Light perception in plants is governed by a series of photoreceptors that can be classified into three groups - the phytochromes, cryptochromes, and phototro-pins. Originally phytochromes were defined as the receptors that were responsible for the red and far-red reversible, plant responses . However they have also been found in bacteria (even in nonphotosynthetic bacteria). They are typically homodimers consisting of two polypeptides with a molecular weight of ~125 kDa, each containing a linear tetrapyrrole (bilin) chromophore that is covalently linked to a conserved cysteine by a thioether bond. Attachment of the bilin prosthetic group is autocatalytic. Phytochromes typically form covalent adducts with phyto-chromobilin (PUB) but can also bind other phycobilin analogs (see Fig. 5.8). The bilins adopt cyclic porphyrin-like conformations in aqueous solution. Upon association with proteins they form more extended conformations that alter the pathways for light deexcitation . The open chain bilin has 64 isomers that differ in their methine bridge configurations (Z/E) and conformations (syn(s)/anti(a)). Phytochromes undergo a cis/trans photoisomerization of the bilin, which leads to substantial changes in the conformation that presumably results in the photo-signaling response that regulates plant growth and development .
One of the distinguishing characteristics of phytochromes is a reversible photoisomerization between a red light-absorbing form known as Pr (kmax = 666 nm), and the far red-absorbing form termed the Pfr form (kmax = 730 nm) . Depending on the species, either Pr or Pfr can be the active form. Photoreversible reactions such as this one play a key role in signal transduction; besides being found in phytochromes they also have an important function in sensory rhodopsin I and photoactive yellow protein . The conformational differences between Pr and Pfr have been observed using several techniques, including limited proteolysis, cysteine labeling, circular dichroism, and chromatography . Gartner and Bra-slavsky have recently written a review of the molecular basis of bilin photochemistry and the role of the photochrome protein .
Although there is no crystal structure of phytochromes, they have been the focus of numerous spectroscopic studies [65,66]. Several intermediates have been trapped by time-resolved experiments in both the Pr:Pfr and the Pfr:Pr interconversions. The Pr:Pfr steady-state ratio is determined by the incident light. It is commonly accepted that the bilin adopts a ZZZ/asa configuration/conformation in Pr that converts to ZZE/ass in Pfr Conformational changes of the protein backbone are required to maintain the high-energy Pfr state. The first step(s) in the photoconversion is a rapid isomerization (picoseconds) around the C15=C16 double bond (see Fig. 5.8). This is followed by a series of slower conformational changes (micro- and milliseconds) that occur in the dark phase. In oat phytochrome (PhyA) three intermediates have been found in the PrgPfr conversion (lumi-R, meta-Ra, and meta-Rc) and two were found in the reverse reaction (lumi-F and meta-F) [67,68].
Recently a combination of resonance Raman spectroscopy and density functional calculations has been used to examine the conformations of the phytochro-mobilin structure of photochrome phyA (oat) . They conclude that the chromophore is in the ZZZasa configuration, and that the reaction cycle is initiated by a ZZZasa (Pr) fi ZZEasa (Lumi-R) photoisomerization followed by thermal relaxation steps that include at least a partial a to s single bond rotation at the methane bridge A-B. This may explain the change in hydrogen bonding of the C=O group of ring A that occurs with the formation of the Pfr precursor meta-Rc .
If phytochromobilin (PUB) is replaced with phycocyanobilin (PCB) the photochemistry remains the same as described above. However if the D ring of the chromophore is modified then differences in the time-course of the photoreaction are observed .
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