Figure 1.
Genes identified for coding enzymes in CO2 fixation pathways in algal species generated by KEGG.
Different colors in the small boxes represent the genes identified from Rhodophyta, Ochrophyta, Chlorophyta, Glaucophyta and Cryptophta, respectively. The numbers within the small boxes are the enzyme commission (EC) number. PEPC: phosphoenolpyruvate carboxylase; PPDK: pyruvate, orthophosphate dikinase; ALT: alanine transaminase; MDH: malate dehydrogenase; ME: malic enzyme; AST: aspartate aminotransferase; PK: pyruvate kinase; PCK: phosphoenolpyruvate carboxykinase.
Table 1.
The numbers of gene in C3 and C4 pathways in algae and tracheophytes species.
Figure 2.
Bayesian phylogenetic trees of PEPC (A) PPDK (B), ALT (C) and PK (D) enzymes with bootstrap values (when >50%) indicated at the nodes.
The PEPCs are classified as PTPCs (in dark gray boxes) and BTPCs (in light gray boxes). ChlP, chlorophytes and plants. Gla, glaucophytes. Rho, rhodophytes. Och, ochrophytes. Cry, cryptophytes. Tri, trichomonad. Amo, amoeba. Cil, ciliates.
Figure 3.
Bayesian phylogenetic trees of MDH (A) and ME (B) enzymes with bootstrap values (when >50%) indicated at the nodes.
The plastic type MDHs are in dark gray boxes, and mitochondrial types in light gray boxes. Eukaryotic MEs cluster in two clades, one clade in dark gray boxes consists of both plastic and mitochondrial type, the other one only contains mitochondrial type. ChlP, chlorophytes and plants. Gla, glaucophytes. Rho, rhodophytes. Och, ochrophytes. Cry, cryptophytes. Tri, trichomonad. Amo, amoeba. Cil, ciliates.
Figure 4.
Bayesian phylogenetic trees of PCK (A) and AST (B) enzymes with bootstrap values (when >50%) indicated at the nodes.
The cytosolic types of AST are in dark gray boxes and mitochondrial types are in light gray boxes. Besides this two clades, some chlorophyte, plant and cryptophyte ASTs are grouped with cyanobacteria (Clade A), which are also in light gray boxes. ChlP, chlorophytes and plants. Gla, glaucophytes. Rho, rhodophytes. Och, ochrophytes. Cry, cryptophytes. Tri, trichomonad. Amo, amoeba. Cil, ciliates.
Figure 5.
Alignments of partial amino acid sequences of PEPC isoenzymes between species of Rhodophyta, Ochrophyta, chlorophytes, Cryptophta, bacteria and archaea.
The deduced PEPC sequences were aligned using ClustalX 1.83 software. Numbering indicates the position of the first and last residue in each aligned sequence. Semi-colons and asterisks indicate identical and conserved amino acids respectively. The C-terminal tetrapeptide (R/K)NTG for BTPCs is highlighted in blue color, whereas QNTG for PTPCs is highlighted in orange. The amino acid residue of No. 774 or around it is highlighted in green (non-photosynthetic PEPCs) or red (C4-type PEPCs).
Figure 6.
Partial sequence alignment of the N-terminal domains of PEPS and PPDK enzymes.
Numbering indicates the position of the first and last residue in each aligned sequence. Proteins with biochemically confirmed enzyme activity are indicated by gray shading. Grey shading indicate the identified sequence signatures specific for PEPS and PPDK respectively.