Nucleomorph

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Nucleomorph chloroplast.svg
Diagram of a four membraned chloroplast containing a nucleomorph.

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. [1] [2]

Contents

Organisms with known nucleomorphs

So far, only two monophyletic groups of organisms are known to contain plastids with a vestigial nucleus or nucleomorph: the cryptomonads [3] of the supergroup Cryptista and the chlorarachniophytes [4] of the supergroup Rhizaria, both of which have examples of sequenced nucleomorph genomes. [3] [4] Studies of the genomic organization and of the molecular phylogeny have shown that the nucleomorph of the cryptomonads used to be the nucleus of a red alga, whereas the nucleomorph of the chlorarchniophytes was the nucleus of a green alga. In both groups of organisms the plastids originate from engulfed photoautotrophic eukaryotes.

Of the two known plastids that contain nucleomorphs, both have four membranes, the nucleomorph residing in the periplastidial compartment, evidence of being engulfed by a eukaryote through phagocytosis. [1]

In addition, some species within the dinoflagellates that have gone through tertiary endosymbiosis also have endosymbionts with both a nucleus and mitochondria present. [5]

Nucleomorph genome

Nucleomorphs represent some of the smallest genomes ever sequenced. After the red or green alga was engulfed by a cryptomonad or chlorarachniophyte, respectively, its genome was reduced. The nucleomorph genomes of both cryptomonads and chlorarachniophytes converged upon a similar size from larger genomes. They retained only three chromosomes and many genes were transferred to the nucleus of the host cell, while others were lost entirely. [1] Chlorarachniophytes contain a nucleomorph genome that is diploid and cryptomonads contain a nucleomorph genome that is tetraploid. [6] The unique combination of host cell and complex plastid results in cells with four genomes: two prokaryotic genomes (mitochondrion and plastid of the red or green algae) and two eukaryotic genomes (nucleus of host cell and nucleomorph).

The model cryptomonad Guillardia theta became an important focus for scientists studying nucleomorphs. Its complete nucleomorph sequence was published in 2001, coming in at 551 Kbp. The G. theta sequence gave insight as to what genes were retained in nucleomorphs. Most of the genes that moved to the host cell involved protein synthesis, leaving behind a compact genome with mostly single-copy “housekeeping” genes (affecting transcription, translation, protein folding and degradation and splicing) and no mobile elements. The genome contains 513 genes, 465 of which code for protein. Thirty genes are considered “plastid” genes, coding for plastid proteins. [1] [7]

The genome sequence of another organism, the chlorarachniophyte Bigelowiella natans indicates that its nucleomorph is probably the vestigial nucleus of a green alga, whereas the nucleomorph in G. theta probably came from a red alga. The B. natans genome is smaller than that of G. theta, with about 373 Kbp and contains 293 protein-coding genes as compared to the 465 genes in G. theta. B. natans also only has 17 genes that code for plastid proteins, again fewer than G. theta. Comparisons between the two organisms have shown that B. natans contains significantly more introns (852) than G. theta (17). B. natans also had smaller introns, ranging from 18-21 bp, whereas G. theta’s introns ranged from 42-52 bp. [1]

Both the genomes of B. natans and G. theta display evidence of genome reduction besides elimination of genes and tiny size, including elevated composition of adenine (A) and thymine (T), and high substitution rates. [4] [7] [8]

Persistence of nucleomorphs

There are no recorded instances of vestigial nuclei in any other secondary plastid-containing organisms, yet they have been retained independently in the cryptomonads and chlorarachniophytes. Plastid gene transfer happens frequently in many organisms, and it is unusual that these nucleomorphs have not disappeared entirely. One theory as to why these nucleomorphs have not disappeared as they have in other groups is that introns present in nucleomorphs are not recognized by host spliceosomes because they are too small and therefore cannot be cut and later incorporated into host DNA.

Nucleomorphs also often code for many of their own critical functions, like transcription and translation. [9] Some say that as long as there exists a gene in the nucleomorph that codes for proteins necessary for the plastid’s functioning that are not produced by the host cell, the nucleomorph will persist. [1] In cryptophytes and chlorarachniophytes all DNA transfer between the nucleomorph and host genome seems to have ceased, but the process is still going on in a few dinoflagellates. [10]

See also

Related Research Articles

<span class="mw-page-title-main">Chloroplast</span> Plant organelle that conducts photosynthesis

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.

<span class="mw-page-title-main">Endosymbiont</span> Organism that lives within the body or cells of another organism

An endosymbiont or endobiont is any organism that lives within the body or cells of another organism most often, though not always, in a mutualistic relationship. This phenomenon is known as endosymbiosis. Examples are nitrogen-fixing bacteria, which live in the root nodules of legumes, single-cell algae inside reef-building corals and bacterial endosymbionts that provide essential nutrients to insects.

<span class="mw-page-title-main">Symbiogenesis</span> Evolutionary theory holding that eukaryotic organelles evolved through symbiosis with prokaryotes

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.

<span class="mw-page-title-main">Cryptomonad</span> Subphylum of algae

The cryptomonads are a group of algae, most of which have plastids. They are common in freshwater, and also occur in marine and brackish habitats. Each cell is around 10–50 μm in size and flattened in shape, with an anterior groove or pocket. At the edge of the pocket there are typically two slightly unequal flagella.

<span class="mw-page-title-main">Plastid</span> Plant cell organelles that perform photosynthesis and store starch

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

<span class="mw-page-title-main">Chlorarachniophyte</span> Group of algae

The chlorarachniophytes are a small group of exclusively marine algae widely distributed in tropical and temperate waters. They are typically mixotrophic, ingesting bacteria and smaller protists as well as conducting photosynthesis. Normally they have the form of small amoebae, with branching cytoplasmic extensions that capture prey and connect the cells together, forming a net. They may also form flagellate zoospores, which characteristically have a single subapical flagellum that spirals backwards around the cell body, and walled coccoid cells.

<span class="mw-page-title-main">Chromista</span> Eukaryotic biological kingdom

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.

Cryptomonas is the name-giving genus of the Cryptomonads established by German biologist Christian Gottfried Ehrenberg in 1831. The algae are common in freshwater habitats and brackish water worldwide and often form blooms in greater depths of lakes. The cells are usually brownish or greenish in color and are characteristic of having a slit-like furrow at the anterior. They are not known to produce any toxins. They are used to feed small zooplankton, which is the food source for small fish in fish farms. Many species of Cryptomonas can only be identified by DNA sequencing. Cryptomonas can be found in several marine ecosystems in Australia and South Korea.

<span class="mw-page-title-main">Archaeplastida</span> Clade of eukaryotes containing land plants and some algae

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.

<span class="mw-page-title-main">Cryptophyceae</span> Class of single-celled organisms

The cryptophyceae are a class of algae, most of which have plastids. About 230 species are known, and they are common in freshwater, and also occur in marine and brackish habitats. Each cell is around 10–50 μm in size and flattened in shape, with an anterior groove or pocket. At the edge of the pocket there are typically two slightly unequal flagella.

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.

<span class="mw-page-title-main">SAR supergroup</span> Eukaryotes superphylum

SAR or Harosa is a highly diverse clade of eukaryotes, often considered a supergroup, that includes stramenopiles (heterokonts), alveolates, and rhizarians. It is a node-based taxon, including all descendants of the three groups' last common ancestor, and comprises most of the now-rejected Chromalveolata. Their sister group has been found to be telonemids, with which they make up the TSAR clade.

<i>Rhodomonas</i> Genus of single-celled organisms

Rhodomonas is a genus of cryptomonads. It is characterized by its red colour, the square-shaped plates of its inner periplast, its short furrow ending in a gullet, and a distinctly shaped chloroplast closely associated with its nucleomorph. Historically, Rhodomonas was characterized by its red chloroplast alone, but this no longer occurs as its taxonomy has become increasingly based on molecular and cellular data. Currently, there is some debate about the taxonomic validity of Rhodomonas as a genus and further research is needed to verify its taxonomic status. Rhodomonas is typically found in marine environments, although freshwater reports exist. It is commonly used as a live feed for various aquaculture species.

<i>Guillardia</i> Genus of single-celled organisms

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

<i>Hemiselmis</i> Genus of single-celled organisms

Hemiselmis is a genus of cryptomonads.

Bigelowiella natans is a species of Chlorarachniophyte alga that is a model organism for the Rhizaria.

Durinskia is a genus of dinoflagellates that can be found in freshwater and marine environments. This genus was created to accommodate its type species, Durinskia baltica, after major classification discrepancies were found. While Durinskia species appear to be typical dinoflagellates that are armored with cellulose plates called theca, the presence of a pennate diatom-derived tertiary endosymbiont is their most defining characteristic. This genus is significant to the study of endosymbiotic events and organelle integration since structures and organelle genomes in the tertiary plastids are not reduced. Like some dinoflagellates, species in Durinskia may cause blooms.

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.

References

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  5. Tertiary Endosymbiosis in Two Dinotoms Has Generated Little Change in the Mitochondrial Genomes of Their Dinoflagellate Hosts and Diatom Endosymbionts - PLOS
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  10. Organellogenesis still a work in progress in novel dinoflagellates

According to GenBank release 164 (Feb 2008), there are 13 Cercozoa and 181 Cryptophyta entries (an entry is the submission of a sequence to the DDBJ/EMBL/GenBank public database of sequences). Most sequenced organisms were:

Guillardia theta: 54; Rhodomonas salina: 18; Cryptomonas sp.: 15; Chlorarachniophyceae sp.:10; Cryptomonas paramecium: 9; Cryptomonas erosa: 7.