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. 2008 Jun;279(6):545-61.
doi: 10.1007/s00438-008-0332-7. Epub 2008 Mar 5.

Aspergillus niger genome-wide analysis reveals a large number of novel alpha-glucan acting enzymes with unexpected expression profiles

Xiao-Lian Yuan  1 , Rachel M van der Kaaij, Cees A M J J van den Hondel, Peter J Punt, Marc J E C van der Maarel, Lubbert Dijkhuizen, Arthur F J Ram
Affiliations

Aspergillus niger genome-wide analysis reveals a large number of novel alpha-glucan acting enzymes with unexpected expression profiles

Xiao-Lian Yuan et al. Mol Genet Genomics. 2008 Jun.

Abstract

The filamentous ascomycete Aspergillus niger is well known for its ability to produce a large variety of enzymes for the degradation of plant polysaccharide material. A major carbon and energy source for this soil fungus is starch, which can be degraded by the concerted action of alpha-amylase, glucoamylase and alpha-glucosidase enzymes, members of the glycoside hydrolase (GH) families 13, 15 and 31, respectively. In this study we have combined analysis of the genome sequence of A. niger CBS 513.88 with microarray experiments to identify novel enzymes from these families and to predict their physiological functions. We have identified 17 previously unknown family GH13, 15 and 31 enzymes in the A. niger genome, all of which have orthologues in other aspergilli. Only two of the newly identified enzymes, a putative alpha-glucosidase (AgdB) and an alpha-amylase (AmyC), were predicted to play a role in starch degradation. The expression of the majority of the genes identified was not induced by maltose as carbon source, and not dependent on the presence of AmyR, the transcriptional regulator for starch degrading enzymes. The possible physiological functions of the other predicted family GH13, GH15 and GH31 enzymes, including intracellular enzymes and cell wall associated proteins, in alternative alpha-glucan modifying processes are discussed.

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Figures

Fig. 1
Fig. 1
Bootstrapped phylogenetic tree of A. niger GH13 (a) and GH31 (b) enzymes and several closest homologues from other species. Newly identified proteins in the genome of A. niger are shown in bold. A description of each protein is listed in Tables 1 and 2. Bootstrap values are indicated on the node of each branch. The tree was created with DNAMAN 4.0 using gap and extension penalties of 10 and 0.5, respectively. The scale bar corresponds to a genetic distance of 0.05 substitution per position
Fig. 2
Fig. 2
Expression profiles of A. niger family GH13, 15 and 31 enzymes. Accession numbers of the gene names are given in Tables 1 and 2. Strain and time points after transfer from the preculture are indicated on the right-hand side. The numeric values and Present/Absent calls from the expression data are provided as Supplementary Tables 1, 2
Fig. 3
Fig. 3
Results of microarray analysis for maltose induced and AmyR dependent genes. Venn-diagram showing the number of genes induced on maltose compared to xylose in A. niger N402, and the number of genes induced in N402 compared to the ΔamyR deletion strain. The number of genes both induced by maltose and dependent on AmyR is indicated in bold. The maltose induced and AmyR dependent genes which are present in both 2 and 8 h after transfer from a preculture are shown in the box
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