Data_Sheet_3_In Silico Analysis of Putative Sugar Transporter Genes in Aspergillus niger Using Phylogeny and Comparative Transcriptomics.pdf

<p>Aspergillus niger is one of the most widely used fungi to study the conversion of the lignocellulosic feedstocks into fermentable sugars. Understanding the sugar uptake system of A. niger is essential to improve the efficiency of the process of fungal plant biomass degradation. In this study, we report a comprehensive characterization of the sugar transportome of A. niger by combining phylogenetic and comparative transcriptomic analyses. We identified 86 putative sugar transporter (ST) genes based on a conserved protein domain search. All these candidates were then classified into nine subfamilies and their functional motifs and possible sugar-specificity were annotated according to phylogenetic analysis and literature mining. Furthermore, we comparatively analyzed the ST gene expression on a large set of fungal growth conditions including mono-, di- and polysaccharides, and mutants of transcriptional regulators. This revealed that transporter genes from the same phylogenetic clade displayed very diverse expression patterns and were regulated by different transcriptional factors. The genome-wide study of STs of A. niger provides new insights into the mechanisms underlying an extremely flexible metabolism and high nutritional versatility of A. niger and will facilitate further biochemical characterization and industrial applications of these candidate STs.</p

Data_Sheet_1_In Silico Analysis of Putative Sugar Transporter Genes in Aspergillus niger Using Phylogeny and Comparative Transcriptomics.xls

<p>Aspergillus niger is one of the most widely used fungi to study the conversion of the lignocellulosic feedstocks into fermentable sugars. Understanding the sugar uptake system of A. niger is essential to improve the efficiency of the process of fungal plant biomass degradation. In this study, we report a comprehensive characterization of the sugar transportome of A. niger by combining phylogenetic and comparative transcriptomic analyses. We identified 86 putative sugar transporter (ST) genes based on a conserved protein domain search. All these candidates were then classified into nine subfamilies and their functional motifs and possible sugar-specificity were annotated according to phylogenetic analysis and literature mining. Furthermore, we comparatively analyzed the ST gene expression on a large set of fungal growth conditions including mono-, di- and polysaccharides, and mutants of transcriptional regulators. This revealed that transporter genes from the same phylogenetic clade displayed very diverse expression patterns and were regulated by different transcriptional factors. The genome-wide study of STs of A. niger provides new insights into the mechanisms underlying an extremely flexible metabolism and high nutritional versatility of A. niger and will facilitate further biochemical characterization and industrial applications of these candidate STs.</p

Data_Sheet_4_In Silico Analysis of Putative Sugar Transporter Genes in Aspergillus niger Using Phylogeny and Comparative Transcriptomics.xls

<p>Aspergillus niger is one of the most widely used fungi to study the conversion of the lignocellulosic feedstocks into fermentable sugars. Understanding the sugar uptake system of A. niger is essential to improve the efficiency of the process of fungal plant biomass degradation. In this study, we report a comprehensive characterization of the sugar transportome of A. niger by combining phylogenetic and comparative transcriptomic analyses. We identified 86 putative sugar transporter (ST) genes based on a conserved protein domain search. All these candidates were then classified into nine subfamilies and their functional motifs and possible sugar-specificity were annotated according to phylogenetic analysis and literature mining. Furthermore, we comparatively analyzed the ST gene expression on a large set of fungal growth conditions including mono-, di- and polysaccharides, and mutants of transcriptional regulators. This revealed that transporter genes from the same phylogenetic clade displayed very diverse expression patterns and were regulated by different transcriptional factors. The genome-wide study of STs of A. niger provides new insights into the mechanisms underlying an extremely flexible metabolism and high nutritional versatility of A. niger and will facilitate further biochemical characterization and industrial applications of these candidate STs.</p

Total carbohydrate content, carbohydrate molar composition and xylan degree of substitution of compost samples obtained at PII, PIII-16, after filling, after pinning, after 1^st and after 2^nd flush.

<p>^aPII: Phase II compost; PIII-16 is Phase III compost after 16 days of mycelium growth (adapted from Jurak et al. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0134169#pone.0134169.ref001" target="_blank">1</a>]).</p><p>^bFilling: compost after filling of compost beds at the farm, Pinning: after mushroom pins appear, 1^st flush: after first flush of mushroom was collected, 2^nd flush: spent compost, after 2^nd flush of mushrooms was collected.</p><p>^cWeight percentage is based on dry matter of composting phases.</p><p>^dAs anhydro-sugars; STDEV < 0.5 for all samples.</p><p>^eRatio mol substituents/100mol of xylosyl residues; abbreviations: Ara, arabinosyl; Xyl, xylosyl; GlcA, glucuronic acid.</p><p>Total carbohydrate content, carbohydrate molar composition and xylan degree of substitution of compost samples obtained at PII, PIII-16, after filling, after pinning, after 1^st and after 2^nd flush.</p

Maximum likelihood (ML) tree of selected fungal FDHs.

<p>Three plant sequences were used as an outgroup. Values over 50% bootstrap support are shown with ML values in red, Neigbor Joining values in purple and Minimum Evolution values in green. The scale bar shows a distance equivalent to 0.1 amino acid substitutions per site. Putative recent gene duplications are indicated by square brackets. Species names are followed by protein IDs from JGI (<a href="http://genome.jgi-psf.org/programs/fungi/index.jsf" target="_blank">http://genome.jgi-psf.org/programs/fungi/index.jsf</a>) or sequence accessions from NCBI database (<a href="http://www.ncbi.nlm.nih.gov/protein" target="_blank">http://www.ncbi.nlm.nih.gov/protein</a>). Proteins of basidiomycetous white-rot and brown-rot species are in blue and red, respectively, while proteins of other basidiomycetes are in black. Ascomycete proteins are in green. The <i>D. squalens</i> proteins are in bold.</p

High performance size exclusion profiles of wheat arabinoxylan (A), birchwood xylan (B), carboxymethyl cellulose (C) and galactomannan (D), after degradation with enzyme extracts obtained from compost of different stages of mushroom growth (24 h incubation).

<p>High performance size exclusion profiles of wheat arabinoxylan (A), birchwood xylan (B), carboxymethyl cellulose (C) and galactomannan (D), after degradation with enzyme extracts obtained from compost of different stages of mushroom growth (24 h incubation).</p

HPAEC elution profile of WAX incubated (24h) first with 1^st flush (e) and then sequentially with pure GH43 AXH-d3 arabinofuranosidase (e*) [17].

<p>Ara = arabinosyl, Xyl = xylosyl, X₂ = xylobiose, X₃ = xylotriose, X₄ = xylotetraose, X₅ = xylopentaose, AXOS = oligomers substituted with arabinose.</p

HPAEC elution profile of WAX (A) and birchwood xylan (B) incubated (24h) with a: PII_end, b: PIII-16, c: Filling, d: Pinning, e: 1^st flush and f: 2^nd flush extracellular enzymes.

<p>Ara = arabinosyl, Xyl = xylosyl, X₂ = xylobiose, X₃ = xylotriose, X₄ = xylotetraose, X₅ = xylopentaose, AXOS = oligomers substituted with arabinose. GlcAXOS = oligomers substituted with 4-<i>O</i>-methyl-glucuronic acid.</p

First screening of extracellular enzyme activities from the compost in PIIend and PIII-16 analyzed by HPSEC after 24 h incubation.

<p>(- no degradation, + partial degradation, ++ complete degradation)</p><p>First screening of extracellular enzyme activities from the compost in PIIend and PIII-16 analyzed by HPSEC after 24 h incubation.</p

Compost sample codes and description.

<p>Compost sample codes and description.</p