Ostreococcus lucimarinus: Difference between revisions

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<ref>[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3847443/ Bartlett et al.: Oncolytic viruses as therapeutic cancer vaccines. Molecular Cancer 2013 12:103.]</ref>
<ref>[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3847443/ Bartlett et al.: Oncolytic viruses as therapeutic cancer vaccines. Molecular Cancer 2013 12:103.]</ref>
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==Section 3==
Include some current research, with at least one figure showing data.<br>
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==Section 4==
==Section 4==

Revision as of 21:48, 30 April 2018

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Introduction


By Sarah Dendy

Ostreococcus are the smallest known eukaryotes1. They are single-celled but contain membrane-bound nuclei and a single chloroplast. They are approximately 1 μm in diameter, and are considered picophytoplankton.

Genomics

Ostreococcus lucimarinus, and a related species, Ostreococcus tauri, have been fully genome-sequenced. The genome of O. lucimarinus is 13.2 million base pairs, distributed on 21 chromosomes1, and is estimated to contain 7,651 genes1. High levels of similarity between O. lucimarinus and O. tauri provide insights to potential evolutionary mechanisms of the sister taxa. O. tauri has a genome of 12.6 million base pairs, which code an estimated 7,892 genes. Of these, 6,753 are orthologous to those of O lucimarinus. O tauri has 20 chromosomes, of which eighteen correspond very closely to those of O. lucimarinus. The other three O. lucimarinus chromosomes do not resemble those of its sister species, nor do they closely resemble anything else in the Ostreococcus genome. The origin of these chromosomes is somewhat mysterious. Chromosome 18, one such mysterious chromosome in O. lucimarinus, is the smallest chromosome of the organism. Its nucleotide sequence aligns with that of O. tauri chromosome 19, with about 5% of nucleotide sequence corresponding between the two species. By contrast, in other chromosomes, these species had 80-90% sequence homology. Chromosome 18 contains an estimated 83 genes, many of which code for proteins that most closely resemble those of bacteria. One enzyme, OSTLU28425, closely resembles the UDP-N-acetylglucosamine 2-epimerase of Microscilla marina, a marine bacterium. Palenik et al (2007) interpret this to indicate recent horizontal gene transfer between the planktonic bacterium and the miniscule planktonic eukaryote. They go on to propose that horizontal gene transfer between planktonic organisms, particularly in genes for sugar-processing or packaging pathways which could alter cell-surface composition and potentially hinder grazers or otherwise change microecological dynamics, will become a recurring theme in plankton genomics. Micronutrients The way in which Ostreococcus processes micronutrients, including metals, distinguishes it from other plankton. O. lucimarinus creates a large number of selenocysteine-containing enzymes (selenoproteins), which are enzymes whose catalytic activity is heightened by substituting a cysteine in an active site to a selenocysteine. Theoretically, this substitution allows cells to have heightened activity from a single enzyme, and therefore need to manufacture fewer enzymes to achieve the same physiological effects. In highly-expressed enzymes, this allows a cell to save molecular resources like nitrogen, because the manufacture of fewer proteins translates to fewer nitrogen atoms being associated with protein backbone. This allows cells to more efficiently use amino acids, which may be valuable at the extremes of livable conditions. However, selenoprotein abundance is limited by availability of selenium, as well as by the evolution of complex recognition systems in coding DNA, which must affix a selenocysteine where typical DNA machinery would recognize a stop codon (TGA). Though iron is a limiting nutrient in many ecosystems, including in marine planktonic ecosystems, Ostreococcus has no described system of iron uptake analogous to those of related organisms, like diatoms. Ostreococcus has no ferric reductase, multicopper oxidase, or ferric permease, all of which are common elements of eukaryotic iron uptake systems (though O. tauri may have a multicopper oxidase, which is not found in any other lineage of the genus). Predicted adaptations to low iron levels are not found in O. lucimarinus. Several iron atoms are required for molecules critical to photosynthesis, the organism’s main means of survival. Also of note, O lucimarinus lacks systems for responding to high levels of copper toxicity through a phytochelatin synthase. This organism presumably must have novel ways of responding to low iron levels, or of responding to copper toxicity, but they are not currently known or described. Furthermore, Ostreococcus requires some of its micronutrients, like vitamin B12, from the environment, because it lacks to genetic pathways to endogenously synthesize this nutrient, but still depends upon it for other physiological functions.

Evolution of the Genus

Ostreococcus has several adaptations specific to allowing its incredibly small size. Comparisons to Chlamydomonas, a closely related genus of photosynthetic diatoms, reveals a large number of genes which are common and well-characterized through the plant kingdom. Some of these well-known genes are nonetheless absent in Ostreococcus, but because Chlamydomonas demonstrates that they already existed in an ancestral phytoplankton phase, a fair assumption is that they have been lost in Ostreococcus. Fascinatingly, one gene which is found in the organelles of plants and algae is actually found in the nuclear genome of Ostreococcus. This gene, CcsA, codes a hydrophobic protein significant to the handling of heme groups in system II cytochrome biogenesis. This is the first described example of presumed gene transfer from the organelle of a cell to the cell nucleus. The implications of this observation are enormous, because organelle genomes are used in countless cell lineages for developing phylogenetic and evolutionary relationships. If horizontal gene transfer, as documented here, occurs between organelles and cell nuclei, many existing taxonomic analyses could be subject to revision with the inclusion of nuclear data. However, this may be a relatively rare occurrence, and perhaps only possible in Ostreococcus because the extreme cell size puts selective pressure on novel gene dynamics and behaviors. Furthermore, probably because pressure toward small cell size has pressured these organisms to reduce their amount of genetic material, Ostreococcus has developed a number of fusion proteins. Around 348 fusion proteins were identified from O. lucimarinus, of which 49 are known to combine multiple enzymatic functions, and the remainder may be either true fusions or combinations of anticipated genes, without additive enzymatic functions. Interestingly, some fusions occur between proteins originating from different biochemical pathways. Also of interest, despite the pressure to reduce genome size through such apparently drastic means as fusing functional proteins, O. lucimarinus still has introns and noncoding sequences in its nuclear DNA. Though several other eukaryotic characteristics, such as broadly-shared chromatin proteins, have been lost in Ostreococcus, the eukaryotic capacity for post-transcriptional splicing remains in this lineage. GapB2 is a gene found in Ostreococcus with significant implications for the evolution of the genus. GapB is an abbreviation for glyceraldehyde-3-phosphate dehydrogenase, which is a cell-signaling component for down-regulating the Calvin cycle in land plants during the night. GapB originates from the duplication of another glyceraldehyde-3-phosphate dehydrogenase gene, known as GapA, with a modification on its C-terminal end from a gene with related function, known as CP12. However, Ostreococcus provides evidence against the duplication-hypothesis for the origin of GapB, because it contains a copy of this gene, as does Mesostigma viride, a phylogenetically separate green algae. If the duplication had arisen once, GapB should appear in only one of these lineages, not both. The fact of its presence may be another example of lateral gene transfer, which is the best existing explanation for several genetic components of the Ostreococccus genus. More data on the rate and character of lateral gene transfer in these organisms would be invaluable to an understanding of their evolution, as well as life histories. Significantly, lateral gene transfer of UDP-N-acetylglucosamine 2-epimerase to Ostreococcus is anticipated from a bacterium, whereas transfer of glyceraldehyde-3-phosphate dehydrogenase B is from an algae, another eukaryote. Also interestingly, Ostreococcus lacks the CP12 gene, which functions in a role similar to that of GapB. Ostreococcus has a genome reduced in size in many areas; possibly, the deletion of CP12 is a continuation on this theme, and represents an instance in which lateral gene transfer allows the recipient organism to capitalize on its new gene repertoire to streamline its genome overall. Yet another protein group valuable for evolutionary study is the polyketide synthase enzymes3, relevant to lipid metabolism. Polyketide synthases are found in Ostreococcus, as well as in the related genus Chlamydomonas. This is extremely unusual, because these enzymes typically occur in fungi and bacteria. Though intuitively this should represent an instance of lateral gene transfer, in fact the polyketide synthases of protists, including Ostreococcus, differ from those of all potential donor lineages. Therefore, it is unlikely that Ostreococcus polyketide synthase originated from a marine bacterium. Whether this enzyme group evolved spontaneously in Ostreococcus and Chlamydomonas, versus in other organisms, or whether it evolved once and was lost in a large number of eukaryotes, is difficult to ascertain from existing data, and not yet known. 1) http://www.pnas.org/content/104/18/7705 2) http://bioinformatics.psb.ugent.be/pdf/JME_64_601_2007.pdf 3) http://bioinformatics.psb.ugent.be/pdf/protist159.pdf



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Section 4

Conclusion

References



Authored for BIOL 238 Microbiology, taught by Joan Slonczewski, 2018, Kenyon College.