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Open Access Research article

Mapping the polysaccharide degradation potential of Aspergillus niger

Mikael R Andersen1, Malene Giese1, Ronald P2 and Jens Nielsen13*

Author Affiliations

1 Department of Systems Biology, Technical University of Denmark, Kgs. Lyngby, Denmark

2 Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands

3 Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden

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BMC Genomics 2012, 13:313  doi:10.1186/1471-2164-13-313

Published: 16 July 2012

Additional files

Additional file 1:

Schematic representation of starch. The nature of the bonds between the sugar units are noted where they are known. The number of sides on the sugar polygons reflect the number of carbons of the sugar. The first carbon is indicated on all sugars with a 1 to clarify the bond configurations. Carbons are numbered clockwise from the first carbon with the two last carbons of the sugar (hexose or pentose) on the same corner of the polygon. The oligos are hypothetical hydrolysis products and sugars that appear due to the action of exo-acting enzymes. The structure is based on ref. [59].

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Additional file 2:

Schematic representation of cellulose. The nature of the bonds between the sugar units are noted where they are known. The number of sides on the sugar polygons reflect the number of carbons of the sugar. The first carbon is indicated on all sugars with a 1 to clarify the bond configurations. Carbons are numbered clockwise from the first carbon with the two last carbons of the sugar (hexose or pentose) on the same corner of the polygon. The oligos are hypothetical hydrolysis products and sugars that appear due to the action of exo-acting enzymes. The structure is based on refs. [20,60].

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Additional file 3:

Schematic representation of pullulan. The nature of the bonds between the sugar units are noted where they are known. The number of sides on the sugar polygons reflect the number of carbons of the sugar. The first carbon is indicated on all sugars with a 1 to clarify the bond configurations. Carbons are numbered clockwise from the first carbon with the two last carbons of the sugar (hexose or pentose) on the same corner of the polygon. The oligos are hypothetical hydrolysis products and sugars that appear due to the action of exo-acting enzymes. The structure is based on refs. [59,61].

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Additional file 4:

Schematic representation of inulin. The nature of the bonds between the sugar units are noted where they are known. The number of sides on the sugar polygons reflect the number of carbons of the sugar. The first carbon is indicated on all sugars with a 1 to clarify the bond configurations. Carbons are numbered clockwise from the first carbon with the two last carbons of the sugar (hexose or pentose) on the same corner of the polygon. The oligos are hypothetical hydrolysis products and sugars that appear due to the action of exo-acting enzymes. The structure is based on ref. [62].

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Open Data

Additional file 5:

Schematic representation of galactomannan. The nature of the bonds between the sugar units are noted where they are known. The number of sides on the sugar polygons reflect the number of carbons of the sugar. The first carbon is indicated on all sugars with a 1 to clarify the bond configurations. Carbons are numbered clockwise from the first carbon with the two last carbons of the sugar (hexose or pentose) on the same corner of the polygon. The oligos are hypothetical hydrolysis products and sugars that appear due to the action of exo-acting enzymes. The structure is based on refs. [20,63].

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Additional file 6:

Schematic representation of insoluble galactoglucomannan. The nature of the bonds between the sugar units are noted where they are known. The number of sides on the sugar polygons reflect the number of carbons of the sugar. The first carbon is indicated on all sugars with a 1 to clarify the bond configurations. Carbons are numbered clockwise from the first carbon with the two last carbons of the sugar (hexose or pentose) on the same corner of the polygon. The oligos are hypothetical hydrolysis products and sugars that appear due to the action of exo-acting enzymes. The structure is based on ref. [20].

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Additional file 7:

Schematic representation of soluble galactoglucomannan. The nature of the bonds between the sugar units are noted where they are known. The number of sides on the sugar polygons reflect the number of carbons of the sugar. The first carbon is indicated on all sugars with a 1 to clarify the bond configurations. Carbons are numbered clockwise from the first carbon with the two last carbons of the sugar (hexose or pentose) on the same corner of the polygon. The oligos are hypothetical hydrolysis products and sugars that appear due to the action of exo-acting enzymes. The structure is based on ref. [18-21].

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Additional file 8:

Schematic representation of smooth pectin. The nature of the bonds between the sugar units are noted where they are known. The number of sides on the sugar polygons reflect the number of carbons of the sugar. The first carbon is indicated on all sugars with a 1 to clarify the bond configurations. Carbons are numbered clockwise from the first carbon with the two last carbons of the sugar (hexose or pentose) on the same corner of the polygon. The oligos are hypothetical hydrolysis products and sugars that appear due to the action of exo-acting enzymes. The structure is based on refs. [20,60].

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Open Data

Additional file 9:

Schematic representation of xylogalactouronan. The nature of the bonds between the sugar units are noted where they are known. The number of sides on the sugar polygons reflect the number of carbons of the sugar. The first carbon is indicated on all sugars with a 1 to clarify the bond configurations. Carbons are numbered clockwise from the first carbon with the two last carbons of the sugar (hexose or pentose) on the same corner of the polygon. The oligos are hypothetical hydrolysis products and sugars that appear due to the action of exo-acting enzymes. The structure is based on refs. [20,64-67].

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Open Data

Additional file 10:

Schematic representation of xylan. The nature of the bonds between the sugar units are noted where they are known. The number of sides on the sugar polygons reflect the number of carbons of the sugar. The first carbon is indicated on all sugars with a 1 to clarify the bond configurations. Carbons are numbered clockwise from the first carbon with the two last carbons of the sugar (hexose or pentose) on the same corner of the polygon. The oligos are hypothetical hydrolysis products and sugars that appear due to the action of exo-acting enzymes. The structure is based on refs. [20,60,68,69].

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Open Data

Additional file 11:

Schematic representation of xyloglucan type XXGG. The nature of the bonds between the sugar units are noted where they are known. The number of sides on the sugar polygons reflect the number of carbons of the sugar. The first carbon is indicated on all sugars with a 1 to clarify the bond configurations. Carbons are numbered clockwise from the first carbon with the two last carbons of the sugar (hexose or pentose) on the same corner of the polygon. The oligos are hypothetical hydrolysis products and sugars that appear due to the action of exo-acting enzymes. The structure is based on refs. [20,70,71].

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Open Data

Additional file 12:

Schematic representation of xyloglucan type XXXG. The nature of the bonds between the sugar units are noted where they are known. The number of sides on the sugar polygons reflect the number of carbons of the sugar. The first carbon is indicated on all sugars with a 1 to clarify the bond configurations. Carbons are numbered clockwise from the first carbon with the two last carbons of the sugar (hexose or pentose) on the same corner of the polygon. The oligos are hypothetical hydrolysis products and sugars that appear due to the action of exo-acting enzymes. The structure is based on refs. [20,70,71].

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Additional file 13:

Schematic representation of arabinogalactan type I. The nature of the bonds between the sugar units are noted where they are known. The number of sides on the sugar polygons reflect the number of carbons of the sugar. The first carbon is indicated on all sugars with a 1 to clarify the bond configurations. Carbons are numbered clockwise from the first carbon with the two last carbons of the sugar (hexose or pentose) on the same corner of the polygon. The oligos are hypothetical hydrolysis products and sugars that appear due to the action of exo-acting enzymes. The structure is based on refs. [12,72,73].

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Additional file 14:

Schematic representation of arabinogalactan type II (protein bound arabinogalactan). The nature of the bonds between the sugar units are noted where they are known. The number of sides on the sugar polygons reflect the number of carbons of the sugar. The first carbon is indicated on all sugars with a 1 to clarify the bond configurations. Carbons are numbered clockwise from the first carbon with the two last carbons of the sugar (hexose or pentose) on the same corner of the polygon. The oligos are hypothetical hydrolysis products and sugars that appear due to the action of exo-acting enzymes. The structure is based on [12,72,74,75].

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Open Data

Additional file 15:

Schematic representation of arabinan. The nature of the bonds between the sugar units are noted where they are known. The number of sides on the sugar polygons reflect the number of carbons of the sugar. The first carbon is indicated on all sugars with a 1 to clarify the bond configurations. Carbons are numbered clockwise from the first carbon with the two last carbons of the sugar (hexose or pentose) on the same corner of the polygon. The oligos are hypothetical hydrolysis products and sugars that appear due to the action of exo-acting enzymes. The structure is based on refs. [76-78].

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Open Data

Additional file 16:

Schematic representation of rhamnogalacturonan type I. The nature of the bonds between the sugar units are noted where they are known. The number of sides on the sugar polygons reflect the number of carbons of the sugar. The first carbon is indicated on all sugars with a 1 to clarify the bond configurations. Carbons are numbered clockwise from the first carbon with the two last carbons of the sugar (hexose or pentose) on the same corner of the polygon. The oligos are hypothetical hydrolysis products and sugars that appear due to the action of exo-acting enzymes. The structure is based on refs. [20,76,77,79,80].

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Open Data

Additional file 17:

Tables of enzymatic activities required for the degradation of 16 different plant-derived polysaccharides. For each isoenzyme, putative or characterized, is noted literature references and the gene ID in the whole genome sequencings of A. niger CBS 513.88 and ATCC 1015 [3-7,10-12,14,18-36,39-41,45-49,51,59-68,70-226].

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Additional file 18:

Full map of 16 polysaccharide structures with the addition of genes fromA. niger ATCC 1015 specific for each type of bond. The nature of the bonds between the sugar units are noted where they are known. The number of sides on the sugar polygons reflect the number of carbons of the sugar. The first carbon is indicated on all sugars with a 1 to clarify the bond configurations. Carbons are numbered clockwise from the first carbon with the two last carbons of the sugar (hexose or pentose) on the same corner of the polygon. The oligos are hypothetical hydrolysis products and sugars that appear due to the action of exo-acting enzymes. Type and approximate 2D orientation is shown for each of the chemical bonds connecting sugars and/or acids. Next to each bond, one can find verified and hypothetical enzymes in A. niger ATCC 1015 capable of catalyzing the hydrolysis of the bond. The bottom panel denotes CAZy-families for each of the genes. See Additional Files 1-16 for details on literature references for structures.

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Additional file 19:

Map of statistically significantly regulated genes coding for carbohydrate-active enzymes in a pairwise comparison of growth on arabinan versus L-arabinose. Genes marked with a red box are significantly up-regulated on arabinan relative to L-arabinose, a green box denotes the opposite, gray boxes means that the gene is found in the A. niger CBS 513.88 sequence, but no bi-directional best hit is found in the A. niger ATCC 1015 sequence. The absence of a box mean that this gene is not statistically significantly regulated in this comparison.

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Additional file 20:

Map of statistically significantly regulated genes coding for carbohydrate-active enzymes in a pairwise comparison of growth on starch versus D-glucose. Genes marked with a red box are significantly up-regulated on starch relative to D-glucose, a green box denotes the opposite, gray boxes means that the gene is found in the A. niger CBS 513.88 sequence, but no bi-directional best hit is found in the A. niger ATCC 1015 sequence. The absence of a box mean that this gene is not statistically significantly regulated in this comparison.

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Additional file 21:

Map of statistically significantly regulated genes coding for carbohydrate-active enzymes in a pairwise comparison of growth on L-arabinose versus D-glucose. Genes marked with a red box are significantly up-regulated on L-arabinose relative to D-glucose, a green box denotes the opposite, gray boxes means that the gene is found in the A. niger CBS 513.88 sequence, but no bi-directional best hit is found in the A. niger ATCC 1015 sequence. The absence of a box mean that this gene is not statistically significantly regulated in this comparison.

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Additional file 22:

Map of statistically significantly regulated genes coding for carbohydrate-active enzymes in a pairwise comparison of growth on starch versus xylan. Genes marked with a red box are significantly up-regulated on starch relative to xylan, a green box denotes the opposite, gray boxes means that the gene is found in the A. niger CBS 513.88 sequence, but no bi-directional best hit is found in the A. niger ATCC 1015 sequence. The absence of a box mean that this gene is not statistically significantly regulated in this comparison.

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Additional file 23:

Clustering of 103 significantly regulated genes coding for enzymes with putative and characterized polysaccharide-activities. All genes were found to be significantly regulated in at least one pairwise-comparison of two carbon sources. Cluster numbers in parentheses is the number of the corresponding cluster(s) in Figure 2. The number of genes in each cluster is shown next to the cluster number. The gene names of known genes found in a particular cluster are found at the bottom of the transcription profile graph of each cluster. The genes were clustered using the ClusterLustre algorithm [50].

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Additional file 24:

24 maps of enzymatic activities present in the expression-based clusters 1-24 of Figure2. Genes marked with a red box are found in the cluster, gray boxes means that the gene is found in the A. niger CBS 513.88 sequence, but no bi-directional best hit is found in the A. niger ATCC 1015 sequence.

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Open Data