Figure 1.
Glycerolipid biosynthesis in eukaryotes.
Cartoons highlighting differences and similarities between the glycerolipid biosynthetic pathways in humans and yeast Saccharomyces cerevisiae.
Figure 2.
Opisthokont relationships and GPAT evolution.
A) Tree illustrating the relative evolutionary history for the eukaryotic emergence, loss and diversification/duplication of GPATs in opisthokonts, in lineages with genome sequences available in the fungi and metazoans with additional taxa from the base of the Opisthokonta supergroup. The apusozoan, T. trahens, was used as the outgroup. The group labeled “SACK” belongs to Saccharomycotina and involves S. cerevisiae, A. gossypii, C.glabrata, and K. lactis To note the Pezizomycotina and Taphrinomycotina form a paraphyletic group of ‘non- Saccharomycotina ascomycota’ which we found to be a useful grouping when considering the evolution of GPATs and are thus colour coded identically. Similarly, all non-tetrapoda metazoans are coded in the same colour. In order to avoid false negative or false positives in our evolutionary deductions, we do not infer any events on lineages where only a single genome was examined. B) Results from the comparative genomic survey and phylogenetic analysis. Individual species from the survey are color coded as in A) and grouped according to established taxonomic classification. The dendrogram is schematic of relationships only and the branch length is not representative of evolutionary distance. Symbols indicate the presence of at least one isoform of a given protein as verified by BLAST, Reciprocal BLAST, hidden Markov model searches, and phylogenetic data as follow: orthologs of Sct1/Gat2(), Gpt2/Gat1(
), as well as new fungal fGPAT-A (
) or fGPAT-B (□) and orthologs of human mitochondrial GPATs (mitoGPATs) GPAT1(▴), GPAT2(▾), putative mitoGPATs (▵), GDPAT (
), DHAPATs (⧫) and putative DHAPATs (pDHAPAT ◊), and orthologs of human microsomal GPATs (eGPATs) GPAT3(▸) and GPAT4(◂) and putative eGPATs (→). Putative orthologs of Sct1 and Gpt2 are shown in grey while strongly supported orthologs are shown in solid black. Blank cells indicate no hits. (p) denotes GDPATs with PTS1 prediction. Designation in a particular orthologous group denotes a prediction of substrate specificity, based on assumed retention between orthologues, and provides hypotheses for future functional testing. (*) The Rhizopus acyltransferase gene groups with moderate support with the DHAPAT genes, but this placement may well be due to its highly divergent sequence. Protein sequences used to initiate the searches: yeast Sct1 (NP_009542.1), yeast Gpt2 (NP_012993.1), human GPAT1 (NP_065969.3), human GPAT2 (NP_997211.2), human DHAPAT (NP_055051.1), human GPAT3 (NP_116106.2), human GPAT4 (NP_848934.1). Note: Putative fungal GDPATs display a peroxisomal target sequence (PTS1) and were hits in a search initiated with mitochondrial human GPAT1.
Figure 3.
Phylogeny of fungal GPAT homologues found in opisthokonts.
Phylogenetic tree of the fungal GPATs. In this and all other phylogenies, node support values are shown in order of Bayesian posterior probabilities, PhyML bootstrap percentages and RaxML bootstrap percentages, or are symbolized as dots, colorized as per the inset to indicate statistical strength. Clades for orthologues of Sct1 and Gpt2 are shaded. For protein accession numbers see Table S3.
Figure 4.
Phylogenetic tree of GDPAT-related genes in opisthokonts.
The clades of mitochondrial GPATs (called mitoGPAT, then enumerated), putative DHAPATs (called pDHAPAT, then enumerated) and fungal GDPATs are shaded. Darker shading in each cluster highlights biochemically characterized enzymes from vertebrates, which includes mammalian GPAT1 and DHAPAT homologues. For protein accession numbers see Table S4.
Figure 5.
Phylogenetic tree of mammalian eGPATs in opisthokonts.
Phylogenetic tree of the emergence of mammalian GPAT3 and GPAT4 homologues (called eGPATs, then enumerated). For protein accession numbers see Table S5.
Figure 6.
Sequence alignments of the catalytic motifs in strongly supported orthologs of biochemically characterized acyltransferases in each of the eGPATs, fungal GPATs (fGPATs-SACK), mitoGPATs and DHAPATs groups were compare to those of fungal GDPATs.
The numbers in the boxes represent the distance between motifs in number of amino-acid residues. Proteins were aligned using Uniprot Align software and acyltransferase motifs recognized as proposed in [18]. Positive, negative and aliphatic residues are highlighted in green, red and yellow respectively. Abbreviations: agos, Ashbya gossypii; amac, Allomyces macrogynus; anid, Aspergillus nidulans; bden, Batrachochytrium dendrobatidis; cgla, Candida glabrata; cimm, Coccidioidies immitis; gall, Gallus gallus; gzea, Gibberella zeae; hsap, Homo sapiens; klac, Kluyveromyces lactis; musm, Mus musculus; ncra, Neurospora crassa; scer, Saccharomyces cerevisiae; spun, Spizellomyces punctatus; xeno or xet, Xenopus tropicalis; ylip, Yarrowia lipolytica.
Table 1.
Acyltransferase motifs and distance between motifs (DBM) in microsomal yeast-like (fGPAT-A), metazoan ER-like (erGPAT), mitoGPATs, DHAPAT and fungal GDPAT (fGDPAT) sets.
Figure 7.
Intracellular distribution of phosphatidic acid biosynthetic and fatty acid oxidation pathways in vertebrate and fungi.