Red algal LHC I genes have similarities with both Chl a/b- and a/c-binding proteins: A 21 kDa polypeptide encoded by LhcaR2 is one of the six LHC I polypeptides

Polypeptides from the PS I holocomplex of the red alga P. cruentum, purified for microsequencing, confirmed that six LHC I polypeptides from SDS-PAGE are distinct apoproteins. Analysis of a cDNA clone, designated as LhcaR2, from a cDNA library, indicates that it shares major structural features with the recently cloned first red algal gene LhcaR1. The LhcaR2 is believed to encode the 21.0 kDa polypeptide of the LHC I complex from comparison of the deduced amino acid sequence and the microsequences of several tryptic digest fragments from the isolated polypeptide. As in chlorophytic and chromophytic LHCs, the essential residues for Chl-binding and helix stabilization in helices 1 and 3 are highly conserved. Relatedness between rhodophytes and the chlorophytes is also inferred from sequence conservation in the N-flanking regions of helices 1 and 3. Conversely, helix 2 exhibited the highest similarity between LHC sequences of Chl a/c-binding chromophytes and the Chl a-binding rhodophytes, with 11 of 22 residues identical or conservatively substituted. Moreover, whereas in chlorophytes, the Q and E Chl-binding residues are separated by seven amino acid residues, they are always separated by 8 residues in rhodophytes and chromophytes. Superimposition of the predicted LhcaR2 sequence with the LHC II model Kühlbrandt et al. (1994) Nature 367: 614–621] shows the same structural features except shortened connecting sequence between helices 1 and 2 on the lumenal side. The chimeric nature of rhodophyte genes, with both chromophytic and chlorophytic features, leads to the suggestion that they reflect attributes of an intermediate stage in LHC apoprotein evolution.