Tracing the evolution of the light-harvesting antennae in chlorophyll a/b-containing organisms

Abstract

The light-harvesting complexes (LHCs) of land plants and green algae have essential roles in light capture and photoprotection. Though the functional diversity of the individual LHC proteins are well described in many land plants, the extent of this family in the majority of green algal groups is unknown. To examine the evolution of the chlorophyll a/b antennae system and to infer its ancestral state, we initiated several expressed sequence tag projects from a taxonomically broad range of chlorophyll a/b-containing protists. This included representatives from the Ulvophyceae (Acetabularia acetabulum), the Mesostigmatophyceae (Mesostigma viride), and the Prasinophyceae (Micromonas sp.), as well as one representative from each of the Euglenozoa (Euglena gracilis) and Chlorarachniophyta (Bigelowiella natans), whose plastids evolved secondarily from a green alga. It is clear that the core antenna system was well developed prior to green algal diversification and likely consisted of the CP29 (Lhcb4) and CP26 (Lhcb5) proteins associated with photosystem II plus a photosystem I antenna composed of proteins encoded by at least Lhca3 and two green algal-specific proteins encoded by the Lhca2 and 9 genes. In organisms containing secondary plastids, we found no evidence for orthologs to the plant/algal antennae with the exception of CP29. We also identified PsbS homologs in the Ulvophyceae and the Prasinophyceae, indicating that this distinctive protein appeared prior to green algal diversification. This analysis provides a snapshot of the antenna systems in diverse green algae, and allows us to infer the changing complexity of the antenna system during green algal evolution.

Figure 1.

Phylogenetic reconstruction of the LHC superfamily. The analysis includes sequences from several major light-harvesting divisions, including LI818 and LI818-like proteins, Chl a/c-binding proteins of the chromalveolates, the cryptomonad/red algal LHCs, the cryptophyte/haptophyte LHCs, and the Chl a/b-binding proteins. A MrBayes tree is shown (−lnL= 13,545.54, α = 1.419) with the support values for all analyses shown at specific nodes in the following order: MrBayes (posterior probabilities), NJD, PHYML. A total of 129 characters were included and the proportion of invariable sites was 0.041. The average sd of the split frequencies was 0.0126. A total of 100 sequences were included in the analyses and all sequences were either novel sequences generated in conjunction with the Protist EST Program (Table II), were present in GenBank, or were retrieved from individual genome projects (C. merolae). P. patens LI818 sequence compiled from individual ESTs available in dbEST (BJ958734, BJ957315, BJ955694, BJ954266, BJ958980, and BJ857081). Sequences from Chl a/b-containing organisms are in bold.

Figure 2.

Phylogenetic reconstruction of the Chl a/b LHC superfamily. A MrBayes tree is shown with the posterior probabilities/support values for all three phylogeny programs shown at specific nodes (MrBayes, ProtDist, and PHYML). A total of 136 amino acid positions and 139 sequences were used with the proportion of invariable sites being 0.040. The γ shape distribution parameter (α) was 1.426 and the −lnL for the tree was 13,126.69. The average sd of the split frequencies was 0.0344. Novel sequences obtained from PEPdb have been differentiated from the other sequences by the addition of a black circle following the sequence names. The Arabidopsis LHC gene family is in bold for easy recognition of the plant LHCs. Solid black boxes surround specific Lhca clades (see text). The conserved trimerization motif for several LHCII sequences is shown, with the conserved residues highlighted.

Figure 3.

Analysis of green algal PsbS proteins. A, hydrophobicity plots of A. acetabulum PsbS1 and O. tauri PsbS sequences calculated with a window size of 19. Putative transmembrane regions are indicated by a white rectangle. Hatched areas identify the location of the putative Chl-binding motifs. TP denotes transit peptide location as determined with ChloroP. B, Phylogenetic analysis of PsbS sequences. A total of 120 amino acid positions were analyzed and the proportion of invariable sites was 0.113. The average sd of the split frequencies was 0.0015. A MrBayes tree is shown with the support values for all three phylogeny programs shown at specific nodes (MrBayes, ProtDist, and PHYML). The γ shape distribution parameter (α) was 4.123 and the −lnL value of the best PHYML tree was 3621.81. C, The conserved Chl-binding motifs for both MSR1 and MSR3 are shown for a variety of LHCs and organisms. The conserved residues in LHCs are highlighted.

Figure 4.

Scheme for the evolution of major LHCs and their relatives in the major photosynthetic eukaryotic groups. An oval indicates an endosymbiotic event. The primary (1°) symbol indicates that the endosymbiont was a cyanobacterium, while secondarily derived plastids (2°) originated from eukaryotic algae as indicated by the solid arrow. A yellow circle denotes a gain of a specific LHC or LHC relative. White rectangles indicate a gene-specific loss. Dotted lines indicate the presence of an alternate timing of an acquisition event. Dashed lines indicate alternative evolutionary pathways. OHP, One-helix protein; PBP, phycobilin protein.