Supplemental Material for Klim et al., 2018

p { margin-bottom: 0.21cm; direction: ltr; color: rgb(0, 0, 10); line-height: 115%; text-align: left; }p.western { font-family: "Calibri", serif; font-size: 11pt; }p.cjk { font-family: "Calibri"; font-size: 11pt; }p.ctl { font-family: "Arial"; font-size: 11pt; }a:link { color: rgb(0, 0, 255); text-decoration: none; } <p><b>Additional file 1.</b> Final alignments (files with .aln.fasta extension) and phylogenetic trees (files with fastree.newick extension) for all the protein families analyzed in the study. Additionally, in case of three protein families: AIF, OMI and caspase/metacaspase the subfolders were created, containing the key subtrees (files in nexml format generated with Dendroscope).</p> <p><br> </p> <p><b>Additional file 2</b><b>.</b> Additional BLASTP results and taxonomy reports conducted to confirm the key results in case of the three protein families: AIF, caspase/metacaspase and htra. BLASTP results and taxonomy reports were obtained with NCBI WWW with two strategies: by selecting only a few eukaryotic proteomes (for the species from Table S2 in Supplementary Methods) as a search database (see file eukaryotic_strategy.pdf) and by extending selected proteomes from the first search strategy with all bacterial and archeal proteomes (see file extended_strategy.pdf). Please see README.md for more details regarding information for given specific file. </p> <p><br> </p> <p><b>Additional file 3. </b>Mega sessions for consensus phylogenetic trees calculated for arbitrarily chosen metacaspases and caspases, OMI/HTRA proteases and AIFs. Separate sessions files are available for calculations based on MLE (maximum likelihood estimation), NJ (neighbor-joining) and ME (minimal evolution).</p> <p><br> </p> <p><b>Additional Figure S1.</b> Competition assay between <i>ndi1</i><i>Δ </i>and wild-type Saccharomyces cerevisiae BY4741 strains under anaerobic conditions.</p> <p><br> </p> <p><b>Additional Figure S2.</b> Growth curves for all tested in this study yeast strains cultivated in prolonged cultures in aerobic (A) or anaerobic (B) conditions. The values of mean and standard deviation from duplicate experiments are shown for each time point.</p> <p><br> </p> <p><b>Additional Figure S3. </b>Yeast strains used in the experimental evolution are unable to grow on medium supplemented with non-fermentable carbon source. Cells grown on glucose-containing (A) and glycerol-containing (B) solid medium. Single colonies were streaked on the appropriate plate and incubated at 28⁰C for 3 days. Wild-type strain shows robust growth on both media, whereas mutant strains grow only on glucose-containing plate.<br> <br> </p

Associations between Trait-Descriptive Words and OGs for Two Illustrative Clusters

<p>“Heat maps” display word–OG association scores (scores greater than 0 are indicated; negative values are set to 0). We considered all words and OGs contributing to the respective cluster with at least one high-confidence association. Protein interaction networks, shown below, were derived from genomic context analysis (see <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0030134#s4" target="_blank">Materials and Methods</a>). (A) Traits and genes related to plant constituent degradation. Functional descriptions are: Plant-degr., involved in plant constituent degradation; Ox, putative oxidoreductases; Arg, Arginine degradation protein/predicted deacylase; UV, UV damage repair endonuclease; those with no description are uncharacterized. Terms related to sporulation reflect a domination of exo- and endospore-forming species from different genera (e.g., <i>Streptomyces, Bacillus,</i> and <i>Clostridium</i>) in these degradation processes. (B) Traits and genes related to food spoilage and poisoning. Some proteins have previously been implicated in virulence of food pathogens such as ManR (“T”), a transcriptional antiterminator involved in resistance to natural food preservatives, and some propanediol degradation proteins (“Prop-diol”). We suggest the involvement of additional proteins in pathogenicity: for example, ethanolamine degradation proteins (“Eth.-amine-usage”; the phospholipid phosphatidyl-ethanolamine, cleaved to ethanolamine by phospholipase, is abundant in the gut [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0030134#pbio-0030134-b14" target="_blank">14</a>]); the cobalt chelatase CbiK (“C”; cobalt is an essential factor for propanediol and ethanolamine utilization [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0030134#pbio-0030134-b14" target="_blank">14</a>]); a phosphotransferase system (“PTS”) involved in sorbitol transport [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0030134#pbio-0030134-b36" target="_blank">36</a>] (sorbitol is an artificial food sweetener naturally found in fruits and may act as an additional carbon source; we suggest that alternatively the chemically similar inositol, cleavage product of another abundant phospholipid, may be utilized). Other proteins that may also be involved are a presumably anaerobically used butyrate kinase (“B”), gamma-glutamylcysteine synthetase (“G”), an electron transport complex protein (“O”), a predicted metal-binding enzyme (“E”), and several uncharacterized proteins (no description).</p