Phytochrome: If It Looks and Smells Like a Histidine Kinase, Is It a Histidine Kinase?

That's all fine and good for cyanobacterial phytochrome, but the real excitement has to do with potential functional homology of plant phytochromes. Specifically, do plant phytochromes possess histidine kinase activity and what then do we make of phytochrome-associated serine kinase activity? As discussed by Quail 1997xQuail, P.H. BioEssay. 1997; 19: 571–579Crossref | PubMedSee all ReferencesQuail 1997, while there is presently no experimental evidence supporting the hypothesis that higher plant phytochromes are histidine kinases, this question must still be considered unresolved. In any case, whether or not they have histidine kinase activity, it is clear from sequence analysis and the discovery of Cph1 that plant phytochromes are evolutionarily related to histidine kinases. Given this, and assuming that phytochrome-associated serine kinase activity is intrinsic to the photoreceptor, there are two general models that seem most probable in accounting for serine kinase activity in a histidine kinase–related protein. The first model postulates that plant phytochromes, and perhaps other proteins like SpoIIAB and the mitochondrial protein kinases, represent nonorthodox members of the sensor kinase family that have altered their substrate specificity from histidines to serines (Figure 2AFigure 2A). In this case, the phosphorylated serines would be expected to be stable regulatory modifications rather than intermediates in phosphotransfer reactions due to the comparatively low energy of a phosphoester bond. As discussed previously, phytochrome autophosphorylation would presumably be a down-regulation mechanism; however, this would not preclude the existence of other substrates for phytochrome kinase activity. In this model then, phytochromes would be functionally similar to the eukaryotic protein serine/threonine/tyrosine kinase family even though they are evolutionarily related to histidine kinases.Figure 2Models of Phytochrome Kinase Activity(A) TKD1 and/or TKD2 directly catalyze the ATP-dependent phosphorylation of an N-terminal serine resulting in the down-regulation of phytochrome activity. A possible mechanism for this down-regulation would be inhibiting phytochrome kinase activity toward a subsequent signaling component X.(B) TKD1 and/or TKD2 exhibit true histidine kinase activity and catalyze the ATP-dependent phosphorylation of a nonconsensus phytochrome histidine residue. The phosphate moiety is subsequently transferred to an N-terminal serine resulting in the down-regulation of phytochrome activity. A possible mechanism for this down-regulation would be by inhibiting phosphotransfer to a response regulator X involved in the signaling pathway.View Large Image | View Hi-Res Image | Download PowerPoint SlideThe alternative model is that plant phytochromes are true histidine kinases that autophosphorylate on a nonconsensus histidine, but the phosphate moiety is then transferred to the N-terminal serine residue (Figure 2BFigure 2B). As previously noted, (Quail 1997xQuail, P.H. BioEssay. 1997; 19: 571–579Crossref | PubMedSee all ReferencesQuail 1997) there are examples of sensor kinases like CheA that autophosphorylate on nonconsensus histidines. Furthermore, there is precedence for the proposed histidine to serine phosphotransfer reaction. CheY mutants lacking the phosphate-accepting aspartate are phosphorylated by CheA on a hydroxy amino acid presumably due to proximity and the high phosphotransfer potential of a phosphohistidine (Bourret et al. 1990xBourret, R.B, Hess, F, and Simon, M.I. Proc. Natl. Acad. Sci. USA. 1990; 87: 41–45Crossref | PubMedSee all ReferencesBourret et al. 1990). One would predict that such a reaction could be favored if an internal hydroxy amino acid were properly spaced and configured relative to a phosphorylated histidine residue. In this regard, we note that the serine phosphorylated in plant phytochromes resides in a 60–100 amino acid N-terminal extension not found in Cph1 (Figure 1DFigure 1D), suggesting that this domain has a function unique to eukaryotic phytochromes. One could envision this model working either with or without a conventional response regulator. In either case, we once again postulate that phytochrome autophosphorylation would serve as a down-regulation mechanism. If response regulators were not involved in signaling, this reaction might simply be an internal feedback mechanism that may or may not have higher levels of regulation beyond phytochrome photoconversion. If response regulators were involved in phytochrome signaling, the N-terminal serine might be acting as an alternate substrate when the response regulator was not available (e.g., due to its subsequent signaling function) or when it was already phosphorylated (Figure 2BFigure 2B). Presently, the proposed histidine-to-serine phosphotransfer reaction in this model can be tested by systematically mutating all phytochrome histidine residues and assaying for an effect on N-terminal serine phosphorylation. Alternatively, the postulated histidine autophosphorylation may be more readily detected in phytochromes where the known serine phosphorylation site was mutated.In summary, we believe that the recurring connections between phytochromes and protein kinases cannot be coincidental and must be indicative of functional importance. Although it is clear that plant phytochromes arose from an ancestral prokaryotic histidine kinase, the fact that they seem to exhibit serine kinase activity indicates that they are atypical members of this superfamily. Therefore, the extent of functional homology between plant phytochromes and histidine kinases is still in question. Resolution of these ambiguities will mark an important step in our understanding of phytochrome function. This obviously is a required step if phytochrome signal transduction involves phosphorylation of subsequent pathway components.