Pathway analysis of the proteomes of red, brown, and green macroalgae

Abstract

Comparative proteomics provides insights into the biochemical pathways of macroalgae. One type of comparative proteomics is pathway analysis, which seeks to identify biological processes and cellular functions impacted by variations in groups of genes. Here we perform pathway analysis of macroalgae, including green (Ulva mutabilis and Ulva prolifera), red (Chondrus crispus, Gracilariopsis chorda and Porphyra umbilicalis), and brown (Ectocarpus siliculosus, Macrocystis pyrifera, Fucus vesiculosus, Saccharina japonica and Undaria pinnatifida) seaweeds. We chose these macroalgae because their whole genomes are publicly available. We determine gene function through mapping to orthologous gene groups in the KEGG database. Our analysis finds a core of approximately fifty pathways that are similar among groups, including central carbon metabolism (amino acid metabolism, nucleotide metabolism) and secondary metabolism (terpenoid biosynthesis, cofactors and vitamins, sulfur metabolism). We also determine numerous pathways that have differential orthologous gene group abundance among the three groups: central metabolic processes (carbon fixation, photosynthesis), secondary metabolism (fatty acid elongation, O-glycan biosynthesis), and also cellular processes (circadian rhythm, longevity regulation). We find both inter- and intra-group differences in the circadian rhythm pathway. For example, transcription factor HY5 is consistent in the red algae and absent from others, whereas, circadian clock associated 1 (CCA1) is present in 2 browns (E. siliculosus and S. japonica) and 2 reds (G. chorda and P. umbilicalis). In both of the green macroalgae and 2 reds (C. crispus and G. chorda) we identified a cryptochrome (CRY), which is a blue light receptor important in circadian rhythm. Overall, we find few orthologous gene groups in the circadian rhythm pathway to be present in the brown macroalgae except for pseudo-response regulator 7, which is consistent with a poorly understood “brown clock”.