Still acting green: continued expression of photosynthetic genes in the heterotrophic Dinoflagellate Pfiesteria piscicida (Peridiniales, Alveolata)

Abstract

The loss of photosynthetic function should lead to the cessation of expression and finally loss of photosynthetic genes in the new heterotroph. Dinoflagellates are known to have lost their photosynthetic ability several times. Dinoflagellates have also acquired photosynthesis from other organisms, either on a long-term basis or as "kleptoplastids" multiple times. The fate of photosynthetic gene expression in heterotrophs can be informative into evolution of gene expression patterns after functional loss, and the dinoflagellates ability to acquire new photosynthetic function through additional endosymbiosis. To explore this we analyzed a large-scale EST database consisting of 151,091 unique sequences (29,170 contigs, 120,921 singletons) obtained from 454 pyrosequencing of the heterotrophic dinoflagellate Pfiesteria piscicida. About 597 contigs from P. piscicida showed significant homology (E-value <e(-30)) with proteins associated with plastid and photosynthetic function. Most of the genes involved in the Calvin-Benson cycle were found, genes of the light-dependent reaction were also identified. Also genes of associated pathways including the chorismate pathway and genes involved in starch metabolism were discovered. BLAST searches and phylogenetic analysis suggest that these plastid-associated genes originated from several different photosynthetic ancestors. The Calvin-Benson cycle genes are mostly associated with genes derived from the secondary plastids of peridinin-containing dinoflagellates, while the light-harvesting genes are derived from diatoms, or diatoms that are tertiary plastids in other dinoflagellates. The continued expression of many genes involved in photosynthetic pathways indicates that the loss of transcriptional regulation may occur well after plastid loss and could explain the organism's ability to "capture" new plastids (i.e. different secondary endosymbiosis or tertiary symbioses) to renew photosynthetic function.

Figure 1. Calvin-Benson cycle and associated pathways.

The genes found in Pfiesteria piscicida EST database were marked in red color.

Figure 2. Maximum likelihood trees (WAG + I + Γ model) inferred from Pfiesteria piscicida protein sequences and assorted “protistan” lineages.

Numbers above nodes indicate posterior probabilities and RAXML bootstrap percentages. * = 1.00 PP and 100% RAxML BP. Values <50% are not shown.

Figure 3. Maximum likelihood trees(RaXML, WAG + I + Γ model) inferred from Pfiesteria piscicida protein sequences and assorted plastid endosymbiont lineages.

psbA protein – alignment length 282 amino acids. Ribose-5-phosphate isomerase protein – alignment length 231 amino acids. Numbers above nodes indicate posterior probabilities and RAXML bootstrap percentages. * = 1.00 PP and 100% RAxML BP. Values <50% are not shown.

Figure 4. A diagram showing chloroplast membrane genes and light reaction center genes.

The genes found in Pfiesteria piscicida EST database are marked in red color.

Figure 5. Multiple alignments of 5′ end sequences of GAPDH and fructose-bisphosphate aldolase showing the location of Spliced Leader sequence and specific primer (black lines on the top).

5′ UTR and open reading frame (ORF) were shown with red arrows.