genes is glucose repressed via a CreA-independent mechanism acting at the level of inducer uptake. Microbial Cell Factories 2012, 11:26.
78. Tani S., Katsuyama Y., Hayashi T., Suzuki H., Kato M., Gomi K., et al. Characterisation of the amyR gene encoding a transcriptional activator for the amylase genes in Aspergillus nidulans. Current Genetics 2001, 39:10-15.
79. Todd R.B., Andrianopoulos A. Evolution of a fungal regulatory gene family: The Zn(II)2Cys6 binuclear cluster DNA binding motif. Fungal Genetics and Biology 1997, 21:388-405.
80. van den Brink J., de Vries R.P. Fungal enzyme sets for plant polysaccharide degradation. Applied Microbiology and Biotechnology 2011, 91(6):1477-1492.
81. vanKuyk P.A., Benen J.A., Wosten H.A., Visser J., de Vries R.P. A broader role for AmyR in Aspergillus niger: Regulation of the utilisation of d-glucose or d-galactose containing oligo- and polysaccharides. Applied Microbiology and Biotechnology 2012, 93:285-293.
82. van Peij N.N.M.E. Transcriptional regulation of the xylanolytic enzyme system of Aspergillus 1999, Molecular Genetics of Industrial Microorganisms, Wageningen University, Wageningen, The Netherlands.
83. van Peij N., Gielkens M.M.C., de Vries R.P., Visser J., de Graaff L.H. The transcriptional activator XlnR regulates both xylanolytic and endoglucanase gene expression in Aspergillus niger. Applied and Environmental Microbiology 1998, 64:3615-3619.
84. van Peij N.N., Visser J., de Graaff L.H. Isolation and analysis of xlnR, encoding a transcriptional activator co-ordinating xylanolytic expression in Aspergillus niger. Molecular Microbiology 1998, 27:131-142.
85. Vincken J.-P., York W.S., Beldman G., Voragen A.G.J. Two general branching patterns of xyloglucan, XXXG and XXGG. Plant Physiology 1997, 114:9-13.
86. Vongsangnak W., Salazar M., Hansen K., Nielsen J. Genome-wide analysis of maltose utilization and regulation in aspergilli. Microbiology 2009, 155:3893-3902.
87. Wang P., Kojima T., Kobayashi T., Nakano H. Comprehensive analysis of the DNA-binding specificity of an Aspergillus nidulans transcription factor, AmyR, using a bead display system. Bioscience, Biotechnology, and Biochemistry 2012, 76(6):1128-1134.
88. Watanabe J., Tanaka H., Mogi Y., Yamazaki T., Suzuki K., Watanabe T., et al. Loss of Aspergillus oryzae amyR function indirectly affects hemicellulolytic and cellulolytic enzyme production. Journal of Bioscience and Bioengineering 2011, 111:408-413.
89. Witteveen C.F.B., Busink R., van de Vondervoort P., Dijkema C., Swart K., Visser J. l-arabinose and d-xylose catabolism in Aspergillus niger. Journal of General Microbiology 1989, 135:2163-2171.
90. Yamane Y., Fujita J., Izuwa S., Fukuchi K., Shimizu R., Hiyoshi A., et al. Properties of cellulose-degrading enzymes from Aspergillus oryzae and their contribution to material utilization and alcohol yield in sake mash fermentation. Journal of Bioscience and Bioengineering 2002, 93:479-484.
91. Yuan X.L., Goosen C., Kools H., van der Maarel M.J., van den Hondel C.A., Dijkhuizen L., et al. Database mining and transcriptional analysis of genes encoding inulin-modifying enzymes of Aspergillus niger. Microbiology 2006, 152:3061-3073.
92. Yuan X.L., Roubos J.A., van den Hondel C.A., Ram A.F. Identification of InuR, a new Zn(II)2Cys6 transcriptional activator involved in the regulation of inulinolytic genes in Aspergillus niger. Molecular Genetics and Genomics 2008, 279:11-26.