A new appraisal of the prokaryotic origin of eukaryotic phytochromes

The evolutionary origin of the phytochromes of eukaryotes is controversial. Three cyanobacterial proteins have been described as "phytochrome-like" an d have been suggested to be potential ancestors of these essential photorec eptors: Cph1 from Synechocystis PCC 6803, showing homology to phytochromes along its entire length and known to attach a chromophore; and PlpA from Sy nechocystis PCC 6803 and RcaE from Fremyella diplosiphon, both showing homo logy to phytochromes most strongly only in the C-terminal region and not kn own to bind a chromophore. We have reexamined the evolution of the photorec eptors using for PCR amplification a highly conserved region encoding the c hromophore-binding domain in both Cph1 and phytochromes of plants and have identified genes for phytochrome-like proteins (PLP) in 11 very diverse cya nobacteria. The predicted gene products contain either a Cys, Arg, Ile, or Leu residue at the putative chromophore binding site. In 10 of the strains examined only a single gene was found, but in Calothrix PCC 7601 two genes (cphA and cphB) were identified. Phylogenetic analysis revealed that genes encoding PLP are homologues that share a common ancestor with the phytochro mes of eukaryotes and diverged before the latter. In contrast, the putative sensory/regulatory proteins, including PlpA and RcaE, that lack a part of the chromophore lyase domain essential for chromophore attachment on the ap ophytochrome, are only distantly related to phytochromes. The Ppr protein o f the anoxygenic photosynthetic bacterium Rhodospirillum centenum and the b acterial phytochrome-like proteins (BphP) of Deinococcus radiodurans and Ps eudomonas aeruginosa fall within the cluster of cyanobacterial phytochromes .