However, the majority of researchers seem to affirm that not only the chloroplasts but also the entire cells of the three lineages are monophyletic. My emphasis. That is all that the authors gave as the criteria of classification of Archaeplastida.
The common origin of the three lineages of Archaeplastida with or without non-photosynthetic clades does not imply that their chloroplasts are cyanobacterial descendants. At this point, I briefly summarize the situation in mitochondria.
The postgenomic era opened a new way of understanding. About proteins were identified in the mitochondrial proteome. This could be a beginning of a new way of thinking of mitochondrial origin. We can imagine various scenarios to explain the situation: 1 Many genes for the future mitochondrial proteins had been acquired by the eukaryotic host before the formation of mitochondria by the acquisition of a proteobacterial endosymbiont.
The old proteins changed their localization and function upon the formation of mitochondria. At the same time, some more proteobacterial enzymes were introduced. Various other scenarios are also probable. Mitochondrial origin might not be a simple event of endosymbiosis, although many researchers still believe that an endosymbiosis of a proteobacterium was essential in establishing the mitochondria.
We now focus on the situation in chloroplasts, which also have similar problems to re-examine. We consider here chloroplast enzymes that are encoded by both nuclear and chloroplast genomes and examine their phylogenetic relationships to the cyanobacterial homologs. Phylogenetic trees of the enzymes described in this section have been published as Supplementary Materials of a previous paper [ 50 ].
Figure 1 presents four types of phylogenetic relationships between the cyanobacterial clade and the chloroplast clade. Type 1 tree indicates that the chloroplast gene originated from cyanobacteria, which is consistent with the idea of chloroplast origin by cyanobacterial endosymbiosis.
When homologs are only found in cyanobacteria and chloroplasts, we cannot determine the position of the root, and hence, the direction of evolution in a strict sense. In some special cases such as PsaA and PsaB, we can root the phylogenetic tree, but in most cases, the root position is undetermined.
These cases are classified as Type 1c. In this case, Gloeobacter or basal Synechococcus are often taken as the root. In the Type 2 tree, the chloroplast clade is sister to the cyanobacterial clade. This means that the chloroplast originated from an ancestor of all extant cyanobacteria, which seems unbelievable. However, we often obtain this type of tree. This could be an artifact of phylogenetic reconstruction, but the tree form is rather robust in most cases, even if taxon samplings and phylogenetic methods are varied.
We will have to find an explanation for this type of tree. Type 3 tree indicates that the chloroplast enzymes originated from bacteria other than cyanobacteria. Type 4 tree shows that eukaryotic enzymes are re-targeted to the chloroplast.
Enzymes found only in cyanobacteria are classified as Type 5. Four major types of phylogenetic relationships between cyanobacterial and chloroplast proteins. Chloroplast-encoded proteins or RNA are marked with an asterisk and colored.
This is an extended, revised version of the original in [ 9 , 50 ]. Peptidoglycan is a meshwork structure that exists between the outer and inner membranes of Gram-negative bacteria including cyanobacteria. In Gram-positive bacteria, a thick layer of peptidoglycan covers the whole cell.
The presence of a wall-like layer in chloroplasts or similar photosynthetic structures was first suggested in P. The chromatophore of Paulinella is now considered a structure that is phylogenetically distinct from the chloroplasts of plants and algae, but in the s, it was identified as a living cyanobacterial cell within the eukaryotic cell. The organelles surrounded by the wall-like layer in Paulinella and Cyanophora were subsequently called cyanelles, meaning cyanobacterial cells living in the cell as an organelle [ 18 ] and were distinguished from the common chloroplasts.
The identity of peptidoglycan in Cyanophora cyanelles was established by chemical analysis [ 66 ]. Peptidoglycan has long been considered important evidence for the endosymbiotic origin of not only cyanelles but also chloroplasts see a microbiology textbook [ 67 ].
The presence of peptidoglycan in green plants was suggested by the genome analysis of the moss P. The complete set of enzymes involved in the synthesis of peptidoglycan was identified in the nuclear genome of P. The presence of peptidoglycan was suggested by treatment with ampicillin, an inhibitor of peptidoglycan synthesis: namely, chloroplast division was inhibited by ampicillin in the moss.
Although the role of peptidoglycan in chloroplast division is still not understood, this was taken as evidence suggesting that peptidoglycan exists in the moss chloroplast. Genes for the complete set of peptidoglycan synthesis enzymes were also found in other organisms, such as green algae Micromonas , charophytes Klebsormidium , liverworts Marchantia , pteridophytes Selaginella , and even in some gymnosperms [ 69 ]. Arabidopsis thaliana also possesses homologs of some of the peptidoglycan synthesis enzymes.
Curiously, AtMurE was shown to be involved in chloroplast development, rather than biosynthesis of a glycan-like substance [ 70 ]. In contrast, all enzymes of peptidoglycan synthesis except MurF are encoded by the chromatophore genome of P.
MurF was found to be encoded by a nuclear gene, which originated from proteobacteria [ 9 , 50 , 71 , 72 , 73 , 74 ]. Peptidoglycan has not been observed by electron microscopy as a clearly defined layer in plant chloroplasts. Subsequently, peptidoglycan materials were located between the outer and inner envelope membranes of moss chloroplasts by quantitative densitometry of transmission electron micrographs [ 76 ].
Note that this conclusion was obtained not only by our study [ 77 ] but also by an independent study [ 78 ]. A class of penicillin-binding proteins PBP encoded by some green algal chloroplast genomes also diverged from cyanobacteria. These results suggest that the peptidoglycan synthesis system was introduced into green algae and glaucophytes from various bacteria. However, important questions remain. First, when or at which stage of evolution was the peptidoglycan synthesis system introduced?
The timing could be either in the common origin of Archaeplastida, or in the common ancestor of green algae and glaucophytes if red algae diverged first , or separately in green algae and glaucophytes. In the first case, red algae must have lost the peptidoglycan synthesis system. Some Cyanophora enzymes are not closely related to green algal homologs and could have different origins.
We also have to consider that many green algae such as Chlamydomonas do not have any peptidoglycan synthesis gene. We have another question: How were the genes introduced into algal cells? If each gene was introduced one by one from different bacteria, then the introduced genes could not function in peptidoglycan synthesis until all necessary genes are provided.
There is no evolutionary advantage of keeping individual genes during the gene acquiring process. A possible scenario might be like this: a complete system of peptidoglycan synthesis was present at first in an organism, and each gene was replaced by horizontal gene transfer. After gene exchanges, a new complete, functional set of genes was introduced into an ancestor of algae either of the three possibilities as above.
Continued studies are necessary on this topic. Chloroplast is the major site of fatty acid synthesis in plant cells. A large proportion of fatty acids produced in the chloroplast are exported to the cytosol for the lipid synthesis in the endoplasmic reticulum ER , while the remaining fatty acids are used for the chloroplast lipid synthesis.
The proportion of the two metabolic flows depends on organisms and tissues. All the enzymes of lipid biosynthesis in the ER of plants and algae are eukaryotic enzymes that have closely related orthologs in other eukaryotes animals and protists.
To discuss the cyanobacterial origin of chloroplasts, we have to examine fatty acid synthesis and lipid synthesis within the chloroplasts. Two types of fatty acid synthases FAS are known: Type II FAS is found in bacteria including cyanobacteria and consists of four separate subunits catalyzing the main cycle of chain elongation.
Type I FAS is a large molecule containing the four enzymatic activities plus acyl carrier protein ACP and other related activities within one or two multifunctional polypeptide s , which is found in the cytosol of fungi and animals. Fungal and animal FAS are also different in the arrangement of enzymatic active centers within the polypeptides. Because plant and algal chloroplasts contain Type II FAS, the fatty acid synthesis activity in the chloroplasts has been compared with the cyanobacterial activity.
Type II FAS is also present in the mitochondria of eukaryotes including animals, plants, and other organisms, but only limited production of fatty acids is ascribed to mitochondria.
Note that all enzymes involved in fatty acid synthesis except some algal enzymes encoded by the chloroplast genome, such as red algal ACP and FabH are encoded by the nuclear genome. Under these circumstances, fatty acid synthesis in the chloroplast was simply believed to originate from cyanobacteria. Recent phylogenetic analysis showed indeed cyanobacterial origin of many components of fatty acid synthesis, but not all Figure 1.
The condensing enzyme called FabF that catalyzes the chain elongation reaction in the chloroplast originates from green sulfur bacteria, whereas the mitochondrial homolog originates from proteobacteria [ 9 , 50 ].
The green bacteria both sulfur and non-sulfur are photosynthetic bacteria that do not produce oxygen but utilize light energy for carbon fixation. Curiously, in many phylogenetic analyses, green bacteria are often found to be the most related group of chloroplasts.
In the chloroplasts, the initial products of FAS are palmitic and stearic acids. In the chloroplasts of green plants and algae, stearic acid is desaturated introduction of a double bond is called desaturation to oleic acid by stearoyl ACP desaturase SAD. Therefore, the primary products of fatty acid synthesis in these chloroplasts are palmitic and oleic acids.
SAD is not present in red algae and glaucophytes, nor in cyanobacteria. Nevertheless, diatoms have homologs of SAD. Desaturation in cyanobacteria, including oleic acid synthesis, uses acyl lipids as the substrate rather than acyl ACP or acyl CoA. A trace amount of phosphatidylcholine is present in the chloroplast. Tri- and tetragalactosyl diacylglycerols are also found in land plants depending on growth conditions. The lack of SQDG and thylakoid membrane in this group of cyanobacteria could be related to each other, but little is known about this question.
Photosynthetic bacteria without oxygen evolution also contain some of these lipids, but not the complete trio. Therefore, the glycolipid trio seemed to be good evidence for the cyanobacterial origin of chloroplasts.
This name had a connotation that the lipid biosynthetic pathway of chloroplast originated from cyanobacteria. However, this turned out to be false. The entire pathways in cyanobacteria and chloroplasts are unrelated in terms of biochemistry and phylogeny Figure 2. Glycolipid biosynthesis pathways in cyanobacteria and chloroplasts.
Cyanobacterial genes are shown in cyan, whereas eukaryotic or non-cyanobacterial genes are shown in green. Note that the biochemical reactions are different in the two steps marked [1] in magenta. In other steps, biochemically identical reactions are catalyzed by structurally unrelated isofunctional non-homologous enzymes marked [2].
Eukaryotic paralogs and phylogenetically distant orthologs are marked [3] and [4], respectively. Essential differences in the galactolipid biosynthetic pathways in cyanobacteria and chloroplasts were found by labeling experiments already in the s [ 80 , 81 ] and the references therein. All genes encoding the galactolipid synthesis enzymes were identified in chloroplasts by the end of the 20th century [ 82 , 83 ], whereas the cyanobacterial genes for the synthesis of galactolipids were identified later [ 84 , 85 , 86 , 87 ].
These are nonhomologous, isofunctional genes. These three kinds of genes are also nonhomologous, isofunctional genes. Acyltransferases that produce lysophosphatidic acid and phosphatidic acid were also identified in the chloroplast in the early days, but cyanobacterial acyltransferases were identified later. Escherichia coli acyltransferases encoded by the plsB and plsC genes were found in the s, but the acyltransferase for the first acylation was identified quite recently in other bacteria including cyanobacteria.
The bacterial system uses acyl phosphate as the acyl donor of the first acylation step and two genes named plsX and plsY were identified [ 92 ]. Identification and phylogenetic analysis [ 93 ] and functional characterization [ 94 ] of the cyanobacterial genes were performed recently. The cyanobacterial pathway of galactolipid synthesis is, therefore, biochemically different from the corresponding pathway in chloroplasts in at least two points see Figure 2.
The second galactosylation step is catalyzed by two different types of galactosyltransferases in cyanobacteria DgdA and chloroplasts DGD1. Note that the chloroplast genome of some red algae in Cyanidiales encodes a dgdA gene [ 96 ]. In addition, phylogenetic analysis of all the enzymes involved in the synthesis of galactolipids revealed that none of the chloroplast enzymes originated from cyanobacteria [ 9 , 50 ]. In terms of biochemical reaction, the second acylation and the dephosphorylation are common in chloroplasts and cyanobacteria.
Nevertheless, phylogenetic analysis showed that the chloroplast enzymes and cyanobacterial enzymes belong to distant clades. Figure 2 shows that all enzymes in the galactolipid synthesis pathway are biochemically or phylogenetically different in cyanobacteria and chloroplasts see Figure 1 for the summary of phylogenetic analysis.
They are classified into three biochemical categories and a phylogenetic category this is shown in magenta brackets in Figure 2. Therefore, the galactolipid biosynthesis system is unrelated to cyanobacteria and chloroplasts, and this is mostly supported by evidence that does not rely on phylogenetic analysis.
ATS2 was based on phylogenetic analysis that robustly supported their distant relationship. Biochemically, the biosynthetic pathways of SQDG and PG are both similar in cyanobacteria and chloroplasts, but the phylogenetic relationship of the enzymes is rather complex [ 50 ]. SqdC replaces SqdX in some cyanobacteria. Schematic phylogenetic trees showing different origins of chloroplast enzymes or RNA within the cyanobacterial diversity.
A Canonical phylogenetic tree of cyanobacteria and chloroplasts. Various clades of cyanobacteria are shown according to [ 53 , 54 ]. Chloroplast-encoded proteins and RNA are shown in green.
Nuclear-encoded chloroplast proteins are shown in black. The clade names are taken from [ 53 ]. According to [ 54 ], G. For simplicity, Clade H is used for G. B Different origins of chloroplast and cyanobacterial RbcL. This diagram, which is consistent with previous results, is still a plausible hypothesis among many other alternatives. Different line colors are used to show different lineages such as cyan for cyanobacteria and green for chloroplast.
Colored protein names are used to show chloroplast-encoded proteins. Chloroplast CDS is likely to originate from cyanobacteria. This is indeed the rare case with Cyanidiales DgdA , in which a direct phylogenetic relationship is demonstrated in cyanobacterial and chloroplast orthologs Type 1 in Figure 1. In summary, chloroplasts and cyanobacteria are similar in the compositions of lipids that make up thylakoid membranes, but they have essentially unrelated pathways of lipid synthesis.
This could be convergent evolution, rather than vertical inheritance, that sustains the functioning of membrane-embedded components of photosynthetic machinery photosystems, electron transfer chain, and ATP synthase.
Many of the enzymes acting within the chloroplasts are eukaryotic enzymes or enzymes that are distantly related to cyanobacterial counterparts. However, many components of the chloroplast fatty acid synthesis system originate from cyanobacteria. The chloroplast genome has been believed as a reduced cyanobacterial genome that was introduced into the hypothetical algal ancestor. Phylogenetic analysis of the rRNAs was the representative support for the cyanobacterial origin of the chloroplast.
However, as pointed out in Section 2. Phylogenetic analysis of chloroplast genome has been traditionally performed with concatenated amino acid sequences of conserved genes [ 53 , 54 ] because chloroplast-encoded proteins e. In practice, we obtain divergent phylogenetic trees for individual chloroplast ribosomal proteins, but a fairly reliable phylogenetic tree of concatenated ribosomal sequences that resembles the tree of rRNA [ 9 , 50 ].
In the phylogenetic trees of the chloroplast rRNA as well as the concatenated chloroplast-encoded proteins, the chloroplast clade branches from the basal clade of cyanobacteria after the clade E, but before the split of the clade A-B1-B2 and the clade C1-C2-C3 Figure 3 A [ 9 , 34 , 35 , 53 , 54 ]. This is the canonical phylogenetic tree of chloroplasts and cyanobacteria that supports the current notion of the cyanobacterial origin of chloroplasts Figure 3 A.
It should be noted, however, that the unity of the chloroplast genome should not be the first assumption to make. Each of the large proteins, such as the large subunit of rubisco, the RNA polymerase subunits, and the two large subunits of Photosystem I reaction center P, has sufficient phylogenetic signals for constructing a reliable, individual phylogenetic tree.
Examination of these individual trees suggested that the relationship between the cyanobacteria and the chloroplasts might not be straightforward as indicated by the canonical tree. The carbon-fixation enzyme, rubisco, was the first to present evidence for the multiple origins of the chloroplast genome.
Let us examine the RbcL phylogeny. The classification of the large subunit of rubisco, RbcL, is quite complicated. Tabita [ 99 ] presented a classification of bacterial and chloroplast RbcL based on biochemical and phylogenetic data. He showed that the red algal rubisco belongs to Form ID, whereas the rubisco of the green plants and algae, as well as many cyanobacteria, belong to Form IB.
This was a novel idea that the chloroplast genome can be a target of horizontal gene transfer. See also Supplementary Material 4 of [ 50 ]. The two types of carboxysomes are biochemically different and correspond to different genomic structures [ , ].
Another complication of the RbcL phylogeny was found in the point of divergence of chloroplasts within the cyanobacterial clade. Note that the C1 clade has Form IA rubisco, which is not related to the chloroplast rubisco. Various analyses using different taxon sampling and different phylogenetic methods gave inconsistent results.
Finally, the previous result is identified as the most plausible hypothesis Figure 3 C. This is really a rare case of difficult phylogenetic analysis, and this tentative conclusion should be re-examined in further studies.
In these phylogenetic trees, only the rpoA tree showed a sister relationship between G. However, in this case, the position of G. Therefore, the phylogenetic relationship of cyanobacterial species is variable depending on genes. These findings as well as previous results [ 9 , 50 ] suggest that the chloroplast genome is not just a reduced form of a single ancestral cyanobacterial genome.
Rather, it could be a chimera resulting from multiple gene transfer events from different clades of cyanobacteria. As described above, the origin of chloroplast psaA and psaB will have to be studied further. Nevertheless, if we never considered a possibility that the chloroplast genome could be a chimera of different cyanobacterial genomes, this is a good occasion to verify or falsify this hypothesis. This was already challenged by a separate origin of the red algal rbcL gene. There could be more examples than those that I described above.
Against the data shown above, various criticisms can be raised. An alternative interpretation could be an ancient gene duplication followed by differential gene loss as in the case of psbA [ ].
Indeed, psaA and psaB show a trace of gene duplication in cyanobacteria. Another alternative is an artifact due to phylogenetic inference. Indeed, the cyanobacterial parts of the trees of rbcL , psaA , psaB , and others as described above are somewhat different compared to the canonical tree.
Gene trees of cyanobacteria will have to be rigorously re-examined before we can conclude a single origin of chloroplast genome within the cyanobacteria based on the concatenated tree, which averages different evolutionary histories of individual genes. POP functions in both mitochondria and chloroplasts in all photosynthetic eukaryotes [ ].
POP is also the mitochondrial replicase in most non-photosynthetic protists such as Tetrahymena and amoebozoa. Nevertheless, this is not valid in most eukaryotes other than animals and fungi. According to the typical endosymbiotic scenario, POP is supposed to replace the proteobacterial DNA polymerase III in the initial eukaryotic cell that engulfed the proteobacterial endosymbiont.
POP became also used in the chloroplasts after the formation of the initial photosynthetic alga [ ]. During the evolution of eukaryotes, various proteins involved in the organellar replication were also replaced by non-cyanobacterial components [ ]. As shown in Figure 1 , the origins of chloroplast replication machinery and the enzymes involved in chloroplast transcription and translation are different in chloroplasts and cyanobacteria.
In other words, discontinuity must be defined by setting a reference to something continuous, which was supposed to be cyanobacterial endosymbiont—chloroplast continuity. In the current state of knowledge, the discontinuity notion could be replaced by diverse origins of various components of the chloroplast nucleoid.
Reproduction by binary fission is an important similarity of chloroplasts and cyanobacteria Item 3 in Table 1. Various prokaryotic components of division machinery are known. FtsZ, which is a tubulin-like protein that forms a ring at the site of cell division in bacteria, is also involved in chloroplast division in both green plants and red algae for reviews, see [ , ].
The division site is determined by the dynamic interaction of MinC, MinD, and MinE in bacteria, whereas the role of MinD and MinE in chloroplast division was identified in plants [ , ]. Nevertheless, the molecular architecture of the chloroplast division rings was elucidated in the model red alga, Cyanidioschyzon merolae [ ]. Phylogenetic analysis of FtsZ proteins showed that the chloroplast clades are sister to the cyanobacterial clade Type 2 tree in Figure 1.
See also Supplementary Material 7 of [ 50 ]. This point was not discussed in the past by researchers e. FtsZ is duplicated into FtsZ1 and Z2 in green algae and plants. FtsZ3 is also present in some plants. Chloroplast MinD only present in glaucophytes, green algae, and plants seemed to originate from cyanobacteria, whereas chloroplast MinE is not directly related to cyanobacterial MinE Figure 1.
MinD diverged from the root of the cyanobacterial clade C1-C2, rather than the base of cyanobacteria Figure 3 A. MinE is a small protein about amino acid residues , and the curious phylogenetic origin could result from insufficient phylogenetic signals.
These findings suggest that FtsZ, MinD, and MinE, which act in cell division in cyanobacteria, were introduced into chloroplasts via divergent processes, rather than by a single event of cyanobacterial endosymbiosis. This should also be studied further in the future.
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The Prokaryotes 2nd Edn. Springer-Verlag: Berlin, pp. A molecular timeline for the origin of photosynthetic eukaryotes. Globally distributed uncultivated oceanic N2-fixing cyanobacteria lack oxygenic photosystem II. Download references. You can also search for this author in PubMed Google Scholar. Reprints and Permissions. Dating the cyanobacterial ancestor of the chloroplast. ISME J 4, — Download citation. Received : 25 September Revised : 18 December Accepted : 06 January Welcome to Owlcation.
Natalie has an MSc in biology and is currently a researcher at Anglian Water. Structure of Plant Cells, Cyanobacteria, and Chloroplasts. Figure 1. Labeled diagram of a plant cell. Related Articles. By precy anza. By Alianess Benny Njuguna. By Jason Ponic.
By Linda Crampton. By L M Reid. By Eugene Brennan. By Rodric Anthony Johnson. By Dean Traylor. By Greg de la Cruz. However, plants still grew in ice-free areas, among them the seed fern Glossopteris , which is known only from Gondwanan landmasses. The seed ferns died out at the end of the Permian, and were replaced by Dicroidium and its relatives, which were also found throughout Gondwanaland.
Early podocarps may also have been present. The appearance of flowering plants. Gymnosperms, especially the cycads, remained the dominant land plants in the Jurassic - million years ago , but the Cretaceous - 65 million years ago saw the rise of the flowering plants angiosperms and their associated insect pollinators an example of coevolution.
There are around , species of angiosperms but they all share a particular set of features: flowers, fruit, and a distinctive life cycle. Because of this, angiosperms are assumed to be a monophyletic group. The angiosperms owe their success to the evolution of the flower.
The flower's pollen and nectar encourage pollinating animals to visit, increasing the odds of fertilisation by ensuring that pollen is transferred efficiently from flower to flower. The flowers of wind-pollinated angiosperms, e. After fertilisation the carpel and other parts of the flower are used to form fruit that aid dispersal of the seeds inside the fruit. In addition, the xylem vessels of angiosperms allow very rapid movement of water through the plant.
This means that flowering plants can keep their stomata open through much of the day, achieving higher photosynthetic rates than gymnosperms; this "spare" photosynthetic capacity can support the development of fruit. Two major groups of angiosperms are the dicotyledons more correctly, "eudicotyledons" and the monocotyledons, which include the grasses.
Grasses evolved in the Eocene As the world began to cool during the Miocene The fragmentation of forest habitats, and spread of grasslands, that accompanied this cooling trend are implicated in the evolution of humans. The Pleistocene Ice Ages were significant in the evolution of New Zealand plants as, together with the new habitats formed by the rise of the Southern Alps, they provided the conditions for the development of our extensive endemic alpine flora.
Other vegetation types are herb fields, grasslands, and shrub-lands, which depending on their situation can be described as coastal, lowland, or montane alpine.
During the last glaciation, , - 10, years ago, mean annual temperatures dropped by 4. There was extensive glaciation along the Southern Alps, extending to sea level on much of the West Coast, and there were small glaciers on the North Island's Tararua ranges and Central Plateau. During the coldest parts of the glacial, so much water was locked up in ice that sea levels were up to m lower and NZ was a continuous land mass.
These extreme conditions had particularly marked effects on the evolution and distribution of New Zealand's diverse alpine flora. Hence our high country plants are probably of relatively recent origin geologically speaking. Alpine plants are those found above the present tree line, but at times during glacial phases they would have extended down to the coast in much of New Zealand.
These plants have likely evolved in NZ by rapid adaptive radiation from lowland species following the end of a glacial period. Alternating warm and cold periods would have driven plant species up and down the emerging mountains, split up habitat zones, and provided a variety of refugia. All these would significantly increase the evolutionary pressures on this particular set of plants.
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