Evolutionary conservation of plant gibberellin signalling pathway components
© Vandenbussche et al; licensee BioMed Central Ltd. 2007
Received: 03 August 2007
Accepted: 29 November 2007
Published: 29 November 2007
Gibberellins (GA) are plant hormones that can regulate germination, elongation growth, and sex determination. They ubiquitously occur in seed plants. The discovery of gibberellin receptors, together with advances in understanding the function of key components of GA signalling in Arabidopsis and rice, reveal a fairly short GA signal transduction route. The pathway essentially consists of GID1 gibberellin receptors that interact with F-box proteins, which in turn regulate degradation of downstream DELLA proteins, suppressors of GA-controlled responses.
Arabidopsis sequences of the gibberellin signalling compounds were used to screen databases from a variety of plants, including protists, for homologues, providing indications for the degree of conservation of the pathway. The pathway as such appears completely absent in protists, the moss Physcomitrella patens shares only a limited homology with the Arabidopsis proteins, thus lacking essential characteristics of the classical GA signalling pathway, while the lycophyte Selaginella moellendorffii contains a possible ortholog for each component. The occurrence of classical GA responses can as yet not be linked with the presence of homologues of the signalling pathway. Alignments and display in neighbour joining trees of the GA signalling components confirm the close relationship of gymnosperms, monocotyledonous and dicotyledonous plants, as suggested from previous studies.
Homologues of the GA-signalling pathway were mainly found in vascular plants. The GA signalling system may have its evolutionary molecular onset in Physcomitrella patens, where GAs at higher concentrations affect gravitropism and elongation growth.
Gibberellins (GAs) are a large family of hormones that are important for a vast array of responses throughout the life cycle of plants. They mainly stimulate germination, cause cell expansion, and regulate flowering time. Due to their high economical relevance, the effects of GAs on cell elongation are subject to intense scientific studies. The green revolution was based on selection for dwarfism in rice and wheat cultivars. Recently it was shown that these dwarfing genes interfere with either the production or the action of GAs . Chemical interference with GA biosynthesis is often used to limit the growth of plants, including trees . GAs were first isolated from Gibberella (Fusarium) fujikuroi . This fungus causes extreme extension growth in rice, named bakanae or "foolish" rice, which hence is far more susceptible to lodging.
Apart from Gibberella, other fungi (Phaeospheria, Aphaceloma sp.) and various bacteria  are able to synthesize GAs. GAs were consequently found in many plant species and are widespread over photosynthesizing organisms. GA-like substances were detected in unicellular and multicellular algae [5–7], in lichens and mosses , and in ferns  But most of all, they are widely accepted as general growth controlling hormones in seed plants .
Presence of GAs in an organism does not necessarily mean that it is responsive to these compounds. For instance, Gibberella itself does not react to exogenous GA . Depending on the species of unicellular algae, GA can slightly increase the biomass . The effects of GAs on elongation growth of unicellular algae are either very small or absent in most species . However, growth increases were reported for the multicellular alga Porphyra in the diploid, filamentous sporophyte conchocelis phase and, in combination with auxin, in stolons of Ulva lactuca [10, 11].
While ABA, auxin, and cytokinin induce specific developmental alterations in mosses like Physcomitrella patens, no such effects have been reported for GA-application [12, 13]. However, some older reports do exist, that GA-application on specific moss species may slightly enhance growth rates [14, 15]. In addition GA-application may interfere with gravitropism in the mosses Ceratodon purpureus  and Pottia intermedia . In fact, to date gibberellins have not been identified in mosses, and it was proposed that the hormonal signalling pathway developed later in land plant evolution . However, as such pathways do not appear completely de novo, precursors from which GA may have been evolved should be present in mosses. Ent-kaurene is the key intermediate in the biosynthesis of gibberellins. Recently, it was shown, that P. patens produces as a secondary metabolite such a tetracyclic diterpene as a volatile compound in huge amounts , and possesses a bifunctional ent-kaurene synthase .
To our knowledge, no reports are available for GA regulated growth in ferns. In contrast, their stimulatory effect on elongation and germination has been extensively documented for seed plants, such as conifers [20, 21] and angiosperms, both mono- and dicotyledonous plants.
Sex determination is another known GA effect. In species as Chara, GA promote antheridia (male sex organ) formation . Likewise, they serve as promoters for antheridia formation in some ferns [23, 24]. Interestingly, in many eudicotyledonous plants as well, GAs promote male flower development . By contrast, in the monocot maize, they promote female flower formation .
Over the last few years, three plant genomes have been entirely sequenced [34–36] and a lot of effort is made to unravel the gene pool of "genomically more complex" plants by expressed sequenced tag (EST) sequencing and assembly. With the variety of open access EST and genome sequence databases, it becomes possible to perform comparative genomics and molecular phylogenetic analysis on a large number of species at a time (plantGDB, ). Based on the aforementioned tools, we investigated the conservation of the GA pathway formed by GID1, SLY1 and DELLA proteins from algae and plants throughout the plant kingdom, using reference species for different major plant groups (Figure 1B). Existing orthologues were retrieved from various higher plants, but are missing from Physcomitrella patens (Pp). The presence of the GA signalling pathway could thus be linked exclusively with vascular plants.
The gibberellin receptors
The GA receptors (GID1) belong to the large family of hormone sensitive lipases and have homologues throughout the plant kingdom, since they are related in sequence to various carboxylesterases . Moreover, the predicted 3D structure of these proteins is similar. However, the GA receptors contain various regions, which distinguish them from their carboxylesterase relatives [28, 38]. Amino acid Arg265 is typically present, while the His340 residue from the catalytic site of the esterases is missing in GID1 proteins.
The seedless vascular plant Selaginella moellendorffii (belonging to the phylum of Lycopodiophyta) has a protein that appears a genuine GA receptor orthologue. It has an overall good aligment (47% similarity) and in contrast to the protein from Pp, it contains the Arg265 residue. It also has a conserved Ile in position 340 instead of a His, typical for known GA receptors.
From the analysis of a limited EST set (~8000) of the fern Adianthum capillus veneris (phylum Pteridophyta, order Polypodiales), we concluded that it has related carboxylesterases, all with the conserved His340 necessary for esterase activity. Yet the EST collection is too small to firmly exclude the existence of genuine GA receptor orthologues.
The SLEEPY homologues
No (E < 1e-4) homologues to the F-box protein SLY1 were found in Chlamydomonas reinhardtii, nor Cyanidioschyzon merolae using TBlastX.
From Selaginella, a protein could be retrieved with homology to the SLY1 over its whole length, including a leucine rich box at the C-terminal end (Figure 4). A reciprocal blast indicates that the protein can be considered as an orthologue of those of higher plants (similarity 51%).
The EST database from the fern Ceratopteris only yielded an F-box protein with a divergent C-terminal end (data not shown). F-box proteins are thus present in ferns, but SLY1 orthologues remain to be discovered.
DELLA related transcription factors
DELLA proteins belong to the GRAS (GAI, RGA, SCARECROW) protein family, specific to plants . The cDNA sequence of RGA1 of Arabidopsis was used in a TBLASTX screen for homologues in other species.
No DELLA homologues (yield is 0 with E = 1e-4) were detected in Cyanidioschyzon merolae or Chlamydomonas reinhardtii.
In contrast, Selaginella contains a clear RGA1 orthologue. The protein (Figure 6) was reconstructed from the genomic sequence, since the matching ESTs do not cover the N-terminal part, possibly due to absence of that part in the EST library. Parts of the sequence from the genomic reconstruction, may represent introns, although the EST that covers the C-terminal part (from position 340 onward in Figure 6) has the same sequence as the genomic.
From a limited EST set (~6000) of the fern Ceratopteris richardii, we only found a scarecrow-like gene (AY974159) as closest homologue to RGA1. However, as for SLY1, considering the small size of the EST collection we cannot exclude the existence of DELLA orthologues in ferns.
It is noteworthy that there are more ESTs with homology to DELLA coding sequences; however, these lack the N-terminal part spanning the DELLA domain (see Additional file 1). This may be either due to a lack of the 5'end of the coding sequence within the available EST collections or simply because some proteins contain only homology to the C-terminal part .
Effect of exogenous GA treatment on Physcomitrella growth
Where on an evolutionary scale did the GA signalling pathway arise?
A central node in evolutionary plant research may be the investigation of mosses for which Pp stands model [47, 48]. GAs are present in various moss species . At present no data on GA content of Physcomitrella are available, but homologues to key enzymes (genes GA1-GA5 of Arabidopsis) of the GA biosynthetic pathway were found (data not shown). Although Physcomitrella has homologues to all three GA signalling components, it is questionable whether they are true orthologues. It is therefore likely that gibberellin signalling does not function in mosses as in vascular plants. Divergence from SLY1 of the F-box protein sequence outside of the F-box, and absence of homology to the "DELLA" region in the closest relative of RGA1, may indicate the existence of other recognition motives between the DELLA-like transcription factor and the SLY1/GID2-like F-box protein. In addition, the DELLA-like protein of Physcomitrella may not be functioning as a GA-regulated repressor of GA response as it is stable upon GA treatment when expressed in Arabidopsis . It could rather play a regulatory role in plant development, being stable upon GA treatment, similarly to the SLR-like GRAS proteins of rice . Furthermore, since "genuine" GA responses in Physcomitrella, e.g. stimulation of growth, are missing, this class of hormones might be less effective in mosses. However, exogenous gibberellins are effective in stimulating growth of seta from the liverwort Pellia epiphylla, suggesting the existence of gibberellin signalling earlier in evolution .
In conclusion, mosses may have lost the capacity of effective GA signalling or use an alternative system to that of vascular plants to pass on the signal. Whether this involves the homologues to the vascular plant pathway is not known. In the future, it may be interesting to study Chara, an even more primitive embryophyte than Physcomitrella, which was reported to be GA-responsive .
The lycophyte Selaginella moellendorffii has clear orthologues for all components of the GA pathway and is to our present knowledge the most primitive species to possess a full-potentially functional – GA signalling pathway; however, phenotypic responses still need to be discovered . Hence, as suggested in earlier studies by its apical growth that is restricted to the sporophyte, the presence of vascular tissue, the formation of roots and leaves, and even by its genome sequences [50, 51], Selaginella is closely related to seed plants. This is confirmed at the level of the molecular components of GA signalling.
GA signalling in non vascular plants?
If the effects shown in those early studies are indeed true GA effects, then it may be that mosses and other clades lost their capacity to respond to GAs (hypothesis 2 in Figure 9). It is however also possible that non-vascular plants have adopted other mechanisms than those operating in vascular plants to pass on the GA signal, eventually serving for other, yet to be discovered, responses. Assuming that GA signalling as we know it is typical for vascular plants, and that non-vascular species have other compounds and an other mechanism to trigger GA-like responses, a parallel with the evolution of GA biosynthesis may exist. The fungus Gibberella has a totally different enzyme set to synthesize GAs than plants . It has therefore been proposed that the synthesis of GAs is a case of convergent evolution in fungi and plants, involving paralogues rather than orthologues.
In ferns, we found homologues to members of the carboxylesterase and scarecrow-like gene families, to which respectively the GA receptors and the DELLA transcription factors belong. Considering the presence of GA responses in ferns  and the limited number of EST sequences available, it can be reasonably assumed that in the future, orthologues to GA signalling components will be found.
Gibberellin as sex determinant
Apart from a possible role in elongation, it is interesting that in non-seed plants as ferns and even Chara, and in some eudicotyledonous plants, male organs are promoted by GAs [23, 25]. At this moment it is not known whether the same receptor, F-box, and DELLA components are involved both in elongation growth and in sex determination. The first function of GAs may have been the stimulation of male gametophyte function. It is therefore possible that GA signalling arose as a sex determinant in the first place. The GA receptors were first implemented as part of the carboxylesterase family, showing homology to PrMC3. Intriguingly, PrMC3 was originally isolated from and shown to be expressed specifically in male cones of Pinus radiata . Future molecular physiological research is necessary to unravel the importance of this family of carboxylesterases in plants and the reason why some of their members are present especially in (male) reproductive organs.
The gibberellin signalling pathway as it is known for Arabidopsis and rice is well conserved in lycophytes, gymnosperms and angiosperms, which reflects a wide spreading among land plants known to date. However, except perhaps for the receptor, the pathway components seem to be missing in the moss Physcomitrella, which indicates that bryophytes may have the evolutionary onset to respond efficiently to gibberellins, which yields other responses (e.g. gravitropism) than in vascular plants. No nuclear EST or genome sequences are available from other non vascular plants and protists such as Charales, nor from multicellular algae, and only limited in ferns. But, a large amount of EST collections and BAC clones of a variety of organisms is awaiting sequencing (CUGI, Clemson, SC). As more genomes will have been sequenced, a more complete picture of the phylogeny of GA signalling will be drawn.
Arabidopsis cDNA sequences from the GID1b, SLY1, and RGA genes were taken from the TAIR website. These sequences were used to search for homologues by tBlastx with default parameters against the unigene collection of Tigr, the citrus HarvEST database (Wanamaker and Close, University of California), the Cosmoss transcriptome and genome (with an eight times sequencing coverage) databases (Stefan Rensing, University Freiburg, Germany), the PHYSCOBASE database , the Selaginella databases at Purdue University , the Cyanidioschyzon merolae database of Tokyo University , the loblolly pine ESTs from the CCGB of the University of Minnesota, the Cycas EST collection from the New York Botanical Garden and the sequenced EST collection of Adiantum capillis veneris, Marchantia polymorpha, Welwitschia mirabilis, Ceratopteris richardii, Mesostigma viridae gathered at plantGDB. Tables with reference numbers can be found in supplemental data (see Additional files 1, 2, 3).
Reconstruction of protein sequences
Retrieved ESTs from Selaginella moellendorffii were used to scan the Sellaginella genome for homologous sequences. 5' and 3' ends were taken to virtually walk over the chromosomes and isolate clones covering about 10 kbp around the original EST (which is homologous to the Arabidopsis sequence). For the Physcomitrella patens F-box protein, the same approach was used. For the the DELLA homologue, the Arabidopsis protein sequences were directly used to scan the genome traces of the Cosmoss dbase (Stefan Rensing, University Freiburg). The retrieved clones (see Additional files 4, 5, 6) were submitted to a PHRAP process to yield contigs. From these contigs, proteins were derived by doing an in silico translation . The Pp F-box protein homologue and DELLA homologue translated as a single exon from the Cosmoss database. A Pp receptor homologue had a predicted intron between R157 and R158 (Figure 2). The predicted intron was left out in the reconstructed protein and was 2 bp out of frame at the 3'end. For the aligment in Figure 2, the sequence of Physcobase contig 12981 was used. In silico translation was also applied to the ESTs from pine. Open reading frames were detected and checked for homology with the original Arabidopsis proteins in a BlastP.
Protein alignments were performed using ClustalW algorithms included in the VectorNTI package (Invitrogen). Multiple alignments of coding sequences and ESTs were done on line, using ClustalW at  (Kyoto University Bioinformatics Center) using default parameters and choosing the PHYLIP output. Neigbour-Joining trees were generated at . Various control runs were done using IUB (at ), Dialign in the Panta rhei package ; University of Bielefeld, Germany) and MAVID  alignment protocols. All controls yielded similar results. Similarity values were calculated with VectorNTI software (Invitrogen).
Gibberellin treatments of Physcomitrella
Physcomitrella patens (Hedw.) B.S.G. was cultured in liquid and solid Knop medium as described earlier . GA3 was purchased by Duchefa (Haarlem, The Netherlands) and a 0.25 M stock solution was prepared in EtOH. For the treatments 5 μl of freshly subcultured moss protonema in liquid culture with a dry weight of 100 mg/l were placed on Knop plates containing 0, 10, 100, 500 and 1000 μM GA3 or control plates containing the corresponding amount of EtOH. After one week of growth at normal conditions (25°C, 16 h light with 55 μmol/sm2, 8 h darkness) the plates were covered with aluminium foil and put upright for 7 days. For documentation the plants were photographed.
gibberellin insensitive dwarf, a GA receptor
SLEEPY, an F-box protein involved in the GA signalling pathway
Repressor of ga1
- one of the DELLA proteins:
acting as a repressor of GA response
Filip Vandenbussche is a post-doctoral fellow of the Research Foundation Flanders (FWO). DVDS and RR acknowledge the Research Foundation Flanders (FWO G.0313.05) and DFG (RE837/7) respectively, for financial support. The authors thank Dr. J. Banks (Purdue University) for access to the Selaginella database.
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