Structure of the Rubisco operon from the unicellular red alga Cyanidium caldarium: evidence for a polyphyletic origin of the plastids

Transcriptome analysis of the effects of different carbon dioxide concentrations on paramylon accumulation in Euglena gracilis Z

Appropriate concentration of carbon dioxide (CO2) will promote algae growth and metabolism. Building upon this finding, the present study investigated the impact of different CO2 concentrations (5% and 20%) on the carbon sequestration capacity of E. gracilis through aeration culturing, employing a combination of physiological analyses and transcriptome analysis. The results demonstrated that under 5% CO2 concentration, the cell density of E. gracilis was 1.79 times higher than that achieved in an air culture condition, and the paramylon content of E. gracilis was found to be 6.18 times higher than that of the air group. Based on transcriptome analysis, the carbon metabolism of E. gracilis was discussed. Significant up-regulation expression of genes associated with carbon synthesis was validated by an increase in paramylon content. This study revealed that under 5% CO2 conditions, E. gracilis exhibited elevated growth rate and enhanced photosynthetic carbon assimilation efficiency.

Differential expression of rubisco in sporophytes and gametophytes of some marine macroalgae

Rubisco (ribulose-1, 5-bisphosphate carboxylase/oxygenase), a key enzyme of photosynthetic CO(2) fixation, is one of the most abundant proteins in both higher plants and algae. In this study, the differential expression of Rubisco in sporophytes and gametophytes of four seaweed species--Porphyra yezoensis, P. haitanensis, Bangia fuscopurpurea (Rhodophyte) and Laminaria japonica (Phaeophyceae)--was studied in terms of the levels of transcription, translation and enzyme activity. Results indicated that both the Rubisco content and the initial carboxylase activity were notably higher in algal gametophytes than in the sporophytes, which suggested that the Rubisco content and the initial carboxylase activity were related to the ploidy of the generations of the four algal species.

Cross species applicability of abundant protein depletion columns for ribulose-1,5-bisphosphate carboxylase/oxygenase

In plants, ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is an important enzyme in the Calvin cycle, catalyzing the first step of carbon fixation. Because of its critical role in photosynthesis, RuBisCO comprises 30-60% of the total protein content in green leaf tissue and represents a major protein which can interfere with determination of lower abundance proteins in plant proteomics. A potential solution to aid in the determination of low level proteins in plant proteomics are RuBisCO immunodepletion columns. Two formats, spin and LC, of Seppro IgY RuBisCO depletion columns were evaluated for cross species applicability. The spin and LC columns were found to deplete arabidopsis RuBisCO by greater than 90 and 98%, respectively, and automation could be achieved with the LC format. Canola RuBisCO was depleted to a similar extent, and there was evidence suggesting that corn and tobacco RuBisCO were also highly depleted in flow through fractions. Model proteins were spiked into samples to provide insight into the degree of non-specific binding. Finally, improved detection and identification of lower abundance proteins was demonstrated after depletion.

Shopping for plastids

Recent suggestions that endosymbionts in a diatom and an amoeba represent independent origins of plastids from those in plants and algae raise again the question of how many times plastids have evolved. In this Opinion article, we review the evidence for a single origin or multiple origins of primary plastids. Although the data are widely taken as supporting a single origin, we stress the assumptions underlying that view, and argue for a more cautious interpretation. We also suggest that the implicit view of plastids being acquired from single ancestors at a single point (or points) in time is an over-simplification.

Speciation and biogeography of the Caloglossa leprieurii complex (Delesseriaceae, Rhodophyta)

Studies on the morphology, reproductive compatibility, life cycle and molecular phylogeny of the euryhaline red alga Caloglossa provide insights into the speciation events and biogeographic patterns. The C. leprieurii complex is separated into three morphotypes based on the number of cell rows at nodes and the blade width. The three morphotypes are reproductively incompatible with each other, and furthermore many mating groups are recognized within the morphotypes. Incomplete reproductive isolation is occasionally seen between geographically distant mating groups, whereas no sexual compatibility occurs between sympatrically or parapatrically distributed mating groups. In the molecular phylogenetic analyses, the C. leprieurii complex is resolved as two clusters that phenotypically correspond to the single and multiple cell row types, respectively. The strains belonging to the same mating group are closely related to each other, without exception, while the mating groups showing incomplete reproductive reactions do not always make a clade. The genetic distance is generally not correlative to the geographic distance, and this is also suggested by the morphological data and crossability. These results indicate that allopatric speciation has frequently occurred in this species complex, although there is some evidence of long-distance dispersal.

Form I Rubiscos from non-green algae are expressed abundantly but not assembled in tobacco chloroplasts

Non-green algae have Rubiscos that are phylogenetically distinct from their counterparts in green algae and higher plants. Some non-green-algal Rubiscos are more specific for CO2, relative to O2, than higher-plant Rubiscos, sometimes coupled with lower Michaelis constants for CO2. If these Rubiscos could be substituted for the higher-plant enzyme, and if they functioned successfully in the higher-plant chloroplast and were regulated appropriately, they would improve the CO2 use and quantum efficiency of higher-plant photosynthesis. To assess the feasibility of expressing non-green algal Rubiscos in higher-plant chloroplasts, we inserted the rbcLS operons from the rhodophyte Galdieria sulphuraria and the diatom Phaeodactylum tricornutum into the inverted repeats of the plastid genome of tobacco, leaving the tobacco rbcL gene unaltered. Homoplasmic transformants were selected. The transgenes directed the synthesis of abundant amounts of transcripts and both subunits of the foreign Rubiscos. In some circumstances, leaves of the transformants with the P. tricornutum Rubisco contained as much foreign Rubisco protein as endogenous tobacco Rubisco (>30% of the soluble leaf protein). However, the subunits of the foreign Rubiscos were not properly folded and/or assembled. All the foreign large subunits and most of the foreign small subunits were recovered in the insoluble fractions of leaf extracts. Edman sequencing yielded the expected N-terminal sequences for the foreign small subunits but the N-termini of the foreign large subunits were blocked. Accumulation of large amounts of denatured foreign Rubisco in the leaves, particularly of the P. tricornutum transformants, caused a reduction in the amount of tobacco Rubisco present, with concomitant reductions in leaf CO2 assimilation and plant growth.

A model for the evolution of the plastid sec apparatus inferred from secY gene phylogeny

Plastids possess a bacteria-like sec apparatus that is involved in protein import into the thylakoid lumen. We have analyzed one of the genes essential for this process, secY. A secY gene from the unicellular red alga Cyanidium caldarium was found to be transcriptionally active, demonstrating for the first time that secY is functional in a plastid. Unlike the situation seen in bacteria the C. caldarium gene is transcribed monocistronically, despite the fact that it is part of a large ribosomal gene cluster that resembles bacterial spc operons. A molecular phylogeny is presented for 8 plastid-encoded secY genes, four of which have not been published yet. In this analysis plastid secY genes fall into two classes. One of these, comprising of genes from multicellular red algae and Cryptophyta, clusters in a neighbour-joining tree with a cyanobacterial counterpart. Separated from the aforesaid are secY genes from Chromophyta, Glaucocystophyta and a unicellular red alga. All plastid and cyanobacterial sequences are located on the same branch, separated from bacterial homologues. We postulate that the two classes of secY genes are paralogous, i.e. their gene products are involved in different protein translocation processes. Based on this assumption a model for the evolution of the plastid sec apparatus is presented.

Isolation, characterization and chromosomal mapping of an actin gene from the primitive red alga Cyanidioschyzon merolae

Based on the results of cytological studies, it has been assumed that Cyanidioschyzon merolae does not contain actin genes. However, Southern hybridization of C. merolae cell-nuclear DNA with a yeast actin-gene probe has been suggested the presence of an actin gene in the C. merolae genome. In the present study, an actin gene was isolated from a C. merolae genomic library using a yeast actin-gene probe. The C. merolae actin gene has no intron. The predicted actin is composed of 377 amino acids and has an estimated molecular mass of 42 003 Da. Southern hybridization indicated that the C. merolae genome contains only one actin gene. This gene is transcribed at a size of 2.4 kb. When Southern hybridization was performed with C. merolae chromosomes separated by pulsed-field gel electrophoresis, a band appeared on unseparated chromosomes XI and XII. A phylogenetic tree based on known eucaryote actin-gene sequences revealed that C. merolae diverged after the division of Protozoa, but before the division of Fungi, Animalia and Chlorophyta.

Partial sequence of ribulose-1,5-bisphosphate carboxylase/oxygenase and the phylogeny of Prochloron and Prochlorococcus (Prochlorales)

The prochlorophytes, oxygenic photosynthetic prokaryotes having no phycobiliprotein but possessing chlorophylls a and b, have been proposed to have a common ancestry with green chloroplasts, yet this is still controversal. We report here that partial sequence comparisons of the large subunit of ribulose-1,5'-bisphosphate carboxylase/oxygenase, including sequence data from two prochlorophytes, Prochlorococcus and Prochloron, indicate that Prochlorococcus is more closely related to a photosynthetic bacterium, Chromatium vinosum (gamma-purple bacteria), than to cyanobacteria, while Prochloron is closely related to the prochlorophyte Prochlorothrix and to cyanobacteria. The molecular phylogenetic tree indicates that a common ancestor of Prochlorococcus and gamma-purple bacteria branched off from the land plant lineage earlier than Prochloron, Prochlorothrix, and cyanobacteria.

The evolutionary origin of red algae as deduced from the nuclear genes encoding cytosolic and chloroplast glyceraldehyde-3-phosphate dehydrogenases from Chondrus crispus

Algae are a heterogeneous group of photosynthetic eukaryotes traditionally separated into three major subdivisions: rhodophytes, chlorophytes, and chromophytes. The evolutionary origin of rhodophytes or red algae and their links to other photosynthetic and nonphotosynthetic eukaryotes have been a matter of much controversy and speculation. Here we present the first cDNAs of nuclear protein genes from red algae: Those encoding cytosolic and chloroplast glyceraldehyde-3-phosphate dehydrogenases (GAPDH) from Chondrus crispus. A phylogenetic analysis including GAPDH gene sequences from a number of eukaryotic taxa, cyanobacteria, and purple bacteria suggests that chloroplasts and rhodoplasts together form a monophyletic group of cyanobacterial descent and that rhodophytes separated from chlorophytes at about the same time as animals and fungi. The composite GAPDH tree further demonstrates that chloroplast and cytosolic GAPDH genes are closely related to their homologs in cyanobacteria and purple bacteria, respectively, the presumptive ancestors of chloroplasts and mitochondria, thereby firmly establishing the endosymbiotic origin of these nuclear genes and their fixation in eukaryotic cells before the rhodophyte/chlorophyte separation. The present data are in conflict with phylogenetic inferences based on plastid-encoded rbcL sequences supporting a polyphyletic origin of rhodoplasts and chloroplasts. Comparison of rbcL to GAPDH phylogenies suggests that rbcL trees may be misleading because they are composed of branches representing ancient duplicated (paralogous) genes.

The gene for ribosomal protein L27 is located on the plastid rather than the nuclear genome of the chlorophyll c-containing alga Pleurochrysis carterae

The gene for ribosomal protein L27 (rpl27) has not been found in plastid genomes. We report here that the rpl27 gene is located in the plastid genome of the prymnesiophyte Pleurochrysis carterae. The deduced amino acid sequence showed 59% identity with E. coli L27. 1.0 kb transcript of the gene was detected by Northern blot analysis. Nucleotide sequence analysis of PCR products suggested that rpl27 is widespread in the genomes of Prymesiophyta and Rhodophyta. In all species of Prymnesiophyta examined in this study, the gene is located at the 3' downstream region of Rubisco operon.

psbD sequences of Bumilleriopsis filiformis (Heterokontophyta, Xanthophyceae) and Porphyridium purpureum (Rhodophyta, Bangiophycidae): evidence for polyphyletic origins of plastids

The nucleotide sequences of the plastidal psbD genes of Bumilleriopsis filiformis and Porphyridium purpureum (encoding the D2 protein of photosystem II) are reported in this paper. The Bumilleriopsis sequence clusters together with Porphyridium when a most parsimonious protein tree of D2 sequences is constructed. A composite D1/D2 protein-similarity network reveals that neither the three red algal sequences nor the two heterokontophyte sequences (Bumilleriopsis, xanthophytes and Ectocarpus, phaeophytes) group together. Therefore, the Heterokontophyta and Rhodophyta may be heterogeneous groups. Instead, it emerges that the D1/D2 proteins of Porphyridium and Bumilleriopsis clearly form a tight cluster. D1 and D2 proteins apparently do not provide a reliable molecular clock. These results fit into hypotheses proposing a polyphyletic origin for complex plastids, even among the supposedly "natural" group of heterokontophytes.

The ribosomal RNA repeats are non-identical and directly oriented in the chloroplast genome of the red alga Porphyra purpurea

A detailed restriction map of the chloroplast genome of the red alga Porphyra purpurea has been constructed. Southern hybridization experiments with cloned or gel-purified restriction fragments and PCR products indicate that the P. purpurea chloroplast genome is approximately 188 kb in size. This circular molecule contains two rRNA-encoding repeats (approximately 4.9 kb) that separate the genome into single-copy regions of 34 kb and 144 kb. Interestingly, these repeats are arranged in a direct orientation. In addition, DNA sequencing of the ends of both repeats revealed that the two rRNA repeats are not identical. No intramolecular recombination between the repeats can be detected. We discuss the possibility that the chloroplast genome of P. purpurea is organized like that of the ancestral chloroplast.

Organization of plastid-encoded ATPase genes and flanking regions including homologues of infB and tsf in the thermophilic red alga Galdieria sulphuraria

We have cloned and sequenced the plastid ATPase operons (atp1 and atp2) and flanking regions from the unicellular red alga Galdieria sulphuraria (Cyanidium caldarium). Six genes (5 atpI, H, G, F, D and A 3) are linked in atp1 encoding ATPase subunits a, c, b, b, delta and alpha, respectively. The atpF gene does not contain an intron and overlaps atpD by 1 bp. As in the genome of chloroplasts from land plants, the cluster is located downstream of rps2, but between this gene and atp1 we found the gene for the prokaryotic translation elongation factor TS. Downstream of atpA, we detected two open reading frames, one encoding a putative transport protein. The genes atpB and atpE, encoding ATPase subunits beta and epsilon, respectively, are linked in atp2, separated by a 2 bp spacer. Upstream of atpB, an uninterrupted orf167 was detected which is homologous to an intron-containing open reading frame in land plant chloroplasts. This orf167 is preceded on the opposite DNA strand by a homologue to initiation factor 2 in prokaryotes. The arrangement of atp1 and atp2 is the same as observed in the multicellular red alga Antithamnion sp., indicating a conserved genome arrangement in the red algal plastid genome. Differences compared to green chloroplast genomes suggest a large phylogenetic distance between red algae and green plants, while similarities in arrangement and sequence to chromophytic ATPase operons support a red algal origin of chlorophyll a/c-containing plastids or alternatively point to a common prokaryotic endosymbiont.

Secondary structure and phylogeny of the chloroplast 23S rRNA gene from the brown alga Pylaiella littoralis

The entire nucleotide sequence of a 23S rRNA gene from the brown alga Pylaiella littoralis (L.) Kjellm has been determined. The predicted length of the 23S rRNA is 2948 nucleotides, including the 4.5S rRNA-like region at the 3' end of the molecule. The putative transcript has been folded into a secondary structure by comparison to existing structure models, and the predicted helical regions were inspected by identifying compensatory downstream base changes. The 23S rRNA secondary structure presented here has features that are unique to P. littoralis (no other chromophyte or red algal 23S rRNA sequences are yet available), but has none of the features specific to the chloroplast rRNAs of green plants and green algae. The Pylaiella sequence was aligned with analogous plastidial and eubacterial gene sequences, and the alignment was used to construct a phylogenetic tree. The plastidial sequences formed a coherent cluster closely associated with the 23S rRNA of the cyanobacterium Anacystis nidulans. Within the plastid group, the P. littoralis sequence was most closely related to that of Euglena gracilis confirming earlier analyses based upon 16S rRNA sequences.

Large ATP synthase operon of the red alga Antithamnion sp. resembles the corresponding operon in cyanobacteria

The large plastid ATP synthase operon of the multicellular red alga Antithamnion sp. was cloned and the sequence of six ATPase genes determined. The operon resembles more the one from cyanobacteria than the ATP synthase operon of the chloroplast genome. The gene order is atpI, H, G, F, D and A, coding for the ATPase subunits a, c, b', b, delta and alpha, respectively. In green plants, the genes atpG and atpD are located in the nucleus. Unlike the situation in three published cyanobacterial ATP synthase operons, atpC, coding for the gamma subunit, is not a part of the rhodoplast operon. A single 4.5 kb transcript was detected with atpG, F, D and A gene probes that could span the whole operon, but no transcript could be detected with atpI and atpH probes. The end of an open reading frame preceding the atp genes shows remarkable homology to elongation factor TS from Escherichia coli. Behind the ATPase cluster, two open reading frames were detected that are not homologous to any known chloroplast gene. One of them may code for a transport protein of unknown specificity. Gene arrangement and sequence comparisons support the hypothesis of a polyphyletic origin of rhodoplasts and chloroplasts.

Structure and organization of rhodophyte and chromophyte plastid genomes: implications for the ancestry of plastids

Plastid genomes of two rhodophytes (Porphyra yezoensis and Griffithsia pacifica) and two chromophytes (Olisthodiscus luteus and Ochromonas danica) were compared with one another and with green plants in terms of overall structure, gene complement and organization. The rhodophyte genomes are moderately colinear in terms of gene organization, and are distinguished by three rearrangements that can most simply be explained by transpositions and a large (approximately 40 kb) inversion. Porphyra contains two loci for ppcBA and Griffithsia has two loci for rpoA. Although there is little similarity in gene organization between the rhodophytes and consensus green plant genome, certain gene clusters found in green plants appear to be conserved in the rhodophytes. The chromophytes Olisthodiscus and Ochromonas contain relatively large plastid inverted repeats that encode several photosynthetic genes in addition to the rRNA genes. With the exception of rbcS, the plastid gene complement in Olisthodiscus is similar to that of green plants, at least for the subset of genes tested. The Ochromonas genome, in contrast, appears unusual in that several of the green plant gene probes hybridizing to Olisthodiscus DNA did not detect similar sequences in Ochromonas DNA. Gene organization within the chromophytes is scrambled relative to each other and to green plants, despite the presence of putatively stabilizing inverted repeats. However, some gene clusters conserved in green plants and rhodophytes are also present in the chromophytes. Comparison of the entire rhodophyte, chromophyte and green plant plastid genomes suggests that despite differences in gene organization, there remain overall similarities in architecture, gene content, and gene sequences among in three lineages. These similarities are discussed with reference to the ancestry of the different plastid types.

Eukaryote-eukaryote endosymbioses: insights from studies of a cryptomonad alga

It has been proposed that those plants which contain photosynthetic plastids surrounded by more than two membranes have arisen through secondary endosymbiotic events. Molecular evidence confirms this proposal, but the nature of the endosymbiont(s) and the number of endosymbioses remain unresolved. Whether plastids arose from one type of prokaryotic ancestor or multiple types is the subject of some controversy. In order to try to resolve this question, the plastid gene content and arrangement has been studied from a cryptomonad alga. Most of the gene clusters common to photosynthetic prokaryotes and plastids are preserved and seventeen genes which are not found on the plastid genomes of land plants have been found. Together with previously published phylogenetic analyses of plastid genes, the present data support the notion that the type of prokaryote involved in the initial endosymbiosis was from within the cyanobacterial assemblage and that an early divergence giving rise to the green plant lineage and the rhodophyte lineage resulted in the differences in plastid gene content and sequence between these two groups. Multiple secondary endosymbiotic events involving a eukaryotic (probably rhodophytic alga) and different hosts are hypothesized to have occurred subsequently, giving rise to the chromophyte, cryptophyte and euglenophyte lineages.

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 plastids 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.

Plastid genomes of the Rhodophyta and Chromophyta constitute a distinct lineage which differs from that of the Chlorophyta and have a composite phylogenetic origin, perhaps like that of the Euglenophyta

A phylogenetic tree has been constructed from comparisons of entire 16S rRNA gene sequences from different prokaryotes and from several algal plastids. According to this study, and to previous work on the ribulose-1,5-bisphosphate carboxylase oxygenase (Rubisco) large and small subunit genes, we postulate that: (1) rhodophyte and chromophyte plastid genomes have a common, composite phylogenetic origin which implies at least two different ancestors, a cyanobacterial and a beta-proteobacterial ancestor; (2) chlorophyte (green algae and land plants) plastids have a cyanobacterial ancestor which probably differs from that of rhodophyte and chromophyte plastids, and in any case constitute a different lineage; (3) euglenophyte plastid genomes also seem to have a composite phylogenetic origin which involves two different lineages.

Targeting proteins to diatom plastids involves transport through an endoplasmic reticulum

Diatoms and related algae, in contrast to higher plants, have a xanthophyll-dominated light harvesting complex and an endoplasmic reticulum (ER) network surrounding the plastid. We have previously demonstrated that polypeptide constituents of the light harvesting complex from the diatom Phaeodactylum tricornutum are nuclear encoded and synthesized as higher molecular weight precursors in the cytoplasm. The amino-termini of the precursor proteins, as deduced from their gene sequences, have features of a signal peptide. Here, we show that the precursor polypeptides can be cotranslationally imported and processed by an in vitro microsomal membrane system, suggesting that cytoplasmically synthesized proteins require a signal peptide to traverse an ER before entering the plastid. These results are discussed in the context of plastid evolution.

Evolution of the Rubisco operon from prokaryotes to algae: structure and analysis of the rbcS gene of the brown alga Pylaiella littoralis

The rbcS gene coding for the small subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) of the brown alga Pylaiella littoralis is located within the plastid genome and is transcribed as a single polycistronic mRNA with the gene for the large subunit of Rubisco, rbcL. The structure of the Rubisco operon from P. littoralis was determined. Molecular phylogenies for rbcS and rbcL with a wide range of prokaryotes and eukaryotes were constructed which are congruent with recent evidence for polyphyletic plastid origins. Both rbcL and rbcS of the beta-purple bacterium Alcaligenes eutrophus clearly cluster with the rhodophyte and chromophyte proteins. The data suggest that the Rubisco operons of red algal and chromophytic plastids derive from beta-purple eubacterial antecedents, rather than the cyanobacterial lineage of eubacteria from which other of their genes derive. This implies a lateral transfer of Rubisco genes from beta-purple eubacterial ancestors to the cyanobacterial ancestor of rhodophyte and chromophyte plastids.

Structural similarities between psbA genes from red and brown algae

The single copy psbA genes from the multicellular red alga Antithamnion spec. and the brown alga Ectocarpus siliculosus have been cloned and sequenced and monocistronic transcripts have been detected. Both genes contain an insertion of 21 bp at the 3' end which was also found in cyanobacteria and which is absent in chloroplasts and the chlorophyll b-containing prochlorophyte Prochlorothrix hollandica. These findings are in agreement with the hypothesis of a polyphyletic origin of plastids. Plastids of red and brown algae appear to be closely related.

Evidence for multiple xenogenous origins of plastids: comparison of psbA-genes with a xanthophyte sequence

When only plastidic features are considered, it is difficult to distinguish between monophyletic and polyphyletic xenogenous origins of plastids. We suggest that a direct comparison of nuclear and plastidic sequence-similarity pattern will help to solve this problem. The D1 amino acid sequence of six major groups of photosynthetic eukaryotes and of the two groups of photosynthetic prokaryotes are now available, including the psbA-gene product from Bumilleriopsis filiformis, which is the first molecular sequence reported for a xanthophycean alga. Evidence is provided for an independent and polyphyletic origin of plastids from five out of the six major taxa of photosynthetic eukaryotes. This conclusion is reached by comparing a plastid-based pattern of D1 similarity with a nucleus-based similarity pattern published recently. Furthermore, the availability of D1 sequences from five eukaryotic algae led to a re-evaluation of the taxonomic position of Prochlorothrix.

Rubisco spacer sequence divergence in the rhodophyte alga Gracilaria verrucosa and closely related species

In the red alga Gracilaria verrucosa, the genes encoding the large and the small subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) are separated by a short spacer of less than 131 bp. Sequencing of PCR-amplified Rubisco spacers from a number of populations of G. verrucosa was performed to assess the feasibility of using this sequence for discriminating among closely related species or populations. Intrapopulation comparisons of the nucleotide sequences of these spacers from five isolates of G. verrucosa, and similar species, demonstrated four main groups. The first group included isolates from Europe and Argentina while the other groups are correlated with the geographical location of their origin.

Structure of the rubisco operon from the multicellular red alga Antithamnion spec

In the multicellular red alga Antithamnion spec. both rubisco genes (rbcL and rbcS) are encoded on the plastid DNA (ptDNA). Both genes are separated by a short A/T-rich spacer of 100 bp and are cotranscribed into an mRNA of approximately 2.7 kb. These findings are in extensive agreement with those obtained from two unicellular red algae (Porphyridium aerugineum and Cyanidium caldarium). The large subunit (LSU) of rubisco shows an amino acid homology of 82-87% with the LSUs from the two unicellular red algae and only about 55% to LSUs from green algae, higher plants and two cyanobacteria. The small subunit (SSU) of rubisco is more similar to those from the unicellular red algae and two algae which are members of the Chromophyta (about 60% homology) than to cyanobacterial and higher plant proteins (27-36% homology). These data indicate that rhodoplasts originated independently from the chloroplast line. The plastids of chromophytes and rhodophytes appear to be closely related.

Rubisco genes indicate a close phylogenetic relation between the plastids of Chromophyta and Rhodophyta

The genes for both subunits of Rubisco (rbcL, rbcS) are located on the plastome of the brown alga Ectocarpus siliculosus (Chromophyta, Phaeophyceae). The organization of these genes in the form of an operon was similar to that found in rhodoplasts, cyanobacteria and the plastids of Cryptomonas phi. Sequence analysis of the complete operon revealed a high degree of homology and great structural similarities to corresponding genes from two red algae. In contrast, sequence homology to Rubisco genes from chloroplasts and cyanobacteria was much lower. This clearly indicated a close phylogenetic relationship between the plastids of Rhodophyta and Chromophyta which seem to have evolved independently from the chloroplasts (polyphyletic origin). Our data suggest that the plastids of Chromophyta and Cryptophyta have originated from endosymbiotic unicellular red algae. Surprisingly, red and brown algal Rubiscos show a significantly higher degree of homology to that from a hydrogen bacterium than to those from cyanobacteria.