Prevalence and environmental abundance of the TSET complex in cosmopolitan algal groups

Abstract

Classical cell biology paradigms are largely established on animal, fungal, and plant models which constitute a small fraction of eukaryotic diversity. Some important cellular machinery has been historically overlooked due to their absence from animals and fungi, e.g., the membrane-trafficking complex TSET involved in plant cell division and endocytosis. Here, we document TSET complexes in distantly related photosynthetic eukaryotic groups (green algae, red algae, haptophytes, cryptophytes, and stramenopiles including diatoms). 3D modeling predicts that at least some stramenopile-encoded subunits share conserved structural features with plant orthologues, and gene expression analysis from the diatom Phaeodactylum tricornutum shows that they are co-expressed with endomembrane trafficking proteins. Finally, diatom TSET genes are detectable in meta-transcriptomic data from Tara Oceans, suggesting functional roles in the wild. These results support the importance of integrating non-model organisms into our understanding of eukaryotic cell biology, as they may reveal underappreciated protein complexes essential for cellular and ecosystem functions.

Keywords: Aquatic biology; Cell biology; Plant biology; Plant development; Plant evolution.

Graphical abstract

Figure 1

Prevalence of TSET in major marine algal groups Illustration of TSET subunit detection in the subgroups of each of four algal groups. Yellow sectors indicate that an orthologue was detected in a single dataset. Gray sectors indicate that orthologues were detected in fewer than 50% of the datasets. Blue sectors indicate that orthologues were detected in ≥50% of the datasets examined. The number of AP1-positive genomes/transcriptome libraries inspected is indicated on the right side of the corresponding group. Branching orders are schematics based on existing taxonomic knowledge for each group, per. (A) Green algae and glaucophytes. (B) Red Algae. (C) Cryptophytes. (D) Haptophytes.

Figure 2

Distribution of TSET across stramenopiles Illustration of TSET subunit detection in the stramenopiles. Yellow sectors indicate that an orthologue was detected in a single dataset. Gray sectors indicate that orthologues were detected in fewer than 50% of the datasets. Blue sectors indicate that orthologues were detected in ≥50% of the datasets examined. The number of AP1-positive genomes/transcriptome libraries inspected is indicated on the right side of the corresponding group. Branching orders are schematics based on existing taxonomic knowledge for each group, per.

Figure 3

Modeling structural conservation between stramenopile and A. thaliana orthologues This figure shows superimposed AlphaFold predicted structures of TSET subunits, with the TM align score of >0.5 indicating structural conservation between the compared subunits. In all cases, taxa are colored as inset.

Figure 4

Subunit docking modeling of TSAUCER-TSPOON subunits For each of the pairs of TSAUCER and TSPOON from A. thaliana, Blastocystis sp., and D. discoideum, the structural models were predicted showing individual structures and potential interactions. Predicted structures are shown to the left, PAE plots shown to the right. pLDDT scores for each predicted structure are near, or above, the confidence threshold (>70), with the experimentally confirmed interacting pair from A. thaliana having the lowest score. The overall quaternary structure of the subunit pairs is relatively concordant.

Figure 5

KEGG functions enriched in genes co-expressed with P. tricornutum TSET Gene co-regulated to four core TSET subunits (Phatr3_J43047 – TCUP, Phatr3_J54511 – TPLATE, Phatr3_J54718 – TSPOON and Phatr3_J46356 – TTRAY) was assessed by Spearman correlation of a meta-dataset of P. tricornutum RNA-seq and microarray data per. The numbers of coregulated genes (r > 0.5) in each category of the “Gene and proteins” classification of the KEGG Mapper Pathway are represented by colored bars, while gray bars represent the total number of genes in the corresponding category. Categories are sorted decreasingly from top to bottom based on their percentage of completeness (shown on the left of the bars). The “Enzymes” category (correlated = 579 genes, total = 1450 genes) and categories containing fewer than 5 genes are not considered. Raw supporting data are provided in Data S6.

Figure 6

Map of Tara Oceans distributions of diatom TSET meta-transcripts Circles represent the mean between surface and DCM samples of the normalized total abundances of all putative TSET subunits transcripts found in each sampling station. The abundance of transcripts is expressed as the percentage of total transcript reads within the station, normalized by the total abundance of diatoms transcript reads within the same station. The presence or absence of the putative TSET subunits transcripts in a station is shown on the corresponding pie chart. Gray crosses indicate the location of all sampling stations. No occurrence of TSAUCER transcripts was detected.

Figure 7

Correlations between the relative abundances of diatom TSET meta-transcripts and Tara Oceans environmental variables (A) Heatmap of the Spearman correlation coefficients between relative transcript abundances and environmental parameters. Normalized relative abundances for each sampling stations were calculated for samples corresponding to the 0.8 to 2000 μm size fraction, collected at the surface (SRF) or at the Deep Chlorophyll Maximum (DCM). Shapes and colors of the ellipses correspond to the correlation coefficient value, empty signs show that no value is available for the corresponding environmental parameter. The “TSAUCER” column is blank as no transcripts were detected. (B) Principal component analysis of Tara environmental conditions and TSET relative abundances. “TSET abundance” corresponds to the normalized total abundances of all putative TSET subunits meta-transcripts found in each sampling station, depth and size fraction. Environmental parameters used for the PCA are listed in A, with the minimal and maximal O₂ depths added. PC1 is positively associated with nitrogen and phosphorus nutrient concentrations, PC2 is positively associated with carbon nutrient and pH, PC3 is associated with depth parameters (salinity, density, photosynthetically active radiations).