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Journal articles on the topic 'Eukaryotic gene'

Author: Grafiati

Published: 4 June 2021

Last updated: 1 February 2022

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1

Hofstatter, Paulo G., Alexander K. Tice, Seungho Kang, Matthew W. Brown, and Daniel J. G. Lahr. "Evolution of bacterial recombinase A ( recA ) in eukaryotes explained by addition of genomic data of key microbial lineages." Proceedings of the Royal Society B: Biological Sciences 283, no. 1840 (2016): 20161453. http://dx.doi.org/10.1098/rspb.2016.1453.

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Recombinase enzymes promote DNA repair by homologous recombination. The genes that encode them are ancestral to life, occurring in all known dominions: viruses, Eubacteria, Archaea and Eukaryota. Bacterial recombinases are also present in viruses and eukaryotic groups (supergroups), presumably via ancestral events of lateral gene transfer. The eukaryotic recA genes have two distinct origins (mitochondrial and plastidial), whose acquisition by eukaryotes was possible via primary (bacteria–eukaryote) and/or secondary (eukaryote–eukaryote) endosymbiotic gene transfers (EGTs). Here we present a co

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2

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 (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 phyl

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3

Hunter, Gary J. "Eukaryotic gene transcription." Biochemical Education 25, no. 3 (1997): 182. http://dx.doi.org/10.1016/s0307-4412(97)84456-1.

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4

Chin, Jason W. "Eukaryotic gene regulation." Chemistry & Biology 7, no. 1 (2000): R26. http://dx.doi.org/10.1016/s1074-5521(00)00071-5.

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5

Garrard, William T. "Eukaryotic gene expression." Trends in Biochemical Sciences 10, no. 2 (1985): 86–87. http://dx.doi.org/10.1016/0968-0004(85)90247-6.

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6

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 (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

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7

Brueckner, Julia, and William F. Martin. "Bacterial Genes Outnumber Archaeal Genes in Eukaryotic Genomes." Genome Biology and Evolution 12, no. 4 (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 th

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8

Liapounova, Natalia A., Vladimir Hampl, Paul M. K. Gordon, Christoph W. Sensen, Lashitew Gedamu, and Joel B. Dacks. "Reconstructing the Mosaic Glycolytic Pathway of the Anaerobic Eukaryote Monocercomonoides." Eukaryotic Cell 5, no. 12 (2006): 2138–46. http://dx.doi.org/10.1128/ec.00258-06.

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ABSTRACT All eukaryotes carry out glycolysis, interestingly, not all using the same enzymes. Anaerobic eukaryotes face the challenge of fewer molecules of ATP extracted per molecule of glucose due to their lack of a complete tricarboxylic acid cycle. This may have pressured anaerobic eukaryotes to acquire the more ATP-efficient alternative glycolytic enzymes, such as pyrophosphate-fructose 6-phosphate phosphotransferase and pyruvate orthophosphate dikinase, through lateral gene transfers from bacteria and other eukaryotes. Most studies of these enzymes in eukaryotes involve pathogenic anaerobe

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9

Whitaker, John W., Glenn A. McConkey, and David R. Westhead. "Prediction of horizontal gene transfers in eukaryotes: approaches and challenges." Biochemical Society Transactions 37, no. 4 (2009): 792–95. http://dx.doi.org/10.1042/bst0370792.

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HGT (horizontal gene transfer) is recognized as an important force in bacterial evolution. Now that many eukaryotic genomes have been sequenced, it has become possible to carry out studies of HGT in eukaryotes. The present review compares the different approaches that exist for identifying HGT genes and assess them in the context of studying eukaryotic evolution. The metabolic evolution resource metaTIGER is then described, with discussion of its application in identification of HGT in eukaryotes.

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10

Johnson, Kristina M., Katherine Mitsouras, and Michael Carey. "Eukaryotic transcription: The core of eukaryotic gene activation." Current Biology 11, no. 13 (2001): R510—R513. http://dx.doi.org/10.1016/s0960-9822(01)00306-2.

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11

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 (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

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12

Tansey, William P. "Eukaryotic Gene Transcription.Stephen Goodbourn." Quarterly Review of Biology 72, no. 4 (1997): 462–63. http://dx.doi.org/10.1086/419976.

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13

Ashwin, S. S., and Masaki Sasai. "2P132 Dynamics of transcriptional apparatus in eukaryotic gene expression(08. Molecular genetics & Gene expression,Poster)." Seibutsu Butsuri 53, supplement1-2 (2013): S180. http://dx.doi.org/10.2142/biophys.53.s180_6.

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14

Kim, Sang-Wan, Shinya Fushinobu, Shengmin Zhou, Takayoshi Wakagi, and Hirofumi Shoun. "Eukaryotic nirK Genes Encoding Copper-Containing Nitrite Reductase: Originating from the Protomitochondrion?" Applied and Environmental Microbiology 75, no. 9 (2009): 2652–58. http://dx.doi.org/10.1128/aem.02536-08.

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ABSTRACT Although denitrification or nitrate respiration has been found among a few eukaryotes, its phylogenetic relationship with the bacterial system remains unclear because orthologous genes involved in the bacterial denitrification system were not identified in these eukaryotes. In this study, we isolated a gene from the denitrifying fungus Fusarium oxysporum that is homologous to the bacterial nirK gene responsible for encoding copper-containing nitrite reductase (NirK). Characterization of the gene and its recombinant protein showed that the fungal nirK gene is the first eukaryotic ortho

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15

Katz, Laura A. "Recent events dominate interdomain lateral gene transfers between prokaryotes and eukaryotes and, with the exception of endosymbiotic gene transfers, few ancient transfer events persist." Philosophical Transactions of the Royal Society B: Biological Sciences 370, no. 1678 (2015): 20140324. http://dx.doi.org/10.1098/rstb.2014.0324.

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While there is compelling evidence for the impact of endosymbiotic gene transfer (EGT; transfer from either mitochondrion or chloroplast to the nucleus) on genome evolution in eukaryotes, the role of interdomain transfer from bacteria and/or archaea (i.e. prokaryotes) is less clear. Lateral gene transfers (LGTs) have been argued to be potential sources of phylogenetic information, particularly for reconstructing deep nodes that are difficult to recover with traditional phylogenetic methods. We sought to identify interdomain LGTs by using a phylogenomic pipeline that generated 13 465 single gen

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16

Anselmetti, Yoann, Nadia El-Mabrouk, Manuel Lafond, and Aïda Ouangraoua. "Gene tree and species tree reconciliation with endosymbiotic gene transfer." Bioinformatics 37, Supplement_1 (2021): i120—i132. http://dx.doi.org/10.1093/bioinformatics/btab328.

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Abstract Motivation It is largely established that all extant mitochondria originated from a unique endosymbiotic event integrating an α−proteobacterial genome into an eukaryotic cell. Subsequently, eukaryote evolution has been marked by episodes of gene transfer, mainly from the mitochondria to the nucleus, resulting in a significant reduction of the mitochondrial genome, eventually completely disappearing in some lineages. However, in other lineages such as in land plants, a high variability in gene repertoire distribution, including genes encoded in both the nuclear and mitochondrial genome

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17

Liu, Huiquan, Yanping Fu, Daohong Jiang, et al. "Widespread Horizontal Gene Transfer from Double-Stranded RNA Viruses to Eukaryotic Nuclear Genomes." Journal of Virology 84, no. 22 (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 cove

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18

Blake, William J., Mads KÆrn, Charles R. Cantor, and J. J. Collins. "Noise in eukaryotic gene expression." Nature 422, no. 6932 (2003): 633–37. http://dx.doi.org/10.1038/nature01546.

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19

Goodbourn, Stephen. "Gene regulation: A eukaryotic perspective." Trends in Genetics 7, no. 10 (1991): 340. http://dx.doi.org/10.1016/0168-9525(91)90426-q.

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20

Lindahl, G. "Gene Regulation: A Eukaryotic Perspective." International Journal of Biochemistry & Cell Biology 35, no. 1 (2003): 111–12. http://dx.doi.org/10.1016/s1357-2725(02)00174-7.

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21

Kornberg, Roger D. "The Eukaryotic Gene Transcription Machinery." Biological Chemistry 382, no. 8 (2001): 1103–7. http://dx.doi.org/10.1515/bc.2001.140.

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Abstract Seven purified proteins may be combined to reconstitute regulated, promoterdependent RNA polymerase II transcription: five general transcription factors, Mediator, and RNA polymerase II. The entire system has been conserved across species from yeast to humans. The structure of RNA polymerase II, consisting of 10 polypeptides with a mass of about 500 kDa, has been determined at atomic resolution. On the basis of this structure, that of an actively transcribing RNA polymerase II complex has been determined as well.

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22

Borodovsky, Mark, Alex Lomsadze, Nikolai Ivanov, and Ryan Mills. "Eukaryotic Gene Prediction Using GeneMark.hmm." Current Protocols in Bioinformatics 1, no. 1 (2003): 4.6.1–4.6.12. http://dx.doi.org/10.1002/0471250953.bi0406s01.

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23

López, Marcela Dávila, and Tore Samuelsson. "eGOB: eukaryotic Gene Order Browser." Bioinformatics 27, no. 8 (2011): 1150–51. http://dx.doi.org/10.1093/bioinformatics/btr075.

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24

Serfling, Edgar, Maria Jasin, and Walter Schaffner. "Enhancers and eukaryotic gene transcription." Trends in Genetics 1 (January 1985): 224–30. http://dx.doi.org/10.1016/0168-9525(85)90088-5.

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25

Marsden, P. "Gene Regulation. A Eukaryotic Perspective." Biochemical Education 19, no. 1 (1991): 44–45. http://dx.doi.org/10.1016/0307-4412(91)90163-3.

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26

Mellor, Jane. "Gene regulation: A eukaryotic perspective." Trends in Biochemical Sciences 16 (January 1991): 482–83. http://dx.doi.org/10.1016/0968-0004(91)90186-y.

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27

Archibald, John M. "Genomic perspectives on the birth and spread of plastids." Proceedings of the National Academy of Sciences 112, no. 33 (2015): 10147–53. http://dx.doi.org/10.1073/pnas.1421374112.

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The endosymbiotic origin of plastids from cyanobacteria was a landmark event in the history of eukaryotic life. Subsequent to the evolution of primary plastids, photosynthesis spread from red and green algae to unrelated eukaryotes by secondary and tertiary endosymbiosis. Although the movement of cyanobacterial genes from endosymbiont to host is well studied, less is known about the migration of eukaryotic genes from one nucleus to the other in the context of serial endosymbiosis. Here I explore the magnitude and potential impact of nucleus-to-nucleus endosymbiotic gene transfer in the evoluti

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28

Richards, Thomas A., Joel B. Dacks, Samantha A. Campbell, et al. "Evolutionary Origins of the Eukaryotic Shikimate Pathway: Gene Fusions, Horizontal Gene Transfer, and Endosymbiotic Replacements." Eukaryotic Cell 5, no. 9 (2006): 1517–31. http://dx.doi.org/10.1128/ec.00106-06.

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ABSTRACT Currently the shikimate pathway is reported as a metabolic feature of prokaryotes, ascomycete fungi, apicomplexans, and plants. The plant shikimate pathway enzymes have similarities to prokaryote homologues and are largely active in chloroplasts, suggesting ancestry from the plastid progenitor genome. Toxoplasma gondii, which also possesses an alga-derived plastid organelle, encodes a shikimate pathway with similarities to ascomycete genes, including a five-enzyme pentafunctional arom. These data suggests that the shikimate pathway and the pentafunctional arom either had an ancient or

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29

Lynch, Michael, and Georgi K. Marinov. "The bioenergetic costs of a gene." Proceedings of the National Academy of Sciences 112, no. 51 (2015): 15690–95. http://dx.doi.org/10.1073/pnas.1514974112.

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An enduring mystery of evolutionary genomics concerns the mechanisms responsible for lineage-specific expansions of genome size in eukaryotes, especially in multicellular species. One idea is that all excess DNA is mutationally hazardous, but weakly enough so that genome-size expansion passively emerges in species experiencing relatively low efficiency of selection owing to small effective population sizes. Another idea is that substantial gene additions were impossible without the energetic boost provided by the colonizing mitochondrion in the eukaryotic lineage. Contrary to this latter view,

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30

Li, Zhichao, and Ralph Bock. "Rapid functional activation of a horizontally transferred eukaryotic gene in a bacterial genome in the absence of selection." Nucleic Acids Research 47, no. 12 (2019): 6351–59. http://dx.doi.org/10.1093/nar/gkz370.

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Abstract Horizontal gene transfer has occurred between organisms of all domains of life and contributed substantially to genome evolution in both prokaryotes and eukaryotes. Phylogenetic evidence suggests that eukaryotic genes horizontally transferred to bacteria provided useful new gene functions that improved metabolic plasticity and facilitated adaptation to new environments. How these eukaryotic genes evolved into functional bacterial genes is not known. Here, we have conducted a genetic screen to identify the mechanisms involved in functional activation of a eukaryotic gene after its tran

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31

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 (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 fro

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32

Madhani, Hiten D. "The Frustrated Gene: Origins of Eukaryotic Gene Expression." Cell 155, no. 4 (2013): 744–49. http://dx.doi.org/10.1016/j.cell.2013.10.003.

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33

Oborník, Miroslav. "Enigmatic Evolutionary History of Porphobilinogen Deaminase in Eukaryotic Phototrophs." Biology 10, no. 5 (2021): 386. http://dx.doi.org/10.3390/biology10050386.

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In most eukaryotic phototrophs, the entire heme synthesis is localized to the plastid, and enzymes of cyanobacterial origin dominate the pathway. Despite that, porphobilinogen deaminase (PBGD), the enzyme responsible for the synthesis of hydroxymethybilane in the plastid, shows phylogenetic affiliation to α-proteobacteria, the supposed ancestor of mitochondria. Surprisingly, no PBGD of such origin is found in the heme pathway of the supposed partners of the primary plastid endosymbiosis, a primarily heterotrophic eukaryote, and a cyanobacterium. It appears that α-proteobacterial PBGD is absent

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34

Weiner, Agnes K. M., Mario A. Cerón-Romero, Ying Yan, and Laura A. Katz. "Phylogenomics of the Epigenetic Toolkit Reveals Punctate Retention of Genes across Eukaryotes." Genome Biology and Evolution 12, no. 12 (2020): 2196–210. http://dx.doi.org/10.1093/gbe/evaa198.

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Abstract Epigenetic processes in eukaryotes play important roles through regulation of gene expression, chromatin structure, and genome rearrangements. The roles of chromatin modification (e.g., DNA methylation and histone modification) and non-protein-coding RNAs have been well studied in animals and plants. With the exception of a few model organisms (e.g., Saccharomyces and Plasmodium), much less is known about epigenetic toolkits across the remainder of the eukaryotic tree of life. Even with limited data, previous work suggested the existence of an ancient epigenetic toolkit in the last eu

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35

Emery-Corbin, Samantha J., Joshua J. Hamey, Brendan R. E. Ansell, et al. "Eukaryote-Conserved Methylarginine Is Absent in Diplomonads and Functionally Compensated in Giardia." Molecular Biology and Evolution 37, no. 12 (2020): 3525–49. http://dx.doi.org/10.1093/molbev/msaa186.

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Abstract Methylation is a common posttranslational modification of arginine and lysine in eukaryotic proteins. Methylproteomes are best characterized for higher eukaryotes, where they are functionally expanded and evolved complex regulation. However, this is not the case for protist species evolved from the earliest eukaryotic lineages. Here, we integrated bioinformatic, proteomic, and drug-screening data sets to comprehensively explore the methylproteome of Giardia duodenalis—a deeply branching parasitic protist. We demonstrate that Giardia and related diplomonads lack arginine-methyltransfer

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36

Salzberg, Steven L., Mihaela Pertea, Arthur L. Delcher, Malcolm J. Gardner, and Hervé Tettelin. "Interpolated Markov Models for Eukaryotic Gene Finding." Genomics 59, no. 1 (1999): 24–31. http://dx.doi.org/10.1006/geno.1999.5854.

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37

Nützmann, Hans-Wilhelm, Daniel Doerr, América Ramírez-Colmenero, et al. "Active and repressed biosynthetic gene clusters have spatially distinct chromosome states." Proceedings of the National Academy of Sciences 117, no. 24 (2020): 13800–13809. http://dx.doi.org/10.1073/pnas.1920474117.

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While colocalization within a bacterial operon enables coexpression of the constituent genes, the mechanistic logic of clustering of nonhomologous monocistronic genes in eukaryotes is not immediately obvious. Biosynthetic gene clusters that encode pathways for specialized metabolites are an exception to the classical eukaryote rule of random gene location and provide paradigmatic exemplars with which to understand eukaryotic cluster dynamics and regulation. Here, using 3C, Hi-C, and Capture Hi-C (CHi-C) organ-specific chromosome conformation capture techniques along with high-resolution micros

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38

Andersson, Jan. "Phylogenomic approaches underestimate eukaryotic gene transfer." Mobile Genetic Elements 2, no. 1 (2012): 59–62. http://dx.doi.org/10.4161/mge.19668.

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39

Bonifer, Constanze. "Developmental regulation of eukaryotic gene loci." Trends in Genetics 16, no. 7 (2000): 310–15. http://dx.doi.org/10.1016/s0168-9525(00)02029-1.

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40

Kitsberg, Daniel, Sara Selig, and Howard Cedar. "Chromosome structure and eukaryotic gene organization." Current Opinion in Genetics & Development 1, no. 4 (1991): 534–37. http://dx.doi.org/10.1016/s0959-437x(05)80204-7.

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41

Fraser, Hunter B., Aaron E. Hirsh, Guri Giaever, Jochen Kumm, and Michael B. Eisen. "Noise Minimization in Eukaryotic Gene Expression." PLoS Biology 2, no. 6 (2004): e137. http://dx.doi.org/10.1371/journal.pbio.0020137.

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42

Lonsdale, David, and Carl Price. "Eukaryotic gene nomenclature—a resolvable problem?" Trends in Biochemical Sciences 21, no. 11 (1996): 443–44. http://dx.doi.org/10.1016/s0968-0004(96)30037-6.

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43

Kelen, Katrien Van Der, Rudi Beyaert, Dirk Inzé, and Lieven De Veylder. "Translational control of eukaryotic gene expression." Critical Reviews in Biochemistry and Molecular Biology 44, no. 4 (2009): 143–68. http://dx.doi.org/10.1080/10409230902882090.

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44

Cramer, P. "Structural biology of eukaryotic gene transcription." Acta Crystallographica Section A Foundations of Crystallography 67, a1 (2011): C172—C173. http://dx.doi.org/10.1107/s0108767311095729.

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45

Keeling, Patrick J., and Jeffrey D. Palmer. "Horizontal gene transfer in eukaryotic evolution." Nature Reviews Genetics 9, no. 8 (2008): 605–18. http://dx.doi.org/10.1038/nrg2386.

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46

Makarov, V. "Computer programs for eukaryotic gene prediction." Briefings in Bioinformatics 3, no. 2 (2002): 195–99. http://dx.doi.org/10.1093/bib/3.2.195.

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47

Wilson, Clive, Hugo J. Bellen, and Walter J. Gehring. "Position Effects on Eukaryotic Gene Expression." Annual Review of Cell Biology 6, no. 1 (1990): 679–714. http://dx.doi.org/10.1146/annurev.cb.06.110190.003335.

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48

Bestor, Timothy H., Vicki L. Chandler, and Andrew P. Feinberg. "Epigenetic effects in eukaryotic gene expression." Developmental Genetics 15, no. 6 (1994): 458–62. http://dx.doi.org/10.1002/dvg.1020150603.

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49

Pescini, R., S. Alouani, A. Proudfoot, et al. "Inducible Inhibition of Eukaryotic Gene Expression." Biochemical and Biophysical Research Communications 202, no. 3 (1994): 1664–67. http://dx.doi.org/10.1006/bbrc.1994.2125.

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50

Brent, Michael R. "How does eukaryotic gene prediction work?" Nature Biotechnology 25, no. 8 (2007): 883–85. http://dx.doi.org/10.1038/nbt0807-883.

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