COMPUTER-ANALYSIS OF PHYTOCHROME SEQUENCES AND REEVALUATION OF THE PHYTOCHROME SECONDARY STRUCTURE BY FOURIER-TRANSFORM INFRARED-SPECTROSCOPY

A repertoire of various methods of computer sequence analysis was appl ied to phytochromes in order to gain new insights into their structure and function, A statistical analysis of 23 complete phytochrome seque nces revealed regions of non-random amino acid composition, which are supposed to be of particular structural or functional importance. All phytochromes other than phyD and phyE from Arabidopsis have at least o ne such region at the N-terminus between residues 2 and 35. A sequence similarity search of current databases indicated striking homologies between all phytochromes and a hypothetical 84.2-kDa protein from the cyanobacterium Synechocystis. Furthermore, scanning the phytochrome se quences for the occurrence of patterns defined in the PROSITE database detected the signature of the WD repeats of the beta-transducin famil y within the functionally important 623-779 region (sequence numbering of phyA from Avena) in a number of phytochromes. A multiple sequence alignment performed with 23 complete phytochrome sequences is made ava ilable via the IMB Jena World-Wide Web server (http://www.imb-jena.de/ PHYTO.html). It can be used as a working tool for future theoretical a nd experimental studies. Based on the multiple alignment striking sequ ence differences between phytochromes A and B were detected directly a t the N-terminal end, where all phytochromes B have an additional stre tch of 15-42 amino acids. There is also a variety of positions with to tally conserved but different amino acids in phytochromes A and B. Mos t of these changes are found in the sequence segment 150-200. It is, t herefore, suggested that this region might be of importance in determi ning the photosensory specificity of the two phytochromes. The seconda ry structure prediction based on the multiple alignment resulted in a small but significant beta-sheet content. This finding is confirmed by a reevaluation of the secondary structure using FTIR spectroscopy. (C ) 1997 Elsevier Science B.V.