title: Taxonomic distribution and origins of the extended LHC (light-harvesting complex) antenna protein superfamily.
abstract: BACKGROUND
  The extended light-harvesting complex (LHC) protein superfamily is a centerpiece of eukaryotic photosynthesis, comprising the LHC family and several families involved in photoprotection, like the LHC-like and the photosystem II subunit S (PSBS). The evolution of this complex superfamily has long remained elusive, partially due to previously missing families.
  
  
  RESULTS
  In this study we present a meticulous search for LHC-like sequences in public genome and expressed sequence tag databases covering twelve representative photosynthetic eukaryotes from the three primary lineages of plants (Plantae): glaucophytes, red algae and green plants (Viridiplantae). By introducing a coherent classification of the different protein families based on both, hidden Markov model analyses and structural predictions, numerous new LHC-like sequences were identified and several new families were described, including the red lineage chlorophyll a/b-binding-like protein (RedCAP) family from red algae and diatoms. The test of alternative topologies of sequences of the highly conserved chlorophyll-binding core structure of LHC and PSBS proteins significantly supports the independent origins of LHC and PSBS families via two unrelated internal gene duplication events. This result was confirmed by the application of cluster likelihood mapping.
  
  
  CONCLUSIONS
  The independent evolution of LHC and PSBS families is supported by strong phylogenetic evidence. In addition, a possible origin of LHC and PSBS families from different homologous members of the stress-enhanced protein subfamily, a diverse and anciently paralogous group of two-helix proteins, seems likely. The new hypothesis for the evolution of the extended LHC protein superfamily proposed here is in agreement with the character evolution analysis that incorporates the distribution of families and subfamilies across taxonomic lineages. Intriguingly, stress-enhanced proteins, which are universally found in the genomes of green plants, red algae, glaucophytes and in diatoms with complex plastids, could represent an important and previously missing link in the evolution of the extended LHC protein superfamily.
authors.affiliation: Department of Biology, University of Konstanz, Konstanz, Germany.
authors.forename: Johannes
authors.initials: J
authors.lastname: Engelken
authors.forename: Henner
authors.initials: H
authors.lastname: Brinkmann
authors.forename: Iwona
authors.initials: I
authors.lastname: Adamska
mesh_terms: D000595:Amino Acid Sequence; D030541:Databases, Genetic; D017377:Diatoms / Q000235:genetics*; D019143:Evolution, Molecular; D045342:Light-Harvesting Protein Complexes / Q000145:classification / Q000235:genetics*; D008969:Molecular Sequence Data; D005810:Multigene Family; D045332:Photosystem II Protein Complex / Q000235:genetics; D010802:Phylogeny; D010944:Plants / Q000235:genetics*; D000461:Rhodophyta / Q000235:genetics*; D017422:Sequence Analysis, DNA
chemical_list: D045342:Light-Harvesting Protein Complexes; D045332:Photosystem II Protein Complex