Transcription profile of <i>C. albicans</i> and <i>S. cerevisiae</i> in xylose

<p>A) From microarray experiments with <i>C. albicans</i> grown in xylose, 175 genes have at least a 2-fold transcription increase in xylose when compared to cells in dextrose. The 44 genes with more than a 5-fold induction in xylose (SX) are shown with their corresponding value. Data for <i>S. cerevisiae</i> is shown for comparison, and in gray-shade if no reciprocal best-hit ortholog is found. B) Transcription modulation of the <i>S. cerevisiae</i> sugar transporters in xylose. The data from the microarray experiments in xylose (SX) and in no-sugar condition (S) is shown for 18 members of the sugar transporter family, relative to cells in dextrose. <i>HXT5</i> and <i>HXT2</i> are likely induced due to the absence of dextrose (glucose). <i>HXT6</i>, <i>HXT7</i> and <i>HXT4</i> are induced specifically by the presence of xylose. <i>HXT4</i>, <i>HXT1</i> and <i>HXT3</i> show a transcriptional reduction only for the no-sugar condition (S), likely due to the absence of sugar. A summary for the transporters description from SGD is reported in the ‘SGD description’ column.</p

The xylose reductase and xylitol dehydrogenase genes from <i>S. cerevisiae</i> complement <i>C. albicans</i> deletion mutants of the equivalent genes.

<p>(A) <i>S. cerevisiae </i><i>GRE3</i> (CA255), and (B) <i>S. cerevisiae </i><i>SOR1</i> (CDH139) complement the <i>C. albicans </i><i>gre3</i> and <i>xyl2</i> deletion mutants respectively. Strains were grown aerobically at 30°C in 2% xylose (SX) or 2% xylitol (ST). The optical density was measured over a period of 14 days, n=3.</p

The xylose isomerase gene <i>XYLA</i> from <i>Piromyces</i><i>sp.</i> complements a double <i>gre3/xyl2</i> deletion or single <i>gre3</i> deletion in <i>C. albicans</i>.

<p>Growth analysis in synthetic medium (SC) with 2% xylose as the sole carbon source for <i>C. albicans</i> strains: <i>gre3-9</i> (<i>gre3</i> deletion), <i>gre3/xyl2-3</i> (<i>gre3 </i><i>xyl2</i> double deletion), CDH128 (<i>gre3/xyl2-3</i> with the integrated <i>Pir</i>.<i>XYLA</i>) and CDH140 (<i>gre3-9</i> with the integrated <i>Pir</i>. <i>XYLA</i>). The optical density was measured over a period of 6 days, n=3. </p

Identification of Spurious Genes

<div><p>Assessing criteria that identify candidate spurious genes in <i>S. cerevisiae,</i> using a reference set of known spurious genes [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0010001#pgen-0010001-b16" target="_blank">16</a>].</p> <p>(A) For every gene in <i>S. cerevisiae,</i> the average Pearson correlation coefficient with all other genes was calculated. Shown are histograms of the correlations associated with genes characterized as spurious in the reading frame conservation test ([<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0010001#pgen-0010001-b16" target="_blank">16</a>]; red) and all genes in the genome (black).</p> <p>(B) The distribution of gene lengths is shown for genes characterized as spurious (red) and for all genes of the genome (black).</p> <p>(C) Assessing the likelihood of being spurious as a function of gene length and correlation score. Shown is the proportion of spurious genes out of all genes whose length and correlation score fall into each of the intervals. The proportion is color-coded according to the color bar shown. <i>S. cerevisiae</i> genes with an ortholog in <i>C. albicans</i> were excluded from the analysis.</p></div

Visualization of Protein Sequence Similarities

<p>Sample from a Web page used by annotators of the <i>C. albicans</i> genome to visualize the significance of the best hit from whole-proteome BLASTP searches. Each putative ORF was compared to the NR database, the <i>Candida</i> ORF list itself (Ca19; showing results from the four top hits), and amino acid sequences from the proteomes of <i>S. cerevisiae</i> (Sac), <i>S. pombe</i> (S.p), <i>M. grisea</i> (Mag), <i>N. crassa</i> (Neu), <i>H. sapiens</i> (H.S), <i>M. musculus</i> (M.m), <i>D. melanogaster</i> (Dro), <i>C. elegans</i> (C.e), and <i>A. thaliana</i> (A.t). The BLASTP <i>e</i>-value from the top hit was converted to a color scale as indicated. Examples of <i>C. albicans</i> genes with interesting similarity patterns are indicated.</p