8.4.2  PHY genes and classes of phytochrome operation

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Figure 8.33    The phytochrome gene family has several members with differing degrees of sequence homology (i.e. molecular similarity), indicated by the branch lengths on these diagrams. Of the Type II phytochromes (PHTB to PHYE), which are a grouping based on physiological response, PHYC appears to be genetically distinct and is more closely related to PHYA. The data are assembled from gene database information for 172 species of flowering plants. Numbers in parentheses represent the number of nucleotide sequences found in each PHY class.

(Based on Mathews and Sharrock 1997; reproduced with permission of Blackwell Science)

We now know that there are at least two main phytochrome response classes (Type I and Type II), and probably more than one gene coding for each. For example, there are five genes (PHYA to PHYE) in the model plant Arabidopsis, and seven in tomato (Smith 1995). In the past, sometimes confusing terminology has reflected our incomplete understanding of the differences between the various forms and genes. What is clear is that Type I responses relate to phytochrome A (phyA) which is the most abundant in dark-grown seedlings, up to 99% of the total phytochrome. Type I is photoreversible, but in the Pfr form phyA is also very unstable with a half-life of about 1 h, so that after exposure of a plant to a few hours of light, most of the phyA has been degraded (Clough and Vierstra 1997). Sometimes this is called ‘light-labile’ phytochrome, but degradation of Type I Pfr continues unabated in the dark. Type II (various versions coded by genes PHYB to PHYE) is present at only a few per cent of the original Type I concentration. Pfr Type II has a much longer half-life, in dark and in light. Type II phytochromes are responsible for classic photoreversible (R-promoted, FR-inhibited) processes and for sensing spectral R:FR ratios. By surveying DNA sequence homology of phytochrome genes across many species, a generic model has been developed of how closely related the various forms are, from which can be deduced their probable evolutionary history (Figure 8.33).

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