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Journal articles on the topic 'Eukaryotic gene'

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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 (October 12, 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 comprehensive phylogenetic analysis of the recA genealogy, with substantially increased taxonomic sampling in the bacteria, viruses, eukaryotes and a special focus on the key eukaryotic supergroup Amoebozoa, earlier represented only by Dictyostelium . We demonstrate that several major eukaryotic lineages have lost the bacterial recombinases (including Opisthokonta and Excavata), whereas others have retained them (Amoebozoa, Archaeplastida and the SAR-supergroups). When absent, the bacterial recA homologues may have been lost entirely (secondary loss of canonical mitochondria) or replaced by other eukaryotic recombinases. RecA proteins have a transit peptide for organellar import, where they act. The reconstruction of the RecA phylogeny with its EGT events presented here retells the intertwined evolutionary history of eukaryotes and bacteria, while further illuminating the events of endosymbiosis in eukaryotes by expanding the collection of widespread genes that provide insight to this deep history.

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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 (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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3

Hunter, Gary J. "Eukaryotic gene transcription." Biochemical Education 25, no. 3 (July 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 (January 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 (February 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 (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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7

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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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 (October 27, 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 anaerobes; Monocercomonoides, an oxymonad belonging to the eukaryotic supergroup Excavata, is a nonpathogenic anaerobe representing an evolutionarily and ecologically distinct sampling of an anaerobic glycolytic pathway. We sequenced cDNA encoding glycolytic enzymes from a previously established cDNA library of Monocercomonoides and analyzed the relationships of these enzymes to those from other organisms spanning the major groups of Eukaryota, Bacteria, and Archaea. We established that, firstly, Monocercomonoides possesses alternative versions of glycolytic enzymes: fructose-6-phosphate phosphotransferase, both pyruvate kinase and pyruvate orthophosphate dikinase, cofactor-independent phosphoglycerate mutase, and fructose-bisphosphate aldolase (class II, type B). Secondly, we found evidence for the monophyly of oxymonads, kinetoplastids, diplomonads, and parabasalids, the major representatives of the Excavata. We also found several prokaryote-to-eukaryote as well as eukaryote-to-eukaryote lateral gene transfers involving glycolytic enzymes from anaerobic eukaryotes, further suggesting that lateral gene transfer was an important factor in the evolution of this pathway for denizens of this environment.

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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 (July 22, 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 (July 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 (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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12

Tansey, William P. "Eukaryotic Gene Transcription.Stephen Goodbourn." Quarterly Review of Biology 72, no. 4 (December 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 (March 6, 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 ortholog of the bacterial counterpart involved in denitrification. Additionally, recent genome analyses have revealed the occurrence of nirK homologs in many fungi and protozoa, although the denitrifying activity of these eukaryotes has never been examined. These eukaryotic homolog genes, together with the fungal nirK gene of F. oxysporum, are grouped in the same branch of the phylogenetic tree as the nirK genes of bacteria, archaea, and eukaryotes, implying that eukaryotic nirK and its homologs evolved from a single ancestor (possibly the protomitochondrion). These results show that the fungal denitrifying system has the same origin as its bacterial counterpart.

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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 (September 26, 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 gene trees and included up to 487 eukaryotes, 303 bacteria and 118 archaea. Our goals include searching for LGTs that unite major eukaryotic clades, and describing the relative contributions of LGT and EGT across the eukaryotic tree of life. Given the difficulties in interpreting single gene trees that aim to capture the approximately 1.8 billion years of eukaryotic evolution, we focus on presence–absence data to identify interdomain transfer events. Specifically, we identify 1138 genes found only in prokaryotes and representatives of three or fewer major clades of eukaryotes (e.g. Amoebozoa, Archaeplastida, Excavata, Opisthokonta, SAR and orphan lineages). The majority of these genes have phylogenetic patterns that are consistent with recent interdomain LGTs and, with the notable exception of EGTs involving photosynthetic eukaryotes, we detect few ancient interdomain LGTs. These analyses suggest that LGTs have probably occurred throughout the history of eukaryotes, but that ancient events are not maintained unless they are associated with endosymbiotic gene transfer among photosynthetic lineages.

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Anselmetti, Yoann, Nadia El-Mabrouk, Manuel Lafond, and Aïda Ouangraoua. "Gene tree and species tree reconciliation with endosymbiotic gene transfer." Bioinformatics 37, Supplement_1 (July 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, is an indication of an ongoing process of Endosymbiotic Gene Transfer (EGT). Understanding how both nuclear and mitochondrial genomes have been shaped by gene loss, duplication and transfer is expected to shed light on a number of open questions regarding the evolution of eukaryotes, including rooting of the eukaryotic tree. Results We address the problem of inferring the evolution of a gene family through duplication, loss and EGT events, the latter considered as a special case of horizontal gene transfer occurring between the mitochondrial and nuclear genomes of the same species (in one direction or the other). We consider both EGT events resulting in maintaining (EGTcopy) or removing (EGTcut) the gene copy in the source genome. We present a linear-time algorithm for computing the DLE (Duplication, Loss and EGT) distance, as well as an optimal reconciled tree, for the unitary cost, and a dynamic programming algorithm allowing to output all optimal reconciliations for an arbitrary cost of operations. We illustrate the application of our EndoRex software and analyze different costs settings parameters on a plant dataset and discuss the resulting reconciled trees. Availability and implementation EndoRex implementation and supporting data are available on the GitHub repository via https://github.com/AEVO-lab/EndoRex.

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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

Blake, William J., Mads KÆrn, Charles R. Cantor, and J. J. Collins. "Noise in eukaryotic gene expression." Nature 422, no. 6932 (April 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 (October 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 (January 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 (August 28, 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 (March 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 (February 10, 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 (January 1991): 44–45. http://dx.doi.org/10.1016/0307-4412(91)90163-3.

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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 (April 20, 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 evolution of complex algae, and the extent to which such transfers compromise our ability to infer the deep structure of the eukaryotic tree of life. In addition to endosymbiotic gene transfer, horizontal gene transfer events occurring before, during, and after endosymbioses further confound our efforts to reconstruct the ancient mergers that forged multiple lines of photosynthetic microbial eukaryotes.

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Richards, Thomas A., Joel B. Dacks, Samantha A. Campbell, Jeffrey L. Blanchard, Peter G. Foster, Rima McLeod, and Craig W. Roberts. "Evolutionary Origins of the Eukaryotic Shikimate Pathway: Gene Fusions, Horizontal Gene Transfer, and Endosymbiotic Replacements." Eukaryotic Cell 5, no. 9 (September 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 origin in the eukaryotes or was conveyed by eukaryote-to-eukaryote horizontal gene transfer (HGT). We expand sampling and analyses of the shikimate pathway genes to include the oomycetes, ciliates, diatoms, basidiomycetes, zygomycetes, and the green and red algae. Sequencing of cDNA from Tetrahymena thermophila confirmed the presence of a pentafused arom, as in fungi and T. gondii. Phylogenies and taxon distribution suggest that the arom gene fusion event may be an ancient eukaryotic innovation. Conversely, the Plantae lineage (represented here by both Viridaeplantae and the red algae) acquired different prokaryotic genes for all seven steps of the shikimate pathway. Two of the phylogenies suggest a derivation of the Plantae genes from the cyanobacterial plastid progenitor genome, but if the full Plantae pathway was originally of cyanobacterial origin, then the five other shikimate pathway genes were obtained from a minimum of two other eubacterial genomes. Thus, the phylogenies demonstrate both separate HGTs and shared derived HGTs within the Plantae clade either by primary HGT transfer or secondarily via the plastid progenitor genome. The shared derived characters support the holophyly of the Plantae lineage and a single ancestral primary plastid endosymbiosis. Our analyses also pinpoints a minimum of 50 gene/domain loss events, demonstrating that loss and replacement events have been an important process in eukaryote genome evolution.

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Lynch, Michael, and Georgi K. Marinov. "The bioenergetic costs of a gene." Proceedings of the National Academy of Sciences 112, no. 51 (November 2, 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, analysis of cellular energetics and genomics data from a wide variety of species indicates that, relative to the lifetime ATP requirements of a cell, the costs of a gene at the DNA, RNA, and protein levels decline with cell volume in both bacteria and eukaryotes. Moreover, these costs are usually sufficiently large to be perceived by natural selection in bacterial populations, but not in eukaryotes experiencing high levels of random genetic drift. Thus, for scaling reasons that are not yet understood, by virtue of their large size alone, eukaryotic cells are subject to a broader set of opportunities for the colonization of novel genes manifesting weakly advantageous or even transiently disadvantageous phenotypic effects. These results indicate that the origin of the mitochondrion was not a prerequisite for genome-size expansion.

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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 (May 20, 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 transfer into a bacterial genome. We integrated a eukaryotic selectable marker gene cassette driven by expression elements from the red alga Porphyridium purpureum into the genome of Escherichia coli. Following growth under non-selective conditions, gene activation events were indentified by antibiotic selection. We show that gene activation in the bacterial recipient occurs at high frequency and involves two major types of spontaneous mutations: deletion and gene amplification. We further show that both mechanisms result in promoter capture and are frequently triggered by microhomology-mediated recombination. Our data suggest that horizontally transferred genes have a high probability of acquiring functionality, resulting in their maintenance if they confer a selective advantage.

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

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Oborník, Miroslav. "Enigmatic Evolutionary History of Porphobilinogen Deaminase in Eukaryotic Phototrophs." Biology 10, no. 5 (April 29, 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 from glaucophytes but is present in rhodophytes, chlorophytes, plants, and most algae with complex plastids. This may suggest that in eukaryotic phototrophs, except for glaucophytes, either the gene from the mitochondrial ancestor was retained while the cyanobacterial and eukaryotic pseudoparalogs were lost in evolution, or the gene was acquired by non-endosymbiotic gene transfer from an unspecified α-proteobacterium and functionally replaced its cyanobacterial and eukaryotic counterparts.

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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 (October 13, 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 eukaryotic common ancestor. We use PhyloToL, our taxon-rich phylogenomic pipeline, to detect homologs of epigenetic genes and evaluate their macroevolutionary patterns among eukaryotes. In addition to data from GenBank, we increase taxon sampling from understudied clades of SAR (Stramenopila, Alveolata, and Rhizaria) and Amoebozoa by adding new single-cell transcriptomes from ciliates, foraminifera, and testate amoebae. We focus on 118 gene families, 94 involved in chromatin modification and 24 involved in non-protein-coding RNA processes based on the epigenetics literature. Our results indicate 1) the presence of a large number of epigenetic gene families in the last eukaryotic common ancestor; 2) differential conservation among major eukaryotic clades, with a notable paucity of genes within Excavata; and 3) punctate distribution of epigenetic gene families between species consistent with rapid evolution leading to gene loss. Together these data demonstrate the power of taxon-rich phylogenomic studies for illuminating evolutionary patterns at scales of >1 billion years of evolution and suggest that macroevolutionary phenomena, such as genome conflict, have shaped the evolution of the eukaryotic epigenetic toolkit.

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Emery-Corbin, Samantha J., Joshua J. Hamey, Brendan R. E. Ansell, Balu Balan, Swapnil Tichkule, Andreas J. Stroehlein, Crystal Cooper, et al. "Eukaryote-Conserved Methylarginine Is Absent in Diplomonads and Functionally Compensated in Giardia." Molecular Biology and Evolution 37, no. 12 (July 23, 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-methyltransferases and have remodeled conserved RGG/RG motifs targeted by these enzymes. We also provide experimental evidence for methylarginine absence in proteomes of Giardia but readily detect methyllysine. We bioinformatically infer 11 lysine-methyltransferases in Giardia, including highly diverged Su(var)3-9, Enhancer-of-zeste and Trithorax proteins with reduced domain architectures, and novel annotations demonstrating conserved methyllysine regulation of eukaryotic elongation factor 1 alpha. Using mass spectrometry, we identify more than 200 methyllysine sites in Giardia, including in species-specific gene families involved in cytoskeletal regulation, enriched in coiled-coil features. Finally, we use known methylation inhibitors to show that methylation plays key roles in replication and cyst formation in this parasite. This study highlights reduced methylation enzymes, sites, and functions early in eukaryote evolution, including absent methylarginine networks in the Diplomonadida. These results challenge the view that arginine methylation is eukaryote conserved and demonstrate that functional compensation of methylarginine was possible preceding expansion and diversification of these key networks in higher eukaryotes.

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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 (July 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, Jesús Emiliano Sotelo-Fonseca, Eva Wegel, Marco Di Stefano, Steven W. Wingett, et al. "Active and repressed biosynthetic gene clusters have spatially distinct chromosome states." Proceedings of the National Academy of Sciences 117, no. 24 (June 3, 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 microscopy, we investigate how chromosome topology relates to transcriptional activity of clustered biosynthetic pathway genes inArabidopsis thaliana. Our analyses reveal that biosynthetic gene clusters are embedded in local hot spots of 3D contacts that segregate cluster regions from the surrounding chromosome environment. The spatial conformation of these cluster-associated domains differs between transcriptionally active and silenced clusters. We further show that silenced clusters associate with heterochromatic chromosomal domains toward the periphery of the nucleus, while transcriptionally active clusters relocate away from the nuclear periphery. Examination of chromosome structure at unrelated clusters in maize, rice, and tomato indicates that integration of clustered pathway genes into distinct topological domains is a common feature in plant genomes. Our results shed light on the potential mechanisms that constrain coexpression within clusters of nonhomologous eukaryotic genes and suggest that gene clustering in the one-dimensional chromosome is accompanied by compartmentalization of the 3D chromosome.

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Andersson, Jan. "Phylogenomic approaches underestimate eukaryotic gene transfer." Mobile Genetic Elements 2, no. 1 (January 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 (July 2000): 310–15. http://dx.doi.org/10.1016/s0168-9525(00)02029-1.

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

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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 (April 27, 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 (November 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 (July 16, 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 (August 22, 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 (August 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 (January 1, 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 (November 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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Pescini, R., S. Alouani, A. Proudfoot, C. Power, J. J. Mermod, J. F. Delamarter, and R. H. Vanhuijsduijnen. "Inducible Inhibition of Eukaryotic Gene Expression." Biochemical and Biophysical Research Communications 202, no. 3 (August 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 (August 2007): 883–85. http://dx.doi.org/10.1038/nbt0807-883.

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