Plastid evolution

Last updated September 01, 2024

A plastid is a membrane-bound organelle found in plants, algae and other eukaryotic organisms that contribute to the production of pigment molecules. Most plastids are photosynthetic, thus leading to color production and energy storage or production. There are many types of plastids in plants alone, but all plastids can be separated based on the number of times they have undergone endosymbiotic events. Currently there are three types of plastids; primary, secondary and tertiary. Endosymbiosis is reputed to have led to the evolution of eukaryotic organisms today, although the timeline is highly debated.^[1]

Primary endosymbiosis

The first plastid is highly accepted within the scientific community to be derived from the engulfment of cyanobacteria ancestor into a eukaryotic organism.^[2] Evidence supporting this belief is found in many morphological similarities such as the presence of a two plasma membranes. It is thought that the first membrane belonged to the cyanobacteria ancestor. During phagocytosis, a vesicle engulfs a molecule with its plasma membrane to allow safe import. When the cyanobacteria became engulfed, the bacterium avoided digestion and led to the double membrane found in primary plastids.^[2] However, in order to live in symbiosis, the eukaryotic cell that engulfed the cyanobacterium must now provide proteins and metabolites to maintain the functions of the bacteria in exchange for energy. Thus, an engulfed cyanobacterium must give up some of its genetic material to allow for endosymbiotic gene transfer to the eukaryote, a phenomenon that is thought to be extremely rare due to the "learned nature" of the interactions that must occur between the cells to allow for processes such as; gene transfer, protein localization, excretion of highly reactive metabolites, and DNA repair.^[1] This would mean, a reduction in genome size, for the cyanobacteria, but also an increase in cytobacterial genes within the eukaryotic genome. The genus of Synechocystis sp., strain PCC6803 is a unicellular fresh water cyanobacteria that encodes 3725 genes, and a 3.9 Mb sized genome.^[3] However, most plastids rarely exceed 200 protein coding genes.^[2] A recent study sequenced the genome of a cyanobacterium that was living extracellularly in endosymbiosis with the water-fern Azolla filiculoides. Endosymbiosis was supported by the fact that the cyanobacterium was unable to grow autonomously, and the observance of the cyanobacterium being vertically transferred between succeeding generations. After cyanobacterium genome analysis, the researchers found that over 30% of the genome was made up of pseudogenes. In addition, roughly 600 transposable elements were found within the genome. The pseudogenes were found in genes such as dnaA, DNA repair genes, glycolysis and nutrient uptake genes. dnaA is essential to initiation of DNA replication in prokaryotic organisms, thus Azolla filiculoides is thought to provide nutrients, and transcriptional factors for DNA replication in exchange for fixed nitrogen that is not readily available in water.^[4] Although the cyanobacterium had not been completely engulfed in the eukaryotic organism, the relationship is thought to demonstrate the precursor to endosymbiotic primary plastids.

Secondary endosymbiosis

Secondary endosymbiosis results in the engulfment of an organism that has already performed primary endosymbiosis. Thus, four plasma membranes are formed. The first originating from the cyanobacteria, the second from the eukaryote that engulfed the cyanobacteria, and the third from the eukaryote who engulfed the primary endosymbiotic eukaryote.^[5] Chloroplasts contain 16S rRNA and 23S rRNA. 16S and 23S rRNA is found only in prokaryotes by definition.^[6] Chloroplasts and mitochondria also replicate semi-autonomously outside of the cell cycle replication system via binary fission.^[6] Consistent with the theory, decreased genome size within the organelle and gene integration into the nucleus occurred. Chloroplasts genomes encode 50-200 proteins, compared to the thousands in cyanobacterium.^[7] Furthermore, in Arabidopsis, nearly 20% of the nuclear genome originate from cyanobacterium, the highly recognized origin of chloroplasts.^[7] Recent studies have been able to identify the speed and size at which chloroplast genes are able to incorporate themselves into the host genome. Using chloroplast transformation genes encoding spectinomycin and kanamycin resistance were inserted into the DNA of chloroplasts found in tobacco plants. After subjecting the plants to spectinomycin and kanamycin selection, some plants began to tolerate spectinomycin and kanamycin.^[7] Roughly 1 in every 5 million cells on the tobacco leaves highly expressed spectinomycin and kanamycin resistant genes.^[7] By using the cells expressing resistances, they were able to grow tobacco from these cell to maturity. Once mature, the plants were mated with wild-type plants, and 50% of the progeny expressed spectinomycin and kanamycin resistance genes. Pollen was thought not to be able to transfer chloroplast DNA in tobacco (which later turned out not to be as true as was thought at the time),^[8] thus leading to believe that the genes were incorporated into the tobaccos genome. Furthermore, 11kb of integrated chloroplast DNA was introduced to the host genome, transferring more DNA that previously predicted at a faster rate than previously predicted.^[7]

Tertiary endosymbiosis

Although previous endosymbiotic events resulted in the increase in the number of membranes, tertiary plastids can have 3-4 membranes. The most largely studied tertiary plastids are found in dinoflagellates.^[9] Tertiary plastids are believed to have been derived from a red algae replacing secondary plastids.^[9] Consistent with our previous rules for reduction in genome size, and incorporation of genes into the host genome, tertiary plastid genome consists of about 14 genes. These genes are broken down further into small minicircles that contain 1-3 genes.^[10] These genomes are circular like prokaryotic genomes. Further, they only encode atpA, atpB, petB, perD, psaA, psaB, psbA-E, psbI, 16S and 23S rRNA. These genes play vital proteins used in photosystem I and II, indicating further their cyanobacterial origin.

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<span class="mw-page-title-main">Cell (biology)</span> Basic unit of many life forms

The cell is the basic structural and functional unit of all forms of life. Every cell consists of cytoplasm enclosed within a membrane; many cells contain organelles, each with a specific function. The term comes from the Latin word cellula meaning 'small room'. Most cells are only visible under a microscope. Cells emerged on Earth about 4 billion years ago. All cells are capable of replication, protein synthesis, and motility.

A chloroplast is a type of membrane-bound organelle known as a plastid that conducts photosynthesis mostly in plant and algal cells. The photosynthetic pigment chlorophyll captures the energy from sunlight, converts it, and stores it in the energy-storage molecules ATP and NADPH while freeing oxygen from water in the cells. The ATP and NADPH is then used to make organic molecules from carbon dioxide in a process known as the Calvin cycle. Chloroplasts carry out a number of other functions, including fatty acid synthesis, amino acid synthesis, and the immune response in plants. The number of chloroplasts per cell varies from one, in unicellular algae, up to 100 in plants like Arabidopsis and wheat.

In cell biology, an organelle is a specialized subunit, usually within a cell, that has a specific function. The name organelle comes from the idea that these structures are parts of cells, as organs are to the body, hence organelle, the suffix -elle being a diminutive. Organelles are either separately enclosed within their own lipid bilayers or are spatially distinct functional units without a surrounding lipid bilayer. Although most organelles are functional units within cells, some function units that extend outside of cells are often termed organelles, such as cilia, the flagellum and archaellum, and the trichocyst.

Symbiogenesis is the leading evolutionary theory of the origin of eukaryotic cells from prokaryotic organisms. The theory holds that mitochondria, plastids such as chloroplasts, and possibly other organelles of eukaryotic cells are descended from formerly free-living prokaryotes taken one inside the other in endosymbiosis. Mitochondria appear to be phylogenetically related to Rickettsiales bacteria, while chloroplasts are thought to be related to cyanobacteria.

Cyanobacteria, also called Cyanobacteriota or Cyanophyta, are a phylum of autotrophic gram-negative bacteria that can obtain biological energy via oxygenic photosynthesis. The name "cyanobacteria" refers to their bluish green (cyan) color, which forms the basis of cyanobacteria's informal common name, blue-green algae, although as prokaryotes they are not scientifically classified as algae.

A plastid is a membrane-bound organelle found in the cells of plants, algae, and some other eukaryotic organisms. Plastids are considered to be intracellular endosymbiotic cyanobacteria.

Chromista is a proposed but polyphyletic biological kingdom, refined from the Chromalveolata, consisting of single-celled and multicellular eukaryotic species that share similar features in their photosynthetic organelles (plastids). It includes all eukaryotes whose plastids contain chlorophyll c and are surrounded by four membranes. If the ancestor already possessed chloroplasts derived by endosymbiosis from red algae, all non-photosynthetic Chromista have secondarily lost the ability to photosynthesise. Its members might have arisen independently as separate evolutionary groups from the last eukaryotic common ancestor.

Nucleomorphs are small, vestigial eukaryotic nuclei found between the inner and outer pairs of membranes in certain plastids. They are thought to be vestiges of primitive red and green algal nuclei that were engulfed by a larger eukaryote. Because the nucleomorph lies between two sets of membranes, nucleomorphs support the endosymbiotic theory and are evidence that the plastids containing them are complex plastids. Having two sets of membranes indicate that the plastid, a prokaryote, was engulfed by a eukaryote, an alga, which was then engulfed by another eukaryote, the host cell, making the plastid an example of secondary endosymbiosis.

Chloroplasts contain several important membranes, vital for their function. Like mitochondria, chloroplasts have a double-membrane envelope, called the chloroplast envelope, but unlike mitochondria, chloroplasts also have internal membrane structures called thylakoids. Furthermore, one or two additional membranes may enclose chloroplasts in organisms that underwent secondary endosymbiosis, such as the euglenids and chlorarachniophytes.

A nuclear gene is a gene that has its DNA nucleotide sequence physically situated within the cell nucleus of a eukaryotic organism. This term is employed to differentiate nuclear genes, which are located in the cell nucleus, from genes that are found in mitochondria or chloroplasts. The vast majority of genes in eukaryotes are nuclear.

The Archaeplastida are a major group of eukaryotes, comprising the photoautotrophic red algae (Rhodophyta), green algae, land plants, and the minor group glaucophytes. It also includes the non-photosynthetic lineage Rhodelphidia, a predatorial (eukaryotrophic) flagellate that is sister to the Rhodophyta, and probably the microscopic picozoans. The Archaeplastida have chloroplasts that are surrounded by two membranes, suggesting that they were acquired directly through a single endosymbiosis event by phagocytosis of a cyanobacterium. All other groups which have chloroplasts, besides the amoeboid genus Paulinella, have chloroplasts surrounded by three or four membranes, suggesting they were acquired secondarily from red or green algae. Unlike red and green algae, glaucophytes have never been involved in secondary endosymbiosis events.

An apicoplast is a derived non-photosynthetic plastid found in most Apicomplexa, including Toxoplasma gondii, and Plasmodium falciparum and other Plasmodium spp., but not in others such as Cryptosporidium. It originated from algae through secondary endosymbiosis; there is debate as to whether this was a green or red alga. The apicoplast is surrounded by four membranes within the outermost part of the endomembrane system. The apicoplast hosts important metabolic pathways like fatty acid synthesis, isoprenoid precursor synthesis and parts of the heme biosynthetic pathway.

A transplastomic plant is a genetically modified plant in which genes are inactivated, modified or new foreign genes are inserted into the DNA of plastids like the chloroplast instead of nuclear DNA.

The following outline is provided as an overview of and topical guide to cell biology:

Paulinella is a genus of at least eleven species including both freshwater and marine amoeboids. Like many members of euglyphids it is covered by rows of siliceous scales, and use filose pseudopods to crawl over the substrate of the benthic zone.

A prokaryote is a single-cell organism whose cell lacks a nucleus and other membrane-bound organelles. The word prokaryote comes from the Ancient Greek πρό 'before' and κάρυον 'nut, kernel'. In the two-empire system arising from the work of Édouard Chatton, prokaryotes were classified within the empire Prokaryota. However in the three-domain system, based upon molecular analysis, prokaryotes are divided into two domains: Bacteria and Archaea. Organisms with nuclei are placed in a third domain, Eukaryota.

Guillardia is a genus of marine biflagellate cryptomonad algae with a plastid obtained through secondary endosymbiosis of a red alga.

The eukaryotes constitute the domain of Eukarya or Eukaryota, organisms whose cells have a membrane-bound nucleus. All animals, plants, fungi, and many unicellular organisms are eukaryotes. They constitute a major group of life forms alongside the two groups of prokaryotes: the Bacteria and the Archaea. Eukaryotes represent a small minority of the number of organisms, but given their generally much larger size, their collective global biomass is much larger than that of prokaryotes.

Chloroplast DNA (cpDNA) is the DNA located in chloroplasts, which are photosynthetic organelles located within the cells of some eukaryotic organisms. Chloroplasts, like other types of plastid, contain a genome separate from that in the cell nucleus. The existence of chloroplast DNA was identified biochemically in 1959, and confirmed by electron microscopy in 1962. The discoveries that the chloroplast contains ribosomes and performs protein synthesis revealed that the chloroplast is genetically semi-autonomous. The first complete chloroplast genome sequences were published in 1986, Nicotiana tabacum (tobacco) by Sugiura and colleagues and Marchantia polymorpha (liverwort) by Ozeki et al. Since then, a great number of chloroplast DNAs from various species have been sequenced.

Eukaryogenesis, the process which created the eukaryotic cell and lineage, is a milestone in the evolution of life, since eukaryotes include all complex cells and almost all multicellular organisms. The process is widely agreed to have involved symbiogenesis, in which an archeon and a bacterium came together to create the first eukaryotic common ancestor (FECA). This cell had a new level of complexity and capability, with a nucleus, at least one centriole and cilium, facultatively aerobic mitochondria, sex, a dormant cyst with a cell wall of chitin and/or cellulose and peroxisomes. It evolved into a population of single-celled organisms that included the last eukaryotic common ancestor (LECA), gaining capabilities along the way, though the sequence of the steps involved has been disputed, and may not have started with symbiogenesis. In turn, the LECA gave rise to the eukaryotes' crown group, containing the ancestors of animals, fungi, plants, and a diverse range of single-celled organisms.

References

1 2 Gray MW (August 2010). "Rethinking plastid evolution". EMBO Reports. 11 (8): 562–3. doi:10.1038/embor.2010.107. PMC 2920437 . PMID 20661242.
1 2 3 Archibald JM (January 2009). "The puzzle of plastid evolution". Current Biology. 19 (2): R81-8. Bibcode:2009CBio...19..R81A. doi: 10.1016/j.cub.2008.11.067 . PMID 19174147.
↑ Nakao M, Okamoto S, Kohara M, Fujishiro T, Fujisawa T, Sato S, Tabata S, Kaneko T, Nakamura Y (January 2010). "CyanoBase: the cyanobacteria genome database update 2010". Nucleic Acids Research. 38 (Database issue): D379-81. doi:10.1093/nar/gkp915. PMC 2808859 . PMID 19880388.
↑ Ran L, Larsson J, Vigil-Stenman T, Nylander JA, Ininbergs K, Zheng WW, Lapidus A, Lowry S, Haselkorn R, Bergman B (July 2010). "Genome erosion in a nitrogen-fixing vertically transmitted endosymbiotic multicellular cyanobacterium". PLOS ONE. 5 (7): e11486. Bibcode:2010PLoSO...511486R. doi: 10.1371/journal.pone.0011486 . PMC 2900214 . PMID 20628610.
↑ McFadden GI (2001). "Primary and Secondary Endosymbiosis and the Origin of Plastids". Journal of Phycology. 37 (6): 951–959. Bibcode:2001JPcgy..37..951M. doi:10.1046/j.1529-8817.2001.01126.x. ISSN 1529-8817. S2CID 51945442.
1 2 Harris EH, Boynton JE, Gillham NW (December 1994). "Chloroplast ribosomes and protein synthesis". Microbiological Reviews. 58 (4): 700–54. doi:10.1128/MMBR.58.4.700-754.1994. PMC 372988 . PMID 7854253.
1 2 3 4 5 Martin W (July 2003). "Gene transfer from organelles to the nucleus: frequent and in big chunks". Proceedings of the National Academy of Sciences of the United States of America. 100 (15): 8612–4. Bibcode:2003PNAS..100.8612M. doi: 10.1073/pnas.1633606100 . PMC 166356 . PMID 12861078.
↑ Ruf, Stephanie; Karcher, Daniel; Bock, Ralph (24 April 2007). "Determining the transgene containment level provided by chloroplast transformation". Proceedings of the National Academy of Sciences. 104 (17): 6998–7002. doi: 10.1073/pnas.0700008104 . PMC 1849964 . PMID 17420459.
1 2 Reyes-Prieto, A.; Yoon, H.S.; Bhattacharya, D. (2009), "Marine Algal Genomics and Evolution", Encyclopedia of Ocean Sciences, Elsevier, pp. 552–559, doi:10.1016/b978-012374473-9.00779-7, ISBN 9780123744739, S2CID 83233023
↑ Yoon, Hwan Su; Hackett, Jeremiah D.; Van Dolah, Frances M.; Nosenko, Tetyana; Lidie, Kristy L.; Bhattacharya, Debashish (2005-03-02). "Tertiary Endosymbiosis Driven Genome Evolution in Dinoflagellate Algae". Molecular Biology and Evolution. 22 (5): 1299–1308. doi: 10.1093/molbev/msi118 . ISSN 1537-1719. PMID 15746017.

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[:3-1] 1 2 Gray MW (August 2010). "Rethinking plastid evolution". EMBO Reports. 11 (8): 562–3. doi:10.1038/embor.2010.107. PMC 2920437 . PMID 20661242.

[:4-2] 1 2 3 Archibald JM (January 2009). "The puzzle of plastid evolution". Current Biology. 19 (2): R81-8. Bibcode:2009CBio...19..R81A. doi: 10.1016/j.cub.2008.11.067 . PMID 19174147.

[3] Nakao M, Okamoto S, Kohara M, Fujishiro T, Fujisawa T, Sato S, Tabata S, Kaneko T, Nakamura Y (January 2010). "CyanoBase: the cyanobacteria genome database update 2010". Nucleic Acids Research. 38 (Database issue): D379-81. doi:10.1093/nar/gkp915. PMC 2808859 . PMID 19880388.

[pmid20628610-4] Ran L, Larsson J, Vigil-Stenman T, Nylander JA, Ininbergs K, Zheng WW, Lapidus A, Lowry S, Haselkorn R, Bergman B (July 2010). "Genome erosion in a nitrogen-fixing vertically transmitted endosymbiotic multicellular cyanobacterium". PLOS ONE. 5 (7): e11486. Bibcode:2010PLoSO...511486R. doi: 10.1371/journal.pone.0011486 . PMC 2900214 . PMID 20628610.

[5] McFadden GI (2001). "Primary and Secondary Endosymbiosis and the Origin of Plastids". Journal of Phycology. 37 (6): 951–959. Bibcode:2001JPcgy..37..951M. doi:10.1046/j.1529-8817.2001.01126.x. ISSN 1529-8817. S2CID 51945442.

[:5-6] 1 2 Harris EH, Boynton JE, Gillham NW (December 1994). "Chloroplast ribosomes and protein synthesis". Microbiological Reviews. 58 (4): 700–54. doi:10.1128/MMBR.58.4.700-754.1994. PMC 372988 . PMID 7854253.

[:6-7] 1 2 3 4 5 Martin W (July 2003). "Gene transfer from organelles to the nucleus: frequent and in big chunks". Proceedings of the National Academy of Sciences of the United States of America. 100 (15): 8612–4. Bibcode:2003PNAS..100.8612M. doi: 10.1073/pnas.1633606100 . PMC 166356 . PMID 12861078.

[8] Ruf, Stephanie; Karcher, Daniel; Bock, Ralph (24 April 2007). "Determining the transgene containment level provided by chloroplast transformation". Proceedings of the National Academy of Sciences. 104 (17): 6998–7002. doi: 10.1073/pnas.0700008104 . PMC 1849964 . PMID 17420459.

[:02-9] 1 2 Reyes-Prieto, A.; Yoon, H.S.; Bhattacharya, D. (2009), "Marine Algal Genomics and Evolution", Encyclopedia of Ocean Sciences, Elsevier, pp. 552–559, doi:10.1016/b978-012374473-9.00779-7, ISBN 9780123744739, S2CID 83233023

[10] Yoon, Hwan Su; Hackett, Jeremiah D.; Van Dolah, Frances M.; Nosenko, Tetyana; Lidie, Kristy L.; Bhattacharya, Debashish (2005-03-02). "Tertiary Endosymbiosis Driven Genome Evolution in Dinoflagellate Algae". Molecular Biology and Evolution. 22 (5): 1299–1308. doi: 10.1093/molbev/msi118 . ISSN 1537-1719. PMID 15746017.

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