Molecular Evolution of Tubulins in Diatoms.
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ABSTRACT:
SUBMITTER: Khabudaev KV
PROVIDER: S-EPMC8776100 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Diatoms are highly productive single-celled algae that form an intricately patterned silica cell wall after every cell division. They take up and utilize silicic acid from seawater via silicon transporter (SIT) proteins. This study examined the evolution of the SIT gene family to identify potential genetic adaptations that enable diatoms to thrive in the modern ocean. By searching for sequence homologs in available databases, the diversity of organisms found to encode SITs increased substantially and included all major diatom lineages and other algal protists. A bacterial-encoded gene with homology to SIT sequences was also identified, suggesting that a lateral gene transfer event occurred between bacterial and protist lineages. In diatoms, the SIT genes diverged and diversified to produce five distinct clades. The most basal SIT clades were widely distributed across diatom lineages, while the more derived clades were lineage-specific, which together produced a distinct repertoire of SIT types among major diatom lineages. Differences in the predicted protein functional domains encoded among SIT clades suggest that the divergence of clades resulted in functional diversification among SITs. Both laboratory cultures and natural communities changed transcription of each SIT clade in response to experimental or environmental growth conditions, with distinct transcriptional patterns observed among clades. Together, these data suggest that the diversification of SITs within diatoms led to specialized adaptations among diatoms lineages, and perhaps their dominant ability to take up silicic acid from seawater in diverse environmental conditions.
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Project description:Codon usage bias (CUB)-preferential use of one of the synonymous codons, has been described in a wide range of organisms from bacteria to mammals, but it has not yet been studied in marine phytoplankton. CUB is thought to be caused by weak selection for translational accuracy and efficiency. Weak selection can overpower genetic drift only in species with large effective population sizes, such as Drosophila that has relatively strong CUB, while organisms with smaller population sizes (e.g., mammals) have weak CUB. Marine plankton species tend to have extremely large populations, suggesting that CUB should be very strong. Here we test this prediction and describe the patterns of codon usage in a wide range of diatom species belonging to 35 genera from 4 classes. We report that most of the diatom species studied have surprisingly modest CUB (mean Effective Number of Codons, ENC = 56), with some exceptions showing stronger codon bias (ENC = 44). Modest codon bias in most studied diatom species may reflect extreme disparity between astronomically large census and modest effective population size (Ne), with fluctuations in population size and linked selection limiting long-term Ne and rendering selection for optimal codons less efficient. For example, genetic diversity (pi ~0.02 at silent sites) in Skeletonema marinoi corresponds to Ne of about 10 million individuals, which is likely many orders of magnitude lower than its census size. Still, Ne ~107 should be large enough to make selection for optimal codons efficient. Thus, we propose that an alternative process-frequent changes of preferred codons, may be a more plausible reason for low CUB despite highly efficient selection for preferred codons in diatom populations. The shifts in the set of optimal codons should result in the changes of the direction of selection for codon usage, so the actual codon usage never catches up with the moving target of the optimal set of codons and the species never develop strong CUB. Indeed, we detected strong shifts in preferential codon usage within some diatom genera, with switches between preferentially GC-rich and AT-rich 3rd codon positions (GC3). For example, GC3 ranges from 0.6 to 1 in most Chaetoceros species, while for Chaetoceros dichaeta GC3 = 0.1. Both variation in selection intensity and mutation spectrum may drive such shifts in codon usage and limit the observed CUB. Our study represents the first genome-wide analysis of CUB in diatoms and the first such analysis for a major phytoplankton group.
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Project description:Diatoms are key players in the global carbon cycle and most aquatic ecosystems. Their cell sizes impact carbon sequestration and energy transfer to higher trophic levels. We report fundamental differences in size distributions of marine and freshwater diatoms, with marine diatoms significantly larger than freshwater species. An evolutionary game theoretical model with empirical allometries of growth and nutrient uptake shows that these differences can be explained by nitrogen versus phosphorus limitation, nutrient fluctuations and mixed layer depth differences. Constant and pulsed phosphorus supply select for small sizes, as does constant nitrogen supply. In contrast, intermediate frequency nitrogen pulses common in the ocean select for large sizes or the evolutionarily stable coexistence of large and small sizes. Size-dependent sinking interacts with mixed layer depth (MLD) to further modulate optimal sizes, with smaller sizes selected for by strong sinking and shallow MLD. In freshwaters, widespread phosphorus limitation, together with strong sinking and shallow MLD produce size distributions with smaller range, means and upper values, compared with the ocean. Shifting patterns of nutrient limitation and mixing may alter diatom size distributions, affecting global carbon cycle and the structure and functioning of aquatic ecosystems.
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Project description:It is of interest to document the molecular docking and dynamic simulations of benzimidazoles with beta-tubulins in the context of anthelmintic activity. We document the compound BI-02 (2-(3,4-dimethyl phenyl)-1H-1,3-benzimidazole (BI-02) with optimal bindig features compared to the standard molecule albendazole (7.0 Kcal/mol) with binding energy -8.50 Kcal/mol and PIC50 value 583.62 nM.
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Project description:Members of the tubulin superfamily are GTPases; the activities of GTPases are necessary for life. The members of the tubulin superfamily are the constituents of the microtubules and the γ-tubulin meshwork. Mutations in members of the tubulin superfamily are involved in developmental brain disorders, and tubulin activities are the target for various chemotherapies. The intricate functions (game) of tubulins depend on the activities of the GTP-binding domain of α-, β-, and γ-tubulin. This review compares the GTP-binding domains of γ-tubulin, α-tubulin, and β-tubulin and, based on their similarities, recapitulates the known functions and the impact of the γ-tubulin GTP-binding domain in the regulation of the γ-tubulin meshwork and cellular homeostasis.
| S-EPMC8065753 | biostudies-literature
Project description:Microtubules are tubulin polymers present in the eukaryotic cytoskeleton essential for structural stability and cell division that are also roadways for intracellular transport of vesicles and organelles. In the human malaria parasite Plasmodium falciparum, apart from providing structural stability and cell division, microtubules also facilitate important biological activities crucial for parasite survival in hosts, such as egression and motility. Hence, parasite structures and processes involving microtubules are among the most important drug targets for discovering much-needed novel Plasmodium inhibitors. The current study aims to construct reliable and high-quality 3D models of α-, β-, and γ-tubulins using various modeling techniques. We identified a common binding pocket specific to Plasmodium α-, β-, and γ-tubulins. Molecular dynamics simulations confirmed the stability of the Plasmodium tubulin 3D structures. The models generated in the present study may be used for protein-protein and protein-drug interaction investigations targeted toward designing malaria parasite tubulin-specific inhibitors.
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Project description:Tubulin is essential to eukaryotic cells and is targeted by several antineoplastics, herbicides, and antimicrobials. We demonstrate that Acanthamoeba spp. are resistant to five antimicrotubule compounds, unlike any other eukaryote studied so far. Resistance correlates with critical amino acid differences within the inhibitor binding sites of the tubulin heterodimers.
| S-EPMC2258519 | biostudies-literature
Project description:Diatoms are important contributors to marine primary production and the ocean carbon cycle, yet the molecular mechanisms that regulate their acclimation and adaptation to temperature are poorly understood. Here we use a transcriptomic approach to investigate the molecular mechanisms associated with temperature acclimation and adaptation in closely related colder- and warmer-adapted diatom species. We find evidence that evolutionary changes in baseline gene expression, which we termed transcriptional investment or divestment, is a key mechanism used by diatoms to adapt to different growth temperatures. Invested and divested pathways indicate that the maintenance of protein processing machinery and membrane structure, important short-term physiological mechanisms used to respond to temperature changes, are key elements associated with adaptation to different growth temperatures. Our results also indicate that evolutionary changes in the transcriptional regulation of acetyl-CoA associated pathways, including lipid and branched chain amino acid metabolism, are used by diatoms to balance photosynthetic light capture and metabolism with changes in growth temperature. Transcriptional investment and divestment can provide a framework to identify mechanisms of acclimation and adaption to temperature.
| S-EPMC6776047 | biostudies-literature
Project description:Diatoms and other chlorophyll-c containing, or chromalveolate, algae are among the most productive and diverse phytoplankton in the ocean. Evolutionarily, chlorophyll-c algae are linked through common, although not necessarily monophyletic, acquisition of plastid endosymbionts of red as well as most likely green algal origin. There is also strong evidence for a relatively high level of lineage-specific bacterial gene acquisition within chromalveolates. Therefore, analyses of gene content and derivation in chromalveolate taxa have indicated particularly diverse origins of their overall gene repertoire. As a single group of functionally related enzymes spanning two distinct gene families, fructose 1,6-bisphosphate aldolases (FBAs) illustrate the influence on core biochemical pathways of specific evolutionary associations among diatoms and other chromalveolates with various plastid-bearing and bacterial endosymbionts. Protein localization and activity, gene expression, and phylogenetic analyses indicate that the pennate diatom Phaeodactylum tricornutum contains five FBA genes with very little overall functional overlap. Three P. tricornutum FBAs, one class I and two class II, are plastid localized, and each appears to have a distinct evolutionary origin as well as function. Class I plastid FBA appears to have been acquired by chromalveolates from a red algal endosymbiont, whereas one copy of class II plastid FBA is likely to have originated from an ancient green algal endosymbiont. The other copy appears to be the result of a chromalveolate-specific gene duplication. Plastid FBA I and chromalveolate-specific class II plastid FBA are localized in the pyrenoid region of the chloroplast where they are associated with ?-carbonic anhydrase, which is known to play a significant role in regulation of the diatom carbon concentrating mechanism. The two pyrenoid-associated FBAs are distinguished by contrasting gene expression profiles under nutrient limiting compared with optimal CO2 fixation conditions, suggestive of a distinct specialized function for each. Cytosolically localized FBAs in P. tricornutum likely play a role in glycolysis and cytoskeleton function and seem to have originated from the stramenopile host cell and from diatom-specific bacterial gene transfer, respectively.
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Project description:BACKGROUND:Diatoms are of great significance to primary productivity in oceans, yet little is known about their biogeographic distribution in oligotrophic rivers. RESULTS:With the help of metabarcoding analysis of 279 samples from the Yangtze River, we provided the first integral biogeographic pattern of planktonic and benthic diatoms over a 6030?km continuum along the world's third largest river. Our study revealed spatial dissimilarity of diatoms under varying landforms, including plateau, mountain, foothill, basin, foothill-mountain, and plain regions, from the river source to the estuary. Environmental drivers of diatom communities were interpreted in terms of photosynthetically active radiation, temperature, channel slope and nutrients, and human interference. Typical benthic diatoms, such as Pinnularia, Paralia, and Aulacoseira, experienced considerable reduction in relative abundance downstream of the Three Gorges Dam and the Xiluodu Dam, two of the world's largest dams. CONCLUSIONS:Our study revealed that benthic diatoms are of particular significance in characterizing motile guild in riverine environments, which provides insights into diatom biogeography and biogeochemical cycles in large river ecosystems.
| S-EPMC6896584 | biostudies-literature