Molecular phylogeny of fucoxanthin‐chlorophyll a/c proteins from Chaetoceros gracilis and Lhcq/Lhcf diversity

Abstract

Diatoms adapt to various aquatic light environments and play major roles in the global carbon cycle using their unique light‐harvesting system, i.e. fucoxanthin chlorophyll a/c binding proteins (FCPs). Structural analyses of photosystem II (PSII)–FCPII and photosystem I (PSI)–FCPI complexes from the diatom Chaetoceros gracilis have revealed the localization and interactions of many FCPs; however, the entire set of FCPs has not been characterized. Here, we identify 46 FCPs in the newly assembled genome and transcriptome of C. gracilis. Phylogenetic analyses suggest that these FCPs can be classified into five subfamilies: Lhcr, Lhcf, Lhcx, Lhcz, and the novel Lhcq, in addition to a distinct type of Lhcr, CgLhcr9. The FCPs in Lhcr, including CgLhcr9 and some Lhcqs, have orthologous proteins in other diatoms, particularly those found in the PSI–FCPI structure. By contrast, the Lhcf subfamily, some of which were found in the PSII–FCPII complex, seems to be diversified in each diatom species, and the number of Lhcqs differs among species, indicating that their diversification may contribute to species‐specific adaptations to light. Further phylogenetic analyses of FCPs/light‐harvesting complex (LHC) proteins using genome data and assembled transcriptomes of other diatoms and microalgae in public databases suggest that our proposed classification of FCPs is common among various red‐lineage algae derived from secondary endosymbiosis of red algae, including Haptophyta. These results provide insights into the loss and gain of FCP/LHC subfamilies during the evolutionary history of the red algal lineage.

Structural basis for different types of hetero-tetrameric light-harvesting complexes in a diatom PSII-FCPII supercomplex

“…This is realized by both high-quality maps that allow us to identify side chains of characteristic amino acid residues in each FCP (Supplementary Fig. 7 ) and the information of the genome of C. gracilis 11 . As a result (Fig.…”

“…Diatoms contain a large number of FCP genes and subunits; for example, the genome of C. gracilis (ChaetoBase; https://chaetoceros.nibb.ac.jp/ ) shows 46 FCP genes 11 . Unlike the green-lineage PSII-LHCII supercomplexes, some of the FCPII subunits in the structures of diatom PSII-FCPII supercomplexes reported previously have not been identified yet 7 , 8 .…”

Structure of PSI-LHCI fromCyanidium caldariumprovides evolutionary insights into conservation and diversity of red-lineage LHCs

“…The amino acid sequences of 16 FCPIs observed in our PSI-FCPI structure 9 were different from those in the PSI-FCPI structures with 24 FCPI subunits 10 . Moreover, the gene names of the 16 FCPIs differ between our structure 9 and the other 10 , which were discussed previously 10,24 . As our PSI-FCPI structure 9 was built according to the genome data of C. gracilis 24 , we performed further data analysis and discussion of the C. caldarium LHCI-2 to LHCI-5 using the structural data of our PSI-FCPI supercomplex 9 (Fig.…”

“…9b). This gene is a RedCAP as discussed in Kumazawa et al 2022 24 . Here we searched this gene in the C. gracilis database, and obtained a gene like RedCAP in C. gracilis , which was termed as CgRedCAP .…”

Origin of the far-red absorbance in eustigmatophyte algae red-shifted Violaxanthin-ChlorophyllaProtein

“…The previously published sets of LHC sequences (excluding LIL1) encoded by the Nannochloropsis oceanica and Microchloropsis (= Nannochloropsis ) gaditana genomes 33,68 were retrieved from the respective databases and further refined by identification of additional, previously missed LHC family members and replacing some of the incorrect gene models with accurate protein sequences derived from transcriptome assemblies. The eustigmatophyte LHC sequences (with technical details listed in Supplementary Table S1) were combined with previously identified LHC sequences from the diatom P. tricornutum 69 and a subset of LHC sequences from the alveolate C. velia , red algae ( Cyanidioschyzon merolae , Galdieria sulphuraria , and Porphyridium purpureum ), the green algal Chlamydomonas reinhardtii , and the plant Arabidopsis thaliana . The sequences were aligned with hmmalign (HMMER package) using the PF00504-derived profile HMM as the template and the --trimm option to remove the unaligned flanking (non-conserved) regions.…”