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Journal articles on the topic 'Eukaryotic cells'

Author: Grafiati

Published: 4 June 2021

Last updated: 30 July 2024

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1

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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2

Brueckner, Julia, and William F. Martin. "Bacterial Genes Outnumber Archaeal Genes in Eukaryotic Genomes." Genome Biology and Evolution 12, no. 4 (March 6, 2020): 282–92. http://dx.doi.org/10.1093/gbe/evaa047.

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Abstract Eukaryotes are typically depicted as descendants of archaea, but their genomes are evolutionary chimeras with genes stemming from archaea and bacteria. Which prokaryotic heritage predominates? Here, we have clustered 19,050,992 protein sequences from 5,443 bacteria and 212 archaea with 3,420,731 protein sequences from 150 eukaryotes spanning six eukaryotic supergroups. By downsampling, we obtain estimates for the bacterial and archaeal proportions. Eukaryotic genomes possess a bacterial majority of genes. On average, the majority of bacterial genes is 56% overall, 53% in eukaryotes that never possessed plastids, and 61% in photosynthetic eukaryotic lineages, where the cyanobacterial ancestor of plastids contributed additional genes to the eukaryotic lineage. Intracellular parasites, which undergo reductive evolution in adaptation to the nutrient rich environment of the cells that they infect, relinquish bacterial genes for metabolic processes. Such adaptive gene loss is most pronounced in the human parasite Encephalitozoon intestinalis with 86% archaeal and 14% bacterial derived genes. The most bacterial eukaryote genome sampled is rice, with 67% bacterial and 33% archaeal genes. The functional dichotomy, initially described for yeast, of archaeal genes being involved in genetic information processing and bacterial genes being involved in metabolic processes is conserved across all eukaryotic supergroups.

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3

Sokol, Kerry A., and Neil E. Olszewski. "The Putative Eukaryote-LikeO-GlcNAc Transferase of the Cyanobacterium Synechococcus elongatus PCC 7942 Hydrolyzes UDP-GlcNAc and Is Involved in Multiple Cellular Processes." Journal of Bacteriology 197, no. 2 (November 10, 2014): 354–61. http://dx.doi.org/10.1128/jb.01948-14.

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The posttranslational addition of a single O-linked β-N-acetylglucosamine (O-GlcNAc) to serine or threonine residues regulates numerous metazoan cellular processes. The enzyme responsible for this modification,O-GlcNAc transferase (OGT), is conserved among a wide variety of organisms and is critical for the viability of many eukaryotes. Although OGTs with domain structures similar to those of eukaryotic OGTs are predicted for many bacterial species, the cellular roles of these OGTs are unknown. We have identified a putative OGT in the cyanobacteriumSynechococcus elongatusPCC 7942 that shows active-site homology and similar domain structure to eukaryotic OGTs. An OGT deletion mutant was created and found to exhibit several phenotypes. Without agitation, mutant cells aggregate and settle out of the medium. The mutant cells have higher free inorganic phosphate levels, wider thylakoid lumen, and differential accumulation of electron-dense inclusion bodies. These phenotypes are rescued by reintroduction of the wild-type OGT but are not fully rescued by OGTs with single amino acid substitutions corresponding to mutations that reduce eukaryotic OGT activity.S. elongatusOGT purified fromEscherichia colihydrolyzed the sugar donor, UDP-GlcNAc, while the mutant OGTs that did not fully rescue the deletion mutant phenotypes had reduced or no activity. These results suggest that bacterial eukaryote-like OGTs, like their eukaryotic counterparts, influence multiple processes.

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4

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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5

Field, Mark C., and Michael P. Rout. "Pore timing: the evolutionary origins of the nucleus and nuclear pore complex." F1000Research 8 (April 3, 2019): 369. http://dx.doi.org/10.12688/f1000research.16402.1.

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The name “eukaryote” is derived from Greek, meaning “true kernel”, and describes the domain of organisms whose cells have a nucleus. The nucleus is thus the defining feature of eukaryotes and distinguishes them from prokaryotes (Archaea and Bacteria), whose cells lack nuclei. Despite this, we discuss the intriguing possibility that organisms on the path from the first eukaryotic common ancestor to the last common ancestor of all eukaryotes did not possess a nucleus at all—at least not in a form we would recognize today—and that the nucleus in fact arrived relatively late in the evolution of eukaryotes. The clues to this alternative evolutionary path lie, most of all, in recent discoveries concerning the structure of the nuclear pore complex. We discuss the evidence for such a possibility and how this impacts our views of eukaryote origins and how eukaryotes have diversified subsequent to their last common ancestor.

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6

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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7

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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8

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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9

Koukal, M., I. Trebichavský, J. Horáček, and V. Štěpánová. "Phages in eukaryotic cells." Folia Microbiologica 30, no. 3 (June 1985): 327–28. http://dx.doi.org/10.1007/bf02923527.

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10

Snider, Martin D. "Glycoproteins in Eukaryotic cells." Cell 40, no. 4 (April 1985): 733. http://dx.doi.org/10.1016/0092-8674(85)90331-9.

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11

Putra, Ramendra Dirgantara, and Diana Lyrawati. "Interactions between Bacteriophages and Eukaryotic Cells." Scientifica 2020 (June 9, 2020): 1–8. http://dx.doi.org/10.1155/2020/3589316.

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As the name implies, bacteriophage is a bacterium-specific virus. It infects and kills the bacterial host. Bacteriophages have gained attention as alternative antimicrobial entities in the science community in the western world since the alarming rise of antibiotic resistance among microbes. Although generally considered as prokaryote-specific viruses, recent studies indicate that bacteriophages can interact with eukaryotic organisms, including humans. In the current review, these interactions are divided into two categories, i.e., indirect and direct interactions, with the involvement of bacteriophages, bacteria, and eukaryotes. We discuss bacteriophage-related diseases, transcytosis of bacteriophages, bacteriophage interactions with cancer cells, collaboration of bacteriophages and eukaryotes against bacterial infections, and horizontal gene transfer between bacteriophages and eukaryotes. Such interactions are crucial for understanding and developing bacteriophages as the therapeutic agents and pharmaceutical delivery systems. With the advancement and combination of in silico, in vitro, and in vivo approaches and clinical trials, bacteriophages definitely serve as useful repertoire for biologic target-based drug development to manage many complex diseases in the future.

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12

de Silva, D. M., C. C. Askwith, and J. Kaplan. "Molecular mechanisms of iron uptake in eukaryotes." Physiological Reviews 76, no. 1 (January 1, 1996): 31–47. http://dx.doi.org/10.1152/physrev.1996.76.1.31.

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Iron serves essential functions in both prokaryotes and eukaryotes, and cells have highly specialized mechanisms for acquiring and handling this metal. The primary mechanism by which the concentration of iron in biologic systems is controlled is through the regulation of iron uptake. Although the role of transferrin in mammalian iron homeostasis has been well characterized, the study of genetic disorders of iron metabolism has revealed other, transferrin-independent, mechanisms by which cells can acquire iron. In an attempt to understand how eukaryotic systems take up this essential element, investigators have begun studying the simple eukaryote Saccharomyces cerevisiae. Several genes have been identified and cloned that act in concert to allow iron acquisition from the environment. Some of these genes appear to have functional homologues in human systems. This review focuses on the recent developments in understanding eukaryotic iron uptake with an emphasis on the genetic and molecular characterization of these systems in both cultured mammalian cells and S. cerevisiae. An unexpected connection between iron and copper homeostasis has been revealed by recent genetic studies, which confirm biologic observations made several decades ago.

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13

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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14

Yusupova, Gulnara, and Marat Yusupov. "Crystal structure of eukaryotic ribosome and its complexes with inhibitors." Philosophical Transactions of the Royal Society B: Biological Sciences 372, no. 1716 (March 19, 2017): 20160184. http://dx.doi.org/10.1098/rstb.2016.0184.

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A high-resolution structure of the eukaryotic ribosome has been determined and has led to increased interest in studying protein biosynthesis and regulation of biosynthesis in cells. The functional complexes of the ribosome crystals obtained from bacteria and yeast have permitted researchers to identify the precise residue positions in different states of ribosome function. This knowledge, together with electron microscopy studies, enhances our understanding of how basic ribosome processes, including mRNA decoding, peptide bond formation, mRNA, and tRNA translocation and cotranslational transport of the nascent peptide, are regulated. In this review, we discuss the crystal structure of the entire 80S ribosome from yeast, which reveals its eukaryotic-specific features, and application of X-ray crystallography of the 80S ribosome for investigation of the binding mode for distinct compounds known to inhibit or modulate the protein-translation function of the ribosome. We also refer to a challenging aspect of the structural study of ribosomes, from higher eukaryotes, where the structures of major distinctive features of higher eukaryote ribosome—the high-eukaryote–specific long ribosomal RNA segments (about 1MDa)—remain unresolved. Presently, the structures of the major part of these high-eukaryotic expansion ribosomal RNA segments still remain unresolved. This article is part of the themed issue ‘Perspectives on the ribosome’.

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15

Kane, Patricia M. "The Where, When, and How of Organelle Acidification by the Yeast Vacuolar H+-ATPase." Microbiology and Molecular Biology Reviews 70, no. 1 (March 2006): 177–91. http://dx.doi.org/10.1128/mmbr.70.1.177-191.2006.

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SUMMARY All eukaryotic cells contain multiple acidic organelles, and V-ATPases are central players in organelle acidification. Not only is the structure of V-ATPases highly conserved among eukaryotes, but there are also many regulatory mechanisms that are similar between fungi and higher eukaryotes. These mechanisms allow cells both to regulate the pHs of different compartments and to respond to changing extracellular conditions. The Saccharomyces cerevisiae V-ATPase has emerged as an important model for V-ATPase structure and function in all eukaryotic cells. This review discusses current knowledge of the structure, function, and regulation of the V-ATPase in S. cerevisiae and also examines the relationship between biosynthesis and transport of V-ATPase and compartment-specific regulation of acidification.

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16

Vellai, T., and G. Vida. "The origin of eukaryotes: the difference between prokaryotic and eukaryotic cells." Proceedings of the Royal Society of London. Series B: Biological Sciences 266, no. 1428 (August 7, 1999): 1571–77. http://dx.doi.org/10.1098/rspb.1999.0817.

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17

Liu, Huiquan, Yanping Fu, Daohong Jiang, Guoqing Li, Jiatao Xie, Jiasen Cheng, Youliang Peng, Said A. Ghabrial, and Xianhong Yi. "Widespread Horizontal Gene Transfer from Double-Stranded RNA Viruses to Eukaryotic Nuclear Genomes." Journal of Virology 84, no. 22 (September 1, 2010): 11876–87. http://dx.doi.org/10.1128/jvi.00955-10.

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ABSTRACT Horizontal gene transfer commonly occurs from cells to viruses but rarely occurs from viruses to their host cells, with the exception of retroviruses and some DNA viruses. However, extensive sequence similarity searches in public genome databases for various organisms showed that the capsid protein and RNA-dependent RNA polymerase genes from totiviruses and partitiviruses have widespread homologs in the nuclear genomes of eukaryotic organisms, including plants, arthropods, fungi, nematodes, and protozoa. PCR amplification and sequencing as well as comparative evidence of junction coverage between virus and host sequences support the conclusion that these viral homologs are real and occur in eukaryotic genomes. Sequence comparison and phylogenetic analysis suggest that these genes were likely transferred horizontally from viruses to eukaryotic genomes. Furthermore, we present evidence showing that some of the transferred genes are conserved and expressed in eukaryotic organisms and suggesting that these viral genes are also functional in the recipient genomes. Our findings imply that horizontal transfer of double-stranded RNA viral genes is widespread among eukaryotes and may give rise to functionally important new genes, thus entailing that RNA viruses may play significant roles in the evolution of eukaryotes.

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18

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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19

Singh, Varsha. "The Origin of Eukaryotic Cells." Resonance 26, no. 4 (April 2021): 479–89. http://dx.doi.org/10.1007/s12045-021-1150-z.

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20

Chen, Liang, Chuan Huang, Xiaolin Wang, and Ge Shan. "Circular RNAs in Eukaryotic Cells." Current Genomics 16, no. 5 (July 10, 2015): 312–18. http://dx.doi.org/10.2174/1389202916666150707161554.

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21

Krysan, K. V. "Extrachromosomal DNA in eukaryotic cells." Biopolymers and Cell 16, no. 4 (July 20, 2000): 301–11. http://dx.doi.org/10.7124/bc.000576.

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22

Bell, Stephen P., and Anindya Dutta. "DNA Replication in Eukaryotic Cells." Annual Review of Biochemistry 71, no. 1 (June 2002): 333–74. http://dx.doi.org/10.1146/annurev.biochem.71.110601.135425.

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23

Mayer, Andreas. "Membrane Fusion in Eukaryotic Cells." Annual Review of Cell and Developmental Biology 18, no. 1 (November 2002): 289–314. http://dx.doi.org/10.1146/annurev.cellbio.18.032202.114809.

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24

Savitskaya, M. A., and G. E. Onishchenko. "Apoptosis in cryopreserved eukaryotic cells." Biochemistry (Moscow) 81, no. 5 (May 2016): 445–52. http://dx.doi.org/10.1134/s0006297916050023.

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25

BATTOGTOKH, DORJSUREN. "FORCED SYNCHRONIZATION OF EUKARYOTIC CELLS." Modern Physics Letters B 21, no. 30 (December 30, 2007): 2033–53. http://dx.doi.org/10.1142/s0217984907014395.

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A comprehensive mathematical model of the budding yeast cell cycle, accounting for several dozen published experiments, has thirty five variables and one hundred and forty parameters.5 Detailed models describing cell cycle regulation in other organisms have also a large number of variables and parameters. Complexity rises further upon integrating the cell cycle network to other pathways in the cell. For some practical and theoretical issues, abundant complexity in realistic models can be tackled by studying first a functional subset of a model to understand the mechanism of a concerned process, and then by revealing the conditions of its occurrence in a detailed model. Here we review this approach applied to the problem of cell synchronization. Using analytic results obtained from a minimal model, we simulate cell synchronization in comprehensive mathematical models for budding and fission yeast cell cycles. Our results demonstrate that an experimental method based on periodic forcing of the synthesis of cell cycle regulators can be a powerful tool for cell synchronization.

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26

Kostianovsky, Mery. "Evolutionary Origin of Eukaryotic Cells." Ultrastructural Pathology 24, no. 2 (January 2000): 59–66. http://dx.doi.org/10.1080/01913120050118521.

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27

van Meer, Gerrit, and Joost C. M. Holthuis. "Sphingolipid transport in eukaryotic cells." Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids 1486, no. 1 (June 2000): 145–70. http://dx.doi.org/10.1016/s1388-1981(00)00054-8.

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28

Kearsey, Stephen E. "DNA replication in eukaryotic cells." Trends in Biochemical Sciences 22, no. 8 (August 1997): 323. http://dx.doi.org/10.1016/s0968-0004(97)82223-2.

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de Nadal, Eulàlia, Francisco X. Real, and Francesc Posas. "Mucins, osmosensors in eukaryotic cells?" Trends in Cell Biology 17, no. 12 (December 2007): 571–74. http://dx.doi.org/10.1016/j.tcb.2007.10.001.

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Go, Young-Mi, and Dean P. Jones. "Redox compartmentalization in eukaryotic cells." Biochimica et Biophysica Acta (BBA) - General Subjects 1780, no. 11 (November 2008): 1273–90. http://dx.doi.org/10.1016/j.bbagen.2008.01.011.

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31

Alpert, C., W. Engst, A. Guehler, T. Oelschlaeger, and M. Blaut. "Bacterial response to eukaryotic cells." Journal of Chromatography A 1082, no. 1 (July 2005): 25–32. http://dx.doi.org/10.1016/j.chroma.2005.03.094.

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Kim, Hae-Young, Dennis Byrne, Paul Hwang, Sandra Collins Thompson, and Paul A. Kitos. "Perceiving mitosis in eukaryotic cells." In Vitro Cellular & Developmental Biology 24, no. 2 (February 1988): 100–107. http://dx.doi.org/10.1007/bf02623886.

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33

Yellin, Florence H., Brenda Farrell, Varun K. A. C. Sreenivasan, and Sean X. Sun. "Electromechanical Model for Eukaryotic Cells." Biophysical Journal 106, no. 2 (January 2014): 574a. http://dx.doi.org/10.1016/j.bpj.2013.11.3182.

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34

Tatosyan, K. A., I. G. Ustyantsev, and D. A. Kramerov. "RNA Degradation in Eukaryotic Cells." Molecular Biology 54, no. 4 (July 2020): 485–502. http://dx.doi.org/10.1134/s0026893320040159.

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35

Falkow, Stanley. "Bacterial entry into eukaryotic cells." Cell 65, no. 7 (June 1991): 1099–102. http://dx.doi.org/10.1016/0092-8674(91)90003-h.

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36

Giron, M. D., C. M. Havel, and J. A. Watson. "Isopentenoid Synthesis in Eukaryotic Cells." Archives of Biochemistry and Biophysics 302, no. 1 (April 1993): 265–71. http://dx.doi.org/10.1006/abbi.1993.1209.

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37

Vogel, Katrin, Maximilian Glettenberg, Hendrik Schroeder, and Christof M. Niemeyer. "DNA-Modification of Eukaryotic Cells." Small 9, no. 2 (October 26, 2012): 255–62. http://dx.doi.org/10.1002/smll.201201852.

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38

Zigmond, Sally H., Ellen F. Foxman, and Jeffrey E. Segall. "Chemotaxis Assays for Eukaryotic Cells." Current Protocols in Cell Biology 00, no. 1 (October 1998): 12.1.1–12.1.29. http://dx.doi.org/10.1002/0471143030.cb1201s00.

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39

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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40

Lake, James A. "Origin of the eukaryotic nucleus: eukaryotes and eocytes are genotypically related." Canadian Journal of Microbiology 35, no. 1 (January 1, 1989): 109–18. http://dx.doi.org/10.1139/m89-017.

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The origin of the eukaryotic nucleus is difficult to reconstruct. While eukaryotic organelles (chloroplast, mitochondrion) are eubacterial endosymbionts, the source of nuclear genes has been obscured by multiple nucleotide substitutions. Using evolutionary parsimony, a newly developed rate-invariant treeing algorithm, the eukaryotic rRNA genes are shown to have evolved from the eocytes, a group of extremely thermophilic, sulfur-metabolizing, anucleate cells. The deepest bifurcation yet found separates the reconstructed tree into two taxonomic divisions. These are a proto-eukaryotic group (karyotes) and an essentially bacterial one (parkaryotes). Within the precision of the rooting procedure, the tree is not consistent with either the prokaryotic–eukaryotic or the archaebacterial–eubacterial–eukaryotic groupings. It implies that the last common ancestor of extant life, and the early ancestors of eukaryotes, very likely lacked nuclei, metabolized sulfur, and lived at near boiling temperatures.Key words: rRNA, evolution, phylogeny, sulfur metabolism.

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Koonin, Eugene V. "Origin of eukaryotes from within archaea, archaeal eukaryome and bursts of gene gain: eukaryogenesis just made easier?" Philosophical Transactions of the Royal Society B: Biological Sciences 370, no. 1678 (September 26, 2015): 20140333. http://dx.doi.org/10.1098/rstb.2014.0333.

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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.

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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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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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Pfannschmidt, Thomas, Matthew J. Terry, Olivier Van Aken, and Pedro M. Quiros. "Retrograde signals from endosymbiotic organelles: a common control principle in eukaryotic cells." Philosophical Transactions of the Royal Society B: Biological Sciences 375, no. 1801 (May 4, 2020): 20190396. http://dx.doi.org/10.1098/rstb.2019.0396.

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Endosymbiotic organelles of eukaryotic cells, the plastids, including chloroplasts and mitochondria, are highly integrated into cellular signalling networks. In both heterotrophic and autotrophic organisms, plastids and/or mitochondria require extensive organelle-to-nucleus communication in order to establish a coordinated expression of their own genomes with the nuclear genome, which encodes the majority of the components of these organelles. This goal is achieved by the use of a variety of signals that inform the cell nucleus about the number and developmental status of the organelles and their reaction to changing external environments. Such signals have been identified in both photosynthetic and non-photosynthetic eukaryotes (known as retrograde signalling and retrograde response, respectively) and, therefore, appear to be universal mechanisms acting in eukaryotes of all kingdoms. In particular, chloroplasts and mitochondria both harbour crucial redox reactions that are the basis of eukaryotic life and are, therefore, especially susceptible to stress from the environment, which they signal to the rest of the cell. These signals are crucial for cell survival, lifespan and environmental adjustment, and regulate quality control and targeted degradation of dysfunctional organelles, metabolic adjustments, and developmental signalling, as well as induction of apoptosis. The functional similarities between retrograde signalling pathways in autotrophic and non-autotrophic organisms are striking, suggesting the existence of common principles in signalling mechanisms or similarities in their evolution. Here, we provide a survey for the newcomers to this field of research and discuss the importance of retrograde signalling in the context of eukaryotic evolution. Furthermore, we discuss commonalities and differences in retrograde signalling mechanisms and propose retrograde signalling as a general signalling mechanism in eukaryotic cells that will be also of interest for the specialist. This article is part of the theme issue ‘Retrograde signalling from endosymbiotic organelles’.

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Williams, Tom A., and T. Martin Embley. "Changing ideas about eukaryotic origins." Philosophical Transactions of the Royal Society B: Biological Sciences 370, no. 1678 (September 26, 2015): 20140318. http://dx.doi.org/10.1098/rstb.2014.0318.

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The origin of eukaryotic cells is one of the most fascinating challenges in biology, and has inspired decades of controversy and debate. Recent work has led to major upheavals in our understanding of eukaryotic origins and has catalysed new debates about the roles of endosymbiosis and gene flow across the tree of life. Improved methods of phylogenetic analysis support scenarios in which the host cell for the mitochondrial endosymbiont was a member of the Archaea, and new technologies for sampling the genomes of environmental prokaryotes have allowed investigators to home in on closer relatives of founding symbiotic partners. The inference and interpretation of phylogenetic trees from genomic data remains at the centre of many of these debates, and there is increasing recognition that trees built using inadequate methods can prove misleading, whether describing the relationship of eukaryotes to other cells or the root of the universal tree. New statistical approaches show promise for addressing these questions but they come with their own computational challenges. The papers in this theme issue discuss recent progress on the origin of eukaryotic cells and genomes, highlight some of the ongoing debates, and suggest possible routes to future progress.

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Salimans, Marcel, Mark Posno, Rob Benne, and Harry O. Voorma. "Regulation of protein synthesis in eukaryotes. Eukaryotic initiation factor eIF-2 and eukaryotic recycling factor eRF from neuroblastoma cells." Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression 825, no. 4 (August 1985): 384–92. http://dx.doi.org/10.1016/0167-4781(85)90065-x.

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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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Singer, S. J., and Abraham Kupfer. "The Directed Migration of Eukaryotic Cells." Annual Review of Cell Biology 2, no. 1 (November 1986): 337–65. http://dx.doi.org/10.1146/annurev.cb.02.110186.002005.

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Merrick, William C., and Graham D. Pavitt. "Protein Synthesis Initiation in Eukaryotic Cells." Cold Spring Harbor Perspectives in Biology 10, no. 12 (May 7, 2018): a033092. http://dx.doi.org/10.1101/cshperspect.a033092.

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Ramsby, Melinda, and Gregory Makowski. "Differential Detergent Fractionation of Eukaryotic Cells." Cold Spring Harbor Protocols 2011, no. 3 (March 2011): prot5592. http://dx.doi.org/10.1101/pdb.prot5592.

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