The phytochrome chromophore

Abstract

For vision to occur, light absorption is an absolute physical requirement. The array of photomorphogenic responses all has one thing in common: these processes are initiated only after photo excitation of a holoprotein. These holoproteins generally contain a polypeptide component and a small, light-absorbing ligand termed the chromophore. Plants have evolved an array of photoreceptor systems to detect the colour, intensity, direction, and periodicity of light. For this, a varying collection of polypeptides and associated chromophores are required. Not surprisingly, many of these receptors have been termed chromes, including the cryptic cryptochromes that detect ultra violet-B (UV-B) and blue (B) light (Lin and Shalitin, 2003), and the phyto (meaning plant) phytochromes that detect UV-B, B, red (R), and far-red (FR) light (Kevei and Nagy, 2003). Additional chromophore-bearing photoreceptors include the B-light detecting phototropins (Christie et al., 2002), the Zeitlupe family of B-light chromo proteins (Imaizumi et al., 2003), and two physiologically distinct systems that detect UV-B (Ulm et al., 2004). The protein component of these latter detection systems awaits identification (see Chapter 14). It should be noted that photosynthesis itself functions in light detection as a receptor, as light-induced redox changes in the plastid provide signalling information to the plant cell (Dietz, 2003). And finally, small molecule absorption of light is also detected by cells (Vladimirov, 1998), albeit as a photo-damage-sensing mechanism (see Chapter 14). Clearly, plants use an array of photochromic perception systems to optimise growth and development to all aspects of the ambient light environment (Sullivan and Deng, 2003). Of these higher-plant photochromic systems, the most thoroughly studied is the phytochrome family of chromoproteins. One extensively characterized group of plant photoreceptors are the R-absorbing and FR-absorbing phytochromes (phys) (see Chapter 7). This family of bilincontaining chromoproteins regulates development throughout the life cycle of plants. They play prominent roles in seed germination and de-etiolation, and control cotyledon, leaf, and stem size by regulating cell division and expansion. Phys also help plants perceive and respond to shading and crowding by neighbouring plants, entrain the circadian timer, and influence the seasonal timing of flowering. Ultimately, phys control plant senescence. Clearly phys control a diverse aspect of biology from the birth to the death of a plant. Despite the wealth of knowledge on phy structure and function, many questions remain as to the nature of it assembly. What is currently known is that phys are homodimeric chromoproteins with each subunit consisting of a linear tetrapyrrole chromophore covalently attached to each polypeptide monomer (Figure 1). The molecular mass of each monomer ranges from 118-127 kD, depending on the phy isoform and the plant species (see Chapter 7). The bilin chromophore, called phytochromobilin (PB), is attached to a ∼300 amino-acid domain within N-terminal half (Bhoo et al., 1997; Lagarias and Rapoport, 1980). Phy apoproteins can autocatalytically bind chromophore in vitro to form the spectrally active holoprotein (Li and Lagarias, 1992). Once assemble, the holoprotein dimer appears as a Y shaped molecule by electron microscopy (Jones and Erickson, 1989; Nakasako et al., 1990). The N-terminal half of phys is both necessary and sufficient for chromophore binding and the spectral properties. The C-terminal half appears to contain domains necessary for homodimerization (Matsushita et al., 2003). Phys have two conformational forms, a R-absorbing form (Pr) and a FRabsorbing form (Pfr) (Figure 2). Pr and Pfr are fully photointerconvertible upon irradiation of R and FR, respectively (Vierstra and Quail, 1983). It is thought that all phys from plants are synthesized in the Pr form, and are converted to Pfr only upon absorption of R. Because physiological responses are initiated as Pfr, this conformation is considered biologically active (see Chapter 17). Whereas FR absorption results in ∼100% photoconvertion of Pfr to Pr, both Pr and Pfr absorb R (Figure 2). This overlap in R absorption results in the total phy pool reaching a photoequilibrium of 86% Pfr and 14% Pr after a saturating R treatment (Vierstra and Quail, 1983). Phys also absorb UV-B and blue light as both Pr and Pfr. This appears to be physiological relevant, as phys assist phototropin and the cryptochromes in mediating blue-light responses (Franklin et al., 2003a), and in phys assisting the uncharacterised UV-B-perception system (Kim et al., 1998). As previously stated, the chromophore of phy is PφB. This molecule is a bile pigment, and as will be described shortly, it is derived from heme. Once the PφB chromophore assembles with a phy isoform, the resulting chromoprotein is poised to initiate photomorphogenic processes. The details of signalling and subsequent physiology are dealt with in great depth in the coming chapters. Within this chapter, I will discuss findings and continuing investigations regarding the roles of tetrapyrroles and the derived bilins in light detection and physiology. As many recent findings on this topic revolve around phy photobiology, this will be the near exclusive focus of this chapter.