Fig 1.
S. schoenii predates on and eliminates S. cerevisiae.
A) S. cerevisiae (H4-GFP) cells collapse after contact-mediated mycoparasitism. Upon physical contact, S. cerevisiae cells vacuolarize (arrowhead), collapse in size and lose their H4-GFP signal (asterisk). B) The area of non-predated and predated S. cerevisiae. While non-predated cells stayed the same size, predated cells shrank significantly. Error bars = 95% CI. Dotted lines; linear regression of slopes, p-value of slopes <0.0001. C) Quantification and timing of predation during co-culture of S. schoenii and S. cerevisiae under different nutritional conditions. Cells were scored hourly on morphology-based viability. Results from two independent replicates, plotted as means with SD error bars.
Fig 2.
In silico analyses suggest S. schoenii is a CTG clade member.
A) A cloudblast of translated S. schoenii ORFs against proteins suggested by nr database. S. schoenii was closely related to several CTG clade members. B) Two CAG-tRNAs were found in the draft S. schoenii genome. C) Alignment of the two S. schoenii CAG-tRNAs with CAG-tRNAs from Saccharomycopsis fermentans [28], C. albicans, C. dubliniensis, C. tropicalis as well as other Leu-tRNAs and Ser-tRNAs from S. cerevisiae and C. albicans. The S. schoenii CAG.2-tRNA aligns the closest with a S. cerevisiae Leu-GAG-tRNA, whereas S. schoenii CAG.1-tRNA aligns closer to the Ser-CAG-tRNAs of other CTG clade yeasts. CAG-tRNA features are color-coded [55–57].
Table 1.
schoenii de novo draft genome assembly and annotation.
S. A) S. schoenii de novo draft genome assembly. B) S. schoenii draft genome annotation. For subsequent functional analyses, the 4,660 genes with homologs were used. a) Identified with tRNA Scan-SE. b) ORF = min 300bp/100aa, ATG start site. c) using the Alternative Yeast Nuclear Code, translation table 12. d) Manual curation of non-overlapping genes. e) Blastx hit score >55. f) deposited by 06.06.17. g) non-overlapping ORFs, any blastx hit bit score >55. h) non-overlapping ORFs, blastx hit bit score <55. C) Gene loss in the sulfate assimilation pathway. D) List of gene expansion. Names of homologous S. cerevisiae or C. albicans genes.
Fig 3.
Proteins and GO term categories increased during starvation and/or predation conditions.
A) Presence and relative abundance of S. schoenii proteins during starvation and predation conditions. Translated genes with homologs to either S. cerevisiae or C. albicans, with a protein abundance at least 10-fold higher during starvation conditions (SD) or predation conditions (SD + S.c.) were selected and listed with its corresponding gene ID. The proteins were curated into three subsets; proteins highly abundant under starvation (green), predation (red) or in both conditions (yellow). B) The top 15 GO term categories of S. schoenii proteins involved in starvation (green), predation (red) or abundant in both conditions, as output from FungiFun2 [54]. Proteins are analyzed in FungiFun2 by their gene name. #Genes/category defines how many genes can theoretically be found in each GO ID, whereas #genes/input defines how many of the submitted genes per total submitted genes belong to each GO ID.
Fig 4.
S. schoenii gene and GO term categories upregulated during gradual nutrient availability and/or predation conditions.
A) Fold upregulation of S. schoenii genes during gradual nutrient availability, compared to S. schoenii on standard media (YPD), without (right) or with (left) S. cerevisiae present as prey. Upregulated genes were manually curated into three categories; mainly upregulated during conditions of Nutrient limitation (CSM, grey), of Methionine deprivation (CSM-Met, blue) or Predation (CSM + S.c., CSM-Met + S.c. or SD + S.c.). Down pointing arrows symbolize genes with two (one arrow) or five (two arrows) fold lower fold increase values when prey was present, compared to when no prey was present, on CSM-Met. B) Top 15 GO term categories of genes upregulated during Nutrient limitation, Methionine deprivation of Predation conditions. Genes are analyzed in FungiFun2 by their gene name. #Genes/category defines how many genes can theoretically be found in each GO ID, whereas #genes/input defines how many of the submitted genes per total submitted genes belong to each GO ID.
Fig 5.
Methionine biosynthesis pathway and sulfur compound uptake genes in S. schoenii.
Genes highlighted in blue were upregulated at least two-fold when methionine was missing compared to present (CSM/CSM-Met). Genes highlighted in red were upregulated at least two-fold when prey was present compared to absent, during methionine deprivation (CSM-Met+S.c./CSM-Met). A) Fold change of S. schoenii gene expression during methionine deprived conditions, when prey was present compared to absent (CSM-Met + S.c./CSM-Met). Dotted lines indicate two-fold changes up or down. B) S. schoenii lacks all genes in the sulfate assimilation pathway, but have two methionine permeases (MUP1, MUP3), two copies of the cysteine transporter YCT1 and several copies of SEO1, a putative sulfur compound permease.