Algal models in plant biology

During the last three decades, plant science has focused on model organism-based approaches, particularly on exploiting the powerful system represented by Arabidopsis thaliana, for which there are a wide range of genetic and genomic resources available. Increasingly, however, there is a tendency to broaden analyses to include multiple study organisms in an attempt to understand biological processes from an evolutionary perspective. An additional advantage of this multi-organism approach is that it has the potential to capture functional variations on a central theme as particular biological processes are likely to have been adapted to the needs of each organism. The exact nature of the organisms selected for such studies depends on the objectives of the study. For recently evolved systems, such as the regulatory processes controlling flowering, for example, the group of organisms will usually need to be quite closely related. By contrast, for ancient, more basic cellular processes such as photosynthesis or primary cell metabolism, for example, it may be of interest to compare much more widely diverged organisms. The objective of this article is to underline the potential of the diverse spectrum of eukaryote species that are grouped under the definition ‘algae’ as study organisms for the latter type of approach. The term ‘algae’ refers to all photosynthetic eukaryotes apart from land plants. Algae is a polyphyletic grouping and includes taxons in five of the eight major eukaryotic groups (Fig. 1). This very broad phylogenetic distribution of photosynthetic organisms in the eukaryotic tree is due to a combination of two factors: (i) the very ancient nature of the initial primary endosymbiotic event that occurred in the green lineage (in which a cyanobacterium was captured and enslaved to become a plastid) and (ii) the subsequent occurrence of multiple secondary and tertiary endosymbiotic events in which a photosynthetic alga was, in turn, captured by a phylogenetically unrelated heterotrophic eukaryote and itself enslaved to become a plastid within the predator cell (Armbrust, 2009; Keeling, 2010). These secondary and tertiary endosymbiotic events are particularly interesting because they have led to plastids being resident in a very diverse range of cellular contexts and because the reiterative ‘Russian doll’ capture process resulted in novel combinations of genomes due to gene transfer processes that occurred during the enslavement. Most of the key endosymbiotic events are very ancient, having occurred before the colonization of the land by photosynthetic organisms (Keeling, 2010) and many of the taxonomic groups that include algal species have no terrestrial members. The marine environment is, therefore, a potentially rich source of novel model photosynthetic organisms. Simplified schema representing the eukaryotic tree (adapted from Baldauf, 2008, with permission from the Editorial Office of the Journal of Systematics and Evolution). Groups that include photosynthetic organisms are indicated by green lettering. A single primary endosymbiotic event was at the origin of the plastids of all the members of the archaeplastida. Photosynthetic species within the stramenopiles, alveolates, haptophytes, cryptophytes, chlorarachnia, and euglenids obtained their plastids through multiple secondary or tertiary endosymbiotic events. Recent work on microalgae illustrates how these organisms are contributing to our understanding of the evolution and diversification of one key cellular process, photosynthesis. Prasinophyte algae, which are major constituents of many marine phytoplankton ecosystems, exhibit many primitive features and are therefore considered to be a basal group for the green lineage (Melkonian, 2001). The identification of a photosynthesis antenna protein that appeared to be associated with both photosystem I (PSI) and PSII initially suggested that this may have been the ancestral situation but genomic analyses showed that these organisms also possess proteins that are incorporated specifically into either PSI or PSII (Six et al., 2005). Interestingly, the PSI antennae system of red algae represents an evolutionary intermediate between the antenna system of prokaryotic cyanobacteria and those of other eukaryotes in the green lineage (Busch et al., 2010). Other intriguing photosynthesis-related phenomena that have been observed in marine phytoplankton algae include evidence for C4 photosynthesis (Reinfelder et al., 2000; Roberts et al., 2007; McGinn and Morel, 2008) and alternative carbon-concentrating mechanisms based, for example, on carbonic anhydrase, which is widespread in marine algae (Kroth et al., 2008). Along with the obvious benefits of photosynthesis as a source of energy for cellular processes, photosynthetic cells have to cope with the risks associated with the absorption of excess light, which can cause oxidative damage to the cell. Work carried out on algae in this domain have identified a remarkable diversity of responses to this problem. Despite being a member of the green lineage, the photosynthetic system of the chlorophyte alga Chlamydomonas differs in several respects from that of land plants (Finazzi et al., 2010). Recent genetic analysis has demonstrated the implication of a light-induced light-harvesting protein, LHCSR (previously called LI818), in the non-photochemical quenching (NPQ) of chlorophyll fluorescence, a mechanism that involves de-excitation of chlorophyll molecules in photosystem II (qE) (Peers et al., 2009). LHCSR proteins are absent from vascular plants, where the PsbS protein plays a major role in qE. Chlamydomonas possesses PsbS genes but the corresponding proteins have not been detected. Moreover, more distantly related algae, such as the diatoms in the chromalveolate group, appear to lack PsbS genes altogether, despite the presence of an unusual xanthophyll-based energy-dissipation system (Lohr and Wilhelm, 1999), which confers a high capacity for NPQ. LHCSR genes have, however, been found in both diatoms and in prymnesiophytes (Peers et al., 2009), although these proteins appear to function slightly differently, at least in diatoms. The Phaeodactylum tricornutum LHCSR, LHCX1, is present under non-stress conditions and modulates NPQ capacity both under stress conditions and during normal light/dark cycles (Bailleul et al., 2010). State transitions, which may provide additional photoprotection in terrestrial plants, have not been observed in diatoms (Owens, 1986). Interestingly, in at least one strain of the prasinophyte alga Ostreococcus a considerable proportion of photosynthetic electron flow is diverted through the chlororespiratory enzyme plastoquinol terminal oxidase (PTOX) (Cardol et al., 2008). It has been suggested that this innovation may allow ATP production under iron starvation conditions, although this idea has recently been contested (Rusch et al., 2010). The red algae also exhibit some unusual features related to photosynthesis. Work on the unicellular species Cyanidioschyzon merolae indicates that, in contrast to green algae and land plants, gene expression in red algal chloroplasts is controlled mainly at the transcriptional level (Apt and Grossman, 1993; Minoda et al., 2005) and that the Rubisco operon is regulated in a nucleus-independent manner in these organelles (Minoda et al., 2010). This latter feature is probably ancient, reflecting the situation at the time that the primary endosymbiosis occurred. Algae that are very distantly related to land plants, such as members of the chromalveolate lineage (which includes stramenopiles and alveolates; Fig. 1), can exhibit unusual metabolic systems due to their having retained different sets of metabolic genes during the long periods for which they have been evolving independently of their green cousins. One interesting example was the discovery of a urea cycle in diatoms (Armbrust et al., 2004), a metabolic pathway that is found in animals but has been lost from green plants and algae. The diatom urea cycle is unlikely to be involved in the production of urea as a waste molecule but is probably integrated into metabolic pathways that produce molecules such as spermine and spermidine and possibly additional long-chain polyamines involved in the precipitation of the silica that makes up the diatoms protective frustule. The recent sequencing of the complete genome of the filamentous brown alga Ectocarpus siliculosus has allowed comparative approaches to be extended to this group of algae and has provided several insights into processes that have played a key role in eukaryotic evolution. For example, inclusion of the Ectocarpus genome data in a broad comparative analysis of genome data has allowed evolutionary scenarios to be proposed for two important metabolic processes, carbon storage and cell wall biosynthesis (Michel et al., 2010,a, b). In both cases, there appear to have been major changes in the metabolic pathways present in the cells of different groups of organisms across the eukaryotic tree over evolutionary time. The recent discovery of starch in cyanobacteria indicates that starch metabolism was probably acquired by the green lineage as a result of the primary endosymbiosis (Deschamps et al., 2008,a). Several lines of evidence, including data based on genome comparisons, indicate that starch metabolism was rapidly transferred to the cytoplasm following the primary endosymbiotic event in the ancestor of the three major lines of the archaeplastida: the glaucophytes, the rhodophytes (red algae), and the chloroplastida (the green lineage). Starch metabolism was then relocated to the plastid at a later stage, but only in the chloroplastida lineage (Deschamps et al., 2008,b). However, starch metabolism is completely absent from the stramenopile lineage, despite the secondary endosymbiotic capture of a red alga. The presence of different carbon storage pathways in stramenopiles and alveolates suggests that they are derived from different secondary endosymbiotic events (Michel et al., 2010,a), and not from the single endosymbiotic event proposed by the chromalveolate hypothesis (Cavalier-Smith, 1999). Similar results were obtained with the analysis of cell wall metabolism. The cell walls of photosynthetic eukaryotes are highly diverse, reflecting both their evolutionary history and the constraints imposed by the environments in which they live (Michel et al., 2010b). For example β-1,3-glucan polymers were probably present in the common eukaryotic ancestor, whereas cellulose would have been acquired from a cyanobacterium during the primary endosymbiosis, and the alginates of brown algae via horizontal transfer from an actinobacterium. As an example of an environmental constraint, sulphated polysaccharides tend to be found predominantly in marine organisms. The presence of a flavonoid pathway in both green plants and in Ectocarpus indicates that this metabolic system evolved in their common ancestor and is, therefore, very ancient. This is not consistent with the proposition that much of the complexity of phenylpropanoid metabolism evolved in land plants after the horizontal transfer of a phenylalanine ammonia lyase gene from a bacterial genome (Emiliani et al., 2009), suggesting rather that this enzyme was integrated into a pre-existing pathway (Cock et al., 2010). The brown algae include organisms that can be considered to have evolved complex, multicellular bodyplans. This is a rare feature amongst the eukaryotes, with only a small number of eukaryote groups exhibiting complex multicellularity (Cock et al., 2010). The Ectocarpus genome was therefore of particular interest as a means to investigate the molecular basis of this phenomenon. Moreover, as complex multicellularity evolved independently in the brown algae, compared with other groups such as the green plants and animals, comparative analyses could potentially distinguish fundamental features associated with the transition to complex multicellularity from features that were contingent on the evolutionary history of each group. Three types of feature were identified that could have been associated with the evolution of complex multicellularity in the brown algae (Cock et al., 2010). The first was the retention of key genes during evolution. Three integrin-like genes and several classes of ion channel were found in the Ectocarpus genome but not in the genomes of other stramenopiles, such as the unicellular diatoms and the oomycetes, which exhibit a primative form of multicellularity. Both of these classes of gene could play important roles in functions linked to multicellularity, the integrin-like genes because of a potential role in cell–cell communication and the ion channels as components of signalling networks, which are thought to be more complex in multicellular organisms. The second type of feature that was identified was a tendency for complexity to be conserved with respect to several key gene families, including transcription factors, small GTPases, and the Rad51 gene family, which is involved in DNA repair and meiosis. This latter observation is consistent with a previous report that the Rad51 family tends to be more complete in multicellular organisms (Lin et al., 2006). Finally, evolution of novel gene families may also have played an important role in the transition to multicellularity. One of the gene families that is predicted to have evolved since the divergence from the diatoms encodes membrane-spanning receptor kinases. These are particularly interesting because the independent emergence of analogous families in the animal and green plant lineages has been associated with the transitions to complex multicellularity in these two lineages (Shui and Bleecker, 2001; Cock et al., 2002). Deep sequencing of small RNA sequences allowed the identification of 26 microRNA genes in the Ectocarpus genome. A large proportion of the putative target genes of these microRNAs encode proteins with leucine-rich repeats, many of which were predicted to have evolved since the divergence of the brown algal and diatom lineages. This is interesting because it has been suggested that the expansion of small-RNA-based gene regulatory processes may have played an important role in the evolution of complex multicellularity in animals (Peterson et al., 2009). The examples given above illustrate the potential of algae as tools to investigate the biology of photosynthetic organisms. The emergence of new algal model organisms in recent years, particularly among marine algae, is an important development that should greatly facilitate the exploitation of algal diversity for plant research. Within the green algae, complete genome sequences of two strains of the picoeukaryote Ostreococcus (Derelle et al., 2006; Palenik et al., 2007) have revealed very compact genomes with a very low level of functional redundancy, the majority of protein functions being encoded by a single gene. This feature, together with the availability of an efficient transformation protocol, makes this organism an attractive candidate for the analysis of cellular processes such as the control of circadian rhythms (Moulager et al., 2010). A complete genome sequence is available for the red alga C. merolae (Matsuzaki et al., 2004), and this organism has proved to be a powerful system for studying several aspects of cell biology including organelle division (Fujiwara et al., 2009; Yoshida et al., 2010), organelle inheritance (Fujiwara et al., 2010) and the mechanisms that co-ordinate organelle and nuclear DNA replication (Kobayashi et al., 2009). Within the stramenopiles, the diatom Phaeodactylum tricornutum is emerging as a useful cellular model, again with a complete genome sequence available (Bowler et al., 2008), several molecular tools (Siaut et al., 2007) and, more recently, the development of an RNA interference-base method for gene knockdown (De Riso et al., 2009). The brown macroalga Ectocarpus is also being developed as a model organism (Peters et al., 2004; Coelho et al., 2007) providing a novel system to study developmental processes such as the regulatory mechanisms that control the life cycle (Peters et al., 2008). As the collections of tools available for these new model organisms are gradually enlarged in the coming years, we can expect them to make many more contributions to our understanding of plant biology. We would like to thank Frédéric Partensky for critically reading the manuscript. Work on Ectocarpus in Roscoff has been supported by the Centre National de Recherche Scientifique, the French GIS ‘Institut de la Génomique Marine’, the European Union network of excellence Marine Genomics Europe, the GIS Europôle Mer, and the University Pierre and Marie Curie.