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COMPUTER SEQUENCE ANALYSIS OF PHYTOCHROME J. Sühnel (jsuehnel@imb-jena.de) Biocomputing, Institute of Molecular Biotechnology, Beutenbergstraße 11, D-07745 Jena G. Hermann (bgh@pop3.uni-jena.de ) Institute of Biochemistry and Biophysics, Friedrich Schiller University Jena, Philosophenweg 12, D-07743 Jena Introduction Materials and Methods Results and Discussion Identification of segments with non-random amino acid composition Sequence similarities between phytochromes and other proteins Motifs Multiple sequence alignment Secondary structure prediction References Introduction The understanding of the mechanism through which phytochrome exerts its biological action is still hampered by the fact that its three-dimensional structure is not known. Indirect structural information was primarily obtained from biochemical and genetic approaches (for more details see Rüdiger and Thümmler, 1991; Furuya and Song, 1994; Quail et al., 1995; Quail, 1997; Song et al., 1997). In the last few years, methods of computer sequence analysis were also used in order to gain new insights into the structure of phytochrome. The results obtained so far suggest, e.g., a structural domain model (Romanowski and Song, 1992) and a three dimensional atomic model of a short sequence region around the chromophore binding site (Parker et al., 1994). Moreover, they indicate that phytochrome might be a light-regulated protein kinase (Schneider-Poetsch et al., 1991; Schneider-Poetsch, 1992). This proposal was further supported on the basis of striking sequence homologies between phytochrome and a regulatory protein of the chromatic adaptation in cyanobacteria which itself is structurally related to sensor histidine kinases (Kehoe and Grossman, 1996). Since over the past years steadily improved methods of computer sequence analysis have been developed and the databases have considerably increased in size, we have recently applied a repertoire of computer methods to the current databases in order to update the information available from sequence analysis (Sühnel et al., 1997). The results obtained are given in full detail on a phytochrome web site of the IMB Jena World-Wide Web server (http://www.imb-jena.de/PHYTO.html). A few selected findings are presented here.