Primitive Eukaryotic Cells Research Articles

The Role of Bacteria-Mitochondria Communication in the Activation of Neuronal Innate Immunity: Implications to Parkinson's Disease.

Mitochondria play a key role in regulating host metabolism, immunity and cellular homeostasis. Remarkably, these organelles are proposed to have evolved from an endosymbiotic association between an alphaproteobacterium and a primitive eukaryotic host cell or an archaeon. This crucial event determined that human cell mitochondria share some features with bacteria, namely cardiolipin, N-formyl peptides, mtDNA and transcription factor A, that can act as mitochondrial-derived damage-associated molecular patterns (DAMPs). The impact of extracellular bacteria on the host act largely through the modulation of mitochondrial activities, and often mitochondria are themselves immunogenic organelles that can trigger protective mechanisms through DAMPs mobilization. In this work, we demonstrate that mesencephalic neurons exposed to an environmental alphaproteobacterium activate innate immunity through toll-like receptor 4 and Nod-like receptor 3. Moreover, we show that mesencephalic neurons increase the expression and aggregation of alpha-synuclein that interacts with mitochondria, leading to their dysfunction. Mitochondrial dynamic alterations also affect mitophagy which favors a positive feedback loop on innate immunity signaling. Our results help to elucidate how bacteria and neuronal mitochondria interact and trigger neuronal damage and neuroinflammation and allow us to discuss the role of bacterial-derived pathogen-associated molecular patterns (PAMPs) in Parkinson's disease etiology.

Evolution: Mitochondrial Ribosomes Across Species.

The ribosome is among the most complex and ancient cellular macromolecular assemblies that plays a central role in protein biosynthesis in all living cells. Its function of translation of genetic information encoded in messenger RNA into protein molecules also extends to subcellular compartments in eukaryotic cells such as apicoplasts, chloroplasts, and mitochondria. The origin of mitochondria is primarily attributed to an early endosymbiotic event between an alpha-proteobacterium and a primitive (archaeal) eukaryotic cell. The timeline of mitochondrial acquisition, the nature of the host, and their diversification have been studied in great detail and are continually being revised as more genomic and structural data emerge. Recent advancements in high-resolution cryo-EM structure determination have provided architectural details of mitochondrial ribosomes (mitoribosomes) from various species, revealing unprecedented diversifications among them. These structures provide novel insights into the evolution of mitoribosomal structure and function. Here, we present a brief overview of the existing mitoribosomal structures in the context of the eukaryotic evolution tree showing their diversification from their last common ancestor.

Central Apparatus, the Molecular Kickstarter of Ciliary and Flagellar Nanomachines.

Motile cilia and homologous organelles, the flagella, are an early evolutionarily invention, enabling primitive eukaryotic cells to survive and reproduce. In animals, cilia have undergone functional and structural speciation giving raise to typical motile cilia, motile nodal cilia, and sensory immotile cilia. In contrast to other cilia types, typical motile cilia are able to beat in complex, two-phase movements. Moreover, they contain many additional structures, including central apparatus, composed of two single microtubules connected by a bridge-like structure and assembling numerous complexes called projections. A growing body of evidence supports the important role of the central apparatus in the generation and regulation of the motile cilia movement. Here we review data concerning the central apparatus structure, protein composition, and the significance of its components in ciliary beating regulation.

Evolution-Driven Versatility of N Terminal Acetylation in Photoautotrophs.

N terminal protein α-acetylation (NTA) is a pervasive protein modification that has recently attracted renewed interest. Early studies on NTA were mostly conducted in yeast and metazoans, providing a detailed portrait of the modification, which was indirectly applied to all eukaryotes. However, new findings originating from photosynthetic organisms have expanded our knowledge of this modification, revealing strong similarities as well as idiosyncratic features. Here, we review the most recent advances on NTA and its dedicated machinery in photosynthetic organisms. We discuss the cytosolic and unique plastid NTA machineries and their critical biological roles in development, stress responses, protein translocation, and stability. These new findings suggest that the multitasking plastid and cytosolic machineries evolved to support the specific needs of photoautotrophs.

Abstract A61: The positive effect of SKD plus IOT and HBO2T in the treatment of cancer

Abstract Background: The aim of this research is to figure out the effectiveness of the Sorush Cancer Treatment Protocol (SCTP), which is based on the Evolutionary Metabolic Hypothesis of Cancer (EMHC) and introducing the Specific Ketogenic Diet (SKD) plus Intravenous Ozone Therapy (IOT) in phase (1) on 54 cancer patients, and combination of hyperbaric oxygen therapy with vitamin/mineral and herbal supplementation beside the SKD and IOT in phase (2) of this research on the remaining 31 cancer patients. Introduction: Cancer based on the introduction of EMHC by Dr. Somayeh Zaminpira and Dr. Sorush Niknamian in 2017 is an evolutionary metabolic disease and through the incline of the reactive oxygen species (ROS) and the Butterfly Effect in normal eukaryotic cells, the mitochondria become damaged or shut down. Cancer cells are primitive eukaryotic cells that have existed since around 1.5 billion years ago before the entrance of mitochondrion as endosymbiont. Materials and Methods: Based on the researches from 1928-2016 and the experimentation of cancer treatments and protocols on cancer patients, we have reached a treatment and decided to test it on 54 voluntary cancer patients in the first stage of their disease. In this treatment we used a 5-day water fasting state, the Specific Ketogenic Diet (SKD) designed by ourselves and Intravenous Ozone Therapy (IOT) in the duration of 90 days (phase 1) and another 90 days (phase 2) with the entrance of hyperbaric oxygen therapy (HBO2T) and several supplements that have been effective in previous studies on cancer patients. We have used the measurement of saliva PH, the MRI device and statistical methods to test the shrinkage of the tumors. Results: After phase (1) of this research on 54 patients, the average percentage decrease in the tumors was 58%, and after phase (2) on 31 remaining cancer patients the average percentage decrease in the tumors was 98.8%. The average saliva PH in the fasting state of the cancer patients improved from acidic to alkaline as well. Conclusion: We have reached an effective cancer treatment based on SCTP by the usage of SKD, IOT, HBO2T and several supplements. There was an obvious improvement of cancer tumor decrease, lifestyle, and saliva PH, and we did not observe any side effects or cachexia in any of the patients. Citation Format: Sorush Niknamian. The positive effect of SKD plus IOT and HBO2T in the treatment of cancer [abstract]. In: Proceedings of the AACR Special Conference on Tumor Immunology and Immunotherapy; 2018 Nov 27-30; Miami Beach, FL. Philadelphia (PA): AACR; Cancer Immunol Res 2020;8(4 Suppl):Abstract nr A61.

Traced on the Timeline: Discovery of Acetylcholine and the Components of the Human Cholinergic System in a Primitive Unicellular Eukaryote Acanthamoeba spp.

Acetylcholine (ACh) is the neurotransmitter of cholinergic signal transduction that affects the target cells via muscarinic (mAChR) and nicotinic (nAChR) cholinergic receptors embedded in the cell membrane. Of the cholinergic receptors that bind to ACh, the mAChRs execute several cognitive and metabolic functions in the human central nervous system (CNS). Very little is known about the origins and autocrine/paracrine roles of the ACh in primitive life forms. With the recent report of the evidence of an ACh binding mAChR1 like receptor in Acanthamoeba spp., it was tempting to investigate the origin and functional roles of cholinergic G-Protein coupled receptors (GPCRs) in the biology of eukaryotes. We inferred the presence of ACh, its synthetic, degradation system, and a signal transduction pathway in an approximately ∼2.0 billion year old primitive eukaryotic cell Acanthamoeba castellanii. Bioinformatics analysis, ligand binding prediction, and docking methods were used to establish the origins of enzymes involved in the synthesis and degradation of ACh. Notably, we provide evidence of the presence of ACh in A. castellanii by colorimetric analysis, which to date is the only report of its presence in this primitive unicellular eukaryote. We show the evidence for the presence of homology of evolutionary conserved key enzymes of the cholinergic system like choline acetyltransferase (ChAT) and acetylcholinesterase (AChE) in A. castellanii spp., which were found to be near identical to their human counterparts. Tracing the origin, functions of ACh, and primeval mAChRs in primitive eukaryotic cells has the potential of uncovering covert cholinergic pathways that can be extended to humans in order to understand the states of cholinergic deficiency in neurodegenerative diseases (ND).

3D-Visualization of the Precise Location of Symbiotic Organelle Crosstalk Throughout Mitosis in the Primitive Unicellular Eukaryotic Cell, C. Merolae

3D-Visualization of the Precise Location of Symbiotic Organelle Crosstalk Throughout Mitosis in the Primitive Unicellular Eukaryotic Cell, C. Merolae

Identification of centromere regions in chromosomes of a unicellular red alga, Cyanidioschyzon merolae

To investigate the evolution of centromere architecture in plant cells, it is important to identify centromere regions of primitive algae, such as Cyanidioschyzon merolae. In a previous genome project, in silico analysis predicted an AT-rich region in each chromosome as putative centromere regions. Here, we identified a centromere position in each chromosome by ChIP-on-chip analysis using an anti-CENP-A antibody. The identified centromeres were of the regional type, about 2–3kb in length and contained no consensus or repeat elements. Centromeres in primitive eukaryotic plant cells may have originated from these regional type centromeres.

Arabidopsis thaliana Tic110, involved in chloroplast protein translocation, contains at least fourteen highly divergent heat-like repeated motifs

Endosymbiotic theory suggests that plastids originated from a photosynthetic bacterium that was engulfed by a primitive eukaryotic cell. In consequence, the chloroplast genome remains affected by this ancestral event, although it is reduced in size and the number of constituent genes. Most parts of the plastid genome have been transferred to the host cell nuclear genome and are nuclear-encoded. Thus, chloroplast proteins are synthesized in the cytosol as precursors with N-terminal extensions called transit peptides. The evolution of import machinery was required to transfer transit peptides to the stroma. Until the present, two protein complexes have been found to mediate the import process: the Toc (outer) and Tic (inner) envelope membrane translocons. The evolutionary origin of many Tic and Toc proteins has been established, but not for the Tic110 subunit. Tic110 binds signal peptides and serves as a scaffold for the recruitment of stromal components. In this study, we analyzed hydrophobic clusters, protein folds, and protein structure homology and we conclude that Tic110 is composed of fourteen repeated motifs related to HEAT-repeats. The explanation for the presence of such repeats in Tic110 is that membrane arrangement is found in separate domains and their probable function in the chloroplast import process is discussed.

Stressed by a Lov Triangle

His-Asp phosphorylation pathways (also known as two-component systems) enable bacteria (and primitive eukaryotic cells and/or eukaryotic organelles) to make important adaptive decisions in response to fluctuations in intra- or extra-cellular chemical and/or physical conditions.…

Bacterial Tubulin Distinct Loop Sequences and Primitive Assembly Properties Support Its Origin from a Eukaryotic Tubulin Ancestor

The structure of the unique bacterial tubulin BtubA/B from Prosthecobacter is very similar to eukaryotic αβ-tubulin but, strikingly, BtubA/B fold without eukaryotic chaperones. Our sequence comparisons indicate that BtubA and BtubB do not really correspond to either α- or β-tubulin but have mosaic sequences with intertwining features from both. Their nucleotide-binding loops are more conserved, and their more divergent sequences correspond to discrete surface zones of tubulin involved in microtubule assembly and binding to eukaryotic cytosolic chaperonin, which is absent from the Prosthecobacter dejongeii draft genome. BtubA/B cooperatively assembles over a wider range of conditions than αβ-tubulin, forming pairs of protofilaments that coalesce into bundles instead of microtubules, and it lacks the ability to differentially interact with divalent cations and bind typical tubulin drugs. Assembled BtubA/B contain close to one bound GTP and GDP. Both BtubA and BtubB subunits hydrolyze GTP, leading to disassembly. The mutant BtubA/B-S144G in the tubulin signature motif GGG(T/S)G(S/T)G has strongly inhibited GTPase, but BtubA-T147G/B does not, suggesting that BtubB is a more active GTPase, like β-tubulin. BtubA/B chimera bearing the β-tubulin loops M, H1-S2, and S9-S10 in BtubB fold, assemble, and have reduced GTPase activity. However, introduction of the α-tubulin loop S9-S10 with its unique eight-residue insertion impaired folding. From the sequence analyses, its primitive assembly features, and the properties of the chimeras, we propose that BtubA/B were acquired shortly after duplication of a spontaneously folding α- and β-tubulin ancestor, possibly by horizontal gene transfer from a primitive eukaryotic cell, followed by divergent evolution.

Les avatars évolutifs du cil/flagelle de la cellule-ancêtre des eucaryotes

The microtubule-based flagellum, or basal body/axoneme, is ancestral: it is a so-called "derived character" defining the extant eukaryote branch, present at the apparition of the early eukaryotic cell. It is a genuine cell compartment. Its structural conservation throughout evolution is remarkable, as well as the molecular conservation of the intraflagellar transport genes. From the start, it links cell sensation and cell locomotion, two properties which require integrated wiring at the cell level. The cell division machinery has been also tightly coupled with this organelle throughout evolution, possibly to ensure the continuity of this cellular polarized organization through division. The association of three basic cell modules, locomotion, sensation and division, all expressing a facet of cell polarity, within the same apparatus, could have given optimal survival value to primitive eukaryotic cells and could explain the evolutionary conservation and success of the basal body/axoneme. In vertebrates, primary cilia are critical sensory organelles, including during early mammalian development. Today the eukaryotic flagellum is not only an important issue for basic cell biology and developmental biology but also for human pathology. Many apparently unrelated severe developmental pathologies turned out to be all connected to the assembly or the function of the primary or beating cilia. The current efforts on human ciliopathies benefit directly from long lasting basic research on the flagellar assembly in experimental models like Chlamydomonas reinhardtii.

Nucleus-Independent Control of the Rubisco Operon by the Plastid-Encoded Transcription Factor Ycf30 in the Red Alga Cyanidioschyzon merolae

Chloroplasts originated from a cyanobacterium, which was engulfed by a primitive eukaryotic host cell. During evolution, chloroplasts have largely lost their autonomy due to the loss of many genes from their own genomes. Consequently, expression of genes encoded in the chloroplast genome is mainly controlled by the factors transferred from the cytosol to chloroplasts. However, chloroplast genomes of glaucophytes and red algae have retained some transcription factors (hypothetical chloroplast open reading frame 27 to 30 [Ycf27-Ycf30]) that are absent from green algae and land plants. Here, we show that the red algal chloroplast up-regulates transcription of the Rubisco operon rbcLS-cbbX via Ycf30 independently of nuclear control. Light-induced transcriptional activation of the Rubisco operon was observed in chloroplasts isolated from the red alga Cyanidioschyzon merolae. The activation was suppressed by 3-(3,4-dichlorophenyl)-1,1-dimethylurea. These results suggest that chloroplast autonomously regulates transcription of the Rubisco operon in response to the activation of photosynthesis driven by the light. Transcriptional activation of the Rubisco operon was specifically repressed by the addition of anti-Ycf30 antibodies. Furthermore, reduced NADP, ribulose-1,5-bisphosphate, and 3-phosphoglyceric acid triggered the up-regulation of Rubisco transcription in the dark, and the activation was dependent on Ycf30. Thus, red algal chloroplasts have retained a nucleus-independent transcriptional regulation of the Rubisco operon to respond to environmental changes. The autonomous system would have been necessary for the initial fixation of cyanobacterial photosynthesis in the ancient nonphotosynthetic eukaryotic host. It has remained functional in the red algal chloroplast over evolutionary time.

5′ and 3′ ends of chloroplast transcripts can both be stabilised by protein ‘caps’: a new model for polycistronic RNA maturation

5′ and 3′ ends of chloroplast transcripts can both be stabilised by protein ‘caps’: a new model for polycistronic RNA maturation

Horizontal gene transfer of an entire metabolic pathway between a eukaryotic alga and its DNA virus

Interactions between viruses and phytoplankton, the main primary producers in the oceans, affect global biogeochemical cycles and climate. Recent studies are increasingly revealing possible cases of gene transfers between cyanobacteria and phages, which might have played significant roles in the evolution of cyanobacteria/phage systems. However, little has been documented about the occurrence of horizontal gene transfer in eukaryotic phytoplankton/virus systems. Here we report phylogenetic evidence for the transfer of seven genes involved in the sphingolipid biosynthesis pathway between the cosmopolitan eukaryotic microalga Emiliania huxleyi and its large DNA virus EhV. PCR assays indicate that these genes are prevalent in E. huxleyi and EhV strains isolated from different geographic locations. Patterns of protein and gene sequence conservation support that these genes are functional in both E. huxleyi and EhV. This is the first clear case of horizontal gene transfer of multiple functionally linked enzymes in a eukaryotic phytoplankton-virus system. We examine arguments for the possible direction of the gene transfer. The virus-to-host direction suggests the existence of ancient viruses that controlled the complex metabolic pathway in order to infect primitive eukaryotic cells. In contrast, the host-to-virus direction suggests that the serial acquisition of genes involved in the same metabolic pathway might have been a strategy for the ancestor of EhVs to stay ahead of their closest relatives in the great evolutionary race for survival.

Evolutionary Dynamics of Introns in Plastid-Derived Genes in Plants: Saturation Nearly Reached but Slow Intron Gain Continues

Some of the principal transitions in the evolution of eukaryotes are characterized by engulfment of prokaryotes by primitive eukaryotic cells. In particular, approximately 1.6 billion years ago, engulfment of a cyanobacterium that became the ancestor of chloroplasts and other plastids gave rise to Plantae, the major branch of eukaryotes comprised of glaucophytes, red algae, green algae, and green plants. After endosymbiosis, there was large-scale migration of genes from the endosymbiont to the nuclear genome of the host such that approximately 18% of the nuclear genes in Arabidopsis appear to be of chloroplast origin. To gain insights into the process of evolution of gene structure in these, originally, intronless genes, we compared the properties and the evolutionary dynamics of introns in genes of plastid origin and ancestral eukaryotic genes in Arabidopsis, poplar, and rice genomes. We found that intron densities in plastid-derived genes were slightly but significantly lower than those in ancestral eukaryotic genes. Although most of the introns in both categories of genes were conserved between monocots (rice) and dicots (Arabidopsis and poplar), lineage-specific intron gain was more pronounced in plastid-derived genes than in ancestral genes, whereas there was no significant difference in the intron loss rates between the 2 classes of genes. Thus, after the transfer to the nuclear genome, the plastid-derived genes have undergone a massive intron invasion that, by the time of the divergence of dicots and monocots (150-200 MYA), yielded intron densities only slightly lower than those in ancestral genes. Nevertheless, the accumulation of introns in plastid-derived genes appears not to have reached saturation and continues to this time, albeit at a low rate. The overall pattern of intron gain and loss in the plastid-derived genes is shaped by this continuing gain and the more general tendency for loss that is characteristic of the recent evolution of plant genes.

MiRNAs control gene expression in the single-cell alga Chlamydomonas reinhardtii

MicroRNAs (miRNAs) in eukaryotes guide post-transcriptional regulation by means of targeted RNA degradation and translational arrest. They are released by a Dicer nuclease as a 21-24-nucleotide RNA duplex from a precursor in which an imperfectly matched inverted repeat forms a partly double-stranded region. One of the two strands is then recruited by an Argonaute nuclease that is the effector protein of the silencing mechanism. Short interfering RNAs (siRNAs), which are similar to miRNAs, are also produced by Dicer but the precursors are perfectly double-stranded RNA. These siRNAs guide post-transcriptional regulation, as with miRNAs, and epigenetic genome modification. Diverse eukaryotes including fungi, plants, protozoans and metazoans produce siRNAs but, until now, miRNAs have not been described in unicellular organisms and it has been suggested that they evolved together with multicellularity in separate plant and animal lineages. Here we show that the unicellular alga Chlamydomonas reinhardtii contains miRNAs, putative evolutionary precursors of miRNAs and species of siRNAs resembling those in higher plants. The common features of miRNAs and siRNAs in an alga and in higher plants indicate that complex RNA-silencing systems evolved before multicellularity and were a feature of primitive eukaryotic cells.

Calcium and cytoskeleton signaling during cell volume regulation in isolated nematocytes of Aiptasia mutabilis (Cnidaria: Anthozoa)

Cell volume regulation has not been completely clarified in Coelenterates. The present investigation focuses on cell volume regulation under anisosmotic conditions, both hyposmotic and hypertonic, and on the underlying signals in nematocytes isolated from the Coelenterate Aiptasia mutabilis living in sea water. Nematocytes, once isolated from acontia, that were submitted to either hyposmotic (35%) and hypertonic shock (45%) show RVD and RVI capabilities, respectively. In order to ascertain the role of Ca2+ in triggering such regulatory mechanisms and the possible involvement of cytoskeleton components, tests were performed by employing either Ca2+ free conditions, Gd3+ as Ca2+ channel blockers, TFP as calmodulin inhibitor, colchicine as microtubule inhibitor and cytochalasin B as microfilament polymerization inhibitor. Results show that isolated nematocytes of A. mutabilis can regulate their volume upon both hyposmotic and hypertonic challenge. Ca2+ both from external medium and from internal stores is needed to perform RVD mechanisms, whereas, intracellular Ca2+ seems to be mainly involved in RVI. Moreover cytoskeletal components may play an important role since a significant RVD and RVI inhibition was observed in treated cells. On the basis of our observations further studies are warranted to further verify the role of signals, including phosphatases and phosphorylases, in cell volume regulation of primitive eukaryotic cells.

Electrostatic considerations in nuclear envelope breakdown and reassembly

I have previously proposed a possible role for electrostatic interactions in the dynamics of chromosome motions during prometaphase, metaphase, and anaphase in primitive eukaryotic cells. The present work focuses on a biophysical mechanism for breakdown and reassembly of the nuclear envelope based on electrostatics. Intracellular pH rises to a peak at mitosis, and decreases through cytokinesis. This result, in conjunction with an observed 50% elevation in the whole cell content of sialic acid preceding mitosis, could set the stage for a precisely timed increase in net negative nuclear envelope charge resulting from an observed release of Ca 2 + from nuclear envelope stores just prior to nuclear envelope breakdown. The resulting increased electrostatic stress in these membranes could provide sufficient electrostatic energy for their breakdown. At late anaphase and early telophase, a decrease in the whole cell content of sialic acid is accompanied by a decline in intracellular pH. These changes would decrease the mutual electrostatic repulsion of membrane fragments, allowing membrane reassembly to occur for the nuclear envelopes of nascent daughter cells.

Electrostatic force in prometaphase, metaphase, and anaphase-Achromosome motions

Primitive cells had to divide using very few biological mechanisms. This work proposes physicochemical mechanisms, based upon nanoscale electrostatics, which explain and unify the motions of chromosomes during prometaphase, metaphase, and anaphase A. In the cytoplasmic medium that exists in biological cells, electrostatic fields are subject to strong attenuation by ionic screening, and therefore decrease rapidly over a distance equal to several Debye lengths. However, the presence of microtubules within cells completely changes the situation. Microtubule dimer subunits are electric dipolar structures, and can act as intermediaries that extend the reach of the electrostatic interaction over cellular distances. Experimental studies have shown that intracellular pH rises to a peak at mitosis, then decreases through cytokinesis. This result, in conjunction with the electric dipole nature of microtubule subunits, is sufficient to explain the dynamics of the above mitotic motions, including their timing and sequencing. The physicochemical mechanisms utilized by primitive eukaryotic cells could provide important clues regarding our understanding of cell division in modern eukaryotic cells.