Modern Eukaryotic Cells Research Articles

Mitochondrial DNA editing inches closer to reality

Over a billion years ago, a single-celled archaean engulfed an overachieving bacterium. The bacterium didn’t perish but instead struck an agreement with its host. For shelter, the bacterium would pay rent by doing what it did best—churn out energy molecules to power both itself and the host cell. This pivotal event in Earth’s history, according to the endosymbiosis theory, allowed the nested cells to harvest energy from the environment like never before, thus starting the march toward complex life. From such simple prokaryotic life forms came nucleus-toting eukaryotes and then their multicellular counterparts, eventually giving rise to the organismic richness across the planet today. With a few exceptions, most modern eukaryotic cells harbor these once-free-roaming bacteria. We call them mitochondria. Over the eons, mitochondria coevolved with their hosts as organelles, but the former bacteria never fully jettisoned their genes. In a last-ditch streak of independence, mitochondria retained 37 genes to

Investigating Human Mitochondrial Genomes in Single Cells.

Mitochondria host multiple copies of their own small circular genome that has been extensively studied to trace the evolution of the modern eukaryotic cell and discover important mutations linked to inherited diseases. Whole genome and exome sequencing have enabled the study of mtDNA in a large number of samples and experimental conditions at single nucleotide resolution, allowing the deciphering of the relationship between inherited mutations and phenotypes and the identification of acquired mtDNA mutations in classical mitochondrial diseases as well as in chronic disorders, ageing and cancer. By applying an ad hoc computational pipeline based on our MToolBox software, we reconstructed mtDNA genomes in single cells using whole genome and exome sequencing data obtained by different amplification methodologies (eWGA, DOP-PCR, MALBAC, MDA) as well as data from single cell Assay for Transposase Accessible Chromatin with high-throughput sequencing (scATAC-seq) in which mtDNA sequences are expected as a byproduct of the technology. We show that assembled mtDNAs, with the exception of those reconstructed by MALBAC and DOP-PCR methods, are quite uniform and suitable for genomic investigations, enabling the study of various biological processes related to cellular heterogeneity such as tumor evolution, neural somatic mosaicism and embryonic development.

A sophisticated, differentiated Golgi in the ancestor of eukaryotes

BackgroundThe Golgi apparatus is a central meeting point for the endocytic and exocytic systems in eukaryotic cells, and the organelle’s dysfunction results in human disease. Its characteristic morphology of multiple differentiated compartments organized into stacked flattened cisternae is one of the most recognizable features of modern eukaryotic cells, and yet how this is maintained is not well understood. The Golgi is also an ancient aspect of eukaryotes, but the extent and nature of its complexity in the ancestor of eukaryotes is unclear. Various proteins have roles in organizing the Golgi, chief among them being the golgins.ResultsWe address Golgi evolution by analyzing genome sequences from organisms which have lost stacked cisternae as a feature of their Golgi and those that have not. Using genomics and immunomicroscopy, we first identify Golgi in the anaerobic amoeba Mastigamoeba balamuthi. We then searched 87 genomes spanning eukaryotic diversity for presence of the most prominent proteins implicated in Golgi structure, focusing on golgins. We show some candidates as animal specific and others as ancestral to eukaryotes.ConclusionsNone of the proteins examined show a phyletic distribution that correlates with the morphology of stacked cisternae, suggesting the possibility of stacking as an emergent property. Strikingly, however, the combination of golgins conserved among diverse eukaryotes allows for the most detailed reconstruction of the organelle to date, showing a sophisticated Golgi with differentiated compartments and trafficking pathways in the common eukaryotic ancestor.

Elemental sulfur reduction to H2S by Tetrahymena thermophila

Eukaryotic nucleocytoplasm is believed to be descended from ancient Archaea that respired on elemental sulfur. If so, a vestige of sulfur reduction might persist in modern eukaryotic cells. That was tested in Tetrahymena thermophila, chosen as a model organism. When oxygenated, the cells consumed H2S rapidly, but when made anoxic they produced H2S mostly by amino acid catabolism. That could be inhibited by adding aminooxyacetic acid, and then H2S production from elemental sulfur became more evident. Anoxic cell lysates produced H2S when provided with sulfur and NADH, but not with either substrate alone. When lysates were fractionated by centrifugation, NADH-dependent H2S production was 83% in the soluble fraction. When intact cells that had just previously oxidized H2S were shifted to anoxia, the cells produced H2S evidently by re-using the oxidized sulfur. After aerobic H2S oxidation was stopped, the oxidation product remained available for H2S production for about 10 min. The observed H2S production is consistent with an evolutionary relationship of nucleocytoplasm to sulfur-reducing Archaea. Mitochondria often are the cellular site of H2S oxidation, suggesting that eukaryotic cells might have evolved from an ancient symbiosis that was based upon sulfur exchange.

Serial endosymbiosis or singular event at the origin of eukaryotes?

‘On the Origin of Mitosing Cells’ heralded a new way of seeing cellular evolution, with symbiosis at its heart. Lynn Margulis (then Sagan) marshalled an impressive array of evidence for endosymbiosis, from cell biology to atmospheric chemistry and Earth history. Despite her emphasis on symbiosis, she saw plenty of evidence for gradualism in eukaryotic evolution, with multiple origins of mitosis and sex, repeated acquisitions of plastids, and putative evolutionary intermediates throughout the microbial world. Later on, Margulis maintained her view of multiple endosymbioses giving rise to other organelles such as hydrogenosomes, in keeping with the polyphyletic assumptions of the serial endosymbiosis theory. She stood at the threshold of the phylogenetic era, and anticipated its potential. Yet while predicting that the nucleotide sequences of genes would enable a detailed reconstruction of eukaryotic evolution, Margulis did not, and could not, imagine the radically different story that would eventually emerge from comparative genomics. The last eukaryotic common ancestor now seems to have been essentially a modern eukaryotic cell that had already evolved mitosis, meiotic sex, organelles and endomembrane systems. The long search for missing evolutionary intermediates has failed to turn up a single example, and those discussed by Margulis turn out to have evolved reductively from more complex ancestors. Strikingly, Margulis argued that all eukaryotes had mitochondria in her 1967 paper (a conclusion that she later disavowed). But she developed her ideas in the context of atmospheric oxygen and aerobic respiration, neither of which is consistent with more recent geological and phylogenetic findings. Instead, a modern synthesis of genomics and bioenergetics points to the endosymbiotic restructuring of eukaryotic genomes in relation to bioenergetic membranes as the singular event that permitted the evolution of morphological complexity.

Tubular microfossils from ∼2.8 to 2.7 Ga-old lacustrine deposits of South Africa: A sign for early origin of eukaryotes?

Unequivocal evidence for Archean eukaryotic life has been long sought for and is a matter of lively debate. In the absence of unambiguous fossils this debate has focused on biogeochemical signatures and molecular phylogenies. Most researchers agree that fossil forms comparable with modern eukaryotic cells can be credibly identified only in Proterozoic (∼1.8–1.6Ga) and younger rocks. Herein, we report for the first time, Neoarchean mineralized tubular microfossils from ∼2.8 to 2.7Ga lacustrine deposits of South Africa. The exceptional preservation of these microfossils allows recognition of important morphological details in petrographic thin section and in HF-macerates that links them to modern siphonous (coenocytic) green or yellow-green microalgae (Chlorophyta and Xanthophyta). The microfossil identification is supported by Raman spectroscopic analyses, EPMA, SEM/BSE and SEM/EDS microprobe analytical results, NanoSIMS elemental mapping and micro-tomographic sectioning of the thalli. All results point to indigenous, bona fide eukaryotic microfossils of algal affinity. These Neoarchean microalgae-like remains and their assumingly combined in vivo and early post-mortem precipitated mineral envelopes greatly improve our knowledge of early life and its habitats and may have far-reaching consequences for the studies of the evolution of life.

Origin of eukaryotes from within archaea, archaeal eukaryome and bursts of gene gain: eukaryogenesis just made easier?

The origin of eukaryotes is a fundamental, forbidding evolutionary puzzle. Comparative genomic analysis clearly shows that the last eukaryotic common ancestor (LECA) possessed most of the signature complex features of modern eukaryotic cells, in particular the mitochondria, the endomembrane system including the nucleus, an advanced cytoskeleton and the ubiquitin network. Numerous duplications of ancestral genes, e.g. DNA polymerases, RNA polymerases and proteasome subunits, also can be traced back to the LECA. Thus, the LECA was not a primitive organism and its emergence must have resulted from extensive evolution towards cellular complexity. However, the scenario of eukaryogenesis, and in particular the relationship between endosymbiosis and the origin of eukaryotes, is far from being clear. Four recent developments provide new clues to the likely routes of eukaryogenesis. First, evolutionary reconstructions suggest complex ancestors for most of the major groups of archaea, with the subsequent evolution dominated by gene loss. Second, homologues of signature eukaryotic proteins, such as actin and tubulin that form the core of the cytoskeleton or the ubiquitin system, have been detected in diverse archaea. The discovery of this ‘dispersed eukaryome’ implies that the archaeal ancestor of eukaryotes was a complex cell that might have been capable of a primitive form of phagocytosis and thus conducive to endosymbiont capture. Third, phylogenomic analyses converge on the origin of most eukaryotic genes of archaeal descent from within the archaeal evolutionary tree, specifically, the TACK superphylum. Fourth, evidence has been presented that the origin of the major archaeal phyla involved massive acquisition of bacterial genes. Taken together, these findings make the symbiogenetic scenario for the origin of eukaryotes considerably more plausible and the origin of the organizational complexity of eukaryotic cells more readily explainable than they appeared until recently.

An inside-out origin for the eukaryotic cell.

BackgroundAlthough the origin of the eukaryotic cell has long been recognized as the single most profound change in cellular organization during the evolution of life on earth, this transition remains poorly understood. Models have always assumed that the nucleus and endomembrane system evolved within the cytoplasm of a prokaryotic cell.ResultsDrawing on diverse aspects of cell biology and phylogenetic data, we invert the traditional interpretation of eukaryotic cell evolution. We propose that an ancestral prokaryotic cell, homologous to the modern-day nucleus, extruded membrane-bound blebs beyond its cell wall. These blebs functioned to facilitate material exchange with ectosymbiotic proto-mitochondria. The cytoplasm was then formed through the expansion of blebs around proto-mitochondria, with continuous spaces between the blebs giving rise to the endoplasmic reticulum, which later evolved into the eukaryotic secretory system. Further bleb-fusion steps yielded a continuous plasma membrane, which served to isolate the endoplasmic reticulum from the environment.ConclusionsThe inside-out theory is consistent with diverse kinds of data and provides an alternative framework by which to explore and understand the dynamic organization of modern eukaryotic cells. It also helps to explain a number of previously enigmatic features of cell biology, including the autonomy of nuclei in syncytia and the subcellular localization of protein N-glycosylation, and makes many predictions, including a novel mechanism of interphase nuclear pore insertion.

S9-6 Elemental sulfur reduction by eukaryotic cytoplasm consistent with an ancient sulfur symbiosis

An accepted theory for the origin of eukaryotic cells postulates a methanogenic ancestor, although no evidence of methanogenesis exists in modern eukaryotic cells. Instead, sulfur reactions are ubiquitous. The seminal event in eukaryotic evolution might have been a sulfur-based symbiosis between a S°-reducing host and a sulfide-oxidizing bacterium. A vestige of those activities might remain in modern cells. To test this, Tetrahymena thermophila was examined as a representative eukaryotic cell. Aerobic cells consumed H 2 S at a rate of 140 nmol (g protein) −1 s −1 . Anoxic cells produced H 2 S at 1.1 nmol g −1 s −1 , but H 2 S production was suppressed by AOAA, an inhibitor of cysteine catabolism. When aerobic cells were fed H 2 S slowly so that all the H 2 S was oxidized, and then made anoxic, H 2 S was produced at up to 3.6 nmol g −1 s −1 , and not inhibited by AOAA. Evidently, H 2 S is oxidized to a compound that is available for H 2 S production. When aerobic incubation was continued after H 2 S addition had stopped, subsequent H 2 S production decreased with t 1/2 = 11 min. When S° was added to 7 mg cells at 85 pmol s −1 , H 2 S production was 4.4 nmol g −1 s −1 and not inhibited by AOAA. When cells were lysed and fractionated, there was NADH-stimulated S° reductase activity in the membrane fraction, distinguishing it from NADPH disulfide oxidoreductases and linking S° reduction to glycolysis. Thus, there is evidence of a sulfur cycle in which S° is reduced in the cytoplasm and H 2 S is oxidized in mitochondria.

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.

Microscale electrostatics in mitosis

Primitive cells had to divide using very few biological mechanisms. This work proposes physicochemical mechanisms, based upon microscale electrostatics, which explain and unify four basic events during mitosis: (1) assembly of the asters, (2) motion of the asters to poles, (3) poleward motion of chromosomes (anaphase A), and (4) cell elongation (anaphase B). 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 changes the situation completely. Microtubule dimer subunits are electric dipolar structures, and can act as intermediaries which extend the reach of the electrostatic interaction over cellular distances. Experimental studies have shown that intracellular pH rises to a peak at mitosis, and decreases through cytokinesis. This result, in conjunction with the electric dipole nature of microtubule subunits, is sufficient to explain the dynamics of the above 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.

Origin of mitochondria in relation to evolutionary history of eukaryotic alanyl-tRNA synthetase.

The origin of the eukaryotic cell remains an unsolved question. Numerous experimental and phylogenetic observations support the symbiotic origin of the modern eukaryotic cell, with its nucleus and (typically) mitochondria. Incorporation of mitochondria has been proposed to precede development of the nucleus, but it is still unclear whether mitochondria were initially part of basal eukaryotes. Data on alanyl-tRNA synthetase from an early eukaryote and other sources are presented and analyzed here. These data are consistent with the notion that mitochondrial genesis did not significantly precede nucleus formation. Moreover, the data raise the possibility that diplomonads are primary amitochondriates that radiated from the eukaryotic lineage before mitochondria became fully integrated as a cellular organelle.

PERSPECTIVE A UNITS-OF-EVOLUTION PERSPECTIVE ON THE ENDOSYMBIONT THEORY OF THE ORIGIN OF THE MITOCHONDRION.

Discussions of mitochondria and their hosts often conceptualize this relationship in a more or less modern form, focusing on the metabolic benefits of mitochondria to the host cell or on the possibility of intragenomic conflict. A more inclusive units-of-evolution perspective recognizes that both costs and benefits must be viewed from the level of the cells that initiated this interaction, the protomitochondrion and the primitive host cell. From this perspective, ecological and physiological considerations become central to the characterization of initial and subsequent host-mitochondria associations. Foremost among these considerations is the generation of superoxide radicals by modern mitochondria and the deleterious effects of these endogenous oxidants on modern eukaryotic cells. Because of their photosynthetic and aerobic ecologies, protomitochondria likely were relatively tolerant of such oxidants; anaerobic, heterotrophic, primitive host cells, on the other hand, likely were not. In the initial association of host and symbiont, the latter may have manipulated the former's life history by means of both endogenous oxidants and a superabundance of ATP. A resolution of this units-of-evolution conflict was necessary to continue this association, and this resolution, in a ritualized form, may have shaped the evolution of many features of modern eukaryotic cells and mitochondria, for example, the messenger functions of calcium ions, the regulatory role of phosphorylation cascades in cell-division cycles, the absence from the mitochondrial genome of replication factors, transcription factors, and adenine nucleotide carrier genes. The initial host-mitochondria interaction may have further channeled the evolution of multicellular eukaryotes, particularly animals, resulting in the association of mitochondria and the germinal plasm and in the use of extracellular ATP and endogenous oxidants as developmental signals. Evolutionary explanations for "free-radical" theories of development and aging are thus suggested.

The Origin of Synergistic Symbiosis

A dominant theme in the history of life has been the evolutionary innovations of cooperative symbioses: the first genomes near the origin of life, integrated prokaryotic cells, the complex symbiotic communities that evolved into modern eukaryotic cells, lichens, mycorrhizae, and so on. In this paper, a mode l of cooperative symbiosis that shows a threshold condition for the evolution of cooperation is analyzed. The threshold is not easily passed, but cooperative evolution proceeds rapidly once a symbiosis overcomes the threshold. In the model presented here, each species has genetic variability for a symbiotic trait. The trait imposes a reproductive cost on its bearer but enhances the reproduction of its partner species. For example, in the origin of genetic systems, the trait may cause biochemical synergism for the rate of replication of primitive RNA strands as in Eigen and Schuster's hypercycle model. Models of growth are contrasted with synergism, which are most appropriate for the evolution of genetic systems and for mutualisms such as lichens, with the strategic and psychological applications of the Prisoner's Dilemma model.

Phylogenetic affinities between eukaryotic cells and a thermophilic mycoplasma

Thermoplasma acidophilum, a thermophilic mycoplasma, has several unusual features suggesting a possible relationship to eukaryotic cells. One feature is a histone-like protein that is associated with the DNA, condensing it into subunits similar to those in eukaryotic chromatin. A second feature is an association of cytoplasmic proteins that resembles eukaryotic actin and myosin. These two components are widely distributed in different groups of eukaryotic cells, but are typically lacking in prokaryotic cells. Furthermore, T. acidophilum lacks cytochromes and respires by enzymes that apparently are not coupled to oxidative phosphorylation. This primitive type of respiration resembles that of microbodies, another feature which is represented in the cytoplasm of all groups of eukaryotic cells. Furthermore, since T. acidophilum lacks a cell wall and appears to have a primitive correlate of endocytosis, it would appear to be mechanically capable of acquiring a symbiotic mitochondrion. Thus, our observations are consistent with the symbiotic hypothesis for the origin of eukaryotic cells. We suggest that an organism similar to T. acidophilum was the host cell for the original symbiosis, becoming the nucleus and cytoplasm of modern eukaryotic cells.