Non-green Algae Research Articles

Energizing the plasmalemma of marine photosynthetic organisms: the role of primary active transport

AbstractGeneration of ion electrochemical potential differences by primary active transport can involve energy inputs from light, from exergonic redox reactions and from exergonic ATP hydrolysis. These electrochemical potential differences are important for homoeostasis, for signalling, and for energizing nutrient influx. The three main ions involved are H+, Na+(efflux) and Cl−(influx). In prokaryotes, fluxes of all three of these ions are energized by ion-pumping rhodopsins, with one archaeal rhodopsin pumping H+intothe cells; among eukaryotes there is also an H+influx rhodopsin inAcetabulariaand (probably) H+efflux in diatoms. Bacteriochlorophyll-based photoreactions export H+from the cytosol in some anoxygenic photosynthetic bacteria, but chlorophyll-based photoreactions in marine cyanobacteria do not lead to export of H+. Exergonic redox reactions export H+and Na+in photosynthetic bacteria, and possibly H+in eukaryotic algae. P-type H+- and/or Na+-ATPases occur in almost all of the photosynthetic marine organisms examined. P-type H+-efflux ATPases occur in charophycean marine algae and flowering plants whereas P-type Na+-ATPases predominate in other marine green algae and non-green algae, possibly with H+-ATPases in some cases. An F-type Cl−-ATPase is known to occur inAcetabularia. Some assignments, on the basis of genomic evidence, of P-type ATPases to H+or Na+as the pumped ion are inconclusive.

The role of Rubisco kinetics and pyrenoid morphology in shaping the CCM of haptophyte microalgae.

The haptophyte algae are a cosmopolitan group of primary producers that contribute significantly to the marine carbon cycle and play a major role in paleo-climate studies. Despite their global importance, little is known about carbon assimilation in haptophytes, in particular the kinetics of their Form 1D CO2-fixing enzyme, Rubisco. Here we examine Rubisco properties of three haptophytes with a range of pyrenoid morphologies (Pleurochrysis carterae, Tisochrysis lutea, and Pavlova lutheri) and the diatom Phaeodactylum tricornutum that exhibit contrasting sensitivities to the trade-offs between substrate affinity (Km) and turnover rate (kcat) for both CO2 and O2. The pyrenoid-containing T. lutea and P. carterae showed lower Rubisco content and carboxylation properties (KC and kCcat) comparable with those of Form 1D-containing non-green algae. In contrast, the pyrenoid-lacking P. lutheri produced Rubisco in 3-fold higher amounts, and displayed a Form 1B Rubisco kCcat-KC relationship and increased CO2/O2 specificity that, when modeled in the context of a C3 leaf, supported equivalent rates of photosynthesis to higher plant Rubisco. Correlation between the differing Rubisco properties and the occurrence and localization of pyrenoids with differing intracellular CO2:O2 microenvironments has probably influenced the divergent evolution of Form 1B and 1D Rubisco kinetics.

Evolutionary rewiring: a modified prokaryotic gene-regulatory pathway in chloroplasts

Photosynthetic electron transport regulates chloroplast gene transcription through the action of a bacterial-type sensor kinase known as chloroplast sensor kinase (CSK). CSK represses photosystem I (PS I) gene transcription in PS I light and thus initiates photosystem stoichiometry adjustment. In cyanobacteria and in non-green algae, CSK homologues co-exist with their response regulator partners in canonical bacterial two-component systems. In green algae and plants, however, no response regulator partner of CSK is found. Yeast two-hybrid analysis has revealed interaction of CSK with sigma factor 1 (SIG1) of chloroplast RNA polymerase. Here we present further evidence for the interaction between CSK and SIG1. We also show that CSK interacts with quinone. Arabidopsis SIG1 becomes phosphorylated in PS I light, which then specifically represses transcription of PS I genes. In view of the identical signalling properties of CSK and SIG1 and of their interactions, we suggest that CSK is a SIG1 kinase. We propose that the selective repression of PS I genes arises from the operation of a gene-regulatory phosphoswitch in SIG1. The CSK-SIG1 system represents a novel, rewired chloroplast-signalling pathway created by evolutionary tinkering. This regulatory system supports a proposal for the selection pressure behind the evolutionary stasis of chloroplast genes.

Inactivation of the conserved open reading frame ycf34 of Synechocystis sp. PCC 6803 interferes with the photosynthetic electron transport chain

Ycf34 is a hypothetical chloroplast open reading frame that is present in the chloroplast genomes of several non-green algae. Ycf34 homologues are also encoded in all sequenced genomes of cyanobacteria. To evaluate the role of Ycf34 we have constructed and analysed a cyanobacterial mutant strain. Inactivation of ycf34 in Synechocystis sp. PCC 6803 showed no obvious phenotype under normal light intensity growth conditions. However, when the cells were grown under low light intensity they contained less and smaller phycobilisome antennae and showed a strongly retarded growth, suggesting an essential role of the Ycf34 polypeptide under light limiting conditions. Northern blot analysis revealed a very weak expression of the phycocyanin operon in the ycf34 mutant under light limiting growth in contrast to the wild type and to normal light conditions. Oxygen evolution and P700 measurements showed impaired electron flow between photosystem II and photosystem I under these conditions which suggest that the impaired antenna size is most likely due to a highly reduced plastoquinone pool which triggers regulation on a transcriptional level. Using a FLAG-tagged Ycf34 we found that this protein is tightly bound to the thylakoid membranes. UV–vis and Mössbauer spectroscopy of the recombinant Ycf34 protein demonstrate the presence of an iron–sulphur cluster. Since Ycf34 lacks homology to known iron–sulphur cluster containing proteins, it might constitute a new type of iron–sulphur protein implicated in redox signalling or in optimising the photosynthetic electron transport chain.

REDOX PROPERTIES ARE CONSERVED IN RUBISCOS FROM DIATOMS AND GREEN ALGAE THROUGH A DIFFERENT PATTERN OF CYSTEINES1

Eukaryotic RUBISCO appears in two sequence‐diverging forms, known as red‐like (present in nongreen algae) and green‐like (of green algae and higher plants) types. Oxidation of cysteines from green‐like RUBISCOs is known to result in conformational changes that inactivate the enzyme and render a relaxed structure more prone to proteolytic attack. These changes may have regulatory value for green algae and higher plants, promoting RUBISCO catabolism under stress conditions. We compare here red‐like RUBISCOs from several diatoms with a representative green‐like RUBISCO from Chlamydomonas reinhardtii, paying special attention to the cysteine‐dependent redox properties. Purified diatom RUBISCO preparations displayed a specific carboxylase activity about one order of magnitude lower than that of the C. reinhardtii P. A. Dang. enzyme. Despite having different patterns of cysteine residues in their primary sequence, the red‐like enzymes from diatoms inactivated also through oxidation of cysteine sulfhydryls to disulfides with a transition midpoint identical to that of the green‐like forms. Cysteine oxidation resulted also in structural modifications of the diatom RUBISCOs, as recognized by a higher sensitivity of the oxidized enzyme to in vitro proteolysis. The coincident redox properties of red‐ and green‐like RUBISCO types suggest that these changes are part of a physiologically significant regulatory mechanism that has been convergently implemented in both groups with a different set of cysteine residues.

Highly Conserved Small Subunit Residues Influence Rubisco Large Subunit Catalysis

The chloroplast enzyme ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) catalyzes the rate-limiting step of photosynthetic CO(2) fixation. With a deeper understanding of its structure-function relationships and competitive inhibition by O(2), it may be possible to engineer an increase in agricultural productivity and renewable energy. The chloroplast-encoded large subunits form the active site, but the nuclear-encoded small subunits can also influence catalytic efficiency and CO(2)/O(2) specificity. To further define the role of the small subunit in Rubisco function, the 10 most conserved residues in all small subunits were substituted with alanine by transformation of a Chlamydomonas reinhardtii mutant that lacks the small subunit gene family. All the mutant strains were able to grow photosynthetically, indicating that none of the residues is essential for function. Three of the substitutions have little or no effect (S16A, P19A, and E92A), one primarily affects holoenzyme stability (L18A), and the remainder affect catalysis with or without some level of associated structural instability (Y32A, E43A, W73A, L78A, P79A, and F81A). Y32A and E43A cause decreases in CO(2)/O(2) specificity. Based on the x-ray crystal structure of Chlamydomonas Rubisco, all but one (Glu-92) of the conserved residues are in contact with large subunits and cluster near the amino- or carboxyl-terminal ends of large subunit alpha-helix 8, which is a structural element of the alpha/beta-barrel active site. Small subunit residues Glu-43 and Trp-73 identify a possible structural connection between active site alpha-helix 8 and the highly variable small subunit loop between beta-strands A and B, which can also influence Rubisco CO(2)/O(2) specificity.

A clade uniting the green algae Mesostigma viride and Chlorokybus atmophyticus represents the deepest branch of the Streptophyta in chloroplast genome-based phylogenies.

BackgroundThe Viridiplantae comprise two major phyla: the Streptophyta, containing the charophycean green algae and all land plants, and the Chlorophyta, containing the remaining green algae. Despite recent progress in unravelling phylogenetic relationships among major green plant lineages, problematic nodes still remain in the green tree of life. One of the major issues concerns the scaly biflagellate Mesostigma viride, which is either regarded as representing the earliest divergence of the Streptophyta or a separate lineage that diverged before the Chlorophyta and Streptophyta. Phylogenies based on chloroplast and mitochondrial genomes support the latter view. Because some green plant lineages are not represented in these phylogenies, sparse taxon sampling has been suspected to yield misleading topologies. Here, we describe the complete chloroplast DNA (cpDNA) sequence of the early-diverging charophycean alga Chlorokybus atmophyticus and present chloroplast genome-based phylogenies with an expanded taxon sampling.ResultsThe 152,254 bp Chlorokybus cpDNA closely resembles its Mesostigma homologue at the gene content and gene order levels. Using various methods of phylogenetic inference, we analyzed amino acid and nucleotide data sets that were derived from 45 protein-coding genes common to the cpDNAs of 37 green algal/land plant taxa and eight non-green algae. Unexpectedly, all best trees recovered a robust clade uniting Chlorokybus and Mesostigma. In protein trees, this clade was sister to all streptophytes and chlorophytes and this placement received moderate support. In contrast, gene trees provided unequivocal support to the notion that the Mesostigma + Chlorokybus clade represents the earliest-diverging branch of the Streptophyta. Independent analyses of structural data (gene content and/or gene order) and of subsets of amino acid data progressively enriched in slow-evolving sites led us to conclude that the latter topology reflects the true organismal relationships.ConclusionIn disclosing a sister relationship between the Mesostigmatales and Chlorokybales, our study resolves the long-standing debate about the nature of the unicellular flagellated ancestors of land plants and alters significantly our concepts regarding the evolution of streptophyte algae. Moreover, in predicting a richer chloroplast gene repertoire than previously inferred for the common ancestor of all streptophytes, our study has contributed to a better understanding of chloroplast genome evolution in the Viridiplantae.

An evolution-based analysis scheme to identify CO2/O2 specificity-determining factors for ribulose 1,5-bisphosphate carboxylase/oxygenase

Ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCo) catalyzes a rate-limiting step in photosynthetic carbon assimilation (reacting with CO2) and its competitive photo-respiratory carbon oxidation (reacting with O2). RuBisCo enzyme with an enhanced CO2/O2 specificity would boost the ability to make great progress in agricultural production and environmental management. RuBisCos in marine non-green algae, resulting from an earlier endo-symbiotic event, diverge greatly from those in green plants and cyanobacteria and, further, have the highest CO2/O2 specificity whereas RuBisCos in cyanobacteria have the lowest. We assumed that there exist different levels of CO2/O2 specificity-determining factors, corresponding to different evolutionary events and specificity levels. Based on this assumption, we devised a scheme to identify these substrate-determining factors. From this analysis, we are able to discover different categories of the CO2/O2 specificity-determining factors that show which residue substitutions account for (relatively) small specificity changes, as happened in green plants, or a tremendous enhancement, as observed in marine non-green algae. Therefore, the analysis can improve our understanding of molecular mechanisms in the substrate specificity development and prioritize candidate specificity-determining surface residues for site-directed mutagenesis.

Algae lacking carbon-concentrating mechanisms

Most of the algae and cyanobacteria that have been critically examined express a carbon-concentrating mechanism (CCM) when grown at, or below, the current atmospheric CO2 concentration. This paper considers algae that appear to lack a CCM. Critical examination of the evidence on which the presence or absence of a CCM is decided shows that more information is frequently needed before the criteria can be fully applied. Examples are the pathways of glycolate metabolism in nongreen algae, and the 13C/12C discrimination shown by form ID Rubisco in vitro. The available evidence suggests that the algae lacking CCMs are some terrestrial green microalgae, some florideophyte freshwater red macroalgae, and a number of florideophyte red macroalgae from the supralittoral, littoral, and sublittoral, and almost all of the freshwater chrysophytes and synurophytes examined. Certain environmental, biochemical, and biophysical factors may permit the occurrence of algae lacking CCMs. The absence of CCMs is presumably the plesiomorphic (i.e., ancestral) condition in cyanobacteria (and algae?).Key words: CO2 diffusion, chrysophyte algae, ecology, evolution, green algae, photosynthesis, red algae.

Chimeric Small Subunits Influence Catalysis without Causing Global Conformational Changes in the Crystal Structure of Ribulose-1,5-bisphosphate Carboxylase/Oxygenase,

Comparison of subunit sequences and X-ray crystal structures of ribulose-1,5-bisphosphate carboxylase/oxygenase indicates that the loop between beta-strands A and B of the small subunit is one of the most variable regions of the holoenzyme. In prokaryotes and nongreen algae, the loop contains 10 residues. In land plants and green algae, the loop is comprised of approximately 22 and 28 residues, respectively. Previous studies indicated that the longer betaA-betaB loop was required for the assembly of cyanobacterial small subunits with plant large subunits in isolated chloroplasts. In the present study, chimeric small subunits were constructed by replacing the loop of the green alga Chlamydomonas reinhardtii with the sequences of Synechococcus or spinach. When these engineered genes were transformed into a Chlamydomonas mutant that lacks small-subunit genes, photosynthesis-competent colonies were recovered, indicating that loop size is not essential for holoenzyme assembly. Whereas the Synechococcus loop causes decreases in carboxylation V(max), K(m)(O(2)), and CO(2)/O(2) specificity, the spinach loop causes complementary decreases in carboxylation V(max), K(m)(O(2)), and K(m)(CO(2)) without a change in specificity. X-ray crystal structures of the engineered proteins reveal remarkable similarity between the introduced betaA-betaB loops and the respective loops in the Synechococcus and spinach enzymes. The side chains of several large-subunit residues are altered in regions previously shown by directed mutagenesis to influence CO(2)/O(2) specificity. Differences in the catalytic properties of divergent Rubisco enzymes may arise from differences in the small-subunit betaA-betaB loop. This loop may be a worthwhile target for genetic engineering aimed at improving photosynthetic CO(2) fixation.

Alanine-scanning mutagenesis of the small-subunit beta A-beta B loop of chloroplast ribulose-1,5-bisphosphate carboxylase/oxygenase: substitution at Arg-71 affects thermal stability and CO2/O2 specificity.

Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) enzymes from different species differ with respect to carboxylation catalytic efficiency and CO2/O2 specificity, but the structural basis for these differences is not known. Whereas much is known about the chloroplast-encoded large subunit, which contains the alpha/beta-barrel active site, much less is known about the role of the nuclear-encoded small subunit in Rubisco structure and function. In particular, a loop between beta-strands A and B contains 21 or more residues in plants and green algae, but only 10 residues in prokaryotes and nongreen algae. To determine the significance of these additional residues, a mutant of the green alga Chlamydomonas reinhardtii, which lacks both small-subunit genes, was used as a host for transformation with directed-mutant genes. Although previous studies had indicated that the betaA-betaB loop was essential for holoenzyme assembly, Ala substitutions at residues conserved among land plants and algae (Arg-59, Tyr-67, Tyr-68, Asp-69, and Arg-71) failed to block assembly or eliminate function. Only the Arg-71 --> Ala substitution causes a substantial decrease in holoenzyme thermal stability. Tyr-68 --> Ala and Asp-69 --> Ala enzymes have lower K(m)(CO2) values, but these improvements are offset by decreases in carboxylation V(max) values. The Arg-71 --> Ala enzyme has a decreased carboxylation V(max) and increased K(m)(CO2) and K(m)(O2) values, which account for an observed 8% decrease in CO2/O2 specificity. Despite the fact that Arg-71 is more than 20 A from the large-subunit active site, it is apparent that the small-subunit betaA-betaB loop region can influence catalytic efficiency and CO2/O2 specificity.

Activation of Rubisco from non-green algae

The CO2 fixing enzyme d-ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) requires both CO2 and Mg2+ for its activation. A molecule of CO2, distinct from the substrate CO2, binds to the e -lysyl amino group of a conserved lysine residue at the active site, forming a carbamate that completes an anionic binding site for the Mg2+. This metal-coordinated carbamate appears to be the general base that carries out several proton abstractions that are essential to the catalytic sequence, a function without precedent elsewhere in biology. Formation of the activated enzyme-CO2-Mg2+ (ECM) complex reaches an equilibrium governed by the CO2 and Mg2+ concentrations: The product of the dissociation constants for CO2 and Mg2+, KcKMg, therefore dictates the extent of activation of Rubisco at particular CO2 and Mg2+ concentrations. It has recently been found that certain non-green algae have Rubiscos with more efficient kinetic properties than those of higher-plant Rubiscos. Consequently, attention has focused on these Rubiscos as potential candidates for transfection into higher plants. Nothing, however, is known about the activation properties of non-green-algal Rubiscos and whether they would be suitable to the conditions prevailing in higher-plant chloroplasts. The carbamylation equilibrium of Rubisco was measured under varying CO2 and Mg2+ concentrations using a method that exploits the difference in binding affinity of the reaction-intermediate analog, 2?-carboxy-d-arabinitol-1,5-bisphosphate, to carbamylated and uncarbamylated active sites. A comparison of data for non-green-algal and higher-plant Rubiscos will be presented.

Microbial ribulose 1,5-bisphosphate carboxylase/oxygenase: A different perspective

Marine and terrestrial photosynthetic and chemoautotrophic microorganisms assimilate considerable amounts of carbon dioxide. Like green plastids, the predominant means by which this process occurs is via the Calvin-Benson-Bassham reductive pentose phosphate pathway, where ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) plays a paramount role. Recent findings indicate that this enzyme is subject to diverse means of control, including specific and elaborate means to guarantee its high rate and extent of synthesis. In addition, powerful and specific means to regulate Rubisco activity is a characteristic feature of many microbial systems. In many respects, the diverse properties of microbial Rubisco enzymes suggest interesting strategies to elucidate the molecular basis of CO2/O2 specificity, the ‘holy grail’ of Rubisco biochemistry. These systems thus provide, as the title suggests, ‘different perspectives’ to this fundamental problem. These include vast possibilities for imaginative biological selection using metabolically versatile organisms with well-defined genetic transfer capabilities to solve important issues of Rubisco specificity and molecular control. This review considers the major issues of Rubisco biochemistry and regulation in photosynthetic microoganisms including proteobacteria, cyanobacteria, marine nongreen algae, as well as other interesting prokaryotic and eukaryotic microbial systems recently shown to possess this enzyme.

The diversity and coevolution of Rubisco, plastids, pyrenoids, and chloroplast-based CO2-concentrating mechanisms in algae

Algae have adopted two primary strategies to maximize the performance of Rubisco in photosynthetic CO2fixation. This has included either the development of a CO2-concentrating mechanism (CCM), based at the level of the chloroplast, or the evolution of the kinetic properties of Rubisco. This review examines the potential diversity of both Rubisco and chloroplast-based CCMs across algal divisions, including both green and nongreen algae, and seeks to highlight recent advances in our understanding of the area and future areas for research. Overall, the available data show that Rubisco enzymes from algae have evolved a higher affinity for CO2when the algae have adopted a strategy for CO2fixation that does not utilise a CCM. This appears to be true of both Green and Red Form I Rubisco enzymes found in green and nongreen algae, respectively. However, the Red Form I Rubisco enzymes present in nongreen algae appear to have reduced oxygenase potential at air level of O2. This has resulted in a photosynthetic physiology with a reduced potential to be inhibited by O2and a reduced need to deal with photorespiration. In the limited number of microalgae that have been examined, there is a strong correlation between the existence of a high-affinity CCM physiology and the presence of pyrenoids in all algae, highlighting the potential importance of these chloroplast Rubisco-containing bodies. However, in macroalgae, there is greater diversity in the apparent relationships between pyrenoids and chloroplast features and the CCM physiology that the species shows. There are many examples of microalgae and macroalgae with variations in the presence and absence of pyrenoids as well as single and multiple chloroplasts per cell. This occurs in both green and nongreen algae and should provide ample material for extending studies in this area. Future research into the function of the pyrenoid and other chloroplast features, such as thylakoids, in the operation of a chloroplast-based CCM needs to be addressed in a diverse range of algal species. This should be approached together with assessment of the coevolution of Rubisco, particularly the evolution of Red Form I Rubisco enzymes, which appear to achieve superior kinetic characteristics when compared with the Rubisco of C3higher plants, which are derived from green algal ancestors.Key words: Rubisco, CO2-concentrating mechanism, carbonic anhydrase, aquatic photosynthesis, algae, pyrenoids, inorganic carbon.

Distribution of fallover in the carboxylase reaction and fallover-inducible sites among ribulose 1,5-bisphosphate carboxylase/oxygenases of photosynthetic organisms.

The biphasic reaction course, fallover, of carboxylation catalysed by ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO) has been known as a characteristic of the enzyme from higher land plants. Fallover consists of hysteresis in the reaction seen during the initial several minutes and a very slow suicide inhibition by inhibitors formed from the substrate ribulose-1,5-bisphosphate (RuBP). This study examined the relationship between occurrence of fallover and non-catalytic RuBP-binding sites, and the putative hysteresis-inducible sites (Lys-21 and Lys-305 of the large subunit in spinach RuBisCO) amongst RuBisCOs of a wide variety of photosynthetic organisms. Fallover could be detected by following the course of the carboxylase reaction at 1 mM RuBP and the non-catalytic binding sites by alleviation of fallover at 5 mM RuBP. RuBisCO from Euglena gracilis showed the same linear reaction course at both RuBP concentrations, indicating an association between an absence of fallover and an absence of the non-catalytic binding sites. This was supported by the results of an equilibrium binding assay for this enzyme with a transition state analogue. Green macroalgae and non-green algae contained the plant-type, fallover enzyme. RuBisCOs from Conjugatae, Closterium ehrenbergii, Gonatozygon monotaenium and Netrium digitus, showed a much smaller decrease in activity at 1 mM RuBP than the spinach enzyme and the reaction courses of these enzymes at 5 mM RuBP were almost linear. RuBisCO of a primitive type Conjugatae, Mesotaenium caldariorum, showed the same linear course at both RuBP concentrations. Sequencing of rbcL of these organisms indicated that Lys-305 was changed into arginine with Lys-21 conserved.

On the delineation and higher-level classification of algae

Biological classification has been successively shaped by Neoplatonism, ideas of plenitude and one-dimensional continuity (the Great Chain of Being), two-dimensional continuity (Linnaeus's map), idealized comparative morphology and development and, through phylogenetic theory, Darwinian descent with modification. Concepts of Algae have thus evolved within a succession of very different paradigms. Algae have been imperfect plants; a segment of the Great Chain; the least-developed members of vegetative form-series; and primitive forms from which plants (and even animals) can be elaborated. The idea of a single grouping of simple organisms, formalized by Bory de Saint-Vincent and others in the early nineteenth century, was developed in a phylogenetic framework by Haeckel as Protista. Most macrophytic algae, however, remained Plants until Copeland merged eukaryotic non-green algae into Protista. Arrangements of algal taxa within form-series, and recognition of Algae and Protista as taxa, are incompatible with Hennigian phylogenetic systematics (cladistics). Developing genomic perspectives threaten to undermine established concepts of organismal lineage and higher-level biological classification.

On the delineation and higher-level classification of algae

Biological classification has been successively shaped by Neoplatonism, ideas of plenitude and one-dimensional continuity (the Great Chain of Being), two-dimensional continuity (Linnaeus's map), idealized comparative morphology and development and, through phylogenetic theory, Darwinian descent with modification. Concepts of Algae have thus evolved within a succession of very different paradigms. Algae have been imperfect plants; a segment of the Great Chain; the least-developed members of vegetative form-series; and primitive forms from which plants (and even animals) can be elaborated. The idea of a single grouping of simple organisms, formalized by Bory de Saint-Vincent and others in the early nineteenth century, was developed in a phylogenetic framework by Haeckel as Protista. Most macrophytic algae, however, remained Plants until Copeland merged eukaryotic non-green algae into Protista. Arrangements of algal taxa within form-series, and recognition of Algae and Protista as taxa, are incompatible with Hennigian phylogenetic systematics (cladistics). Developing genomic perspectives threaten to undermine established concepts of organismal lineage and higher-level biological classification.

Plastid genomes of three non-green algae are sequenced

Plastid genomes of three non-green algae are sequenced

Gene phylogenies and the endosymbiotic origin of plastids

The endosymbiotic origin of chloroplasts from cyanobacteria has long been suspected and has been confirmed in recent years by many lines of evidence. Debate now is centered on whether plastids are derived from a single endosymbiotic event or from multiple events involving several photosynthetic prokaryotes and/or eukaryotes. Phylogenetic analysis was undertaken using the inferred amino acid sequences from the genes psbA, rbcL, rbcS, tufA and atpB and a published analysis (Douglas and Turner, 1991) of nucleotide sequences of small subunit (SSU) rRNA to examine the relationships among purple bacteria, cyanobacteria and the plastids of non-green algae (including rhodophytes, chromophytes, a cryptophyte and a glaucophyte), green algae, euglenoids and land plants. Relationships within and among groups are generally consistent among all the trees; for example, prochlorophytes cluster with cyanobacteria (and not with green plastids) in each of the trees and rhodophytes are ancestral to or the sister group of the chromophyte algae. One notable exception is that Euglenophytes are associated with the green plastid lineage in psbA, rbcL, rbcS and tufA trees and with the non-green plastid lineage in SSU rRNA trees. Analysis of psbA, tufA, atpB and SSU rRNA sequences suggests that only a single bacterial endosympbiotic event occurred leading to plastics in the various algal and plant lineages. In contrast, analysis of rbcL and rbcS sequences strongly suggests that plastids are polyphyletic in origin, with plastids being derived independently from both purple bacteria and cyanobacteria. A hypothesis consistent with these discordant trees is that a single bacterial endosymbiotic event occurred leading to all plastids, followed by the lateral transfer of the rbcLS operon from a purple bacterium to a rhodophyte.

Organization of the chloroplast genome in the red alga Porphyra yezoensis

A comprehensive assessment of the origin and evolution of plastids will require more information on the nature of plastid genomes from non-green algae. I have constructed a physical map of the chloroplast genome from the red alga Porphyra yezoensis. The 185 kb circular genome contains ribosomal RNA encoding inverted repeats (6.6 kb), and is divided into small and large singlecopy regions of approxiamtely 16 kb and 156 kb respectively. The Porphyra genome contains several genes not found in higher plant chloroplasts. Genes encoding the pigmented, light-harvesting phycobiliproteins are organized relatively close to one another on the genome, and represent components of a multi-gene family. the phycocyanin biliprotein genes (ppcBA) map in two single-copy regions, suggesting either duplicated genes or a transsplicing mechanism. In contrast to higher plants, the tufA and rbcS genes are chloroplast-encoded in Porphyra, and rbcS is clustered with the rbcL gene, suggesting an operon type of arrangement. The Porphyra chloroplast genome is distinctive, also, in that part of it has sequence homology to plasmid-like DNA molecules which co-isolate with the chloroplast DNA.