Partial nucleotide sequence of phytochrome from the zygnematophycean green alga Mougeotia

Algal photoreceptors: in vivo functions and potential applications

Many algae, particularly microalgae, possess a sophisticated light-sensing system including photoreceptors and light-modulated signaling pathways to sense environmental information and secure the survival in a rapidly changing environment. Over the last couple of years, the multifaceted world of algal photobiology has enriched our understanding of the light absorption mechanisms and in vivo function of photoreceptors. Moreover, specific light-sensitive modules have already paved the way for the development of optogenetic tools to generate light switches for precise and spatial control of signaling pathways in individual cells and even in complex biological systems.

Red light and calmodulin regulate the expression of the psbA binding protein genes in Chlamydomonas reinhardtii

In the unicellular green alga Chlamydomonas reinhardtii, translation of the chloroplast-encoded psbA mRNA is regulated by the light-dependent binding of a nuclear-encoded protein complex (RB38, RB47, RB55 and RB60) to the 5'-untranslated region of the RNA. Despite the absence of any report identifying a red light photoreceptor within this alga, we show that the expression of the rb38, rb47 and rb60 genes, as well as the nuclear-encoded psbO gene that directs the synthesis of OEE1 (oxygen evolving enhancer 1), is differentially regulated by red light. Further elucidation of the signal transduction pathway shows that calmodulin is an important messenger in the signaling cascade that leads to the expression of rb38, rb60 and psbO, and that a chloroplast signal affects rb47 at the translational level. While there may be several factors involved in the cascade of events from the perception of red light to the expression of the rb and psbO genes, our data suggest the involvement of a red light photoreceptor. Future studies will elucidate this receptor and the additional components of this red light signaling expression pathway in C. reinhardtii.

Phytochrome of the green alga Mougeotia: cDNA sequence, autoregulation and phylogenetic position

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.

Atypical phytochrome gene structure in the green alga Mesotaenium caldariorum

The phytochrome photoreceptor in the green alga Mesotaenium caldariorum is encoded by a small family of highly related genes. DNA sequence analysis of two of the algal phytochrome genes indicates an atypical gene structure with numerous long introns. The two genes, termed mesphy1a and mesphy1b, encode polypeptides which differ by one amino acid in the region of overlap that was sequenced. RT-PCR studies have established the intron-exon junctions of both genes and show that both are expressed. RNA blot analysis indicates a single transcript of ca. 4.1 kb in length. The deduced amino acid sequence of the mesphy1b gene reveals that the photoreceptor consists of 1142 amino acids, with an overall structure similar to other phytochromes. Phylogenetic analyses indicate that the algal phytochrome falls into a distinct subfamily with other lower plant phytochromes. Profile analysis of an internal repeat found within the central hinge region of the phytochrome polypeptide indicates an evolutionary relatedness to the photoactive yellow protein from the purple bacterium Ectothiorhodospira halophila, to several bacterial sensor kinase family members, and to a family of eukaryotic regulatory proteins which includes the period clock (per) and single-minded (sim) gene products of Drosophila. Since mutations which alter phytochrome activity cluster within the region delimited by these direct repeats (P.H. Quail et al., Science 268 (1995): 675-680), this conserved motif may play an important role in the signal transducing function of these disparate protein families.

Homology at the amino acid level between plant phytochromes and a regulator of asexual sporulation in Emericella (= Aspergillus) nidulans

Protein sequence comparison between the N-terminal regions of the BRLA (bristle A) protein of the ascomycete fungus Aspergillus nidulans and a number of plant phytochromes has demonstrated a moderate level of sequence similarity. The region of similarity corresponds to the phytochrome domains believed to be responsible for photoreception and which undergo light-induced conformational changes, although a putative chromophore-binding site is not evident. Over 22% of residues are conserved and 24% conservatively substituted between residues 1 and 272 of BRLA and the N-terminal domains of Type 1 phytochromes from dicotyledonous species. A lower level of similarity, but over the same region, is observed in comparison with a wider range of phytochromes. Given the known role of BRLA as a transcriptional activator involved in conidiation, and the red/far-red reversible photoregulation of this developmental process, the similarity with phytochromes may be significant.

Mosses do express conventional, distantly B-type-related phytochromes. Phytochrome of Physcomitrella patens (Hedw.)

We have screened a cDNA library of the moss Physcomitrella patens (Hedw.) for phytochrome sequences. The isolated sequences turned out to encode a phytochrome dissimilar to the phytochrome type postulated for the moss Ceratodon [(1992) Plant Mol. Biol. 20, 1003-1017] Physcomitrella phytochrome was completely alignable to fern phytochrome (Selaginella) and phytochromes of higher plants. The frequency of clones encoding this phytochrome indicated that a Ceratodon-like type should only be expressed, if at all, with lower frequencies than the sequenced phytochrome cDNA. Sequence differences between lower plant phytochromes are small as compared to phytochrome types of higher plants.

Phytochrome evolution: a phylogenetic tree with the first complete sequence of phytochrome from a cryptogamic plant (Selaginella martensii spring)

We have sequenced cDNA and genomic clones coding for phytochrome of the fern Selaginella. On the amino acid level, this phytochrome shares sequence homologies with phytochromes of higher plants which range between 62 (phytochrome B of Arabidopsis) and 55 (56)% [phytochrome C of Arabidopsis (Avena)]. Introns in the Selaginella gene are short and occupy positions known from phytochrome sequences of higher plants. A rooted phylogenetic tree based on mutation distances puts Selaginella phytochrome closest to the hypothetical ancestor. A similar tree arises if the tree is constructed with partial sequences (about 200 amino acids) around the chromophore attachment site. An extension of this tree by sequences of other cryptogamic plants (Mougeotia, Ceratodon, Psilotum) shows all these sequences including those of the phytochromes B and C of Arabidopsis on a branch, well separated from the branch formed by phytochromes known to accumulate in etiolated plants. The rooted phytochrome phylogenetic tree, however, is difficult to reconcile with the fossil record.