Summary of abundance changes of proteins involved in purine biosynthesis pathways.

<p>Fold increase (↑) or decrease (↓) of protein, relative to the respective control. CADRE ID., <i>A. fumigatus</i> gene annotation nomenclature according to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0106942#pone.0106942-Nierman1" target="_blank">[1]</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0106942#pone.0106942-Mabey1" target="_blank">[71]</a>; Spot No, according to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0106942#pone-0106942-g002" target="_blank">Figure 2</a>.</p><p>*Change in protein abundance was reported previously <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0106942#pone.0106942-Carberry2" target="_blank">[20]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0106942#pone.0106942-Lessing1" target="_blank">[23]</a>.</p><p>Summary of abundance changes of proteins involved in purine biosynthesis pathways.</p

Proteins (n = 13) exhibiting significant differential abundance1 in A. fumigatus ATCC26933 following the co-addition of gliotoxin and H2O2, relative to H2O2 alone.

<p>Data extracted from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0106942#pone.0106942.s004" target="_blank">Tables S3</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0106942#pone.0106942.s005" target="_blank">S4</a> and re-charted for clarity. Proteins detected with a significant change in abundance in H₂O₂ compared to the control are also reported.</p>1<p><i>p</i><0.05; Fold increase (↑) or decrease (↓) of protein in the co-additive condition, relative to the solvent control, gliotoxin alone or H₂O₂ alone. Co-addition: incubation with both gliotoxin and H₂O₂. CADRE ID., <i>A. fumigatus</i> gene annotation nomenclature according to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0106942#pone.0106942-Nierman1" target="_blank">[1]</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0106942#pone.0106942-Mabey1" target="_blank">[71]</a>; Spot No, according to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0106942#pone-0106942-g002" target="_blank">Figure 2</a>. Numbers in bold indicate fold change of proteins (<i>n</i> = 13) differentially regulated in the co-addition, relative to H₂O₂ alone.</p><p>Proteins (n = 13) exhibiting significant differential abundance1 in A. fumigatus ATCC26933 following the co-addition of gliotoxin and H2O2, relative to H2O2 alone.</p

<i>A. fumigatus</i> proteins, involved in secondary metabolism, and identified by shotgun mass spectrometry.

<p>CADRE ID., <i>A. fumigatus</i> gene annotation nomenclature according to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0106942#pone.0106942-Nierman1" target="_blank">[1]</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0106942#pone.0106942-Mabey1" target="_blank">[71]</a>.</p>a<p>Cluster numbers and LaeA regulation as denoted in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0106942#pone.0106942-Perrin1" target="_blank">[38]</a>.</p><p><i>A. fumigatus</i> proteins, involved in secondary metabolism, and identified by shotgun mass spectrometry.</p

Overview of <i>A. fumigatus</i> shotgun proteomic data.

<p>(a) Proteome map showing distribution of <i>A. fumigatus</i> proteins based on theoretical M_r and p<i>I</i> where proteins identified by shotgun mass spectrometry (<i>n</i> = 414; red) are shown overlaid on the total <i>A. fumigatus</i> proteome (black). tM_r, theoretical molecular mass, axis drawn on logarithmic scale; tp<i>I</i>, theoretical isoelectric point, axis drawn on linear scale. (b, c) Distribution of proteins identified by shotgun mass spectrometry (MS) according to their relative hydrophobicity and the number of putative transmembrane regions per protein. The number of putative transmembrane regions on each protein identified by shotgun MS is shown. (d) Distribution of functional annotations of <i>A. fumigatus</i> proteins identified using shotgun proteomics strategy. GO, KEGG and FunCat classification schemes were used for functional annotation utilizing the FungiFun application. A number of proteins (<i>n</i> = 23) were identified that possessed no functional classification using this system. (e) The functional categorization of the proteins identified here, based on the FunCat annotation scheme, are shown. <i>Note:</i> GRAVY, grand average of hydropathy; TM, transmembrane; MS, mass spectrometry. (f) LC-MS detection of SM in <i>A. fumigatus</i> organic extracts from AMM cultures and (g) Czapek-Dox cultures (BPC: Base Peak Chromatogram; EIC: Extracted Ion Chromatogram).</p

2-D analysis reveals differential proteomic response <i>of A. fumigatus</i> to a combination of gliotoxin and H₂O₂.

<p>2-D proteome maps of <i>A. fumigatus</i> ATCC26933 (a) solvent control, (b) following exposure to gliotoxin (10 µg/ml) for 4 h, (c) following exposure to 2 mM H₂O₂ for 4 h, (d) following exposure to a combination of gliotoxin (10 µg/ml) and H₂O₂ (2 mM) for 4 h. The proteins were first separated on pH 4–7 strips followed by SDS-PAGE. Proteins found to be significantly differentially expressed (<i>p</i><0.05), after analysis using Progenesis SameSpot software, are numbered. (e) Increased expression of the gliotoxin oxidoreductase GliT in response to gliotoxin but not H₂O₂. GliT expression was increased following exposure to exogenous gliotoxin alone (5.1 fold) and in combination with H₂O₂ (4.8 fold), relative to the solvent control. No significant difference in expression of GliT was detected upon exposure of <i>A. fumigatus</i> to H₂O₂ alone, relative to the control (<i>p</i>>0.05), indicating GliT expression is mediated by gliotoxin only.</p

Distribution of single nucleotide polymorphisms in a mutation-accumulation experiment.

<p>(A) Normalized mean number of single nucleotide polymorphisms (SNPs) per chromosome after experimental evolution of 5 <i>S. cerevisiae</i> lineages for up to 2200 generations. The number of SNPs per chromosome was normalized by length to that of the longest chromosome (chrIV) and error bars represent the standard deviation. (B) The number of SNPs detected in the genome of each lineage increased linearly with the number of generations for total, non-synonymous and synonymous SNPs. (C) The fraction of SSDs (black columns) and WGDs (grey columns) affected by non-synonymous single nucleotide polymorphisms (Nsyn-SNPs) across the five mutation-accumulation (MA1 to MA5) experimental lines. In all five MA lines, the fraction of SSDs with Nsyn-SNPs is larger than that of WGDs. The fraction of SSDs that have fixed Nsyn-SNPs is significantly larger than that of WGDs in four of the five MA experimental lines (significance is indicated by * = <i>P</i><0.05; ** = <i>P</i><0.01 and *** = <i>P</i><0.001).</p

Gliotoxin attenuates H₂O₂-induced ROS formation.

<p>(a) Neither methanol (solvent control) or gliotoxin induce significant ROS formation in <i>A. fumigatus</i>, however H₂O₂ exposure leads to clear formation of ROS. Co-addition of gliotoxin dissipates ROS as judged by reduced fluorescence. (b) Gliotoxin significantly reduces H₂O₂-induced ROS levels during co-incubation with H₂O₂ (<i>p</i>>0.0001).</p

Distinct functional fates for genes duplicated by small-scale duplication (SSD) and whole-genome duplication (WGD).

<p>(A) After the duplication of a gene by SSD (circles), one of the gene copies (black circle) maintains the ancestral functions (squares), while the other (white circle) loses (discontinuous lines) some ancestral functions while establishing novel genetic interactions (functions) through the process of neo-functionalization. (B) Genes duplicated by WGD sub-functionalize through the partitioning of ancestral functions so that each gene copy specializes in a subset of the ancestral functions.</p

Small-scale duplication (SSD) generates gene copies sharing more ancestral functions than whole-genome duplication (WGD).

<p>We tested the partitioning of ancestral functions after duplication by SSD and WGD. We calculated partitioning of ancestral functions by estimating the proportion of shared genetic interactions between the copies of a duplicated gene. This proportion was calculated as <i>Θ_SSD|WGD</i> = (2<i>n_S(i,j)</i>)/(<i>GI_i</i>+<i>GI_j</i>), with <i>n_S(i,j)</i> being the number of genetic interactions (<i>GI</i>) in common between gene copies <i>i</i> and <i>j</i>. To determine the significance of this partitioning (or sharing) we compared <i>Θ_SSD|WGD</i> to that calculated for a distribution of such values estimated from 10⁶ randomly paired singletons. WGDs shared on average (solid green arrow line) as many GIs as random pairs of singletons (for example, the mean indicated by an arrow is within the 90% density of the curve), indicating that they have partitioned their ancestral functions to a point that they could be almost considered as singletons. Conversely, SSD gene copies share ancestral functions (solid red arrow line) significantly more than expected by chance (indicated by asterisks *). The classification of the average number of shared partners between duplicates for different categories of amino acid sequence divergence (amino acid divergence between duplicates was estimated using JTT model) followed the same patterns, with all divergence bins (bins were built with 0.2 divergence levels intervals, except for the first bin) of WGDs (green dashed lines) being not significant while bins of SSDs (red dashed lines) being significant (*: <i>P</i><0.01, **: <i>P</i><10⁻⁶).</p

Interaction partners of duplicated genes are more functionally related than those of singletons.

<p>(A) We calculated the functional relatedness of the interaction partners (blue circles) of a gene as the proportion of links (<i>l</i>) between these partners (black thick lines) taking into account the number of partners (<i>n</i>): <i>k</i> = 2<i>l</i>/<i>n</i>(<i>n</i>−1). For example, in (A), there are 7 links between the 5 partners of a gene (black circle), which yields k = 2×7/5×4 = 0.7. (B) Clustering coefficients for singletons, small-scale duplications (SSDs) and whole-genome duplications (WGDs). The columns represent the mean clustering coefficient and the standard error of the mean associated to that particular set of genes. Probabilities were calculated by the Wilcoxon rank test. Duplicates interact with genes more functionally related than those with which singletons interact. SSDs interact with genes that are more functionally dispersed (unrelated) than the interaction partners of WGDs.</p