Introduction Aspergillus niger 2001 2001 2006 2006 1998 http://www.cazy.org 1999 8 2001 1986 2000 1999 A. niger A. niger 1984 2003 1997 1990 1990 2006 2001 2002a 1999 2000 2001 2004 2000 2001 A. niger 1953 1965 1972 ags d ags1 Schizosaccharomyces pombe 1998 ags1 2005 2006 Histoplasma capsulatum AMY1 H. capsulatum 2004 2006 S. pombe 2006 aah3 agtA A. niger 2007a A. niger 2007 Aspergillus A. niger amyR S. pombe H. capsulatum Material and methods A. niger A. niger 2007 A. niger 1 2 1998 http://hmmer.wustl.edu/ http://www.cazy.org 1999 http://www.ncbi.nlm.nih.gov/entrez/ http://www.expasy.org/sprot/ A. niger 2004 http://www.ebi.ac.uk/Wise2/ Table 1 A. niger Accession no. Gene Family Enzyme activity a b Proposed biological function c An11g03340 aamA GH13 Acid α-amylase SS   Starch degradation 1 An12g06930 amyA GH13 α-Amylase SS +970; +252 Starch degradation 2 An05g02100 amyB GH13 α-Amylase SS +252 Starch degradation 2 An04g06930 amyC GH13 α-Amylase SS +787; +664; −531 Starch degradation 3 An09g03100 agtA GH13 α-Glucanotransferase SS, GPI  Cell wall α-glucan synthesis 4 An12g02460 agtB GH13 α-Glucanotransferase SS, GPI +810 Cell wall α-glucan synthesis 4 An15g07800 agtC GH13 Putative α-glucanotransferase SS, GPI  Cell wall α-glucan synthesis 4 An02g13240 agdC GH13 Putative α-glucosidase  +368 Unknown  An13g03710 agdD GH13 Putative α-glucosidase   Unknown  An01g13610 amyD GH13 Putative α-amylase  +504; −32 Cell wall α-glucan synthesis  An09g03110 amyE GH13 Putative α-amylase  −76 Cell wall α-glucan synthesis  An01g06120 gdbA GH13 Glycogen debranching enzyme −487; +393 Glycogen metabolism  An14g04190 gbeA GH13 Glycogen branching enzyme  Glycogen metabolism  An04g09890 agsA GH13 Putative α-glucan synthase SS  Cell wall α-glucan synthesis 5 An15g07810 agsB GH13 Putative α-glucan synthase SS +287 Cell wall α-glucan synthesis 5 An12g02450 agsC GH13 Putative α-glucan synthase SS −973; +622, −185 Cell wall α-glucan synthesis 5 An02g03260 agsD GH13 Putative α-glucan synthase SS  Cell wall α-glucan synthesis 5 An09g03070 agsE GH13 Putative α-glucan synthase SS  Cell wall α-glucan synthesis 5 An03g06550 glaA GH15 Glucoamylase SS, SBD −792; −669; +423; −301 Starch degradation 6 An12g03070 glaB GH15 Putative glucoamylase  −878 Unknown  An04g06920 agdA GH31 α-Glucosidase SS +574; +191,  Starch degradation 7 An01g10930 agdB GH31 Putative α-glucosidase SS +904; −334 Starch degradation  An09g05880 agdE GH31 Putative α-glucosidase II SS  Protein glycosylation  An18g05620 agdF GH31 Unknown   Unknown  An07g00350 agdG GH31 Unknown SS +402 Unknown  An09g03300 axlA GH31 Putative α-xylosidase SS +126 Xyloglucan degradation  An01g04880 axlB GH31 Putative α-xylosidase  +430; +138,  Xyloglucan degradation  The newly identified proteins are indicated in bold a SS  GPI  SBD b c 1990 1990 2007 2005 1984 1997 Table 2 1 Accession no. Name Family Enzyme activity a Biological function Organism b BAA78714  AndGbe1 GH13 Glycogen branching enzyme  Glycogen metabolism A. nidulans 1 BAA34996 ScGdb1 GH13 Glycogen debranching enzyme  Glycogen metabolism S. cerevisiae 2 P19571 BsAmyA GH13 α-Amylase SS Starch degradation Bacillus  3 CAA54266 BsAglA GH13 α-Glucosidase  Starch degradation Bacillus  4 CAA21237  SpAah1 GH13 Unknown SS, GPI α-Glucan biosynthesis S. pombe 5 CAA91249 SpAah2 GH13 Unknown SS, GPI α-Glucan biosynthesis S. pombe 5 CAB40006 SpAah3 GH13 Unknown SS, GPI α-Glucan biosynthesis S. pombe 5 CAA16864 SpAah4 GH13 Unknown SS, GPI α-Glucan biosynthesis S. pombe 5 ABK62854 HcAmy1 GH13 Unknown α-Glucan biosynthesis H. capsulatum 6 ABF50883 AN7345.2 GH31 α/β-Glucosidase SS Starch/cellulose degradation A. nidulans 7 ABF50846 AN7505.2 GH31 α-Xylosidase  Xylan degradation A. nidulans 7 BAB39856 AndAgdB GH31 α-Glucosidase SS Starch degradation A. nidulans 8 AAU87580  TrAguII GH31 α-Glucosidase II SS Protein glycosylation T. reesei 9 A45249 CAMAL2 GH31 Maltase  Maltose degradation C. albicans 10 A. niger a SS  GPI b 2002 2000 1988 1994 2006 2006 2006 2002b 2005 1992 http://www.cbs.dtu.dk/services/SignalP/ 2004 http://mendel.imp.ac.at/sat/gpi/gpi_server 2004 http://www.ncbi.nlm.nih.gov/BLAST/ 2004 1994 Strains and transformations A. niger cpsA1 A. niger 1988 pyrG 1987 amyR A. niger Aspergillus 1991 Aspergillus A. niger 1992 Escherichia coli 1990 A. niger A. niger amyR Nsi amyR amyR Bam Eco Nsi Sal amyR Nsi Sal BamH Sal A. oryzae pyrG 1989 pyrG Bam Eco amyR amyR amy Eco pyrG + amyR amyR amyR amyR Culture conditions, RNA preparation, microarray experiments and data analysis A. niger amyR ® Aspergillus niger 6 −1 ΔamyR A. niger P http://www.ebi.ac.uk/miamexpress P Results A. niger 2001 A. niger A. niger 2007 1 A. niger A. niger 1 A. niger A. niger amyR 2 amyR A. niger A. fumigatus 2005 A. nidulans 2005 A. oryzae 2005 Fig. 1 A. niger a b A. niger bold 1 2 Bootstrap values scale bar  Fig. 2 A. niger 1 2 right-hand side  Identification and transcriptional regulation of GH13 family members A. niger 1 3 A. niger 1 Table 3 A. niger S. pombe H. capsulatu m  The seven residues generally conserved in family GH13 are indicated in bold and the three catalytic residues are additionally underlined. The group to which the proteins are assigned, as described in this paper, is indicated 1990 A. niger amyC agdA amyR aamA A. niger 2 aamA amyR amyA amyB A. niger 2 Discussion amyC aamA amyC amyR amyC 1 A. niger aamA A. nidulans A. fumigatus A. niger glaA aamA aamA aamA A. niger A. niger A. niger 2006 g t 2007a g p i 1997 1 3 1999 2003 2004 3 A. niger agtB agtC agtA amyR 2 agtB agtC 3 A. oryzae A. nidulans A. fumigatus Bacillus 1994 agdC agdD 2 2007b H. capsulatum Bacillus 1988 amyD amyE 2 A. niger Aspergillus A. niger amyE A. nidulans A. oryzae A. niger Aspergillus A. niger amyR 2 2005 agsB agsC agtC agtB agsC agtB agsB agtC agsA agsD AgsE 2 A. niger Aspergillus A. niger Identification and transcriptional regulation of GH15 family members A. niger 1984 A. niger glaA 1990 glaA glaB 2 Identification and transcriptional regulation of GH31 family members A. niger aglA 1997 A. niger A. nidulans 1992 1 A. nidulans 2006 2002b agdB agdA amyR aamA glaA agdA agdB 2 Trichoderma reesei 2005 2005 agdE 2 A. nidulans 2006 axlA 2 axlA 2 A. fumigatus A. nidulans A. oryzae A. niger Genome-wide analysis of AmyR dependent maltose induced genes using microarrays A. niger aamA glaA agdA agdB 2 P amyR P 3 4 5 2004 aamA glaA agdA agdB 4 Candida intermedia 2006 amyR Kluyveromyces lactis 1998 Fig. 3 Venn-diagram A. niger amyR bold box  Table 4 A. niger a b c N402 xylose Call ΔamyR Call Fold induction P Putative function Maltose vs xylose ΔamyR Carbohydrate transport and metabolism An11g03340 3.15 ± 0.12 P 0.08 ± 0.04 A 0.13 ± 0.09 A 38.6 24.2 0.080 Acid alpha-amylase AamA An04g06920 85.96 ± 22.54 P 6.24 ± 0.98 P 5.03 ± 0.03 P 13.8 17.1 0.064 Extracellular alpha-glucosidase AgdA An01g10930 96.50 ± 31.50 P 10.47 ± 2.59 P 8.35 ± 2.13 P 9.2 11.5 0.062 Extracellular alpha-glucosidase AgdB An03g06550 117.80 ± 43.16 P 13.78 ± 4.14 P 5.85 ± 0.47 P 8.5 20.1 0.072 Glucoamylase GlaA  An15g03940 152.30 ± 19.00 P 65.74 ± 3.04 P 70.59 ± 2.88 P 2.3 2.2 0.074 Putative monosaccharide transporter Energy An11g02550 58.87 ± 3.86 P 10.13 ± 1.41 P 25.27 ± 5.35 P 5.8 2.3 0.033 Putative phosphoenolpyruvate carboxykinase  a b P c P  M  A 2004 Table 5 A. niger a b c N402 xylose Call ΔamyR Call Fold induction P Putative function Maltose vs xylose ΔamyR Carbohydrate transport and metabolism An11g03340 65.26 ± 7.48 P 0.58 ± 0.57 A 0.08 ± 0.01 A 113.0 808.4 0.004 Acid alpha-amylase AamA An01g10930 49.46 ± 3.42 P 2.37 ± 0.08 P 6.84 ± 1.99 P 20.9 7.2 0.006 Extracellular alpha-glucosidase AgdB An04g06920 179.10 ± 13.90 P 9.89 ± 3.63 P 3.36 ± 0.46 P 17.6 51.7 0.012 Extracellular alpha-glucosidase AgdA An02g03540 62.79 ± 8.36 P 8.81 ± 0.61 P 0.96 ± 0.82 P, A 6.7 61.9 0.012 Putative hexose transport protein MstC An15g03940 144.40 ± 6.80 P 35.93 ± 2.72 P 3.04 ± 0.03 P, M 4.0 47.6 0.003 Putative monosaccharide transporter An03g06550 239.30 ± 2.05 P 83.03 ± 4.35 P 19.03 ± 1.75 P 2.9 12.6 0.012 Glucoamylase GlaA  An04g06930 4.36 ± 0.50 P 1.50 ± 0.16 P 1.40 ± 0.03 P 2.9 3.1 0.062 Extracellular alpha-amylase AmyC An09g04810 18.47 ± 0.44 P 6.46 ± 0.35 P 2.52 ± 0.02 P 2.9 7.4 0.003 Putative hexose transporter An12g07450 137.60 ± 13.00 P 51.57 ± 11.82 P 52.50 ± 6.31 P 2.7 2.6 0.064 Sugar/H+ symporter MstA Energy An03g06270 4.72 ± 0.29 P 1.59 ± 0.14 A 0.20 ± 0.25 A 3.3 25.6 0.035 Putative isoamyl alcohol oxidase  An16g06010 5.18 ± 1.55 P 1.80 ± 0.39 P 0.22 ± 0.02 A 2.9 23.8 0.032 Putative phosphoglycerate mutase Amino acid transport and metabolism An03g00280 8.35 ± 0.90 P 3.57 ± 0.74 P, A 0.12 ± 0.06 A 2.3 68.0 0.050 Similarity to tyrosinase protein  Cell rescue, defence and virulence            An14g05730 3.99 ± 0.59 P 0.23 ± 0.03 A 1.37 ± 0.73 P, A 18.8 3.2 0.037 Similarity to integral membrane protein  An03g00290 5.96 ± 0.89 P 1.68 ± 0.47 P 0.64 ± 0.21 P 3.5 9.3 0.068 Similarity to integral membrane protein  An06g00490 8.14 ± 0.89 P 3.81 ± 0.30 P, A 2.23 ± 0.44 A 2.1 3.7 0.066 Similarity to integral membrane protein Protein fate An18g04260 5.44 ± 0.40 P 2.57 ± 0.07 P 1.77 ± 0.28 M, A 2.1 3.1 0.056 Similarity to UDP-galactose transporter Unclassified An16g01290 15.04 ± 0.28 P 5.22 ± 1.69 P, A 1.97 ± 0.26 A 2.6 6.9 0.027 Unknown  An09g06130 12.62 ± 2.51 P 5.41 ± 0.93 P 2.69 ± 0.30 P, A 2.3 4.7 0.059 Unknown a,b,c 4 amyR ΔamyR ΔamyR amyR P 3 5 aamA, glaA, agdA, agdB amyC 4 5 glaA aamA agdB amyC amyC amyR P P amyR amyR amyR Discussion A. niger 2007 A. niger Aspergillus A. niger 1 amyC A. niger amyC amyC agdA amyR A. nidulans A. oryzae 2000 A. fumigatus 1995 1989 amyA amyB A. niger A. niger 2007 A. niger amyA/B A. niger amyA/B A. niger 2006 amyA/amyB A. niger ΔaamA aamA glaA 2006 amyA/B agtC, amyD, agdD, agdG glaB A. niger 2006 2007a S. pombe 3 2006 A. niger agtA 2007a agt Aspergillus A. niger agt Aspergillus niger 2006 H. capsulatum AMY1 2006 Aspergilli A. niger A. nidulans A. oryzae AMY1 ags agt 2007b amyD amyE A. niger Bacillus C. albicans A. niger 1997 2000 A. niger Aspergillus 2007 2007 A. niger A. nidulans 2007 A. niger aamA glaA agdA agdB Results 5 2004 mstC 5 amyR mstC amyR amyR amyR aamA 1 aamA aamA A. niger Electronic supplementary material Below is the link to the electronic supplementary material.
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