Sequence similarities of phytochrome to protein kinases: implication for the structure, function and evolution of the phytochrome gene family

Abstract

Phytochrome, the best characterised plant photoreceptor, is encoded by a small multigene family within the plant kingdom. The different phytochrome types are composed of a conserved light-sensing chromophore domain of about 80 kDa and a less-conserved C-terminal domain of about 50 kDa. The C-terminus of phytochrome of the moss Ceratodon purpureus is homologous to the catalytic domain of eukaryotic serinelthreonine or tyrosine protein kinases; in contrast, for all other phytochromes (conventional phytochromes) sequence similarities within the C-terminal domain to the catalytic domain of bacterial histidine kinases have been reported. We performed careful sequence comparisons of the putative catalytic domains of phytochrome with each other, with authentic serine/threonine, tyrosine and with histidine kinases. We report that conventional phytochromes exhibit structural elements of the catalytic domains of both histidine and, to a lesser extent, of serine/threonine and tyrosine kinases. The significance of these observations is discussed in the framework of the structure, function and evolution of phytochrome.

Characterization and expression of the phytochrome gene family in the moss Ceratodon purpureus

“…We have provisionally called the new phytochrome gene CpPHY2. The 3Ј coding region of CpPHY2 is homologous to the catalytic domain of two-component transmitter histidine kinases, a typical feature of conventional-type phytochromes (Schneider-Poetsch et al, 1991;Thü mmler et al, 1995a) and exhibits about 85% nucleotide sequence identity to conventional-type phytochrome from the moss Physcomitrella (X75025; Kolukisaoglu et al, 1993). ZAPc23 also represents a 5Ј-truncated cDNA clone (Figure 1).…”

“…Intron 1 is present at the identical location in CpPHY1, intron 2 of CpPHY2, which is located close to an additional intron found in soybean PHYB (Hughes et al, 1996), is close to intron 2 present in CpPHY1; intron 2 marks the transition point of the chromophore and the kinase domain in CpPHY1 (Thü mmler et al, 1992(Thü mmler et al, , 1995a. Intron 1 and 2 sequences are not conserved in CpPHY1 and 2, but the 5Ј coding regions of CpPHY1 and 2 (chromophore domains) are very well conserved (96% sequence identity over 777 amino acids); additionally, 102 nucleotides within the 5Ј UTRs of CpPHY1 and 2 (-102 to 0) are 100% conserved.…”

A possible tyrosine phosphorylation of phytochrome

“…Based on sequence analyses of phytochromes from various species, it has previously been proposed by Schneider-Poetsch and colleagues [30,31], and more recently by Thfimmler et al [32], that phytochrome may function as a protein-tyrosine kinase. Schneider-Poetsch's proposal was based on the observation that a C-terminal portion of phytochromes from various species share an approx.…”

“…However, biochemical support in favor of this hypothesis has not been forthcoming and mutational analyses of the conserved histidine present in oat phytochrome A, as well as mutagenesis of other nearby residues that are conserved between all known phytochromes and the bacterial sensor proteins, failed to produce altered phenotypes when expressed in transgenic Arabidopsis [2]. The more recent proposal of Thfimmler et al [32] notes limited sequence homologies between the C-terminal domains of various phytochromes and the catalytic domains of eukaryotic histidine, serine/threonine and tyrosine kinases, but does not present experimental verification of this proposal. Although our results neither prove nor refute these hypotheses, they do suggest that further investigations are warranted.…”

Fundamental and biotechnological applications of phytochrome transgenes

“…In addition to bound chromophore, phytochrome activity requires a sequence in the COOH-terminus, as a 68 kDa NH2-terminal fragment that contained the chromophore-binding region was spectrally active but lacked light-mediated inhibition of hypocoty] elongation (Boylan & Quail 1991). Catalytic activity has been attributed to the COOH-terminal region of phytochrome, based on homology with bacterial sensor proteins (Schneider-Poetsch 1992; Thummler et al 1995).…”