Toward systems biology in brown algae to explore acclimation and adaptation to the shore environment

Brown algae belong to a phylogenetic lineage distantly related to land plants and animals. They are almost exclusively found in the intertidal zone, a harsh and frequently changing environment where organisms are submitted to marine and terrestrial constraints. In relation with their unique evolutionary history and their habitat, they feature several peculiarities, including at the level of their primary and secondary metabolism. The establishment of Ectocarpus siliculosus as a model organism for brown algae has represented a framework in which several omics techniques have been developed, in particular, to study the response of these organisms to abiotic stresses. With the recent publication of medium to high throughput profiling data, it is now possible to envision integrating observations at the cellular scale to apply systems biology approaches. As a first step, we propose a protocol focusing on integrating heterogeneous knowledge gained on brown algal metabolism. The resulting abstraction of the system will then help understanding how brown algae cope with changes in abiotic parameters within their unique habitat, and to decipher some of the mechanisms underlying their (1) acclimation and (2) adaptation, respectively consequences of (1) the behavior or (2) the topology of the system resulting from the integrative approach.     

Development and physiology of the brown alga Ectocarpus siliculosus: two centuries of research

Brown algae share several important features with land plants, such as their photoautotrophic nature and their cellulose-containing wall, but the two groups are distantly related from an evolutionary point of view. The heterokont phylum, to which the brown algae belong, is a eukaryotic crown group that is phylogenetically distinct not only from the green lineage, but also from the red algae and the opisthokont phylum (fungi and animals). As a result of this independent evolutionary history, the brown algae exhibit many novel features and, moreover, have evolved complex multicellular development independently of the other major groups already mentioned. In 2004, a consortium of laboratories, including the Station Biologique in Roscoff and Genoscope, initiated a project to sequence the genome of Ectocarpus siliculosus, a small filamentous brown alga that is found in temperate, coastal environments throughout the globe. The E. siliculosus genome, which is currently being annotated, is expected to be the first completely characterized genome of a multicellular alga. In this review we look back over two centuries of work on this brown alga and highlight the advances that have led to the choice of E. siliculosus as a genomic and genetic model organism for the brown algae.     

ETOILE regulates developmental patterning in the filamentous brown alga Ectocarpus siliculosus

Brown algae are multicellular marine organisms evolutionarily distant from both metazoans and land plants. The molecular or cellular mechanisms that govern the developmental patterning in brown algae are poorly characterized. Here, we report the first morphogenetic mutant, étoile (etl), produced in the brown algal model Ectocarpus siliculosus. Genetic, cellular, and morphometric analyses showed that a single recessive locus, ETL, regulates cell differentiation: etl cells display thickening of the extracellular matrix (ECM), and the elongated, apical, and actively dividing E cells are underrepresented. As a result of this defect, the overrepresentation of round, branch-initiating R cells in the etl mutant leads to the rapid induction of the branching process at the expense of the uniaxial growth in the primary filament. Computational modeling allowed the simulation of the etl mutant phenotype by including a modified response to the neighborhood information in the division rules used to specify wild-type development. Microarray experiments supported the hypothesis of a defect in cell-cell communication, as primarily Lin-Notch-domain transmembrane proteins, which share similarities with metazoan Notch proteins involved in binary cell differentiation were repressed in etl. Thus, our study highlights the role of the ECM and of novel transmembrane proteins in cell-cell communication during the establishment of the developmental pattern in this brown alga.     

A REEVALUATION OF THE ZOSTEROPHYLLOPHYTINA WITH COMMENTS ON THE ORIGIN OF LYCOPODS

The primary paleobotanical literature pertaining to Zosterophyllophytina (a now extinct group of Devonian vascular plants) was reexamined for evidence concerning the activity of the apex of fertile shoots as it might be revealed by the presence or absence of terminally located sporangia (terminate or nonterminate axes, respectively). The symmetry of sporangial arrangement (radial or bilateral), the presence or absence of enations, circinate axial tips, and the shape of the vascular strand were also recorded. We found terminate axes usually are (but not invariably) associated with radial symmetry and nonterminate axes are typically bilateral in symmetry. Other morphological features are consistent with this observation, e.g., enations, circinate tips, and (when preserved) elliptic vascular strands are found in association with bilateral symmetry and nonterminate axes. We hypothesize that there are two distinct patterns of fertile axial growth within the Zosterophyllophytina. Nonetheless, all taxa currently assigned to the zosterophyllophytes share a reniform or globose sporangial shape and a distal line of dehiscence. Accordingly, we view Zosterophyllophytina as a monophyletic group of plants, whose members show two distinct patterns of growth in their fertile axes. We speculate that lycopods arose from an early zosterophyllophytelike group characterized by nonterminate, radially symmetrical fertile axes. We speculate that zosterophyllophytes with terminate fertile axes and those with nonterminate, bilaterally symmetrical fertile axes were phylogenetic deadends.     

Plant Proteus: brown algal morphological plasticity and underlying developmental mechanisms

Brown algae are multicellular photosynthetic marine organisms, ubiquitous on rocky intertidal shores at cold and temperate latitudes. Nevertheless, little is known about many aspects of their biology, particularly their development. Given their phylogenetic distance (1.6 billion years) from other plant organisms (land plants, and green and red algae), brown algae harbor a high, as-yet undiscovered diversity of biological mechanisms governing their development. They also show great morphological plasticity, responding to specific environmental constraints, such as sea currents, reduced light availability, grazer attacks, desiccation and UV exposure. Here, we show that brown algal morphogenesis is rather simple and flexible, and review recent genomic data on the cellular and molecular mechanisms known to date that can possibly account for this developmental strategy.     

Beyond bilateral symmetry: geometric morphometric methods for any type of symmetry

Background

Studies of symmetric structures have made important contributions to evolutionary biology, for example, by using fluctuating asymmetry as a measure of developmental instability or for investigating the mechanisms of morphological integration. Most analyses of symmetry and asymmetry have focused on organisms or parts with bilateral symmetry. This is not the only type of symmetry in biological shapes, however, because a multitude of other types of symmetry exists in plants and animals. For instance, some organisms have two axes of reflection symmetry (biradial symmetry; e.g. many algae, corals and flowers) or rotational symmetry (e.g. sea urchins and many flowers). So far, there is no general method for the shape analysis of these types of symmetry.

Results

We generalize the morphometric methods currently used for the shape analysis of bilaterally symmetric objects so that they can be used for analyzing any type of symmetry. Our framework uses a mathematical definition of symmetry based on the theory of symmetry groups. This approach can be used to divide shape variation into a component of symmetric variation among individuals and one or more components of asymmetry. We illustrate this approach with data from a colonial coral that has ambiguous symmetry and thus can be analyzed in multiple ways. Our results demonstrate that asymmetric variation predominates in this dataset and that its amount depends on the type of symmetry considered in the analysis.

Conclusions

The framework for analyzing symmetry and asymmetry is suitable for studying structures with any type of symmetry in two or three dimensions. Studies of complex symmetries are promising for many contexts in evolutionary biology, such as fluctuating asymmetry, because these structures can potentially provide more information than structures with bilateral symmetry.     

Pollen Organ Telangiopsis sp. of Late Devonian Seed Plant and Associated Vegetative Frond

Pollen organ Telangiopsis sp., associated with but not attached to vegetative fronds, has been collected from the Upper Devonian (Famennian) Wutong Formation, Dongzhi County, Anhui Province, China. Fertile axes with terminal pollen organs are dichotomous for 2–4 times and may be proximally attached by fragmentary pinnules. Pollen organs are synangiate and borne on the top of a short stalk. Synangia are radial in symmetry and each consists of 4–8 elongate microsporangia fused at base. Microsporangia have a longitudinal dehiscence line and show a tapered apex. The associated stem is spiny and bears a vegetative frond which bifurcates once at the basalmost part. Frond rachises possess one order of pinna arranged alternately. Pinnules are borne alternately, planate, highly dissected, and equally dichotomous for 2–3 times. Comparisons among Late Devonian seed plants recognize several branching patterns in the fertile fronds/axes bearing terminal pollen organs. Telangiopsis sp. reinforces that the Late Devonian pollen organs are synangiate usually with basally fused microsporangia. It is suggested that the evolutionary divergence of radial and bilateral symmetries of pollen organs may have occurred in the Famennian, when the earliest seed plants evolved planate and sometimes laminate pinnules.     

Dead-end evolution of the Cnidaria as deduced from 5S ribosomal RNA sequences

Using nucleotide sequences of 5S ribosomal RNAs from 2 hydrozoan jellyfishes, 3 scyphozoan jellyfishes and 2 sea anemones, a phylogenetic tree of Cnidaria has been constructed to elucidate the evolutionary relationships of radial and bilateral symmetries. The 3 classes of Cnidaria examined herein belong to one branch, which does not include other metazoan phyla such as the Platyhelminthes. The Hydrozoa (having radial symmetry without septa) and the Scyphozoa (having radial symmetry with septa) are more closely related to each other than to the Anthozoa (having bilateral symmetry with septa). In classical taxonomy, multicellular animals are considered to have evolved through organisms with radial symmetry (e.g., Cnidaria) to bilateral symmetry. Our results, however, indicate that the emergence of the Bilateria was earlier than that of the Radiata, suggesting (in opposition to Haeckel's view) that the radial symmetry of Cnidaria is an evolutionary dead end.     

Origin and Early Evolution of Plant Body Symmetry and Gravity Responses

Land plant bodies exhibit both apical–basal and radial symmetry, and they are able to detect and respond to gravitational forces. These attributes were, likely important factors in the success of earliest plants on land. This study focuses on features of charophycean green algae likely to have been pre‐adaptive to early establishment of plant symmetry and gravitational responses, though most modern charophyceans occupy aquatic habitats where the buoyancy of water counteracts the effects of gravity. Trait mapping suggests that even the earliest‐divergent modern members of the streptophyte clade have bodies whose symmetry departs significantly from the spherical condition, and that cellular mechanisms defining aspects of radial symmetry and polarized tip growth originated early. Genes, cell biological approaches, and taxa are identified for which further exploration is likely to illuminate early evolution of plant body symmetry and gravity responses.     

生长素在植物胚胎早期发育中的作用

有性生殖是有花植物的一个重要特征, 胚胎则是实现有性生殖和世代交替的重要载体。植物胚胎从双受精开始, 经历了合子极性建立、顶基轴形成、细胞层分化和器官形成等过程, 这些过程都受到生长素的调控。近年来的研究表明, 生长素在生物合成、极性运输和信号转导3个层面上调控胚胎的发育过程。该文以双子叶植物拟南芥(Arabidopsis thaliana)为例, 综述了生长素对胚胎早期发育过程, 包括合子极性和顶基轴建立、表皮原特化和对称模式转变、胚根原特化和根尖分生组织形成及茎尖分生组织形成等发育的调控机制。     

Evolutionary Trends in the Flowers of Asteridae: Is Polyandry an Alternative to Zygomorphy?

Background and Aims

Floral symmetry presents two main states in angiosperms, actinomorphy (polysymmetry or radial symmetry) and zygomorphy (monosymmetry or bilateral symmetry). Transitions from actinomorphy to zygomorphy have occurred repeatedly among flowering plants, possibly in coadaptation with specialized pollinators. In this paper, the rules controlling the evolution of floral symmetry were investigated to determine in which architectural context zygomorphy can evolve.

Methods

Floral traits potentially associated with perianth symmetry shifts in Asteridae, one of the major clades of the core eudicots, were selected: namely the perianth merism, the presence and number of spurs, and the androecium organ number. The evolution of these characters was optimized on a composite tree. Correlations between symmetry and the other morphological traits were then examined using a phylogenetic comparative method.

Key Results

The analyses reveal that the evolution of floral symmetry in Asteridae is conditioned by both androecium organ number and perianth merism and that zygomorphy is a prerequisite to the emergence of spurs.

Conclusions

The statistically significant correlation between perianth zygomorphy and oligandry suggests that the evolution of floral symmetry could be canalized by developmental or spatial constraint. Interestingly, the evolution of polyandry in an actinomorphic context appears as an alternative evolutionary pathway to zygomorphy in Asteridae. These results may be interpreted either in terms of plant–pollinator adaptation or in terms of developmental or physical constraints. The results are discussed in relation to current knowledge about the molecular bases underlying floral symmetry.Key words: Floral symmetry, architectural constraints, Asteridae, comparative analysis, composite tree, correlated evolution, evolutionary scenario     

Building divergent body plans with similar genetic pathways

Deuterostome animals exhibit widely divergent body plans. Echinoderms have either radial or bilateral symmetry, hemichordates include bilateral enteropneust worms and colonial pterobranchs, and chordates possess a defined dorsal-ventral axis imposed on their anterior-posterior axis. Tunicates are chordates only as larvae, following metamorphosis the adults acquire a body plan unique for the deuterostomes. This paper examines larval and adult body plans in the deuterostomes and discusses two distinct ways of evolving divergent body plans. First, echinoderms and hemichordates have similar feeding larvae, but build a new adult body within or around their larvae. In hemichordates and many direct-developing echinoderms, the adult is built onto the larva, with the larval axes becoming the adult axes and the larval mouth becoming the adult mouth. In contrast, indirect-developing echinoderms undergo radical metamorphosis where adult axes are not the same as larval axes. A second way of evolving a divergent body plan is to become colonial, as seen in hemichordates and tunicates. Early embryonic development and gastrulation are similar in all deuterostomes, but, in chordates, the anterior-posterior axis is established at right angles to the animal-vegetal axis, in contrast to hemichordates and indirect-developing echinoderms. Hox gene sequences and anterior-posterior expression patterns illuminate deuterostome phylogenetic relationships and the evolution of unique adult body plans within monophyletic groups. Many genes that are considered vertebrate 'mesodermal' genes, such as nodal and brachyury T, are likely to ancestrally have been involved in the formation of the mouth and anus, and later were evolutionarily co-opted into mesoderm during vertebrate development.     

Symmetry and crystallography: New facilities in the graphic software MANOSK

The new routine SYMCRY of the graphies program MANOSK is described in this paper. It is designed to analyze interactions between molecular structures related by crystalline symmetry. The symetric objects can be described in the same referential, to be manipulated as an entity, or in a referential of their own, to undergo correlative real-time movements (via the dials), given the symmetry constraints. Crystal packing can be observed, and any command of the main software MANOSK is available for the symmetric objects, including storage of the coordinates of symmetries in the final orientation.     

Automated segmentation of molecular subunits in electron cryomicroscopy density maps

Electron cryomicroscopy (cryoEM) is capable of imaging large macromolecular machines composed of multiple components. However, it is currently only possible to achieve moderate resolution at which it may be possible to computationally extract the individual components in the machine. In this work, we present application details of an automated method for detecting and segmenting the components of a large machine in an experimentally determined density map. This method is applicable to object with and without symmetry and takes advantage of global and local symmetry axes if present. We have applied this segmentation algorithm to several cryoEM data sets already deposited in EMDB with various complexities, symmetries and resolutions and validated the results using manually segmented density and available structures of the components in the PDB. As such, automated segmentation could become a useful tool for the analysis of the ever-increasing number of structures of macromolecular machines derived from cryoEM.     

Finding and using local symmetry in identifying lower domain movements in hexon subunits of the herpes simplex virus type 1 B capsid

A characteristic of virus assembly is the use of symmetry to construct a complex capsid from a limited number of different proteins. Many spherical viruses display not only icosahedral symmetry, but also local symmetries, which further increase the redundancy of their structural proteins. We have developed a computational procedure for evaluating the quality of these local symmetries that allows us to probe the extent of local structural variations among subunits. This type of analysis can also provide orientation parameters for carrying out non-icosahedral averaging of quasi-equivalent subunits during three-dimensional structural determination. We have used this procedure to analyze the three types of hexon (P, E and C) in the 8.5 A resolution map of the herpes simplex virus type 1 (HSV-1) B capsid, determined by electron cryomicroscopy. The comparison of the three hexons showed that they have good overall 6-fold symmetry and are almost identical throughout most of their lengths. The largest difference among the three lies near the inner surface in a region of about 34 A in thickness. In this region, the P hexon displays slightly lower 6-fold symmetry than the C and E hexons. More detailed analysis showed that parts of two of the P hexon subunits are displaced counterclockwise with respect to their expected 6-fold positions. The most highly displaced subunit interacts with a subunit from an adjacent P hexon (P'). Using the local 6-fold symmetry axis of the P hexon as a rotation axis, we examined the geometrical relationships among the local symmetry axes of the surrounding capsomeres. Deviations from exact symmetry are also found among these local symmetry axes. The relevance of these findings to the process of capsid assembly is considered.     

Essays on the application of nonclassical symmetries to natural biomorphs

The following symmetries are conventionally termed "nonclassical": conformal symmetry, inversion symmetry, Mikheev homology, curvilinear symmetry, colour symmetry, and antisymmetry. These symmetries are applicable to biomorphs differing in linear dimensions and proportions (such as the shells of bivalves, crustaceans, diatoms, etc.) and to such three-dimensional biomorphs as gastropod shells. These three-dimensional objects used to be substituted so far with two-dimensional images. The shift transformation causing inhomogeneous deformations is discussed in the framework of Mikheev homologies. Antisymmetry and colour symmetry are discussed by the example of flowers, duckweed plants, and the crustacean chela. Early stages of cleavage, like colloid crystals, may be represented as polyhedrons. They have Euler characteristics and face symbols, and, because of this, stages of cleavage may have symmetries of crystals. Mastering nonclassical symmetries may promote the progress of biosymmetrics. The potential of discrete (arithmetical) biomorphology in taxonomy and the potential of continuous (geomertical) biomorphology in biosymmetrics are discussed.     

Qualitative and quantitative determination of pheromone secretion in female gametes of Ectocarpus siliculosus (Phaeophyceae)

Pheromone secretion in living female gametes of Ectocarpus siliculosus was examined by closed-loop extraction and gas chromatography. The pheromone (ectocarpene) recovery efficiency was calibrated with synthetic ectocarpene and was found to depend strongly on the volume of the closed-loop system. Maximum extraction efficiency of ectocarpene (17.4%) was obtained with a small-volume system. In addition to the main compound ectocarpene, the pheromone bouquet of E. siliculosus contained minor amounts of hormosirene, multifidene and dictyotene, which until now are known only as sperm-attractants in other brown algae. The pheromone bouquet was identical in 4 clones of different geographic origins. Settled female gametes of Ectocarpus siliculosus continued to secrete pheromone and to attract male gametes for up to 7 h after their release with an ectocarpene secretion rate of 1 x 10(5) molecules s-1 cell-1.     

Symmetry of priapulids (Priapulida). 2. Symmetry of larvae

Larvae of priapulids are characterized by radial symmetry evident from both external and internal characters of the introvert and lorica. The bilaterality appears as a result of a combination of several radial symmetries: pentaradial symmetry of the teeth, octaradial symmetry of the primary scalids, 25-radial symmetry of scalids, biradial symmetry of the neck, and biradial and decaradial symmetry of the trunk. Internal radiality is exhibited by musculature and the circumpharyngeal nerve ring. Internal bilaterality is evident from the position of the ventral nerve cord and excretory elements. Externally, the bilaterality is determined by the position of the anal tubulus and two shortened midventral rows of scalids bordering the ventral nerve cord. The lorical elements define the biradial symmetry that is missing in adult priapulids. The radial symmetry of larvae is a secondary appearance considered an evolutionary adaptation to a lifestyle within the three-dimensional environment of the benthic sediment.