A cDNA clone encoding phytochrome (apoprotein) of the zygnematophycean green alga Mougeotia scalaris has been isolated and sequenced. The clone consisted of 3372 bp, encoded 1124 amino acids, and showed strainspecific nucleotide exchanges for M. scalaris, originating from different habitats. No indication was found of multiple phytochrome genes in Mougeotia. The 5' non-coding region of the Mougeotia PHY cDNA harbours a striking stem-loop structure. Homologies with higher-plant phytochromes were 52-53% for PHYA and 57-59% for PHYB. Highest homology scores were found with lower-plant phytochromes, for example 67% for Selaginella (Lycopodiopsida), 64% for Physcomitrella (Bryopsida) and 73% for Mesotaenium (Zygnematophyceae). In an unrooted phylogenetic tree, the position of Mougeotia PHY appeared most distant to all other known PHYs. The amino acids Gly-Val in the chromophore-binding domain (-Arg-Gly-Val-His-Gly-Cys-) were characteristic of the zygnematophycean PHYs known to date. There was no indication of a transmembrane region in Mougeotia phytochrome in particular, but a carboxyl-terminal 16-mer three-fold repeat in both, Mougeotia and Mesotaenium PHYs may represent a microtubule-binding domain. Unexpected for a non-angiosperm phytochrome, its expression was autoregulated in Mougeotia in a red/far-red reversible manner: under Pr conditions, phytochrome mRNA levels were tenfold higher than under Pfr conditions.

Following polymerase chain reaction, a fragment of about 800 bp was amplified from genomic Mougeotia DNA using oligonucleotides directed to conserved regions of known phytochrome genes. The nucleotide sequence points to a different exon/intron structure in the neighborhood of the chromophore attachment site of this Mougeotia phytochrome gene, as compared to other phytochromes. Alignment of the derived amino acid sequence to phytochromes of higher and lower plants shows highest homology (> 60%) to type II (green type) phytochrome, while Northern blot analysis of total Mougeotia RNA indicates down-regulation of the phytochrome transcription in light. Signal pattern of hybridized genomic DNA after digestion reveals the presence of probably only one phytochrome gene in Mougeotia.