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Hisayoshi Nozaki - One of the best experts on this subject based on the ideXlab platform.
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A new scenario of plastid evolution: plastid primary endosymbiosis before the divergence of the “Plantae,” emended
Journal of Plant Research, 2005Co-Authors: Hisayoshi NozakiAbstract:A recent hypothesis on the origin of eukaryotic phototrophs proposes that red algae, green plants (land plants plus green algae), and glaucophytes constitute the primary photosynthetic eukaryotes, whose plastids may have originated directly from a cyanobacterium-like prokaryote via primary endosymbiosis, whereas the plastids of other lineages of eukaryotic phototrophs appear to be the result of secondary Endosymbiotic Events involving a phototrophic eukaryote and a host cell. However, the phylogenetic relationships among the three lineages of primary photosynthetic eukaryotes remained unresolved because previous nuclear multigene phylogenies used incomplete red algal gene sequences derived mainly from Porphyra (Rhodophyceae, one of the two lineages of the Rhodophyta), and lacked sequences from the Cyanidiophyceae (the other red algal lineage). Recently, the complete nuclear genome sequences from the red alga Cyanidioschyzon merolae 10D of the Cyanidiophyceae were determined. Using this genomic information, nuclear multigene phylogenetic analyses of various lineages of mitochondrion-containing eukaryotes were conducted. Since bacterial and amitochondrial eukaryotic genes present serious problems to eukaryotic phylogenies, basal eukaryotes were deduced based on the paralogous comparison of the concatenated α- and β-tubulin. The comparison demonstrated that cellular slime molds (Amoebozoa) represent the most basal position within the mitochondrion-containing organisms. With the cellular slime molds as the outgroup, phylogenetic analyses based on a 1,525-amino acid sequence of four concatenated nuclear genes [actin, elongation factor-1α( EF-1α ), α-tubulin, and β-tubulin] resolved the presence of two large, robust monophyletic groups and the basal eukaryotic lineages (Amoebozoa). One of the two groups corresponded to the Opisthokonta (Metazoa and Fungi), whereas the other included various lineages containing primary and secondary plastids (red algae, green plants, glaucophytes, euglenoids, heterokonts, and apicomplexans), Ciliophora, Kinetoplastida, dinoflagellates, and Heterolobosea, for which the red algae represented the most basal lineage. Therefore, the plastid primary endosymbiosis likely occurred once in the common ancestor of the latter group, and the primary plastids were subsequently lost in the ancestor(s) of organisms within the group that now lacks primary plastids. A new concept of Plantae was proposed for phototrophic and nonphototrophic organisms belonging to this group on the basis of their common history of plastid primary endosymbiosis. This new scenario of plastid evolution is discussed here, and is compared with recent genome information and findings on the secondary endosymbiosis of the Euglena plastid.
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a new scenario of plastid evolution plastid primary endosymbiosis before the divergence of the plantae emended
Journal of Plant Research, 2005Co-Authors: Hisayoshi NozakiAbstract:A recent hypothesis on the origin of eukaryotic phototrophs proposes that red algae, green plants (land plants plus green algae), and glaucophytes constitute the primary photosynthetic eukaryotes, whose plastids may have originated directly from a cyanobacterium-like prokaryote via primary endosymbiosis, whereas the plastids of other lineages of eukaryotic phototrophs appear to be the result of secondary Endosymbiotic Events involving a phototrophic eukaryote and a host cell. However, the phylogenetic relationships among the three lineages of primary photosynthetic eukaryotes remained unresolved because previous nuclear multigene phylogenies used incomplete red algal gene sequences derived mainly from Porphyra (Rhodophyceae, one of the two lineages of the Rhodophyta), and lacked sequences from the Cyanidiophyceae (the other red algal lineage). Recently, the complete nuclear genome sequences from the red alga Cyanidioschyzon merolae 10D of the Cyanidiophyceae were determined. Using this genomic information, nuclear multigene phylogenetic analyses of various lineages of mitochondrion-containing eukaryotes were conducted. Since bacterial and amitochondrial eukaryotic genes present serious problems to eukaryotic phylogenies, basal eukaryotes were deduced based on the paralogous comparison of the concatenated α- and β-tubulin. The comparison demonstrated that cellular slime molds (Amoebozoa) represent the most basal position within the mitochondrion-containing organisms. With the cellular slime molds as the outgroup, phylogenetic analyses based on a 1,525-amino acid sequence of four concatenated nuclear genes [actin, elongation factor-1α( EF-1α), α-tubulin, and β-tubulin] resolved the presence of two large, robust monophyletic groups and the basal eukaryotic lineages (Amoebozoa). One of the two groups corresponded to the Opisthokonta (Metazoa and Fungi), whereas the other included various lineages containing primary and secondary plastids (red algae, green plants, glaucophytes, euglenoids, heterokonts, and apicomplexans), Ciliophora, Kinetoplastida, dinoflagellates, and Heterolobosea, for which the red algae represented the most basal lineage. Therefore, the plastid primary endosymbiosis likely occurred once in the common ancestor of the latter group, and the primary plastids were subsequently lost in the ancestor(s) of organisms within the group that now lacks primary plastids. A new concept of Plantae was proposed for phototrophic and nonphototrophic organisms belonging to this group on the basis of their common history of plastid primary endosymbiosis. This new scenario of plastid evolution is discussed here, and is compared with recent genome information and findings on the secondary endosymbiosis of the Euglena plastid.
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Cyanobacterial Genes Transmitted to the Nucleus Before Divergence of Red Algae in the Chromista
Journal of Molecular Evolution, 2004Co-Authors: Hisayoshi Nozaki, Motomichi Matsuzaki, Osami Misumi, Haruko Kuroiwa, Masami Hasegawa, Tetsuya Higashiyama, Tadasu Shin-i, Yuji Kohara, Naotake Ogasawara, Tsuneyoshi KuroiwaAbstract:The plastids of red algae, green plants, and glaucophytes may have originated directly from a cyanobacterium-like prokaryote via primary endosymbiosis. In contrast, the plastids of other lineages of eukaryotic phototrophs appear to be the result of secondary or tertiary Endosymbiotic Events involving a phototrophic eukaryote and a eukaryotic host cell. Although phylogenetic analyses of multiple plastid genes from a wide range of eukaryotic lineages have been carried out, the phylogenetic positions of the secondary plastids of the Chromista (Heterokontophyta, Haptophyta and Cryptophyta) are ambiguous in a range of different analyses. This ambiguity may be the result of unusual substitutions or bias in the plastid genes established by the secondary endosymbiosis. In this study, we carried out phylogenetic analyses of five nuclear genes of cyanobacterial origin (6-phosphogluconate dehydrogenase [ gnd ], oxygen-evolving-enhancer [ psbO ], phosphoglycerate kinase [ pgk ], delta-aminolevulinic acid dehydratase [ aladh ], and ATP synthase gamma [ atpC ] genes), using the genome sequence data from the primitive red alga Cyanidioschyzon merolae 10D. The sequence data robustly resolved the origin of the cyanobacterial genes in the nuclei of the Chromista (Heterokontophyta and Haptophyta) and Dinophyta, before the divergence of the extant red algae (including Porphyra [Rhodophyceae] and Cyanidioschyzon [Cyadidiophyceae]). Although it is likely that gnd genes in the Chromista were transmitted from the cyanobacterium-like ancestor of plastids in the primary endosymbiosis, other genes might have been transferred from nuclei of a red algal ancestor in the secondary endosymbiosis. Therefore, the results indicate that the Chromista might have originated from the ancient secondary endosymbiosis before the divergence of extant red algae.
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Phylogeny of Plastids Based on Cladistic Analysis of Gene Loss Inferred from Complete Plastid Genome Sequences
Journal of Molecular Evolution, 2003Co-Authors: Hisayoshi Nozaki, Njij Ohta, Motomichi Matsuzaki, Osami Misumi, Tsuneyoshi KuroiwaAbstract:Based on the recent hypothesis on the origin of eukaryotic phototrophs, red algae, green plants, and glaucophytes constitute the “primary photosynthetic eukaryotes” (whose plastids may have originated directly from a cyanobacterium-like prokaryote via primary endosymbiosis), whereas the plastids of other lineages of eukaryotic phototrophs appear to be the result of secondary or tertiary Endosymbiotic Events (involving a phototrophic eukaryote and a host cell). Although phylogenetic analyses using multiple plastid genes from a wide range of eukaryotic lineages have been carried out, some of the major phylogenetic relationships of plastids remain ambiguous or conflict between different phylogenetic methods used for nucleotide or amino acid substitutions. Therefore, an alternative methodology to infer the plastid phylogeny is needed. Here, we carried out a cladistic analysis of the “loss of plastid genes” after primary endosymbiosis using complete plastid genome sequences from a wide range of eukaryotic phototrophs. Since it is extremely unlikely that plastid genes are regained during plastid evolution, we used the irreversible Camin-Sokal model for our cladistic analysis of the loss of plastid genes. The cladistic analysis of the 274 plastid protein-coding genes resolved the 20 operational taxonomic units representing a wide range of eukaryotic lineages (including three secondary plastid-containing groups) into two large monophyletic groups with high bootstrap values: one corresponded to the red lineage and the other consisted of a large clade composed of the green lineage (green plants and Euglena ) and the basal glaucophyte plastid. Although the sister relationship between the green lineage and the Glaucophyta was not resolved in recent phylogenetic studies using amino acid substitutions from multiple plastid genes, it is consistent with the rbcL gene phylogeny and with a recent phylogenetic study using multiple nuclear genes. In addition, our analysis robustly resolved the conflicting/ambiguous phylogenetic positions of secondary plastids in previous phylogenetic studies: the Euglena plastid was sister to the chlorophycean ( Chlamydomonas ) lineage, and the secondary plastids from the diatom ( Odontiella ) and cryptophyte ( Guillardia ) were monophyletic within the red lineage.
Karl J. Niklas - One of the best experts on this subject based on the ideXlab platform.
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Macroevolution via secondary endosymbiosis: a Neo-Goldschmidtian view of unicellular hopeful monsters and Darwin’s primordial intermediate form
Theory in Biosciences, 2008Co-Authors: Ulrich Kutschera, Karl J. NiklasAbstract:Seventy-five years ago, the geneticist Richard Goldschmidt hypothesized that single mutations affecting development could result in major phenotypic changes in a single generation to produce unique organisms within animal populations that he called “hopeful monsters”. Three decades ago, Sarah P. Gibbs proposed that photosynthetic unicellular micro-organisms like euglenoids and dinoflagellates are the products of a process now called “secondary endosymbiosis” (i.e., the evolution of a chloroplast surrounded by three or four membranes resulting from the incorporation of a eukaryotic alga by a eukaryotic heterotrophic host cell). In this article, we explore the evidence for Goldschmidt’s “hopeful monster” concept and expand the scope of this theory to include the macroevolutionary emergence of organisms like Euglena and Chlorarachnion from secondary Endosymbiotic Events. We argue that a Neo-Goldschmidtian perspective leads to the conclusion that cell chimeras such as euglenids and dinoflagellates, which are important groups of phytoplankton in freshwater and marine ecosystems, should be interpreted as “successful monsters”. In addition, we argue that Charles Darwin had euglenoids (infusoria) in mind when he speculated on the “primordial intermediate form”, although his Proto-Euglena-hypothesis for the origin of the last common ancestor of all forms of life is no longer acceptable.
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macroevolution via secondary endosymbiosis a neo goldschmidtian view of unicellular hopeful monsters and darwin s primordial intermediate form
Theory in Biosciences, 2008Co-Authors: Ulrich Kutschera, Karl J. NiklasAbstract:Seventy-five years ago, the geneticist Richard Goldschmidt hypothesized that single mutations affecting development could result in major phenotypic changes in a single generation to produce unique organisms within animal populations that he called "hopeful monsters". Three decades ago, Sarah P. Gibbs proposed that photosynthetic unicellular micro-organisms like euglenoids and dinoflagellates are the products of a process now called "secondary endosymbiosis" (i.e., the evolution of a chloroplast surrounded by three or four membranes resulting from the incorporation of a eukaryotic alga by a eukaryotic heterotrophic host cell). In this article, we explore the evidence for Goldschmidt's "hopeful monster" concept and expand the scope of this theory to include the macroevolutionary emergence of organisms like Euglena and Chlorarachnion from secondary Endosymbiotic Events. We argue that a Neo-Goldschmidtian perspective leads to the conclusion that cell chimeras such as euglenids and dinoflagellates, which are important groups of phytoplankton in freshwater and marine ecosystems, should be interpreted as "successful monsters". In addition, we argue that Charles Darwin had euglenoids (infusoria) in mind when he speculated on the "primordial intermediate form", although his Proto-Euglena-hypothesis for the origin of the last common ancestor of all forms of life is no longer acceptable.
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The Cell Walls that Bind the Tree of Life
BioScience, 2004Co-Authors: Karl J. NiklasAbstract:Abstract Cell walls have evolved independently in many phyletically diverse clades, including the Eubacteria and Archaebacteria. However, a review of the available genetic and biochemical evidence indicates that the machinery responsible for synthesizing the cell walls of land plants, of their nearest algal relatives (the charophytes), and of some very ancient algal lineages (chlorophytes, rhodophytes, and phaeophytes) can be traced back to ancient primary Endosymbiotic Events involving Eubacteria (specifically cyanobacteria and proteobacteria). Lateral gene transfers attending secondary Endosymbiotic Events appear to be responsible for manufacturing the cell walls of more recently evolved photoautotrophic and heterotrophic lineages (e.g., euglenoids and tunicates). Recent research into the genetic basis of cell wall synthesis and chemical composition in bacteria, algae, and land plants continues to shed light on the phylogenetic relationships among a broad spectrum of evolutionarily and ecologically dive...
Dagmar B Stengel - One of the best experts on this subject based on the ideXlab platform.
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evolution and diversity of plant cell walls from algae to flowering plants
Annual Review of Plant Biology, 2011Co-Authors: Zoe A Popper, Gurvan Michel, Cecile Herve, David S Domozych, William G T Willats, Maria G Tuohy, Bernard Kloareg, Dagmar B StengelAbstract:All photosynthetic multicellular Eukaryotes, including land plants and algae, have cells that are surrounded by a dynamic, complex, carbohydrate-rich cell wall. The cell wall exerts considerable biological and biomechanical control over individual cells and organisms, thus playing a key role in their environmental interactions. This has resulted in compositional variation that is dependent on developmental stage, cell type, and season. Further variation is evident that has a phylogenetic basis. Plants and algae have a complex phylogenetic history, including acquisition of genes responsible for carbohydrate synthesis and modification through a series of primary (leading to red algae, green algae, and land plants) and secondary (generating brown algae, diatoms, and dinoflagellates) Endosymbiotic Events. Therefore, organisms that have the shared features of photosynthesis and possession of a cell wall do not form a monophyletic group. Yet they contain some common wall components that can be explained increas...
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Evolution and Diversity of Plant Cell Walls: From Algae to Flowering Plants
Annual Review of Plant Biology, 2011Co-Authors: Zoe A Popper, Gurvan Michel, Cecile Herve, David S Domozych, William G T Willats, Maria G Tuohy, Bernard Kloareg, Dagmar B StengelAbstract:All photosynthetic multicellular Eukaryotes, including land plants and algae, have cells that are surrounded by a dynamic, complex, carbohydrate-rich cell wall. The cell wall exerts considerable biological and biomechanical control over individual cells and organisms, thus playing a key role in their environmental interactions. This has resulted in compositional variation that is dependent on developmental stage, cell type, and season. Further variation is evident that has a phylogenetic basis. Plants and algae have a complex phylogenetic history, including acquisition of genes responsible for carbohydrate synthesis and modification through a series of primary (leading to red algae, green algae, and land plants) and secondary (generating brown algae, diatoms, and dinoflagellates) Endosymbiotic Events. Therefore, organisms that have the shared features of photosynthesis and possession of a cell wall do not form a monophyletic group. Yet they contain some common wall components that can be explained increasingly by genetic and biochemical evidence.
Patrick J. Keeling - One of the best experts on this subject based on the ideXlab platform.
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The Number, Speed, and Impact of Plastid Endosymbioses in Eukaryotic Evolution
Annual review of plant biology, 2013Co-Authors: Patrick J. KeelingAbstract:Plastids (chloroplasts) have long been recognized to have originated by endosymbiosis of a cyanobacterium, but their subsequent evolutionary history has proved complex because they have also moved between eukaryotes during additional rounds of secondary and tertiary endosymbioses. Much of this history has been revealed by genomic analyses, but some debates remain unresolved, in particular those relating to secondary red plastids of the chromalveolates, especially cryptomonads. Here, I examine several fundamental questions and assumptions about endosymbiosis and plastid evolution, including the number of Endosymbiotic Events needed to explain plastid diversity, whether the genetic contribution of the endosymbionts to the host genome goes far beyond plastid-targeted genes, and whether organelle origins are best viewed as a singular transition involving one symbiont or as a gradual transition involving a long line of transient food/symbionts. I also discuss a possible link between transporters and the evolut...
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multiple gene phylogenies support the monophyly of cryptomonad and haptophyte host lineages
Current Biology, 2007Co-Authors: Nicola J Patron, Yuji Inagaki, Patrick J. KeelingAbstract:Cryptomonad algae acquired their plastids by the secondary Endosymbiotic uptake of a eukaryotic red alga. Several other algal lineages acquired plastids through such an event [1], but cryptomonads are distinguished by the retention of a relic red algal nucleus, the nucleomorph [2]. The nucleomorph (and its absence in other lineages) can reveal a great deal about the process and history of endosymbiosis, but only if we know the relationship between cryptomonads and other algae, and this has been controversial. Several recent analyses have suggested a relationship between plastids of cryptomonads and some or all other red alga-containing lineages [3-6], but we must also know whether host nuclear genes mirror this relationship to determine the number of Endosymbiotic Events, and this has not been demonstrated. We have carried out an expressed sequence tag (EST) survey of the cryptomonad Guillardia theta. Phylogenetic analyses of 102 orthologous nucleus-encoded proteins (18,425 amino acid alignment positions) show a robust sister-group relationship between cryptomonads and the haptophyte algae, which also have a red secondary plastid. This relationship demonstrates that loss of nucleomorphs must have taken place in haptophytes independently of any other red alga-containing lineages and that the ancestor of both already contained a red algal endosymbiont.
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Diversity and evolutionary history of plastids and their hosts.
American journal of botany, 2004Co-Authors: Patrick J. KeelingAbstract:By synthesizing data from individual gene phylogenies, large concatenated gene trees, and other kinds of molecular, morphological, and biochemical markers, we begin to see the broad outlines of a global phylogenetic tree of eukaryotes. This tree is apparently composed of five large assemblages, or "supergroups." Plants and algae, or more generally eukaryotes with plastids (the photosynthetic organelle of plants and algae and their nonphotosynthetic derivatives) are scattered among four of the five supergroups. This is because plastids have had a complex evolutionary history involving several Endosymbiotic Events that have led to their transmission from one group to another. Here, the history of the plastid and of its various hosts is reviewed with particular attention to the number and nature of the Endosymbiotic Events that led to the current distribution of plastids. There is accumulating evidence to support a single primary origin of plastids from a cyanobacterium (with one intriguing possible exception in the little-studied amoeba Paulinella), followed by the diversification of glaucophytes, red and green algae, with plants evolving from green algae. Following this, some of these algae were themselves involved in secondary Endosymbiotic Events. The best current evidence indicates that two independent secondary endosymbioses involving green algae gave rise to euglenids and chlorarachniophytes, whereas a single endosymbiosis with a red algae gave rise to the chromalveolates, a diverse group including cryptomonads, haptophytes, heterokonts, and alveolates. Dinoflagellates (alveolates) have since taken up other algae in serial secondary and tertiary endosymbioses, raising a number of controversies over the origin of their plastids, and by extension, the recently discovered cryptic plastid of the closely related apicomplexan parasites.
Gurvan Michel - One of the best experts on this subject based on the ideXlab platform.
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Evolution and diversity of plant cell walls: from algae to flowering plants
'Annual Reviews', 2017Co-Authors: Popper, Zoë A., Gurvan Michel, Hervé Cécile, Domozych, David S., Willats, William G.t., Tuohy, Maria G., Kloareg Bernard, Stengel, Dagmar B.Abstract:All photosynthetic multicellular Eukaryotes, including land plants and algae, have cells that are surrounded by a dynamic, complex, carbohydrate-rich cell wall. The cell wall exerts considerable biological and biomechanical control over individual cells and organisms, thus playing a key role in their environmental interactions. This has resulted in compositional variation that is dependent on developmental stage, cell type, and season. Further variation is evident that has a phylogenetic basis. Plants and algae have a complex phylogenetic history, including acquisition of genes responsible for carbohydrate synthesis and modification through a series of primary (leading to red algae, green algae, and land plants) and secondary (generating brown algae, diatoms, and dinoflagellates) Endosymbiotic Events. Therefore, organisms that have the shared features of photosynthesis and possession of a cell wall do not form a monophyletic group. Yet they contain some common wall components that can be explained increasingly by genetic and biochemical evidence.peer-reviewe
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evolution and diversity of plant cell walls from algae to flowering plants
Annual Review of Plant Biology, 2011Co-Authors: Zoe A Popper, Gurvan Michel, Cecile Herve, David S Domozych, William G T Willats, Maria G Tuohy, Bernard Kloareg, Dagmar B StengelAbstract:All photosynthetic multicellular Eukaryotes, including land plants and algae, have cells that are surrounded by a dynamic, complex, carbohydrate-rich cell wall. The cell wall exerts considerable biological and biomechanical control over individual cells and organisms, thus playing a key role in their environmental interactions. This has resulted in compositional variation that is dependent on developmental stage, cell type, and season. Further variation is evident that has a phylogenetic basis. Plants and algae have a complex phylogenetic history, including acquisition of genes responsible for carbohydrate synthesis and modification through a series of primary (leading to red algae, green algae, and land plants) and secondary (generating brown algae, diatoms, and dinoflagellates) Endosymbiotic Events. Therefore, organisms that have the shared features of photosynthesis and possession of a cell wall do not form a monophyletic group. Yet they contain some common wall components that can be explained increas...
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Evolution and Diversity of Plant Cell Walls: From Algae to Flowering Plants
Annual Review of Plant Biology, 2011Co-Authors: Zoe A Popper, Gurvan Michel, Cecile Herve, David S Domozych, William G T Willats, Maria G Tuohy, Bernard Kloareg, Dagmar B StengelAbstract:All photosynthetic multicellular Eukaryotes, including land plants and algae, have cells that are surrounded by a dynamic, complex, carbohydrate-rich cell wall. The cell wall exerts considerable biological and biomechanical control over individual cells and organisms, thus playing a key role in their environmental interactions. This has resulted in compositional variation that is dependent on developmental stage, cell type, and season. Further variation is evident that has a phylogenetic basis. Plants and algae have a complex phylogenetic history, including acquisition of genes responsible for carbohydrate synthesis and modification through a series of primary (leading to red algae, green algae, and land plants) and secondary (generating brown algae, diatoms, and dinoflagellates) Endosymbiotic Events. Therefore, organisms that have the shared features of photosynthesis and possession of a cell wall do not form a monophyletic group. Yet they contain some common wall components that can be explained increasingly by genetic and biochemical evidence.