Genomic insights into the lifestyles, functional capacities and oleagenicity of members of the fungal family Trichosporonaceae

Abstract

Trichosporonaceae incorporates six genera of physiologically and ecologically diverse fungi including both human pathogenic taxa as well as yeasts of biotechnological interest, especially those oleagenic taxa that accumulate large amounts of single cell oils (SCOs). Here, we have undertaken comparative genomic analysis of thirty-three members of the family with a view to gain insight into the molecular determinants underlying their lifestyles and niche specializations. Phylogenomic analysis revealed potential misidentification of three strains which could impact subsequent analyses. Evaluation of the predicted proteins coding sequences showed that the free-living members of the family harbour greater numbers of carbohydrate active enzymes (CAZYmes), metallo- and serine peptidases compared to their host-associated counterparts. Phylogenies of selected lipid biosynthetic enzymes encoded in the genomes of the studied strains revealed disparate evolutionary histories for some proteins inconsistent with the core genome phylogeny. However, the documented oleagenic members distinctly cluster based on the constitution of the upstream regulatory regions of genes encoding acetyl-CoA carboxylase (ACC), ATP-citrate synthase (ACS) and isocitrate dehydrogenase [NADP] (ICDH), which are among the major proteins in the lipid biosynthetic pathway of these yeasts, suggesting a possible pattern in the regulation of these genes.

Figure 1

Phylogenomic analysis of members of the family Trichosporonaceae. The maximum likelihood (ML) tree was inferred from the concatenated protein alignment (223,082 amino acids) of 405 proteins present in single copies among the haploid genomes and only in duplicate copies in the hybrid genomes. The phylogeny was generated using IQ-TREE version 1.6.7 based on the LG + F + R10 model. The ML was generated with confidence values based on 1,000 bootstrap replicates. The documented oil accumulating members of the family are indicated in blue fonts. The labels ‘_1’ and ‘_2’ indicate the two sets of single copy orthologs (SCOs) in the hybrid genomes, where the letter shows higher amino acid similarity to the closest haploid genome.

Figure 2

Comparison of number of proteins associated with (a) CAZymes and (b) MEROPS among thirty-three strains of Trichosporonaceae. CAZymes; AA: auxillary activities, CBM: carbohydrate-binding modules, CE: carbohydrate esterases, GH: glycoside hydrolases and GT: glycosyltransferases. MEROPS; A: aspartic peptidases, C: cysteine peptidases, M: metallo-peptidases, N: asparagine peptide lyases, S: serine peptidases, T: threonine peptidases, and I: protease inhibitors.

Figure 3

Illustration of the initiation of the biochemical oil production in yeasts showing the steps within the pathway catalysed by the studied enzymes under nitrogen limitation. ACC, acetyl-CoA carboxylase, AMPD, AMP deaminase, ACS, ATP-citrate synthase, FASI & II, fatty acid synthase subunits alpha and beta and ICDH, isocitrate dehydrogenase [NADP]. × and ↑ indicates the inhibition of ICDH and increased activity of AMPD under nitrogen limitation. Modified from

Figure 4

Evolutionary analyses of the ICDH protein and the upstream region of its gene among thirty-three strains of Trichosporonaceae. (a) ML tree of ICDH (380 amino acids long trimmed alignment) generated using IQ-TREE version 1.6.7 with confidence values based on 1,000 bootstrap replicates. (b) Distribution of predicted transcription factor binding sites 600 nucleotide bases upstream of the transcription initiation site of ICDH gene clustered using hierarchical clustering on principal components (HCPC) in R. The documented oil accumulating members of the family are indicated in blue fonts in the phylogeny and with blue arrows in the HCPC.

Figure 5

Evolutionary analyses of the ACS protein and the upstream region of its gene among thirty-three strains of Trichosporonaceae. (a) ML tree of ACS (1,097 amino acids long trimmed alignment) generated using IQ-TREE version 1.6.7 with confidence values based on 1,000 bootstrap replicates. (b) Distribution of predicted transcription factor binding sites 600 nucleotide bases upstream of the transcription initiation site of ACS gene clustered using hierarchical clustering on principal components (HCPC) in R. The documented oil accumulating members of the family are indicated in blue fonts in the phylogeny and with blue arrows in the HCPC.

Figure 6

Evolutionary analyses of the ACC protein and the upstream region of its gene among thirty-three strains of Trichosporonaceae. (a) ML tree of ACC (2094 amino acids long trimmed alignment) generated using IQ-TREE version 1.6.7 with confidence values based on 1,000 bootstrap replicates. (b) Distribution of predicted transcription factor binding sites 600 nucleotide bases upstream of the transcription initiation site of ACC gene clustered using hierarchical clustering on principal components (HCPC) in R. The documented oil accumulating members of the family are indicated in blue fonts in the phylogeny and with blue arrows in the HCPC.