Environmental photoperception is essential to optimal growth and development of plants. In the natural environment, plants are exposed to extremes in light intensity and spectral quality and therefore must continuously optimize light capture for photosynthesis. This is accomplished by the action of phytochrome, a molecular light sensor which serves to mediate adaptive changes in gene expression, growth rate or chloroplast orientation. The recent identification and cloning of phytochrome from the cyanobacterium Synechocystis sp PCC6803 in my laboratory provides invaluable information on the structure of the photoreceptor from the simplest organism known to possess it. DNA and protein sequence comparisons with more than 25 full-length phytochromes have considerably extended models of the structure, function and evolution of this important plant photoreceptor. Our ongoing studies will lead to new information about the ancestral origin of different domains of the phytochrome mol ecule and insight into the evolution of biochemical function of this photoreceptor family. Firstly, we plan to further evaluate the significance of the roughly 250 amino acid direct repeats which comprise the C-terminus of phytochromes, the bacterial sensor proteins and the other eukaryotic protein homologs. This will be accomplished using PROFILESS and PROFILEMAKE to identify the entire superfamily of proteins, which exhibit a dual 'transmitter-like' kinase domain. Multiple sequence alignments of this superfamily using the programs MSA, CLUSTAL and SAGA will enable us to further define this new 'motif'. This information is a prerequisite for determining phylogenetic relationships between different family members with PHYLIP. Secondly, we will perform recursive Profile Searches and multiple sequence alignments of the various members of the bacterial receiver family in order to identify common structural motifs with orf2, the potential 'substrate' of the cyanobacterial phytochrome S6803phy1. This information should be useful for identification and cloning of molecules, which interact with phytochrome in plants by PCR, or through their identification in the plant EST databases. In addition, homology modeling of orf2 and cheY, for which a crystal structure is known, will be initiated. Thirdly, we will identify other homologs of the 'photosensory domain' of phytochrome by adding cyanobacterial members of this family to our peptide profiles. In this way, we hope to identify new members of this family in species hithertofore thought to lack phytochromes (e.g. yeast, insects and mammals). We will also identify potential homologs of the chromophore-binding domain of the phytochrome photoreceptor. This information should extend our understanding of the evolution and possibly biochemical function of this important photoreceptor. Fourthly, we propose to analyze the phytochrome protein sequence alignments in terms of differences rather than similarities. This type of analysis could provide new clues into regions that confer phytochrome """"""""species-specific"""""""" functions.
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