Journal articles: 'Eukaryotic cell'

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Martin, William F., Sriram Garg, and Verena Zimorski. "Endosymbiotic theories for eukaryote origin." Philosophical Transactions of the Royal Society B: Biological Sciences 370, no. 1678 (September 26, 2015): 20140330. http://dx.doi.org/10.1098/rstb.2014.0330.

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For over 100 years, endosymbiotic theories have figured in thoughts about the differences between prokaryotic and eukaryotic cells. More than 20 different versions of endosymbiotic theory have been presented in the literature to explain the origin of eukaryotes and their mitochondria. Very few of those models account for eukaryotic anaerobes. The role of energy and the energetic constraints that prokaryotic cell organization placed on evolutionary innovation in cell history has recently come to bear on endosymbiotic theory. Only cells that possessed mitochondria had the bioenergetic means to attain eukaryotic cell complexity, which is why there are no true intermediates in the prokaryote-to-eukaryote transition. Current versions of endosymbiotic theory have it that the host was an archaeon (an archaebacterium), not a eukaryote. Hence the evolutionary history and biology of archaea increasingly comes to bear on eukaryotic origins, more than ever before. Here, we have compiled a survey of endosymbiotic theories for the origin of eukaryotes and mitochondria, and for the origin of the eukaryotic nucleus, summarizing the essentials of each and contrasting some of their predictions to the observations. A new aspect of endosymbiosis in eukaryote evolution comes into focus from these considerations: the host for the origin of plastids was a facultative anaerobe.

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Martijn, Joran, and Thijs J. G. Ettema. "From archaeon to eukaryote: the evolutionary dark ages of the eukaryotic cell." Biochemical Society Transactions 41, no. 1 (January 29, 2013): 451–57. http://dx.doi.org/10.1042/bst20120292.

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The evolutionary origin of the eukaryotic cell represents an enigmatic, yet largely incomplete, puzzle. Several mutually incompatible scenarios have been proposed to explain how the eukaryotic domain of life could have emerged. To date, convincing evidence for these scenarios in the form of intermediate stages of the proposed eukaryogenesis trajectories is lacking, presenting the emergence of the complex features of the eukaryotic cell as an evolutionary deus ex machina. However, recent advances in the field of phylogenomics have started to lend support for a model that places a cellular fusion event at the basis of the origin of eukaryotes (symbiogenesis), involving the merger of an as yet unknown archaeal lineage that most probably belongs to the recently proposed ‘TACK superphylum’ (comprising Thaumarchaeota, Aigarchaeota, Crenarchaeota and Korarchaeota) with an alphaproteobacterium (the protomitochondrion). Interestingly, an increasing number of so-called ESPs (eukaryotic signature proteins) is being discovered in recently sequenced archaeal genomes, indicating that the archaeal ancestor of the eukaryotic cell might have been more eukaryotic in nature than presumed previously, and might, for example, have comprised primitive phagocytotic capabilities. In the present paper, we review the evolutionary transition from archaeon to eukaryote, and propose a new model for the emergence of the eukaryotic cell, the ‘PhAT (phagocytosing archaeon theory)’, which explains the emergence of the cellular and genomic features of eukaryotes in the light of a transiently complex phagocytosing archaeon.

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Ku, Chuan, and Arnau Sebé-Pedrós. "Using single-cell transcriptomics to understand functional states and interactions in microbial eukaryotes." Philosophical Transactions of the Royal Society B: Biological Sciences 374, no. 1786 (October 7, 2019): 20190098. http://dx.doi.org/10.1098/rstb.2019.0098.

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Understanding the diversity and evolution of eukaryotic microorganisms remains one of the major challenges of modern biology. In recent years, we have advanced in the discovery and phylogenetic placement of new eukaryotic species and lineages, which in turn completely transformed our view on the eukaryotic tree of life. But we remain ignorant of the life cycles, physiology and cellular states of most of these microbial eukaryotes, as well as of their interactions with other organisms. Here, we discuss how high-throughput genome-wide gene expression analysis of eukaryotic single cells can shed light on protist biology. First, we review different single-cell transcriptomics methodologies with particular focus on microbial eukaryote applications. Then, we discuss single-cell gene expression analysis of protists in culture and what can be learnt from these approaches. Finally, we envision the application of single-cell transcriptomics to protist communities to interrogate not only community components, but also the gene expression signatures of distinct cellular and physiological states, as well as the transcriptional dynamics of interspecific interactions. Overall, we argue that single-cell transcriptomics can significantly contribute to our understanding of the biology of microbial eukaryotes. This article is part of a discussion meeting issue ‘Single cell ecology’.

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Lane, Nick. "Origin of the Eukaryotic Cell." Molecular Frontiers Journal 01, no. 02 (December 2017): 108–20. http://dx.doi.org/10.1142/s2529732517400120.

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All complex life on Earth is composed of ‘eukaryotic’ cells. Eukaryotes arose just once in 4 billion years, via an endosymbiosis — bacteria entered a simple host cell, evolving into mitochondria, the ‘powerhouses’ of complex cells. Mitochondria lost most of their genes, retaining only those needed for respiration, giving eukaryotes ‘multi-bacterial’ power without the costs of maintaining thousands of complete bacterial genomes. These energy savings supported a substantial expansion in nuclear genome size, and far more protein synthesis from each gene.

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Chiyomaru, Katsumi, and Kazuhiro Takemoto. "Revisiting the hypothesis of an energetic barrier to genome complexity between eukaryotes and prokaryotes." Royal Society Open Science 7, no. 2 (February 2020): 191859. http://dx.doi.org/10.1098/rsos.191859.

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The absence of genome complexity in prokaryotes, being the evolutionary precursors to eukaryotic cells comprising all complex life (the prokaryote–eukaryote divide), is a long-standing question in evolutionary biology. A previous study hypothesized that the divide exists because prokaryotic genome size is constrained by bioenergetics (prokaryotic power per gene or genome being significantly lower than eukaryotic ones). However, this hypothesis was evaluated using a relatively small dataset due to lack of data availability at the time, and is therefore controversial. Accordingly, we constructed a larger dataset of genomes, metabolic rates, cell sizes and ploidy levels to investigate whether an energetic barrier to genome complexity exists between eukaryotes and prokaryotes while statistically controlling for the confounding effects of cell size and phylogenetic signals. Notably, we showed that the differences in bioenergetics between prokaryotes and eukaryotes were less significant than those previously reported. More importantly, we found a limited contribution of power per genome and power per gene to the prokaryote–eukaryote dichotomy. Our findings indicate that the prokaryote–eukaryote divide is hard to explain from the energetic perspective. However, our findings may not entirely discount the traditional hypothesis; in contrast, they indicate the need for more careful examination.

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Goodsell, David S. "Eukaryotic cell panorama." Biochemistry and Molecular Biology Education 39, no. 2 (March 2011): 91–101. http://dx.doi.org/10.1002/bmb.20494.

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Akiyoshi, Bungo, and Keith Gull. "Evolutionary cell biology of chromosome segregation: insights from trypanosomes." Open Biology 3, no. 5 (May 2013): 130023. http://dx.doi.org/10.1098/rsob.130023.

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Faithful transmission of genetic material is essential for the survival of all organisms. Eukaryotic chromosome segregation is driven by the kinetochore that assembles onto centromeric DNA to capture spindle microtubules and govern the movement of chromosomes. Its molecular mechanism has been actively studied in conventional model eukaryotes, such as yeasts, worms, flies and human. However, these organisms are closely related in the evolutionary time scale and it therefore remains unclear whether all eukaryotes use a similar mechanism. The evolutionary origins of the segregation apparatus also remain enigmatic. To gain insights into these questions, it is critical to perform comparative studies. Here, we review our current understanding of the mitotic mechanism in Trypanosoma brucei , an experimentally tractable kinetoplastid parasite that branched early in eukaryotic history. No canonical kinetochore component has been identified, and the design principle of kinetochores might be fundamentally different in kinetoplastids. Furthermore, these organisms do not appear to possess a functional spindle checkpoint that monitors kinetochore–microtubule attachments. With these unique features and the long evolutionary distance from other eukaryotes, understanding the mechanism of chromosome segregation in T. brucei should reveal fundamental requirements for the eukaryotic segregation machinery, and may also provide hints about the origin and evolution of the segregation apparatus.

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Cavalier-Smith, Thomas. "Kingdoms Protozoa and Chromista and the eozoan root of the eukaryotic tree." Biology Letters 6, no. 3 (December 23, 2009): 342–45. http://dx.doi.org/10.1098/rsbl.2009.0948.

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I discuss eukaryotic deep phylogeny and reclassify the basal eukaryotic kingdom Protozoa and derived kingdom Chromista in the light of multigene trees. I transfer the formerly protozoan Heliozoa and infrakingdoms Alveolata and Rhizaria into Chromista, which is sister to kingdom Plantae and arguably originated by synergistic double internal enslavement of green algal and red algal cells. I establish new subkingdoms (Harosa; Hacrobia) for the expanded Chromista. The protozoan phylum Euglenozoa differs immensely from other eukaryotes in its nuclear genome organization (trans-spliced multicistronic transcripts), mitochondrial DNA organization, cytochrome c -type biogenesis, cell structure and arguably primitive mitochondrial protein-import and nuclear DNA prereplication machineries. The bacteria-like absence of mitochondrial outer-membrane channel Tom40 and DNA replication origin-recognition complexes from trypanosomatid Euglenozoa roots the eukaryotic tree between Euglenozoa and all other eukaryotes (neokaryotes), or within Euglenozoa. Given their unique properties, I segregate Euglenozoa from infrakingdom Excavata (now comprising only phyla Percolozoa, Loukozoa, Metamonada), grouping infrakingdoms Euglenozoa and Excavata as the ancestral protozoan subkingdom Eozoa. I place phylum Apusozoa within the derived protozoan subkingdom Sarcomastigota. Clarifying early eukaryote evolution requires intensive study of properties distinguishing Euglenozoa from neokaryotes and Eozoa from neozoa (eukaryotes except Eozoa; ancestrally defined by haem lyase).

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Goley, Erin D. "Tiny cells meet big questions: a closer look at bacterial cell biology." Molecular Biology of the Cell 24, no. 8 (April 15, 2013): 1099–102. http://dx.doi.org/10.1091/mbc.e12-11-0788.

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While studying actin assembly as a graduate student with Matt Welch at the University of California at Berkeley, my interest was piqued by reports of surprising observations in bacteria: the identification of numerous cytoskeletal proteins, actin homologues fulfilling spindle-like functions, and even the presence of membrane-bound organelles. Curiosity about these phenomena drew me to Lucy Shapiro's lab at Stanford University for my postdoctoral research. In the Shapiro lab, and now in my lab at Johns Hopkins, I have focused on investigating the mechanisms of bacterial cytokinesis. Spending time as both a eukaryotic cell biologist and a bacterial cell biologist has convinced me that bacterial cells present the same questions as eukaryotic cells: How are chromosomes organized and accurately segregated? How is force generated for cytokinesis? How is polarity established? How are signals transduced within and between cells? These problems are conceptually similar between eukaryotes and bacteria, although their solutions can differ significantly in specifics. In this Perspective, I provide a broad view of cell biological phenomena in bacteria, the technical challenges facing those of us who peer into bacterial cells, and areas of common ground as research in eukaryotic and bacterial cell biology moves forward.

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Mills, Daniel B. "The origin of phagocytosis in Earth history." Interface Focus 10, no. 4 (June 12, 2020): 20200019. http://dx.doi.org/10.1098/rsfs.2020.0019.

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Phagocytosis, or ‘cell eating’, is a eukaryote-specific process where particulate matter is engulfed via invaginations of the plasma membrane. The origin of phagocytosis has been central to discussions on eukaryogenesis for decades, where it is argued as being either a prerequisite for, or consequence of, the acquisition of the ancestral mitochondrion. Recently, genomic and cytological evidence has increasingly supported the view that the pre-mitochondrial host cell—a bona fide archaeon branching within the ‘Asgard’ archaea—was incapable of phagocytosis and used alternative mechanisms to incorporate the alphaproteobacterial ancestor of mitochondria. Indeed, the diversity and variability of proteins associated with phagosomes across the eukaryotic tree suggest that phagocytosis, as seen in a variety of extant eukaryotes, may have evolved independently several times within the eukaryotic crown-group. Since phagocytosis is critical to the functioning of modern marine food webs (without it, there would be no microbial loop or animal life), multiple late origins of phagocytosis could help explain why many of the ecological and evolutionary innovations of the Neoproterozoic Era (e.g. the advent of eukaryotic biomineralization, the ‘Rise of Algae’ and the origin of animals) happened when they did.

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Nurse, Paul. "Eukaryotic Cell-Cycle Control." Biochemical Society Transactions 20, no. 2 (May 1, 1992): 239–42. http://dx.doi.org/10.1042/bst0200239.

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Porter, Susannah M., and Leigh Anne Riedman. "Frameworks for Interpreting the Early Fossil Record of Eukaryotes." Annual Review of Microbiology 77, no. 1 (September 15, 2023): 173–91. http://dx.doi.org/10.1146/annurev-micro-032421-113254.

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The origin of modern eukaryotes is one of the key transitions in life's history, and also one of the least understood. Although the fossil record provides the most direct view of this process, interpreting the fossils of early eukaryotes and eukaryote-grade organisms is not straightforward. We present two end-member models for the evolution of modern (i.e., crown) eukaryotes—one in which modern eukaryotes evolved early, and another in which they evolved late—and interpret key fossils within these frameworks, including where they might fit in eukaryote phylogeny and what they may tell us about the evolution of eukaryotic cell biology and ecology. Each model has different implications for understanding the rise of complex life on Earth, including different roles of Earth surface oxygenation, and makes different predictions that future paleontological studies can test.

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Martin Embley, T. "Multiple secondary origins of the anaerobic lifestyle in eukaryotes." Philosophical Transactions of the Royal Society B: Biological Sciences 361, no. 1470 (May 3, 2006): 1055–67. http://dx.doi.org/10.1098/rstb.2006.1844.

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Classical ideas for early eukaryotic evolution often posited a period of anaerobic evolution producing a nucleated phagocytic cell to engulf the mitochondrial endosymbiont, whose presence allowed the host to colonize emerging aerobic environments. This idea was given credence by the existence of contemporary anaerobic eukaryotes that were thought to primitively lack mitochondria, thus providing examples of the type of host cell needed. However, the groups key to this hypothesis have now been shown to contain previously overlooked mitochondrial homologues called hydrogenosomes or mitosomes; organelles that share common ancestry with mitochondria but which do not carry out aerobic respiration. Mapping these data on the unfolding eukaryotic tree reveals that secondary adaptation to anaerobic habitats is a reoccurring theme among eukaryotes. The apparent ubiquity of mitochondrial homologues bears testament to the importance of the mitochondrial endosymbiosis, perhaps as a founding event, in eukaryotic evolution. Comparative study of different mitochondrial homologues is needed to determine their fundamental importance for contemporary eukaryotic cells.

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BALUsKA, F. "Eukaryotic Cells and their Cell Bodies: Cell Theory Revised." Annals of Botany 94, no. 1 (May 20, 2004): 9–32. http://dx.doi.org/10.1093/aob/mch109.

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Speijer, Dave, Julius Lukeš, and Marek Eliáš. "Sex is a ubiquitous, ancient, and inherent attribute of eukaryotic life." Proceedings of the National Academy of Sciences 112, no. 29 (July 21, 2015): 8827–34. http://dx.doi.org/10.1073/pnas.1501725112.

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Sexual reproduction and clonality in eukaryotes are mostly seen as exclusive, the latter being rather exceptional. This view might be biased by focusing almost exclusively on metazoans. We analyze and discuss reproduction in the context of extant eukaryotic diversity, paying special attention to protists. We present results of phylogenetically extended searches for homologs of two proteins functioning in cell and nuclear fusion, respectively (HAP2 and GEX1), providing indirect evidence for these processes in several eukaryotic lineages where sex has not been observed yet. We argue that (i) the debate on the relative significance of sex and clonality in eukaryotes is confounded by not appropriately distinguishing multicellular and unicellular organisms; (ii) eukaryotic sex is extremely widespread and already present in the last eukaryotic common ancestor; and (iii) the general mode of existence of eukaryotes is best described by clonally propagating cell lines with episodic sex triggered by external or internal clues. However, important questions concern the relative longevity of true clonal species (i.e., species not able to return to sexual procreation anymore). Long-lived clonal species seem strikingly rare. We analyze their properties in the light of meiotic sex development from existing prokaryotic repair mechanisms. Based on these considerations, we speculate that eukaryotic sex likely developed as a cellular survival strategy, possibly in the context of internal reactive oxygen species stress generated by a (proto) mitochondrion. Thus, in the context of the symbiogenic model of eukaryotic origin, sex might directly result from the very evolutionary mode by which eukaryotic cells arose.

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Thomason, P., and R. Kay. "Eukaryotic signal transduction via histidine-aspartate phosphorelay." Journal of Cell Science 113, no. 18 (September 15, 2000): 3141–50. http://dx.doi.org/10.1242/jcs.113.18.3141.

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Transmembrane signal transduction is a feature common to all eukaryotic and prokaryotic cells. We now understand that a subset of the signalling mechanisms used by eukaryotes and prokaryotes are not just similar in principle, but actually use homologous proteins. These are the histidine-aspartate phosphorelays, signalling systems of eubacterial origin, now known to be widespread in eukaryotes outside the animal kingdom. Genome projects are revealing that His-Asp phosphorelays are present as multigene families in lower eukaryotes and in plants. A major challenge is to understand how these ‘novel’ signal transduction systems form integrated networks with the more familiar signalling mechanisms also present in eukaryotic cells. Already, phosphorelays have been characterised that regulate MAP kinase cascades and the cAMP/PKA pathway. The probable absence of His-Asp phosphorelays from animals has generated interest in their potential as targets for anti-microbial therapy, including antifungals. Recent findings suggest that this approach holds promise.

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Ku, Chuan, Shijulal Nelson-Sathi, Mayo Roettger, Sriram Garg, Einat Hazkani-Covo, and William F. Martin. "Endosymbiotic gene transfer from prokaryotic pangenomes: Inherited chimerism in eukaryotes." Proceedings of the National Academy of Sciences 112, no. 33 (March 2, 2015): 10139–46. http://dx.doi.org/10.1073/pnas.1421385112.

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Endosymbiotic theory in eukaryotic-cell evolution rests upon a foundation of three cornerstone partners—the plastid (a cyanobacterium), the mitochondrion (a proteobacterium), and its host (an archaeon)—and carries a corollary that, over time, the majority of genes once present in the organelle genomes were relinquished to the chromosomes of the host (endosymbiotic gene transfer). However, notwithstanding eukaryote-specific gene inventions, single-gene phylogenies have never traced eukaryotic genes to three single prokaryotic sources, an issue that hinges crucially upon factors influencing phylogenetic inference. In the age of genomes, single-gene trees, once used to test the predictions of endosymbiotic theory, now spawn new theories that stand to eventually replace endosymbiotic theory with descriptive, gene tree-based variants featuring supernumerary symbionts: prokaryotic partners distinct from the cornerstone trio and whose existence is inferred solely from single-gene trees. We reason that the endosymbiotic ancestors of mitochondria and chloroplasts brought into the eukaryotic—and plant and algal—lineage a genome-sized sample of genes from the proteobacterial and cyanobacterial pangenomes of their respective day and that, even if molecular phylogeny were artifact-free, sampling prokaryotic pangenomes through endosymbiotic gene transfer would lead to inherited chimerism. Recombination in prokaryotes (transduction, conjugation, transformation) differs from recombination in eukaryotes (sex). Prokaryotic recombination leads to pangenomes, and eukaryotic recombination leads to vertical inheritance. Viewed from the perspective of endosymbiotic theory, the critical transition at the eukaryote origin that allowed escape from Muller’s ratchet—the origin of eukaryotic recombination, or sex—might have required surprisingly little evolutionary innovation.

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HOEIJMAKERS, J. H. J. "How Relevant is the Escherichia coli UvrABC Model for Excision Repair in Eukaryotes?" Journal of Cell Science 100, no. 4 (December 1, 1991): 687–91. http://dx.doi.org/10.1242/jcs.100.4.687.

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Knowledge about the DNA excision repair system is increasing rapidly. A detailed model for this process in Escherichia coli has emerged in which a lesion in the DNA is first recognized by the UvrA2B helicase complex. Subsequently, UvrC mediates incision on both sites of the DNA injury. Finally, the concerted action of helicase II (UvrD), polymerase and ligase takes care of removal of the damage-containing oligonucleotide, DNA resynthesis and sealing of the residual nick. In the eukaryotes, yeast and mammals a total of 10 excision repair genes have been analysed thus far. However, little is still known about the molecular mechanism of this repair reaction. Amino acid sequence comparison suggests that at least three DNA helicases operate in eukaryotic nucleotide excision. In addition, a striking sequence conservation is noted between human and yeast repair proteins. But no eukaryotic homologs of the UvrABC proteins have been identified. In this Commentary the parallels and differences between the prokaryotic and eukaryotic excision repair pathways are weighed in an attempt to assess the relevance of the E. coli model for the eukaryotic system.

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WALKER, GISELLE, RICHARD G. DORRELL, ALEXANDER SCHLACHT, and JOEL B. DACKS. "Eukaryotic systematics: a user's guide for cell biologists and parasitologists." Parasitology 138, no. 13 (February 15, 2011): 1638–63. http://dx.doi.org/10.1017/s0031182010001708.

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SUMMARYSingle-celled parasites like Entamoeba, Trypanosoma, Phytophthora and Plasmodium wreak untold havoc on human habitat and health. Understanding the position of the various protistan pathogens in the larger context of eukaryotic diversity informs our study of how these parasites operate on a cellular level, as well as how they have evolved. Here, we review the literature that has brought our understanding of eukaryotic relationships from an idea of parasites as primitive cells to a crystallized view of diversity that encompasses 6 major divisions, or supergroups, of eukaryotes. We provide an updated taxonomic scheme (for 2011), based on extensive genomic, ultrastructural and phylogenetic evidence, with three differing levels of taxonomic detail for ease of referencing and accessibility (see supplementary material at Cambridge Journals On-line). Two of the most pressing issues in cellular evolution, the root of the eukaryotic tree and the evolution of photosynthesis in complex algae, are also discussed along with ideas about what the new generation of genome sequencing technologies may contribute to the field of eukaryotic systematics. We hope that, armed with this user's guide, cell biologists and parasitologists will be encouraged about taking an increasingly evolutionary point of view in the battle against parasites representing real dangers to our livelihoods and lives.

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Di Timoteo, Gaia, Francesca Rossi, and Irene Bozzoni. "Circular RNAs in cell differentiation and development." Development 147, no. 16 (August 15, 2020): dev182725. http://dx.doi.org/10.1242/dev.182725.

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ABSTRACTIn recent years, circular RNAs (circRNAs) – a novel class of RNA molecules characterized by their covalently closed circular structure – have emerged as a complex family of eukaryotic transcripts with important biological features. Besides their peculiar structure, which makes them particularly stable molecules, they have attracted much interest because their expression is strongly tissue and cell specific. Moreover, many circRNAs are conserved across eukaryotes, localized in particular subcellular compartments, and can play disparate molecular functions. The discovery of circRNAs has therefore added not only another layer of gene expression regulation but also an additional degree of complexity to our understanding of the structure, function and evolution of eukaryotic genomes. In this Review, we summarize current knowledge of circRNAs and discuss the possible functions of circRNAs in cell differentiation and development.

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Brunet, Thibaut, and Detlev Arendt. "From damage response to action potentials: early evolution of neural and contractile modules in stem eukaryotes." Philosophical Transactions of the Royal Society B: Biological Sciences 371, no. 1685 (January 5, 2016): 20150043. http://dx.doi.org/10.1098/rstb.2015.0043.

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Eukaryotic cells convert external stimuli into membrane depolarization, which in turn triggers effector responses such as secretion and contraction. Here, we put forward an evolutionary hypothesis for the origin of the depolarization–contraction–secretion (DCS) coupling, the functional core of animal neuromuscular circuits. We propose that DCS coupling evolved in unicellular stem eukaryotes as part of an ‘emergency response’ to calcium influx upon membrane rupture. We detail how this initial response was subsequently modified into an ancient mechanosensory–effector arc, present in the last eukaryotic common ancestor, which enabled contractile amoeboid movement that is widespread in extant eukaryotes. Elaborating on calcium-triggered membrane depolarization, we reason that the first action potentials evolved alongside the membrane of sensory-motile cilia, with the first voltage-sensitive sodium/calcium channels (Na v /Ca v ) enabling a fast and coordinated response of the entire cilium to mechanosensory stimuli. From the cilium, action potentials then spread across the entire cell, enabling global cellular responses such as concerted contraction in several independent eukaryote lineages. In animals, this process led to the invention of mechanosensory contractile cells. These gave rise to mechanosensory receptor cells, neurons and muscle cells by division of labour and can be regarded as the founder cell type of the nervous system.

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Pérez-Vargas, Jimena, Thomas Krey, Clari Valansi, Ori Avinoam, Ahmed Haouz, Marc Jamin, Hadas Raveh-Barak, Benjamin Podbilewicz, and Félix A. Rey. "Structural Basis of Eukaryotic Cell-Cell Fusion." Cell 157, no. 2 (April 2014): 407–19. http://dx.doi.org/10.1016/j.cell.2014.02.020.

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Tarrason Risa, Gabriel, Fredrik Hurtig, Sian Bray, Anne E. Hafner, Lena Harker-Kirschneck, Peter Faull, Colin Davis, et al. "The proteasome controls ESCRT-III–mediated cell division in an archaeon." Science 369, no. 6504 (August 6, 2020): eaaz2532. http://dx.doi.org/10.1126/science.aaz2532.

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Sulfolobus acidocaldarius is the closest experimentally tractable archaeal relative of eukaryotes and, despite lacking obvious cyclin-dependent kinase and cyclin homologs, has an ordered eukaryote-like cell cycle with distinct phases of DNA replication and division. Here, in exploring the mechanism of cell division in S. acidocaldarius, we identify a role for the archaeal proteasome in regulating the transition from the end of one cell cycle to the beginning of the next. Further, we identify the archaeal ESCRT-III homolog, CdvB, as a key target of the proteasome and show that its degradation triggers division by allowing constriction of the CdvB1:CdvB2 ESCRT-III division ring. These findings offer a minimal mechanism for ESCRT-III–mediated membrane remodeling and point to a conserved role for the proteasome in eukaryotic and archaeal cell cycle control.

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Pujic, Zac, Duncan Mortimer, Julia Feldner, and Geoffrey Goodhill. "Assays for Eukaryotic Cell Chemotaxis." Combinatorial Chemistry & High Throughput Screening 12, no. 6 (July 1, 2009): 580–88. http://dx.doi.org/10.2174/138620709788681952.

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Dunlap, Jay C. "New Directions at Eukaryotic Cell." Eukaryotic Cell 9, no. 1 (December 4, 2009): 20. http://dx.doi.org/10.1128/ec.00340-09.

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Reggiori, Fulvio, and Daniel J. Klionsky. "Autophagy in the Eukaryotic Cell." Eukaryotic Cell 1, no. 1 (February 2002): 11–21. http://dx.doi.org/10.1128/ec.01.1.11-21.2002.

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Archibald, John M. "Endosymbiosis and Eukaryotic Cell Evolution." Current Biology 25, no. 19 (October 2015): R911—R921. http://dx.doi.org/10.1016/j.cub.2015.07.055.

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Baluška, František, and Stefano Mancuso. "Synaptic view of eukaryotic cell." International Journal of General Systems 43, no. 7 (June 10, 2014): 740–56. http://dx.doi.org/10.1080/03081079.2014.920999.

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Scott, G. Kenneth. "Proteinases and eukaryotic cell growth." Comparative Biochemistry and Physiology Part B: Comparative Biochemistry 87, no. 1 (January 1987): 1–10. http://dx.doi.org/10.1016/0305-0491(87)90462-7.

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Radzvilavicius, Arunas L., and Neil W. Blackstone. "Conflict and cooperation in eukaryogenesis: implications for the timing of endosymbiosis and the evolution of sex." Journal of The Royal Society Interface 12, no. 111 (October 2015): 20150584. http://dx.doi.org/10.1098/rsif.2015.0584.

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Roughly 1.5–2.0 Gya, the eukaryotic cell evolved from an endosymbiosis of an archaeal host and proteobacterial symbionts. The timing of this endosymbiosis relative to the evolution of eukaryotic features remains subject to considerable debate, yet the evolutionary process itself constrains the timing of these events. Endosymbiosis entailed levels-of-selection conflicts, and mechanisms of conflict mediation had to evolve for eukaryogenesis to proceed. The initial mechanisms of conflict mediation (e.g. signalling with calcium and soluble adenylyl cyclase, substrate carriers, adenine nucleotide translocase, uncouplers) led to metabolic homeostasis in the eukaryotic cell. Later mechanisms (e.g. mitochondrial gene loss) contributed to the chimeric eukaryotic genome. These integral features of eukaryotes were derived because of, and therefore subsequent to, endosymbiosis. Perhaps the greatest opportunity for conflict arose with the emergence of eukaryotic sex, involving whole-cell fusion. A simple model demonstrates that competition on the lower level severely hinders the evolution of sex. Cytoplasmic mixing, however, is beneficial for non-cooperative endosymbionts, which could have used their aerobic metabolism to manipulate the life history of the host. While early evolution of sex may have facilitated symbiont acquisition, sex would have also destabilized the subsequent endosymbiosis. More plausibly, the evolution of sex and the true nucleus concluded the transition.

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Cooper, Stephen. "Cell cycle controls in eukaryotic cells: A reply." Journal of Theoretical Biology 127, no. 2 (July 1987): 247–49. http://dx.doi.org/10.1016/s0022-5193(87)80134-0.

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Rivett, A. J. "Eukaryotic protein degradation." Current Opinion in Cell Biology 2, no. 6 (December 1990): 1143–49. http://dx.doi.org/10.1016/0955-0674(90)90168-e.

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Diffley, John F. X. "Eukaryotic DNA replication." Current Opinion in Cell Biology 6, no. 3 (June 1994): 368–72. http://dx.doi.org/10.1016/0955-0674(94)90028-0.

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Wang, Thomas A., and Joachim J. Li. "Eukaryotic DNA replication." Current Opinion in Cell Biology 7, no. 3 (January 1995): 414–20. http://dx.doi.org/10.1016/0955-0674(95)80098-0.

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Mathews, Christopher K., and Mary B. Slabaugh. "Eukaryotic DNA metabolism." Experimental Cell Research 162, no. 2 (February 1986): 285–95. http://dx.doi.org/10.1016/0014-4827(86)90335-6.

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Bansal, Suneyna, and Aditya Mittal. "A statistical anomaly indicates symbiotic origins of eukaryotic membranes." Molecular Biology of the Cell 26, no. 7 (April 2015): 1238–48. http://dx.doi.org/10.1091/mbc.e14-06-1078.

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Compositional analyses of nucleic acids and proteins have shed light on possible origins of living cells. In this work, rigorous compositional analyses of ∼5000 plasma membrane lipid constituents of 273 species in the three life domains (archaea, eubacteria, and eukaryotes) revealed a remarkable statistical paradox, indicating symbiotic origins of eukaryotic cells involving eubacteria. For lipids common to plasma membranes of the three domains, the number of carbon atoms in eubacteria was found to be similar to that in eukaryotes. However, mutually exclusive subsets of same data show exactly the opposite—the number of carbon atoms in lipids of eukaryotes was higher than in eubacteria. This statistical paradox, called Simpson's paradox, was absent for lipids in archaea and for lipids not common to plasma membranes of the three domains. This indicates the presence of interaction(s) and/or association(s) in lipids forming plasma membranes of eubacteria and eukaryotes but not for those in archaea. Further inspection of membrane lipid structures affecting physicochemical properties of plasma membranes provides the first evidence (to our knowledge) on the symbiotic origins of eukaryotic cells based on the “third front” (i.e., lipids) in addition to the growing compositional data from nucleic acids and proteins.

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Embley, Martin, Mark van der Giezen, David S. Horner, Patricia L. Dyal, and Peter Foster. "Mitochondria and hydrogenosomes are two forms of the same fundamental organelle." Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences 358, no. 1429 (January 29, 2003): 191–203. http://dx.doi.org/10.1098/rstb.2002.1190.

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Published data suggest that hydrogenosomes, organelles found in diverse anaerobic eukaryotes that make energy and hydrogen, were once mitochondria. As hydrogenosomes generally lack a genome, the conversion is probably one way. The sources of the key hydrogenosomal enzymes, pyruvate : ferredoxin oxidoreductase (PFO) and hydrogenase, are not resolved by current phylogenetic analyses, but it is likely that both were present at an early stage of eukaryotic evolution. Once thought to be restricted to a few unusual anaerobic eukaryotes, the proteins are intimately integrated into the fabric of diverse eukaryotic cells, where they are targeted to different cell compartments, and not just hydrogenosomes. There is no evidence supporting the view that PFO and hydrogenase originated from the mitochondrial endosymbiont, as posited by the hydrogen hypothesis for eukaryogenesis. Other organelles derived from mitochondria have now been described in anaerobic and parasitic microbial eukaryotes, including species that were once thought to have diverged before the mitochondrial symbiosis. It thus seems possible that all eukaryotes may eventually be shown to contain an organelle of mitochondrial ancestry, to which different types of biochemistry can be targeted. It remains to be seen if, despite their obvious differences, this family of organelles shares a common function of importance for the eukaryotic cell, other than energy production, that might provide the underlying selection pressure for organelle retention.

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D’Archivio, Simon, and Bill Wickstead. "Trypanosome outer kinetochore proteins suggest conservation of chromosome segregation machinery across eukaryotes." Journal of Cell Biology 216, no. 2 (December 29, 2016): 379–91. http://dx.doi.org/10.1083/jcb.201608043.

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Kinetochores are multiprotein complexes that couple eukaryotic chromosomes to the mitotic spindle to ensure proper segregation. The model for kinetochore assembly is conserved between humans and yeast, and homologues of several components are widely distributed in eukaryotes, but key components are absent in some lineages. The recent discovery in a lineage of protozoa called kinetoplastids of unconventional kinetochores with no apparent homology to model organisms suggests that more than one system for eukaryotic chromosome segregation may exist. In this study, we report a new family of proteins distantly related to outer kinetochore proteins Ndc80 and Nuf2. The family member in kinetoplastids, KKT-interacting protein 1 (KKIP1), associates with the kinetochore, and its depletion causes severe defects in karyokinesis, loss of individual chromosomes, and gross defects in spindle assembly or stability. Immunopurification of KKIP1 from stabilized kinetochores identifies six further components, which form part of a trypanosome outer kinetochore complex. These findings suggest that kinetochores in organisms such as kinetoplastids are built from a divergent, but not ancestrally distinct, set of components and that Ndc80/Nuf2-like proteins are universal in eukaryotic division.

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Liston, David R., and Patricia J. Johnson. "Analysis of a Ubiquitous Promoter Element in a Primitive Eukaryote: Early Evolution of the Initiator Element." Molecular and Cellular Biology 19, no. 3 (March 1, 1999): 2380–88. http://dx.doi.org/10.1128/mcb.19.3.2380.

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ABSTRACTTypical metazoan core promoter elements, such as TATA boxes and Inr motifs, have yet to be identified in early-evolving eukaryotes, underscoring the extensive divergence of these organisms. Towards the identification of core promoters in protists, we have studied transcription of protein-encoding genes in one of the earliest-diverging lineages of Eukaryota, that represented by the parasitic protistTrichomonas vaginalis. A highly conserved element, comprised of a motif similar to a metazoan initiator (Inr) element, surrounds the start site of transcription in all examinedT. vaginalisgenes. In contrast, a metazoan-like TATA element appears to be absent in trichomonad promoters. We demonstrate that the conserved motif found inT. vaginalisprotein-encoding genes is an Inr promoter element. This trichomonad Inr is essential for transcription, responsible for accurate start site selection, and interchangeable between genes, demonstrating its role as a core promoter element. The sequence requirements of the trichomonad Inr are similar to metazoan Inrs and can be replaced by a mammalian Inr. These studies show that the Inr is a ubiquitous, core promoter element for protein-encoding genes in an early-evolving eukaryote. Functional and structural similarities between this protist Inr and the metazoan Inr strongly indicate that the Inr promoter element evolved early in eukaryotic evolution.

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Tromer, Eelco C., Jolien J. E. van Hooff, Geert J. P. L. Kops, and Berend Snel. "Mosaic origin of the eukaryotic kinetochore." Proceedings of the National Academy of Sciences 116, no. 26 (May 24, 2019): 12873–82. http://dx.doi.org/10.1073/pnas.1821945116.

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The emergence of eukaryotes from ancient prokaryotic lineages embodied a remarkable increase in cellular complexity. While prokaryotes operate simple systems to connect DNA to the segregation machinery during cell division, eukaryotes use a highly complex protein assembly known as the kinetochore. Although conceptually similar, prokaryotic segregation systems and the eukaryotic kinetochore are not homologous. Here we investigate the origins of the kinetochore before the last eukaryotic common ancestor (LECA) using phylogenetic trees, sensitive profile-versus-profile homology detection, and structural comparisons of its protein components. We show that LECA’s kinetochore proteins share deep evolutionary histories with proteins involved in a few prokaryotic systems and a multitude of eukaryotic processes, including ubiquitination, transcription, and flagellar and vesicular transport systems. We find that gene duplications played a major role in shaping the kinetochore; more than half of LECA’s kinetochore proteins have other kinetochore proteins as closest homologs. Some of these have no detectable homology to any other eukaryotic protein, suggesting that they arose as kinetochore-specific folds before LECA. We propose that the primordial kinetochore evolved from proteins involved in various (pre)eukaryotic systems as well as evolutionarily novel folds, after which a subset duplicated to give rise to the complex kinetochore of LECA.

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Daniels, Jan-Peter, Keith Gull, and Bill Wickstead. "Cell Biology of the Trypanosome Genome." Microbiology and Molecular Biology Reviews 74, no. 4 (December 2010): 552–69. http://dx.doi.org/10.1128/mmbr.00024-10.

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SUMMARY Trypanosomes are a group of protozoan eukaryotes, many of which are major parasites of humans and livestock. The genomes of trypanosomes and their modes of gene expression differ in several important aspects from those of other eukaryotic model organisms. Protein-coding genes are organized in large directional gene clusters on a genome-wide scale, and their polycistronic transcription is not generally regulated at initiation. Transcripts from these polycistrons are processed by global trans-splicing of pre-mRNA. Furthermore, in African trypanosomes, some protein-coding genes are transcribed by a multifunctional RNA polymerase I from a specialized extranucleolar compartment. The primary DNA sequence of the trypanosome genomes and their cellular organization have usually been treated as separate entities. However, it is becoming increasingly clear that in order to understand how a genome functions in a living cell, we will need to unravel how the one-dimensional genomic sequence and its trans-acting factors are arranged in the three-dimensional space of the eukaryotic nucleus. Understanding this cell biology of the genome will be crucial if we are to elucidate the genetic control mechanisms of parasitism. Here, we integrate the concepts of nuclear architecture, deduced largely from studies of yeast and mammalian nuclei, with recent developments in our knowledge of the trypanosome genome, gene expression, and nuclear organization. We also compare this nuclear organization to those in other systems in order to shed light on the evolution of nuclear architecture in eukaryotes.

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Kelly, Thomas, and A. John Callegari. "Dynamics of DNA replication in a eukaryotic cell." Proceedings of the National Academy of Sciences 116, no. 11 (February 4, 2019): 4973–82. http://dx.doi.org/10.1073/pnas.1818680116.

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Each genomic locus in a eukaryotic cell has a distinct average time of replication during S phase that depends on the spatial and temporal pattern of replication initiation events. Replication timing can affect genomic integrity because late replication is associated with an increased mutation rate. For most eukaryotes, the features of the genome that specify the location and timing of initiation events are unknown. To investigate these features for the fission yeast, Schizosaccharomyces pombe, we developed an integrative model to analyze large single-molecule and global genomic datasets. The model provides an accurate description of the complex dynamics of S. pombe DNA replication at high resolution. We present evidence that there are many more potential initiation sites in the S. pombe genome than previously identified and that the distribution of these sites is primarily determined by two factors: the sequence preferences of the origin recognition complex (ORC), and the interference of transcription with the assembly or stability of prereplication complexes (pre-RCs). We suggest that in addition to directly interfering with initiation, transcription has driven the evolution of the binding properties of ORC in S. pombe and other eukaryotic species to target pre-RC assembly to regions of the genome that are less likely to be transcribed.

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Leger, Michelle M., Markéta Petrů, Vojtěch Žárský, Laura Eme, Čestmír Vlček, Tommy Harding, B. Franz Lang, Marek Eliáš, Pavel Doležal, and Andrew J. Roger. "An ancestral bacterial division system is widespread in eukaryotic mitochondria." Proceedings of the National Academy of Sciences 112, no. 33 (March 23, 2015): 10239–46. http://dx.doi.org/10.1073/pnas.1421392112.

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Bacterial division initiates at the site of a contractile Z-ring composed of polymerized FtsZ. The location of the Z-ring in the cell is controlled by a system of three mutually antagonistic proteins, MinC, MinD, and MinE. Plastid division is also known to be dependent on homologs of these proteins, derived from the ancestral cyanobacterial endosymbiont that gave rise to plastids. In contrast, the mitochondria of model systems such asSaccharomyces cerevisiae, mammals, andArabidopsis thalianaseem to have replaced the ancestral α-proteobacterial Min-based division machinery with host-derived dynamin-related proteins that form outer contractile rings. Here, we show that the mitochondrial division system of these model organisms is the exception, rather than the rule, for eukaryotes. We describe endosymbiont-derived, bacterial-like division systems comprising FtsZ and Min proteins in diverse less-studied eukaryote protistan lineages, including jakobid and heterolobosean excavates, a malawimonad, stramenopiles, amoebozoans, a breviate, and an apusomonad. For two of these taxa, the amoebozoanDictyostelium purpureumand the jakobidAndalucia incarcerata, we confirm a mitochondrial localization of these proteins by their heterologous expression inSaccharomyces cerevisiae. The discovery of a proteobacterial-like division system in mitochondria of diverse eukaryotic lineages suggests that it was the ancestral feature of all eukaryotic mitochondria and has been supplanted by a host-derived system multiple times in distinct eukaryote lineages.

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WALTER, PETER. "The Membranes of a Eukaryotic Cell." American Zoologist 29, no. 2 (May 1989): 501–10. http://dx.doi.org/10.1093/icb/29.2.501.

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Mullard, Asher. "Eukaryotic cell, now showing in 3D." Nature Reviews Molecular Cell Biology 8, no. 4 (April 2007): 273. http://dx.doi.org/10.1038/nrm2157.

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MCGARRITY, GERARD J., and HITOSHI KOTANI. "Ureaplasma-eukaryotic cell interactions in vitro." Pediatric Infectious Disease Journal 5, Supplement (November 1986): S316–318. http://dx.doi.org/10.1097/00006454-198611010-00026.

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Zhaxybayeva, Olga. "The Mystery of Eukaryotic Cell Origin." BioScience 62, no. 11 (November 2012): 997–98. http://dx.doi.org/10.1525/bio.2012.62.11.12.

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ROBINSON, ARTHUR C., JOHN F. COLLINS, and WILLIAM D. DONACHIE. "Prokaryotic and eukaryotic cell-cycle proteins." Nature 328, no. 6133 (August 1987): 766. http://dx.doi.org/10.1038/328766a0.

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Krylov, Dmitri M., Kim Nasmyth, and Eugene V. Koonin. "Evolution of Eukaryotic Cell Cycle Regulation." Current Biology 13, no. 2 (January 2003): 173–77. http://dx.doi.org/10.1016/s0960-9822(03)00008-3.

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Gupta, Radhey S., and G. Brian Golding. "The origin of the eukaryotic cell." Trends in Biochemical Sciences 21, no. 5 (May 1996): 166–71. http://dx.doi.org/10.1016/s0968-0004(96)20013-1.

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Journal articles on the topic 'Eukaryotic cell'

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