Phylogenetic analysis of the phytochrome superfamily reveals distinct microbial subfamilies of photoreceptors

Abstract

Phys (phytochromes) are a superfamily of photochromic photoreceptors that employ a bilin-type chromophore to sense red and far-red light. Although originally thought to be restricted to plants, accumulating genetic and genomic analyses now indicate that they are also prevalent among micro-organisms. By a combination of phylogenetic and biochemical studies, we have expanded the Phy superfamily and organized its members into distinct functional clades which include the phys (plant Phys), BphPs (bacteriophytochromes), Cphs (cyanobacterial Phys), Fphs (fungal Phys) and a collection of Phy-like sequences. All contain a signature GAF (cGMP phosphodiesterase/adenylate cyclase/FhlA) domain, which houses the bilin lyase activity. A PHY domain (uppercase letters are used to denote the PHY domain specifically), which helps stabilize the Pfr form (far-red-light-absorbing form of Phy), is downstream of the GAF region in all but the Phy-like sequences. The phy, Cph, BphP and Fph families also include a PLD [N-terminal PAS (Per/Arnt/Sim)-like domain] upstream of the GAF domain. Site-directed mutagenesis of conserved residues within the GAF and PLD motifs supports their importance in chromophore binding and/or spectral activity. In agreement with Lamparter, Carrascal, Michael, Martinez, Rottwinkel and Abian [(2004) Biochemistry 43, 3659-3669], a conserved cysteine within the PLD of several BphPs was found to be necessary for binding the chromophore via the C-3 vinyl side chain on the bilin A ring. Phy-type sequences were also discovered in the actinobacterium Kineococcus radiotolerans and collections of microorganisms obtained from marine and extremely acidic environments, thus expanding further the range of these photoreceptors. Based on their organization and distribution, the evolution of the Phy superfamily into distinct photoreceptor types is proposed.

The Structure of Phytochrome: A Picture Is Worth a Thousand Spectra

“…Unlike the phycobiliproteins, which utilize C-S lyases for covalent attachment of their bilin chromophores (Schluchter and Glazer, 1999), plant phytochromes do not require enzymes or cofactors to assist the covalent assembly reaction (Terry et al, 1993). The same is true for cyanobacterial, fungal, and bacteriophytochromes (Karniol et al, 2005). While recent work implicates the importance of the P2 domain for proper holoprotein assembly of a cyanobacterial phytochrome (Zhao et al, 2004), the more distantly related phytochromes of the Cph2 subfamily lack this domain altogether but are nevertheless able to support bilin attachment (Wu and Lagarias, 2000).…”

“…In more primitive plants and algae, atypical phytochromes have been described in which the C-terminal region has been replaced by fortuitous gene fusions with phototropins and other eukaryotic Ser/Thr kinases (Thü mmler et al, 1992;Nozue et al, 1998;Suetsugu et al, 2005). Bacteriophytochromes that lack recognizable kinase output domains have also been reported (Giraud et al, 2002;Karniol et al, 2005). It thus appears that the primary mechanism of light perception, arguably shared by the conserved photosensory core of all phytochromes, has been evolutionarily co-opted to regulate output domains with different molecular architectures.…”

“…In all phytochromes, the bilin chromophore precursor is covalently attached to the protein via a thioether linkage between a Cys residue and the bilin A-ring ( Figure 1A). Plant and cyanobacterial phytochromes utilize a conserved Cys residue in the P3 domain (Lagarias and Rapoport, 1980;Hü bschmann et al, 2001), whereas bacteriophytochromes (and probably fungal phytochromes) instead utilize a different Cys in the P2 region (Lamparter et al, 2004;Karniol et al, 2005;Tasler et al, 2005) (Figure 1C). Unlike the phycobiliproteins, which utilize C-S lyases for covalent attachment of their bilin chromophores (Schluchter and Glazer, 1999), plant phytochromes do not require enzymes or cofactors to assist the covalent assembly reaction (Terry et al, 1993).…”

“…Plant phytochromes (Phy family) are members of a more widespread family of photosensors that are found in cyanobacteria (cyanobacterial phytochromes Cph1 and Cph2) as well as in purple and nonphotosynthetic bacteria (bacteriophytochromes; BphP) and even fungi (fungal phytochromes; Fph family) (Montgomery and Lagarias, 2002;Blumenstein et al, 2005;Froehlich et al, 2005;Karniol et al, 2005). Members of the extended family of phytochrome proteins share a common N-terminal photosensory core, with three blocks of homology sometimes referred to as P2, P3, and P4 (Montgomery and Lagarias, 2002) (Figure 1C).…”

Evolutionary Studies Illuminate the Structural-Functional Model of Plant Phytochromes

“…Currently, high-resolution structures of the photosensory core of prokaryotic phytochromes are available; this region is homologous with the sensory module of plant phytochromes (Montgomery and Lagarias, 2002;Lamparter, 2004;Karniol et al, 2005) and consists of PAS, GAF, and PHY domains ( Figure 3B). It is necessary for photoreversibility (Rockwell et al, 2006) and is sufficient for signaling when fused with dimerization and nuclear localization signals (Matsushita et al, 2003;Oka et al, 2004).…”