Phytochromes

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 [59]. 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 [60]. 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 [61].

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) [62]. 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 [11]. The conformational differences between Pr and Pfr have been observed using several techniques, including limited proteolysis, cysteine labeling, circular dichroism, and chromatography [63]. Gartner and Bra-slavsky have recently written a review of the molecular basis of bilin photochemistry and the role of the photochrome protein [64].

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) [69]. 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 [65].

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 [68].

COOH COOH

COOH COOH

3E-phytochromobilin (POB)

COOH COOH

COOH COOH

Fig. 5.8 Phytochrome autocatalytically forms adducts with phytochromobilin (PUB) as well phycobilin analogs, such as phytocyanobilin (PCB). The bilins are covalently attached by means of a thioester bond through the site, indicated with the arrow, and photoisomerize around the C15=C16 double bond.

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