title: Streptophyte phytochromes exhibit an N-terminus of cyanobacterial origin and a C-terminus of proteobacterial origin.
abstract: BACKGROUND
  Phytochromes are red light-sensitive photoreceptors that control a variety of developmental processes in plants, algae, bacteria and fungi. Prototypical phytochromes exhibit an N-terminal tridomain (PGP) consisting of PAS, GAF and PHY domains and a C-terminal histidine kinase (HK).
  
  
  RESULTS
  The mode of evolution of streptophyte, fungal and diatom phytochromes from bacteria is analyzed using two programs for sequence alignment and six programs for tree construction. Our results suggest that Bacteroidetes present the most ancient types of phytochromes. We found many examples of lateral gene transfer and rearrangements of PGP and HK sequences. The PGP and HK of streptophyte phytochromes seem to have different origins. In the most likely scenario, PGP was inherited from cyanobacteria, whereas the C-terminal portion originated from a proteobacterial protein with multiple PAS domains and a C-terminal HK. The plant PhyA and PhyB lineages go back to an early gene duplication event before the diversification of streptophytes. Fungal and diatom PGPs could have a common prokaryotic origin within proteobacteria. Early gene duplication is also obvious in fungal phytochromes.
  
  
  CONCLUSIONS
  The dominant question of the origin of plant phytochromes is difficult to tackle because the patterns differ among phylogenetic trees. We could partially overcome this problem by combining several alignment and tree construction algorithms and comparing many trees. A rearrangement of PGP and HK can directly explain the insertion of the two PAS domains by which streptophyte phytochromes are distinguished from all other phytochromes.
authors.affiliation: Karlsruhe Institute of Technology (KIT), Botanical Institute, Kaiserstr. 2, Karlsruhe, D-76128, Germany. thosten.buchberger@gmail.com.
authors.forename: Thorsten
authors.initials: T
authors.lastname: Buchberger
authors.affiliation: Karlsruhe Institute of Technology (KIT), Botanical Institute, Kaiserstr. 2, Karlsruhe, D-76128, Germany. tilman.lamparter@kit.edu.
authors.forename: Tilman
authors.initials: T
authors.lastname: Lamparter
mesh_terms: D000465:Algorithms; D001105:Archaea / Q000145:classification / Q000235:genetics / Q000378:metabolism; D041963:Bacteroidetes / Q000145:classification / Q000235:genetics / Q000378:metabolism; D005075:Biological Evolution; D000458:Cyanobacteria / Q000145:classification / Q000235:genetics / Q000378:metabolism; D005658:Fungi / Q000145:classification / Q000235:genetics / Q000378:metabolism; D020440:Gene Duplication; D015870:Gene Expression; D022761:Gene Transfer, Horizontal; D000071677:Histidine Kinase; D010802:Phylogeny; D051942:Phytochrome A / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D051939:Phytochrome B / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D010940:Plant Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D011494:Protein Kinases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D017434:Protein Structure, Tertiary; D020560:Proteobacteria / Q000145:classification / Q000235:genetics / Q000378:metabolism; D057949:Streptophyta / Q000145:classification / Q000235:genetics* / Q000378:metabolism
chemical_list: D051942:Phytochrome A; D010940:Plant Proteins; D051939:Phytochrome B; D011494:Protein Kinases; D000071677:Histidine Kinase