Identification and Molecular Evolution of Novel Phospholipase D Enzymes in Taxonomically Dispersed Algae using Biocomputational Analyses

BELIGNI, MV; TEN HAVE A

Rosario

Congreso; 4th International Conference of Iberoamerican Society of Bioinformatcis and 4th Congress of the Asocación Argentina de Bioinformática y Biología Computacional; 2013

Asocación Argentina de Bioinformática y Biología Computacional

Phospholipase D (PLD) is a key enzyme in phospholipid metabolism that catalyzes the hydrolysis ofphosphatidylcholine to form phosphatidic acid (PA), a signaling molecule [1]. Due to the importance oflipid biochemistry in algae and the poor characterization of PA formation in these organisms, we setout to study PLDs in algae and started with a biocomputational meta-analysis. We performed datamining, starting with a high-quality seed dataset of PLDs from reference organisms, by means ofiterative HMMer profiling of the complete proteomes from microalgae and related organisms. Figure1A is a taxonomic tree showing the species used for data mining. Since algae belong to three differentkingdoms, representative members of the important taxonomic groups related to algae were includedfor analysis.The presence of two HxKxxxxD (HKD) domains was used as a preliminary rule for the identification ofa protein as a PLD. Sequences containing only one HKD were eliminated in each cycle except for thelast one. Sequences with two HKDs (or canonical PLDs, called hereafter PLDs) were separated fromsequences with only one HKD domain (PLD homologs). Since complete proteomes for theRhodophyta and Dinophyta groups are scarce or not available, TBLASTN with genome sequenceswere performed to augment the information from these two groups.Algae possess less PLDs than higher plants, consistent with their lower signaling complexity. All landplants analyzed have ten PLDs or more, whereas algae typically have one to four, with the exceptionof the dinoflagellate Alexandrium tamarense, which has at least seven PLDs.Figure 1B shows a phylogenetic tree of PLDs. Plants have mainly C2- and PX-PH-PLDs, based on theregulatory domains they contain. Most algal PLDs belong to the C2 type, while none of the themappear to be PX-PH-PLDs. A few PLDs from chromalveolata algae (diatoms, dinoflagellates, rhizaria)appear to be related to rice signal peptide PLD (SP-PLD) [2]. A few PLDs from A. tamarense are, toour surprise, associated to Phytophthora infestans PLD-like proteins [3]. In addition, a group of PLDsfrom mamiellophycean green algae (Ostreococcus tauri, Ostreococcus lucimarinus and Micromonaspusilla) are conserved with PLD-like cardiolipin synthases (c-PLDs) from chromalveolata parasites.Hence, it appears that algal PLDs have evolved form a number of ancestors, often but not alwaysexplained by their taxonomic classification.A few intriguing ideas arise from this analysis. For example, PLD activity was measured inChlamydomonas reinhardtii [4], a green alga with no detected PLDs. However, one PLD homolog witha single HKD was identified (data not shown), opening the possibility that some algae might performthe catalytic function of PLDs through homodimeric interaction between PLD homologouspolypeptides.