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Gross MR, Hsu R, Deitsch KW. Evolution of transcriptional control of antigenic variation and virulence in human and ape malaria parasites. BMC Ecol Evol 2021; 21:139. [PMID: 34238209 PMCID: PMC8265125 DOI: 10.1186/s12862-021-01872-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 07/02/2021] [Indexed: 11/13/2022] Open
Abstract
Background The most severe form of human malaria is caused by the protozoan parasite Plasmodium falciparum. This unicellular organism is a member of a subgenus of Plasmodium called the Laverania that infects apes, with P. falciparum being the only member that infects humans. The exceptional virulence of this species to humans can be largely attributed to a family of variant surface antigens placed by the parasites onto the surface of infected red blood cells that mediate adherence to the vascular endothelium. These proteins are encoded by a large, multicopy gene family called var, with each var gene encoding a different form of the protein. By changing which var gene is expressed, parasites avoid immune recognition, a process called antigenic variation that underlies the chronic nature of malaria infections. Results Here we show that the common ancestor of the branch of the Laverania lineage that includes the human parasite underwent a remarkable change in the organization and structure of elements linked to the complex transcriptional regulation displayed by the var gene family. Unlike the other members of the Laverania, the clade that gave rise to P. falciparum evolved distinct subsets of var genes distinguishable by different upstream transcriptional regulatory regions that have been associated with different expression profiles and virulence properties. In addition, two uniquely conserved var genes that have been proposed to play a role in coordinating transcriptional switching similarly arose uniquely within this clade. We hypothesize that these changes originated at a time of dramatic climatic change on the African continent that is predicted to have led to significant changes in transmission dynamics, thus selecting for patterns of antigenic variation that enabled lengthier, more chronic infections. Conclusions These observations suggest that changes in transmission dynamics selected for significant alterations in the transcriptional regulatory mechanisms that mediate antigenic variation in the parasite lineage that includes P. falciparum. These changes likely underlie the chronic nature of these infections as well as their exceptional virulence. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01872-z.
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Affiliation(s)
- Mackensie R Gross
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, USA
| | - Rosie Hsu
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, USA
| | - Kirk W Deitsch
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, USA.
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2
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Exploration of space to achieve scientific breakthroughs. Biotechnol Adv 2020; 43:107572. [PMID: 32540473 DOI: 10.1016/j.biotechadv.2020.107572] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 05/05/2020] [Accepted: 05/29/2020] [Indexed: 12/13/2022]
Abstract
Living organisms adapt to changing environments using their amazing flexibility to remodel themselves by a process called evolution. Environmental stress causes selective pressure and is associated with genetic and phenotypic shifts for better modifications, maintenance, and functioning of organismal systems. The natural evolution process can be used in complement to rational strain engineering for the development of desired traits or phenotypes as well as for the production of novel biomaterials through the imposition of one or more selective pressures. Space provides a unique environment of stressors (e.g., weightlessness and high radiation) that organisms have never experienced on Earth. Cells in the outer space reorganize and develop or activate a range of molecular responses that lead to changes in cellular properties. Exposure of cells to the outer space will lead to the development of novel variants more efficiently than on Earth. For instance, natural crop varieties can be generated with higher nutrition value, yield, and improved features, such as resistance against high and low temperatures, salt stress, and microbial and pest attacks. The review summarizes the literature on the parameters of outer space that affect the growth and behavior of cells and organisms as well as complex colloidal systems. We illustrate an understanding of gravity-related basic biological mechanisms and enlighten the possibility to explore the outer space environment for application-oriented aspects. This will stimulate biological research in the pursuit of innovative approaches for the future of agriculture and health on Earth.
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Evolution of Host Specificity by Malaria Parasites through Altered Mechanisms Controlling Genome Maintenance. mBio 2020; 11:mBio.03272-19. [PMID: 32184256 PMCID: PMC7078485 DOI: 10.1128/mbio.03272-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Malaria remains one of the most prevalent and deadly infectious diseases of the developing world, causing approximately 228 million clinical cases and nearly half a million deaths annually. The disease is caused by protozoan parasites of the genus Plasmodium, and of the five species capable of infecting humans, infections with P. falciparum are the most severe. In addition to the parasites that infect people, there are hundreds of additional species that infect birds, reptiles, and other mammals, each exquisitely evolved to meet the specific challenges inherent to survival within their respective hosts. By comparing the unique strategies that each species has evolved, key insights into host-parasite interactions can be gained, including discoveries regarding the pathogenesis of human disease. Here, we describe the surprising observation that closely related parasites with different hosts have evolved remarkably different methods for repairing their genomes. This observation has important implications for the ability of parasites to maintain chronic infections and for the development of host immunity. The protozoan parasites that cause malaria infect a wide variety of vertebrate hosts, including birds, reptiles, and mammals, and the evolutionary pressures inherent to the host-parasite relationship have profoundly shaped the genomes of both host and parasite. Here, we report that these selective pressures have resulted in unexpected alterations to one of the most basic aspects of eukaryotic biology, the maintenance of genome integrity through DNA repair. Malaria parasites that infect humans continuously generate genetic diversity within their antigen-encoding gene families through frequent ectopic recombination between gene family members, a process that is a crucial feature of the persistence of malaria globally. The continuous generation of antigen diversity ensures that different parasite isolates are antigenically distinct, thus preventing extensive cross-reactive immunity and enabling parasites to maintain stable transmission within human populations. However, the molecular basis of the recombination between gene family members is not well understood. Through computational analyses of the antigen-encoding, multicopy gene families of different Plasmodium species, we report the unexpected observation that malaria parasites that infect rodents do not display the same degree of antigen diversity as observed in Plasmodium falciparum and appear to undergo significantly less ectopic recombination. Using comparative genomics, we also identify key molecular components of the diversification process, thus shedding new light on how malaria parasites balance the maintenance of genome integrity with the requirement for continuous genetic diversification.
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Horizontal Gene Transfer as an Indispensable Driver for Evolution of Neocallimastigomycota into a Distinct Gut-Dwelling Fungal Lineage. Appl Environ Microbiol 2019; 85:AEM.00988-19. [PMID: 31126947 DOI: 10.1128/aem.00988-19] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 05/19/2019] [Indexed: 01/01/2023] Open
Abstract
Survival and growth of the anaerobic gut fungi (AGF; Neocallimastigomycota) in the herbivorous gut necessitate the possession of multiple abilities absent in other fungal lineages. We hypothesized that horizontal gene transfer (HGT) was instrumental in forging the evolution of AGF into a phylogenetically distinct gut-dwelling fungal lineage. The patterns of HGT were evaluated in the transcriptomes of 27 AGF strains, 22 of which were isolated and sequenced in this study, and 4 AGF genomes broadly covering the breadth of AGF diversity. We identified 277 distinct incidents of HGT in AGF transcriptomes, with subsequent gene duplication resulting in an HGT frequency of 2 to 3.5% in AGF genomes. The majority of HGT events were AGF specific (91.7%) and wide (70.8%), indicating their occurrence at early stages of AGF evolution. The acquired genes allowed AGF to expand their substrate utilization range, provided new venues for electron disposal, augmented their biosynthetic capabilities, and facilitated their adaptation to anaerobiosis. The majority of donors were anaerobic fermentative bacteria prevalent in the herbivorous gut. This study strongly indicates that HGT indispensably forged the evolution of AGF as a distinct fungal phylum and provides a unique example of the role of HGT in shaping the evolution of a high-rank taxonomic eukaryotic lineage.IMPORTANCE The anaerobic gut fungi (AGF) represent a distinct basal phylum lineage (Neocallimastigomycota) commonly encountered in the rumen and alimentary tracts of herbivores. Survival and growth of anaerobic gut fungi in these anaerobic, eutrophic, and prokaryote-dominated habitats necessitates the acquisition of several traits absent in other fungal lineages. We assess here the role of horizontal gene transfer as a relatively fast mechanism for trait acquisition by the Neocallimastigomycota postsequestration in the herbivorous gut. Analysis of 27 transcriptomes that represent the broad diversity of Neocallimastigomycota identified 277 distinct HGT events, with subsequent gene duplication resulting in an HGT frequency of 2 to 3.5% in AGF genomes. These HGT events have allowed AGF to survive in the herbivorous gut by expanding their substrate utilization range, augmenting their biosynthetic pathway, providing new routes for electron disposal by expanding fermentative capacities, and facilitating their adaptation to anaerobiosis. HGT in the AGF is also shown to be mainly a cross-kingdom affair, with the majority of donors belonging to the bacteria. This study represents a unique example of the role of HGT in shaping the evolution of a high-rank taxonomic eukaryotic lineage.
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5
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Independent evolution of complex development in animals and plants: deep homology and lateral gene transfer. Dev Genes Evol 2019; 229:25-34. [PMID: 30685797 DOI: 10.1007/s00427-019-00626-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 01/10/2019] [Indexed: 01/25/2023]
Abstract
The evolution of multicellularity is a premier example of phenotypic convergence: simple multicellularity evolved independently many times, and complex multicellular phenotypes are found in several distant groups. Furthermore, both animal and plant lineages have independently reached extreme levels of morphological, functional, and developmental complexity. This study explores the genetic basis for the parallel evolution of complex multicellularity and development in the animal and green plant (i.e., green algae and land plants) lineages. Specifically, the study (i) identifies the SAND domain-a DNA-binding domain with important roles in the regulation of cell proliferation and differentiation, as unique to animals, green algae, and land plants; and (ii) suggests that the parallel deployment of this ancestral domain in similar regulatory roles could have contributed to the independent evolution of complex development in these distant groups. Given the deep animal-green plant divergence, the limited distribution of the SAND domain is best explained by invoking a lateral gene transfer (LGT) event from a green alga to an early metazoan. The presence of a sequence motif specifically shared by a family of SAND-containing transcription factors involved in the evolution of complex multicellularity in volvocine algae and two types of SAND proteins that emerged early in the evolution of animals is consistent with this scenario. Overall, these findings imply that (i) in addition to be involved in the evolution of similar phenotypes, deep homologous sequences can also contribute to shaping parallel evolutionary trajectories in distant lineages, and (ii) LGT could provide an additional source of latent homologous sequences that can be deployed in analogous roles and affect the evolutionary potentials of distantly related groups.
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Abstract
Organisms with identical genome sequences can show substantial differences in their phenotypes owing to epigenetic changes that result in different use of their genes. Epigenetic regulation of gene expression plays a key role in the control of several fundamental processes in the biology of malaria parasites, including antigenic variation and sexual differentiation. Some of the histone modifications and chromatin-modifying enzymes that control the epigenetic states of malaria genes have been characterized, and their functions are beginning to be unraveled. The fundamental principles of epigenetic regulation of gene expression appear to be conserved between malaria parasites and model eukaryotes, but important peculiarities exist. Here, we review the current knowledge of malaria epigenetics and discuss how it can be exploited for the development of new molecular markers and new types of drugs that may contribute to malaria eradication efforts.
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Affiliation(s)
- Alfred Cortés
- ISGlobal, Barcelona Centre for International Health Research (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Catalonia 08036, Spain.,ICREA, Barcelona, Catalonia 08010, Spain
| | - Kirk W Deitsch
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York 10065
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7
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Pasini EM, Böhme U, Rutledge GG, Voorberg-Van der Wel A, Sanders M, Berriman M, Kocken CH, Otto TD. An improved Plasmodium cynomolgi genome assembly reveals an unexpected methyltransferase gene expansion. Wellcome Open Res 2017; 2:42. [PMID: 28748222 PMCID: PMC5500898 DOI: 10.12688/wellcomeopenres.11864.1] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2017] [Indexed: 11/20/2022] Open
Abstract
Background:
Plasmodium cynomolgi, a non-human primate malaria parasite species, has been an important model parasite since its discovery in 1907. Similarities in the biology of
P. cynomolgi to the closely related, but less tractable, human malaria parasite
P. vivax make it the model parasite of choice for liver biology and vaccine studies pertinent to
P. vivax malaria. Molecular and genome-scale studies of
P. cynomolgi have relied on the current reference genome sequence, which remains highly fragmented with 1,649 unassigned scaffolds and little representation of the subtelomeres. Methods: Using long-read sequence data (Pacific Biosciences SMRT technology), we assembled and annotated a new reference genome sequence, PcyM, sourced from an Indian rhesus monkey. We compare the newly assembled genome sequence with those of several other
Plasmodium species, including a re-annotated
P. coatneyi assembly. Results: The new PcyM genome assembly is of significantly higher quality than the existing reference, comprising only 56 pieces, no gaps and an improved average gene length. Detailed manual curation has ensured a comprehensive annotation of the genome with 6,632 genes, nearly 1,000 more than previously attributed to
P. cynomolgi. The new assembly also has an improved representation of the subtelomeric regions, which account for nearly 40% of the sequence. Within the subtelomeres, we identified more than 1300
Plasmodium interspersed repeat (
pir) genes, as well as a striking expansion of 36 methyltransferase pseudogenes that originated from a single copy on chromosome 9. Conclusions: The manually curated PcyM reference genome sequence is an important new resource for the malaria research community. The high quality and contiguity of the data have enabled the discovery of a novel expansion of methyltransferase in the subtelomeres, and illustrates the new comparative genomics capabilities that are being unlocked by complete reference genomes.
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Affiliation(s)
- Erica M Pasini
- Biomedical Primate Research Centre, Rijswijk, Lange Kleiweg 161, 2288GJ Rijswijk, Netherlands
| | - Ulrike Böhme
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Gavin G Rutledge
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | | | - Mandy Sanders
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Matt Berriman
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Clemens Hm Kocken
- Biomedical Primate Research Centre, Rijswijk, Lange Kleiweg 161, 2288GJ Rijswijk, Netherlands
| | - Thomas Dan Otto
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
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8
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Eichenberger RM, Ramakrishnan C, Russo G, Deplazes P, Hehl AB. Genome-wide analysis of gene expression and protein secretion of Babesia canis during virulent infection identifies potential pathogenicity factors. Sci Rep 2017; 7:3357. [PMID: 28611446 PMCID: PMC5469757 DOI: 10.1038/s41598-017-03445-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 04/27/2017] [Indexed: 12/14/2022] Open
Abstract
Infections of dogs with virulent strains of Babesia canis are characterized by rapid onset and high mortality, comparable to complicated human malaria. As in other apicomplexan parasites, most Babesia virulence factors responsible for survival and pathogenicity are secreted to the host cell surface and beyond where they remodel and biochemically modify the infected cell interacting with host proteins in a very specific manner. Here, we investigated factors secreted by B. canis during acute infections in dogs and report on in silico predictions and experimental analysis of the parasite’s exportome. As a backdrop, we generated a fully annotated B. canis genome sequence of a virulent Hungarian field isolate (strain BcH-CHIPZ) underpinned by extensive genome-wide RNA-seq analysis. We find evidence for conserved factors in apicomplexan hemoparasites involved in immune-evasion (e.g. VESA-protein family), proteins secreted across the iRBC membrane into the host bloodstream (e.g. SA- and Bc28 protein families), potential moonlighting proteins (e.g. profilin and histones), and uncharacterized antigens present during acute crisis in dogs. The combined data provides a first predicted and partially validated set of potential virulence factors exported during fatal infections, which can be exploited for urgently needed innovative intervention strategies aimed at facilitating diagnosis and management of canine babesiosis.
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Affiliation(s)
| | | | | | - Peter Deplazes
- Institute of Parasitology, University of Zurich, Zurich, Switzerland
| | - Adrian B Hehl
- Institute of Parasitology, University of Zurich, Zurich, Switzerland.
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9
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Abstract
Complications arising from malaria are a concern for public health authorities worldwide, since the annual caseload in humans usually exceeds millions. Of more than 160 species of Plasmodium, only 4 infect humans, with the most severe cases ascribed to Plasmodium falciparum and the most prevalent to Plasmodium vivax. Over the past 70 years, since World War II, when the first antimalarial drugs were widely used, many efforts have been made to combat this disease, including vectorial control, new drug discoveries and genetic and molecular approaches. Molecular approaches, such as glycobiology, may lead to new therapeutic targets (both in the host and the parasites), since all interactions are mediated by carbohydrates or glycan moieties decorating both cellular surfaces from parasite and host cells. In this review, we address the carbohydrate-mediated glycobiology that directly affects Plasmodium survival or host resistance.
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Affiliation(s)
- Pollyanna S Gomes
- Departamento de Imunologia, Instituto de Microbiologia, Universidade Federal do Rio de JaneiroRio de Janeiro, Brazil
| | - Daniel F Feijó
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz (Fiocruz)Salvador, Brazil
| | - Alexandre Morrot
- Departamento de Imunologia, Instituto de Microbiologia, Universidade Federal do Rio de JaneiroRio de Janeiro, Brazil.,Instituto Oswaldo CruzFiocruz, Rio de Janeiro, Brazil
| | - Celio G Freire-de-Lima
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de JaneiroRio de Janeiro, Brazil
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Caljon G, De Muylder G, Durnez L, Jennes W, Vanaerschot M, Dujardin JC. Alice in microbes' land: adaptations and counter-adaptations of vector-borne parasitic protozoa and their hosts. FEMS Microbiol Rev 2016; 40:664-85. [PMID: 27400870 DOI: 10.1093/femsre/fuw018] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/03/2016] [Indexed: 12/24/2022] Open
Abstract
In the present review, we aim to provide a general introduction to different facets of the arms race between pathogens and their hosts/environment, emphasizing its evolutionary aspects. We focus on vector-borne parasitic protozoa, which have to adapt to both invertebrate and vertebrate hosts. Using Leishmania, Trypanosoma and Plasmodium as main models, we review successively (i) the adaptations and counter-adaptations of parasites and their invertebrate host, (ii) the adaptations and counter-adaptations of parasites and their vertebrate host and (iii) the impact of human interventions (chemotherapy, vaccination, vector control and environmental changes) on these adaptations. We conclude by discussing the practical impact this knowledge can have on translational research and public health.
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Affiliation(s)
- Guy Caljon
- Institute of Tropical Medicine, Department of Biomedical Sciences, Nationalestraat 155, B-2000 Antwerp, Belgium University of Antwerp, Department of Biomedical Sciences, Laboratory of Microbiology, Parasitology and Health, Universiteitsplein 1, B-2610 Wilrijk, Belgium
| | - Géraldine De Muylder
- Institute of Tropical Medicine, Department of Biomedical Sciences, Nationalestraat 155, B-2000 Antwerp, Belgium
| | - Lies Durnez
- Institute of Tropical Medicine, Department of Biomedical Sciences, Nationalestraat 155, B-2000 Antwerp, Belgium
| | - Wim Jennes
- Institute of Tropical Medicine, Department of Biomedical Sciences, Nationalestraat 155, B-2000 Antwerp, Belgium
| | - Manu Vanaerschot
- Institute of Tropical Medicine, Department of Biomedical Sciences, Nationalestraat 155, B-2000 Antwerp, Belgium Columbia University, College of Physicians and Surgeons, Department of Microbiology and Immunology, Fidock Lab, New York, NY 10032, USA
| | - Jean-Claude Dujardin
- Institute of Tropical Medicine, Department of Biomedical Sciences, Nationalestraat 155, B-2000 Antwerp, Belgium University of Antwerp, Department of Biomedical Sciences, Laboratory of Microbiology, Parasitology and Health, Universiteitsplein 1, B-2610 Wilrijk, Belgium
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11
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Minarovits J, Banati F, Szenthe K, Niller HH. Epigenetic Regulation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 879:1-25. [DOI: 10.1007/978-3-319-24738-0_1] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Abstract
All living organisms require protein degradation to terminate biological processes and remove damaged proteins. One such machine is the 20S proteasome, a specialized barrel-shaped and compartmentalized multicatalytic protease. The activity of the 20S proteasome generally requires the binding of regulators/proteasome activators (PAs), which control the entrance of substrates. These include the PA700 (19S complex), which assembles with the 20S and forms the 26S proteasome and allows the efficient degradation of proteins usually labeled by ubiquitin tags, PA200 and PA28, which are involved in proteolysis through ubiquitin-independent mechanisms and PI31, which was initially identified as a 20S inhibitor in vitro. Unlike 20S proteasome, shown to be present in all Eukaryotes and Archaea, the evolutionary history of PAs remained fragmentary. Here, we made a comprehensive survey and phylogenetic analyses of the four types of regulators in 17 clades covering most of the eukaryotic supergroups. We found remarkable conservation of each PA700 subunit in all eukaryotes, indicating that the current complex PA700 structure was already set up in the last eukaryotic common ancestor (LECA). Also present in LECA, PA200, PA28, and PI31 showed a more contrasted evolutionary picture, because many lineages have subsequently lost one or two of them. The paramount conservation of PA700 composition in all eukaryotes and the dynamic evolution of PA200, PA28, and PI31 are discussed in the light of current knowledge on their physiological roles.
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Affiliation(s)
- Philippe Fort
- CNRS, CRBM, UMR5237, Montpellier, France Université de Montpellier, France
| | - Andrey V Kajava
- CNRS, CRBM, UMR5237, Montpellier, France Université de Montpellier, France Institut de Biologie Computationnelle, Montpellier, France
| | - Fredéric Delsuc
- Université de Montpellier, France CNRS, IRD, Institut des Sciences de l'Evolution, UMR 5554, Montpellier, France
| | - Olivier Coux
- CNRS, CRBM, UMR5237, Montpellier, France Université de Montpellier, France
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Simonti CN, Pollard KS, Schröder S, He D, Bruneau BG, Ott M, Capra JA. Evolution of lysine acetylation in the RNA polymerase II C-terminal domain. BMC Evol Biol 2015; 15:35. [PMID: 25887984 PMCID: PMC4362643 DOI: 10.1186/s12862-015-0327-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 02/24/2015] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND RPB1, the largest subunit of RNA polymerase II, contains a highly modifiable C-terminal domain (CTD) that consists of variations of a consensus heptad repeat sequence (Y1S2P3T4S5P6S7). The consensus CTD repeat motif and tandem organization represent the ancestral state of eukaryotic RPB1, but across eukaryotes CTDs show considerable diversity in repeat organization and sequence content. These differences may reflect lineage-specific CTD functions mediated by protein interactions. Mammalian CTDs contain eight non-consensus repeats with a lysine in the seventh position (K7). Posttranslational acetylation of these sites was recently shown to be required for proper polymerase pausing and regulation of two growth factor-regulated genes. RESULTS To investigate the origins and function of RPB1 CTD acetylation (acRPB1), we computationally reconstructed the evolution of the CTD repeat sequence across eukaryotes and analyzed the evolution and function of genes dysregulated when acRPB1 is disrupted. Modeling the evolutionary dynamics of CTD repeat count and sequence content across diverse eukaryotes revealed an expansion of the CTD in the ancestors of Metazoa. The new CTD repeats introduced the potential for acRPB1 due to the appearance of distal repeats with lysine at position seven. This was followed by a further increase in the number of lysine-containing repeats in developmentally complex clades like Deuterostomia. Mouse genes enriched for acRPB1 occupancy at their promoters and genes with significant expression changes when acRPB1 is disrupted are enriched for several functions, such as growth factor response, gene regulation, cellular adhesion, and vascular development. Genes occupied and regulated by acRPB1 show significant enrichment for evolutionary origins in the early history of eukaryotes through early vertebrates. CONCLUSIONS Our combined functional and evolutionary analyses show that RPB1 CTD acetylation was possible in the early history of animals, and that the K7 content of the CTD expanded in specific developmentally complex metazoan lineages. The functional analysis of genes regulated by acRPB1 highlight functions involved in the origin of and diversification of complex Metazoa. This suggests that acRPB1 may have played a role in the success of animals.
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Affiliation(s)
- Corinne N Simonti
- Center for Human Genetics Research, Vanderbilt University, Nashville, TN, 37232, USA.
| | - Katherine S Pollard
- Gladstone Institutes, University of California, San Francisco, San Francisco, CA, 94158, USA. .,Department of Epidemiology & Biostatistics and Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, 94158, USA.
| | - Sebastian Schröder
- Gladstone Institutes, University of California, San Francisco, San Francisco, CA, 94158, USA.
| | - Daniel He
- Gladstone Institutes, University of California, San Francisco, San Francisco, CA, 94158, USA.
| | - Benoit G Bruneau
- Gladstone Institutes, University of California, San Francisco, San Francisco, CA, 94158, USA.
| | - Melanie Ott
- Gladstone Institutes, University of California, San Francisco, San Francisco, CA, 94158, USA.
| | - John A Capra
- Center for Human Genetics Research, Vanderbilt University, Nashville, TN, 37232, USA. .,Departments of Biological Sciences and Biomedical Informatics, Vanderbilt University, Nashville, TN, 37232, USA.
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14
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Jenkins AM, Muskavitch MAT. Evolution of an epigenetic gene ensemble within the genus Anopheles. Genome Biol Evol 2015; 7:901-15. [PMID: 25724208 PMCID: PMC5322554 DOI: 10.1093/gbe/evv041] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Epigenetic control of gene expression has important implications for the regulation of developmental processes, for mediating homeostasis and responses to the external environment, and for transgenerational inheritance of gene expression patterns. Genes that mediate epigenetic control have been well-characterized in Drosophila melanogaster, and we have identified and analyzed an orthologous gene ensemble in Anopheles gambiae that comprises 169 orthologs related to a 215-member epigenetic gene ensemble in D. melanogaster. We find that this ensemble is highly conserved among anopheline mosquitoes, as we identify only seven gene family expansion/contraction events within the ensemble among 12 mosquito species we have studied within the genus Anopheles. Comparative analyses of the epigenetic gene expression across the genera Drosophila and Anopheles reveal distinct tissue-associated expression patterns in the two genera, but similar temporal expression patterns. The A. gambiae complex and D. melanogaster subgroup epigenetic gene ensembles exhibit similar evolutionary rates, as assessed by their respective dN/dS values. These differences in tissue-associated expression patterns, in contrast to similarities in evolutionary rates and temporal expression patterns, may imply that some members of the epigenetic gene ensemble have been redeployed within one or both genera, in comparison to the most recent common ancestor of these two clades. Members of this epigenetic gene ensemble may constitute another set of potential targets for vector control and enable further reductions in the burden of human malaria, by analogy to recent success in development of small molecule antagonists for mammalian epigenetic machinery.
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Affiliation(s)
| | - Marc A T Muskavitch
- Department of Biology, Boston College Discovery Research, Biogen Idec, Cambridge, Massachusetts
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15
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Mitosis, microtubule dynamics and the evolution of kinesins. Exp Cell Res 2015; 334:61-9. [PMID: 25708751 DOI: 10.1016/j.yexcr.2015.02.010] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 02/10/2015] [Indexed: 12/20/2022]
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Djuika CF, Huerta-Cepas J, Przyborski JM, Deil S, Sanchez CP, Doerks T, Bork P, Lanzer M, Deponte M. Prokaryotic ancestry and gene fusion of a dual localized peroxiredoxin in malaria parasites. MICROBIAL CELL 2015; 2:5-13. [PMID: 28357258 PMCID: PMC5361646 DOI: 10.15698/mic2015.01.182] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Horizontal gene transfer has emerged as a crucial driving force for the evolution of eukaryotes. This also includes Plasmodium falciparum and related economically and clinically relevant apicomplexan parasites, whose rather small genomes have been shaped not only by natural selection in different host populations but also by horizontal gene transfer following endosymbiosis. However, there is rather little reliable data on horizontal gene transfer between animal hosts or bacteria and apicomplexan parasites. Here we show that apicomplexan homologues of peroxiredoxin 5 (Prx5) have a prokaryotic ancestry and therefore represent a special subclass of Prx5 isoforms in eukaryotes. Using two different immunobiochemical approaches, we found that the P. falciparum Prx5 homologue is dually localized to the parasite plastid and cytosol. This dual localization is reflected by a modular Plasmodium-specific gene architecture consisting of two exons. Despite the plastid localization, our phylogenetic analyses contradict an acquisition by secondary endosymbiosis and support a gene fusion event following a horizontal prokaryote-to-eukaryote gene transfer in early apicomplexans. The results provide unexpected insights into the evolution of apicomplexan parasites as well as the molecular evolution of peroxiredoxins, an important family of ubiquitous, usually highly concentrated thiol-dependent hydroperoxidases that exert functions as detoxifying enzymes, redox sensors and chaperones.
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Affiliation(s)
- Carine F Djuika
- Department of Parasitology, Ruprecht-Karls University, D-69120 Heidelberg, Germany
| | - Jaime Huerta-Cepas
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), D-69117 Heidelberg, Germany
| | - Jude M Przyborski
- Department of Parasitology, Philipps University, D-35043 Marburg, Germany
| | - Sophia Deil
- Department of Parasitology, Ruprecht-Karls University, D-69120 Heidelberg, Germany
| | - Cecilia P Sanchez
- Department of Parasitology, Ruprecht-Karls University, D-69120 Heidelberg, Germany
| | - Tobias Doerks
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), D-69117 Heidelberg, Germany
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), D-69117 Heidelberg, Germany
| | - Michael Lanzer
- Department of Parasitology, Ruprecht-Karls University, D-69120 Heidelberg, Germany
| | - Marcel Deponte
- Department of Parasitology, Ruprecht-Karls University, D-69120 Heidelberg, Germany
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17
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Weyenberg G, Huggins PM, Schardl CL, Howe DK, Yoshida R. kdetrees: Non-parametric estimation of phylogenetic tree distributions. Bioinformatics 2014; 30:2280-7. [PMID: 24764459 PMCID: PMC4176058 DOI: 10.1093/bioinformatics/btu258] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Revised: 04/04/2014] [Accepted: 04/22/2014] [Indexed: 01/14/2023] Open
Abstract
MOTIVATION Although the majority of gene histories found in a clade of organisms are expected to be generated by a common process (e.g. the coalescent process), it is well known that numerous other coexisting processes (e.g. horizontal gene transfers, gene duplication and subsequent neofunctionalization) will cause some genes to exhibit a history distinct from those of the majority of genes. Such 'outlying' gene trees are considered to be biologically interesting, and identifying these genes has become an important problem in phylogenetics. RESULTS We propose and implement kdetrees, a non-parametric method for estimating distributions of phylogenetic trees, with the goal of identifying trees that are significantly different from the rest of the trees in the sample. Our method compares favorably with a similar recently published method, featuring an improvement of one polynomial order of computational complexity (to quadratic in the number of trees analyzed), with simulation studies suggesting only a small penalty to classification accuracy. Application of kdetrees to a set of Apicomplexa genes identified several unreliable sequence alignments that had escaped previous detection, as well as a gene independently reported as a possible case of horizontal gene transfer. We also analyze a set of Epichloë genes, fungi symbiotic with grasses, successfully identifying a contrived instance of paralogy. AVAILABILITY AND IMPLEMENTATION Our method for estimating tree distributions and identifying outlying trees is implemented as the R package kdetrees and is available for download from CRAN.
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Affiliation(s)
- Grady Weyenberg
- Department of Statistics, University of Kentucky, Lexington, KY 40536, Robotics Institute, Carnegie Mellon University, Pittsburgh, PA 15213, Plant Pathology Department and Department of Veterinary Science, University of Kentucky, Lexington, KY 40546, USA
| | - Peter M Huggins
- Department of Statistics, University of Kentucky, Lexington, KY 40536, Robotics Institute, Carnegie Mellon University, Pittsburgh, PA 15213, Plant Pathology Department and Department of Veterinary Science, University of Kentucky, Lexington, KY 40546, USA
| | - Christopher L Schardl
- Department of Statistics, University of Kentucky, Lexington, KY 40536, Robotics Institute, Carnegie Mellon University, Pittsburgh, PA 15213, Plant Pathology Department and Department of Veterinary Science, University of Kentucky, Lexington, KY 40546, USA
| | - Daniel K Howe
- Department of Statistics, University of Kentucky, Lexington, KY 40536, Robotics Institute, Carnegie Mellon University, Pittsburgh, PA 15213, Plant Pathology Department and Department of Veterinary Science, University of Kentucky, Lexington, KY 40546, USA
| | - Ruriko Yoshida
- Department of Statistics, University of Kentucky, Lexington, KY 40536, Robotics Institute, Carnegie Mellon University, Pittsburgh, PA 15213, Plant Pathology Department and Department of Veterinary Science, University of Kentucky, Lexington, KY 40546, USA
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18
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Oberstaller J, Pumpalova Y, Schieler A, Llinás M, Kissinger JC. The Cryptosporidium parvum ApiAP2 gene family: insights into the evolution of apicomplexan AP2 regulatory systems. Nucleic Acids Res 2014; 42:8271-84. [PMID: 24957599 PMCID: PMC4117751 DOI: 10.1093/nar/gku500] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 05/15/2014] [Accepted: 05/19/2014] [Indexed: 01/13/2023] Open
Abstract
We provide the first comprehensive analysis of any transcription factor family in Cryptosporidium, a basal-branching apicomplexan that is the second leading cause of infant diarrhea globally. AP2 domain-containing proteins have evolved to be the major regulatory family in the phylum to the exclusion of canonical regulators. We show that apicomplexan and perkinsid AP2 domains cluster distinctly from other chromalveolate AP2s. Protein-binding specificity assays of C. parvum AP2 domains combined with motif conservation upstream of co-regulated gene clusters allowed the construction of putative AP2 regulons across the in vitro life cycle. Orthologous Apicomplexan AP2 (ApiAP2) expression has been rearranged relative to the malaria parasite P. falciparum, suggesting ApiAP2 network rewiring during evolution. C. hominis orthologs of putative C. parvum ApiAP2 proteins and target genes show greater than average variation. C. parvum AP2 domains display reduced binding diversity relative to P. falciparum, with multiple domains binding the 5'-TGCAT-3', 5'-CACACA-3' and G-box motifs (5'-G[T/C]GGGG-3'). Many overrepresented motifs in C. parvum upstream regions are not AP2 binding motifs. We propose that C. parvum is less reliant on ApiAP2 regulators in part because it utilizes E2F/DP1 transcription factors. C. parvum may provide clues to the ancestral state of apicomplexan transcriptional regulation, pre-AP2 domination.
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Affiliation(s)
- Jenna Oberstaller
- Department of Genetics, University of Georgia, Athens, GA 30602, USA Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA
| | - Yoanna Pumpalova
- Department of Molecular Biology and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Ariel Schieler
- Department of Molecular Biology and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Manuel Llinás
- Department of Molecular Biology and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Jessica C Kissinger
- Department of Genetics, University of Georgia, Athens, GA 30602, USA Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
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19
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Evolutionary diversity and taxon-specific modifications of the RNA polymerase II C-terminal domain. Proc Natl Acad Sci U S A 2014; 111:5920-5. [PMID: 24711388 DOI: 10.1073/pnas.1323616111] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In model eukaryotes, the C-terminal domain (CTD) of the largest subunit of DNA-dependent RNA polymerase II (RNAP II) is composed of tandemly repeated heptads with the consensus sequence YSPTSPS. The core motif and tandem structure generally are conserved across model taxa, including animals, yeasts and higher plants. Broader investigations revealed that CTDs of many organisms deviate substantially from this canonical structure; however, limited sampling made it difficult to determine whether disordered sequences reflect the CTD's ancestral state or degeneration from ancestral repetitive structures. Therefore, we undertook, to our knowledge, the broadest investigation to date of the evolution of the RNAP II CTD across eukaryotic diversity. Our results indicate that a tandemly repeated CTD existed in the ancestors of each major taxon, and that degeneration and reinvention of this ordered structure are common features of CTD evolution. Lineage-specific CTD modifications appear to be associated with greater developmental complexity in multicellular organisms, a pattern taken to an extreme in fungi and red algae, in which the CTD has undergone dramatic to complete alteration during the transition from unicellular to developmentally complex forms. Overall, loss and reinvention of repeats have punctuated CTD evolution, occurring independently and sometimes repeatedly in various groups.
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20
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Ukaegbu UE, Kishore SP, Kwiatkowski DL, Pandarinath C, Dahan-Pasternak N, Dzikowski R, Deitsch KW. Recruitment of PfSET2 by RNA polymerase II to variant antigen encoding loci contributes to antigenic variation in P. falciparum. PLoS Pathog 2014; 10:e1003854. [PMID: 24391504 PMCID: PMC3879369 DOI: 10.1371/journal.ppat.1003854] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Accepted: 11/12/2013] [Indexed: 11/18/2022] Open
Abstract
Histone modifications are important regulators of gene expression in all eukaryotes. In Plasmodium falciparum, these epigenetic marks regulate expression of genes involved in several aspects of host-parasite interactions, including antigenic variation. While the identities and genomic positions of many histone modifications have now been cataloged, how they are targeted to defined genomic regions remains poorly understood. For example, how variant antigen encoding loci (var) are targeted for deposition of unique histone marks is a mystery that continues to perplex the field. Here we describe the recruitment of an ortholog of the histone modifier SET2 to var genes through direct interactions with the C-terminal domain (CTD) of RNA polymerase II. In higher eukaryotes, SET2 is a histone methyltransferase recruited by RNA pol II during mRNA transcription; however, the ortholog in P. falciparum (PfSET2) has an atypical architecture and its role in regulating transcription is unknown. Here we show that PfSET2 binds to the unphosphorylated form of the CTD, a property inconsistent with its recruitment during mRNA synthesis. Further, we show that H3K36me3, the epigenetic mark deposited by PfSET2, is enriched at both active and silent var gene loci, providing additional evidence that its recruitment is not associated with mRNA production. Over-expression of a dominant negative form of PfSET2 designed to disrupt binding to RNA pol II induced rapid var gene expression switching, confirming both the importance of PfSET2 in var gene regulation and a role for RNA pol II in its recruitment. RNA pol II is known to transcribe non-coding RNAs from both active and silent var genes, providing a possible mechanism by which it could recruit PfSET2 to var loci. This work unifies previous reports of histone modifications, the production of ncRNAs, and the promoter activity of var introns into a mechanism that contributes to antigenic variation by malaria parasites. Chemical modifications to histones, the proteins that serve as the primary units of chromatin, often determine whether specific genes are actively transcribed or condensed into transcriptionally silent regions of the genome. In the malaria parasite Plasmodium falciparum, histone modifications have been shown to play a significant role in controlling gene expression involved in many aspects of their lifecycle, including the complex gene expression patterns associated with antigenic variation. The various histone modifications that are found within the parasite's genome have now been extensively cataloged, and the enzymes that are responsible for adding and removing them have been identified. However, how these enzymes are recruited to specific regions of the genome to coordinate gene expression is not understood. In this paper, we provide the first evidence for recruitment of a unique histone methyltransferase to specific regions of the genome through its tethering to RNA polymerase II. We find that disruption of this interaction results in major changes in expression patterns of genes involved in antigenic variation, demonstrating the importance of regulated recruitment of histone modifiers for parasite biology.
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Affiliation(s)
- Uchechi E Ukaegbu
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, United States of America
| | - Sandeep P Kishore
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, United States of America
| | - Dacia L Kwiatkowski
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, United States of America
| | - Chethan Pandarinath
- Program in Computational Biology, Weill Medical College of Cornell University, New York, New York, United States of America
| | - Noa Dahan-Pasternak
- Department of Microbiology and Molecular Genetics, The Institute for Medical Research Israel-Canada, The Kuvin Center for the Study of Infectious and Tropical Diseases, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Ron Dzikowski
- Department of Microbiology and Molecular Genetics, The Institute for Medical Research Israel-Canada, The Kuvin Center for the Study of Infectious and Tropical Diseases, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Kirk W Deitsch
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, United States of America
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21
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Duffy MF, Selvarajah SA, Josling GA, Petter M. Epigenetic regulation of the Plasmodium falciparum genome. Brief Funct Genomics 2013; 13:203-16. [PMID: 24326119 DOI: 10.1093/bfgp/elt047] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Recent research has highlighted some unique aspects of chromatin biology in the malaria parasite Plasmodium falciparum. During its erythrocytic lifecycle P. falciparum maintains its genome primarily as unstructured euchromatin. Indeed there is no clear role for chromatin-mediated silencing of the majority of the developmentally expressed genes in P. falciparum. However discontinuous stretches of heterochromatin are critical for variegated expression of contingency genes that mediate key pathogenic processes in malaria. These range from invasion of erythrocytes and antigenic variation to solute transport and growth adaptation in response to environmental changes. Despite lack of structure within euchromatin the nucleus maintains functional compartments that regulate expression of many genes at the nuclear periphery, particularly genes with clonally variant expression. The typical components of the chromatin regulatory machinery are present in P. falciparum; however, some of these appear to have evolved novel species-specific functions, e.g. the dynamic regulation of histone variants at virulence gene promoters. The parasite also appears to have repeatedly acquired chromatin regulatory proteins through lateral transfer from endosymbionts and from the host. P. falciparum chromatin regulators have been successfully targeted with multiple drugs in laboratory studies; hopefully their functional divergence from human counterparts will allow the development of parasite-specific inhibitors.
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Abstract
SUMMARY From hundreds of independent transitions from a free-living existence to a parasitic mode of life, separate parasite lineages have converged over evolutionary time to share traits and exploit their hosts in similar ways. Here, we first summarize the evidence that, at a phenotypic level, eukaryotic parasite lineages have all converged toward only six general parasitic strategies: parasitoid, parasitic castrator, directly transmitted parasite, trophically transmitted parasite, vector-transmitted parasite or micropredator. We argue that these strategies represent adaptive peaks, with the similarities among unrelated taxa within any strategy extending to all basic aspects of host exploitation and transmission among hosts and transcending phylogenetic boundaries. Then, we extend our examination of convergent patterns by looking at the evolution of parasite genomes. Despite the limited taxonomic coverage of sequenced parasite genomes currently available, we find some evidence of parallel evolution among unrelated parasite taxa with respect to genome reduction or compaction, and gene losses or gains. Matching such changes in parasite genomes with the broad phenotypic traits that define the convergence of parasites toward only six strategies of host exploitation is not possible at present. Nevertheless, as more parasite genomes become available, we may be able to detect clear trends in the evolution of parasitic genome architectures representing true convergent adaptive peaks, the genomic equivalents of the phenotypic strategies used by all parasites.
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Niller HH, Banati F, Nagy K, Buzas K, Minarovits J. Update on microbe-induced epigenetic changes: bacterial effectors and viral oncoproteins as epigenetic dysregulators. Future Virol 2013. [DOI: 10.2217/fvl.13.97] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Pathoepigenetics is a new discipline describing how disturbances in epigenetic regulation alter the epigenotype and gene-expression pattern of human, animal or plant cells. Such ‘epigenetic reprogramming’ may play an important role in the initiation and progression of a wide variety of diseases. Infectious diseases also belong to this category: recent data demonstrated that microbial pathogens, including bacteria and viruses, are capable of dysregulating the epigenetic machinery of their host cell. The resulting heritable changes in host cell gene expression may favor the colonization, growth or spread of infectious pathogens. It may also facilitate the establishment of latency and malignant cell transformation. In this article, we review how bacterial epigenetic effectors and inflammatory processes elicited by bacteria alter the host cell epigenotype, and describe how oncoproteins encoded by human tumor viruses act as epigenetic dysregulators to alter the phenotype and behavior of host cells.
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Affiliation(s)
- Hans Helmut Niller
- Institute for Medical Microbiology & Hygiene, University of Regensburg, Franz-Josef-Strauss Allee 11, Regensburg D93053, Germany
| | - Ferenc Banati
- RT-Europe Nonprofit Research Center, H-9200 Mosonmagyarovar, Pozsonyi út 88, Hungary
| | - Katalin Nagy
- University of Szeged, Faculty of Dentistry, Department of Oral Surgery, H-6720 Szeged, Tisza Lajos Krt. 64, Hungary
| | - Krisztina Buzas
- University of Szeged, Faculty of Dentistry, Department of Oral Biology & Experimental Dental Research, H-6720 Szeged, Tisza Lajos Krt. 64, Hungary
| | - Janos Minarovits
- University of Szeged, Faculty of Dentistry, Department of Oral Biology & Experimental Dental Research, H-6720 Szeged, Tisza Lajos Krt. 64, Hungary
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Barteneva NS, Maltsev N, Vorobjev IA. Microvesicles and intercellular communication in the context of parasitism. Front Cell Infect Microbiol 2013; 3:49. [PMID: 24032108 PMCID: PMC3764926 DOI: 10.3389/fcimb.2013.00049] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 08/20/2013] [Indexed: 01/18/2023] Open
Abstract
There is a rapidly growing body of evidence that production of microvesicles (MVs) is a universal feature of cellular life. MVs can incorporate microRNA (miRNA), mRNA, mtDNA, DNA and retrotransposons, camouflage viruses/viral components from immune surveillance, and transfer cargo between cells. These properties make MVs an essential player in intercellular communication. Increasing evidence supports the notion that MVs can also act as long-distance vehicles for RNA molecules and participate in metabolic synchronization and reprogramming eukaryotic cells including stem and germinal cells. MV ability to carry on DNA and their general distribution makes them attractive candidates for horizontal gene transfer, particularly between multi-cellular organisms and their parasites; this suggests important implications for the co-evolution of parasites and their hosts. In this review, we provide current understanding of the roles played by MVs in intracellular pathogens and parasitic infections. We also discuss the possible role of MVs in co-infection and host shifting.
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Affiliation(s)
- Natasha S Barteneva
- Program in Cellular and Molecular Medicine, Children's Hospital Boston and Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA. Natasha.Barteneva@ childrens.harvard.edu
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