Figure 1.
Quaternary structure of the GAPDH A2B2 heterotetramer (PDB: 2PKQ) from Spinacia oleracea (spinach).
Crystallographic subunits O (GapB) and R (GapA) are show in blue and orange respectively. Bound NADPH in the co-enzyme binding domain drawn as a van der Waals space-filling model coloured by element type according to the Visual Molecular Dynamics (VMD) program. Sulfate ions in the Ps and Pi in purple, also as space-filling models. The O and R subunit are related by the R axis of symmetry. The P and Q subunits are shown in the background.
Figure 2.
A simplified representation of the organismal phylogeny for relevant taxa in this study.
Green oval represents the endosymbiotic event in the ancestor of the Archaeplastida (Green Algae, Red Algae, Glaucophytes, Land Plants, etc) that gave rise to the modern chloroplast. Gap2 of cyanobacteria became the GapA of the Archaeplastida, with a further gene duplication event in land plants giving rise to GapB. Many of the relationships between eukaryotic supergroups are currently unresolved, and are represented with multifurcations. Indicated with red ovals are lineages that contain the GapC1 gene. While the gene itself is monophyletic, it is unlikely that the lineages that harbour the red-algal derived plastids they are found in represent a clade, with the Haptophytes and Cryptophytes having uncertain affiliation but probably not with the Stramenopiles and Alveolata as once was thought.
Figure 3.
Simplified maximum-likelihood phylogenetic tree of GAPH, shown as arbitrarily rooted with cyanobacterial sequences.
Cytosolic GAPDH collapsed clades are coloured in blue. Gap A/B and Gap2 are in green, with GapC1 in red. Several ciliates form the immediate outgroup to GapC1 sequences, although without bootstrap support. Only bootstrap support values above 50 are shown. Several clades, indicated as Mixed Eukaryotic Groups, belong sequences from taxa that do not form monophyletic clades. Given the many paralogs included in this analysis, and the fact that it is a single gene phylogeny, this is not unexpected. In the majority of these groups taxa are predominantly from a single supergroup with the addition of a few “rogue” taxa. The full phylogenetic tree can be found in data S1.