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Nowell RW, Rodriguez F, Hecox-Lea BJ, Mark Welch DB, Arkhipova IR, Barraclough TG, Wilson CG. Bdelloid rotifers deploy horizontally acquired biosynthetic genes against a fungal pathogen. Nat Commun 2024; 15:5787. [PMID: 39025839 PMCID: PMC11258130 DOI: 10.1038/s41467-024-49919-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 06/18/2024] [Indexed: 07/20/2024] Open
Abstract
Coevolutionary antagonism generates relentless selection that can favour genetic exchange, including transfer of antibiotic synthesis and resistance genes among bacteria, and sexual recombination of disease resistance alleles in eukaryotes. We report an unusual link between biological conflict and DNA transfer in bdelloid rotifers, microscopic animals whose genomes show elevated levels of horizontal gene transfer from non-metazoan taxa. When rotifers were challenged with a fungal pathogen, horizontally acquired genes were over twice as likely to be upregulated as other genes - a stronger enrichment than observed for abiotic stressors. Among hundreds of upregulated genes, the most markedly overrepresented were clusters resembling bacterial polyketide and nonribosomal peptide synthetases that produce antibiotics. Upregulation of these clusters in a pathogen-resistant rotifer species was nearly ten times stronger than in a susceptible species. By acquiring, domesticating, and expressing non-metazoan biosynthetic pathways, bdelloids may have evolved to resist natural enemies using antimicrobial mechanisms absent from other animals.
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Affiliation(s)
- Reuben W Nowell
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
- Department of Life Sciences, Imperial College London; Silwood Park Campus, Buckhurst Road, Ascot, Berkshire, SL5 7PY, UK
- Institute of Ecology and Evolution, University of Edinburgh; Ashworth Laboratories, Charlotte Auerbach Road, Edinburgh, EH9 3FL, UK
- Biological and Environmental Sciences, University of Stirling, Stirling, FK9 4LA, UK
| | - Fernando Rodriguez
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, USA
| | - Bette J Hecox-Lea
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, USA
| | - David B Mark Welch
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, USA
| | - Irina R Arkhipova
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, USA
| | - Timothy G Barraclough
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
- Department of Life Sciences, Imperial College London; Silwood Park Campus, Buckhurst Road, Ascot, Berkshire, SL5 7PY, UK
| | - Christopher G Wilson
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK.
- Department of Life Sciences, Imperial College London; Silwood Park Campus, Buckhurst Road, Ascot, Berkshire, SL5 7PY, UK.
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2
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Wilson CG, Pieszko T, Nowell RW, Barraclough TG. Recombination in bdelloid rotifer genomes: asexuality, transfer and stress. Trends Genet 2024; 40:422-436. [PMID: 38458877 DOI: 10.1016/j.tig.2024.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 03/10/2024]
Abstract
Bdelloid rotifers constitute a class of microscopic animals living in freshwater habitats worldwide. Several strange features of bdelloids have drawn attention: their ability to tolerate desiccation and other stresses, a lack of reported males across the clade despite centuries of study, and unusually high numbers of horizontally acquired, non-metazoan genes. Genome sequencing is transforming our understanding of their lifestyle and its consequences, while in turn providing wider insights about recombination and genome organisation in animals. Many questions remain, not least how to reconcile apparent genomic signatures of sex with the continued absence of reported males, why bdelloids have so many horizontally acquired genes, and how their remarkable ability to survive stress interacts with recombination and other genomic processes.
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Affiliation(s)
- Christopher G Wilson
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford OX1 3SZ, UK.
| | - Tymoteusz Pieszko
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford OX1 3SZ, UK
| | - Reuben W Nowell
- Institute of Ecology and Evolution, Ashworth Laboratories, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK; Biological and Environmental Sciences, School of Natural Sciences, University of Stirling, Stirling FK9 4LA, UK
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3
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Felipe Benites L, Stephens TG, Van Etten J, James T, Christian WC, Barry K, Grigoriev IV, McDermott TR, Bhattacharya D. Hot springs viruses at Yellowstone National Park have ancient origins and are adapted to thermophilic hosts. Commun Biol 2024; 7:312. [PMID: 38594478 PMCID: PMC11003980 DOI: 10.1038/s42003-024-05931-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 02/16/2024] [Indexed: 04/11/2024] Open
Abstract
Geothermal springs house unicellular red algae in the class Cyanidiophyceae that dominate the microbial biomass at these sites. Little is known about host-virus interactions in these environments. We analyzed the virus community associated with red algal mats in three neighboring habitats (creek, endolithic, soil) at Lemonade Creek, Yellowstone National Park (YNP), USA. We find that despite proximity, each habitat houses a unique collection of viruses, with the giant viruses, Megaviricetes, dominant in all three. The early branching phylogenetic position of genes encoded on metagenome assembled virus genomes (vMAGs) suggests that the YNP lineages are of ancient origin and not due to multiple invasions from mesophilic habitats. The existence of genomic footprints of adaptation to thermophily in the vMAGs is consistent with this idea. The Cyanidiophyceae at geothermal sites originated ca. 1.5 Bya and are therefore relevant to understanding biotic interactions on the early Earth.
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Affiliation(s)
- L Felipe Benites
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Timothy G Stephens
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Julia Van Etten
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
- Graduate Program in Ecology and Evolution, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Timeeka James
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - William C Christian
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, Montana, USA
| | - Kerrie Barry
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Igor V Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Timothy R McDermott
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA.
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4
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Moris VC, Bruneau L, Berthe J, Heuskin AC, Penninckx S, Ritter S, Weber U, Durante M, Danchin EGJ, Hespeels B, Doninck KV. Ionizing radiation responses appear incidental to desiccation responses in the bdelloid rotifer Adineta vaga. BMC Biol 2024; 22:11. [PMID: 38273318 PMCID: PMC10809525 DOI: 10.1186/s12915-023-01807-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 12/21/2023] [Indexed: 01/27/2024] Open
Abstract
BACKGROUND The remarkable resistance to ionizing radiation found in anhydrobiotic organisms, such as some bacteria, tardigrades, and bdelloid rotifers has been hypothesized to be incidental to their desiccation resistance. Both stresses produce reactive oxygen species and cause damage to DNA and other macromolecules. However, this hypothesis has only been investigated in a few species. RESULTS In this study, we analyzed the transcriptomic response of the bdelloid rotifer Adineta vaga to desiccation and to low- (X-rays) and high- (Fe) LET radiation to highlight the molecular and genetic mechanisms triggered by both stresses. We identified numerous genes encoding antioxidants, but also chaperones, that are constitutively highly expressed, which may contribute to the protection of proteins against oxidative stress during desiccation and ionizing radiation. We also detected a transcriptomic response common to desiccation and ionizing radiation with the over-expression of genes mainly involved in DNA repair and protein modifications but also genes with unknown functions that were bdelloid-specific. A distinct transcriptomic response specific to rehydration was also found, with the over-expression of genes mainly encoding Late Embryogenesis Abundant proteins, specific heat shock proteins, and glucose repressive proteins. CONCLUSIONS These results suggest that the extreme resistance of bdelloid rotifers to radiation might indeed be a consequence of their capacity to resist complete desiccation. This study paves the way to functional genetic experiments on A. vaga targeting promising candidate proteins playing central roles in radiation and desiccation resistance.
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Affiliation(s)
- Victoria C Moris
- Laboratory of Evolutionary Genetics and Ecology (LEGE), Department of Biology - URBE, University of Namur, Rue de Bruxelles, 61, B-5000, Namur, Belgium.
- Laboratory of Molecular Biology & Evolution (MBE), Department of Biology, Université Libre de Bruxelles, 1000, Brussels, Belgium.
| | - Lucie Bruneau
- Laboratory of Evolutionary Genetics and Ecology (LEGE), Department of Biology - URBE, University of Namur, Rue de Bruxelles, 61, B-5000, Namur, Belgium
| | - Jérémy Berthe
- Laboratory of Evolutionary Genetics and Ecology (LEGE), Department of Biology - URBE, University of Namur, Rue de Bruxelles, 61, B-5000, Namur, Belgium
| | - Anne-Catherine Heuskin
- Namur Research Institute for Life Sciences (NARILIS), Laboratory of Analysis By Nuclear Reactions (LARN), University of Namur, Rue de Bruxelles, 61, B-5000, Namur, Belgium
| | - Sébastien Penninckx
- Medical Physics Department, Institut Jules Bordet - Université Libre de Bruxelles, 90 Rue Meylemeersch, 1070, Brussels, Belgium
| | - Sylvia Ritter
- Biophysics Department, GSI Helmholtzzentrum Für Schwerionenforschung, Darmstadt, Germany
| | - Uli Weber
- Biophysics Department, GSI Helmholtzzentrum Für Schwerionenforschung, Darmstadt, Germany
| | - Marco Durante
- Biophysics Department, GSI Helmholtzzentrum Für Schwerionenforschung, Darmstadt, Germany
- Institute of Condensed Matter Physics, Technische Universität Darmstadt, Darmstadt, Germany
| | - Etienne G J Danchin
- Institut Sophia Agrobiotech, INRAE, Université Côte d'Azur, CNRS, 06903, Sophia Antipolis, France
| | - Boris Hespeels
- Laboratory of Evolutionary Genetics and Ecology (LEGE), Department of Biology - URBE, University of Namur, Rue de Bruxelles, 61, B-5000, Namur, Belgium
| | - Karine Van Doninck
- Laboratory of Evolutionary Genetics and Ecology (LEGE), Department of Biology - URBE, University of Namur, Rue de Bruxelles, 61, B-5000, Namur, Belgium
- Laboratory of Molecular Biology & Evolution (MBE), Department of Biology, Université Libre de Bruxelles, 1000, Brussels, Belgium
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5
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Nicolas E, Simion P, Guérineau M, Terwagne M, Colinet M, Virgo J, Lingurski M, Boutsen A, Dieu M, Hallet B, Van Doninck K. Horizontal acquisition of a DNA ligase improves DNA damage tolerance in eukaryotes. Nat Commun 2023; 14:7638. [PMID: 37993452 PMCID: PMC10665377 DOI: 10.1038/s41467-023-43075-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 10/30/2023] [Indexed: 11/24/2023] Open
Abstract
Bdelloid rotifers are part of the restricted circle of multicellular animals that can withstand a wide range of genotoxic stresses at any stage of their life cycle. In this study, bdelloid rotifer Adineta vaga is used as a model to decipher the molecular basis of their extreme tolerance. Proteomic analysis shows that a specific DNA ligase, different from those usually involved in DNA repair in eukaryotes, is strongly over-represented upon ionizing radiation. A phylogenetic analysis reveals its orthology to prokaryotic DNA ligase E, and its horizontal acquisition by bdelloid rotifers and plausibly other eukaryotes. The fungus Mortierella verticillata, having a single copy of this DNA Ligase E homolog, also exhibits an increased radiation tolerance with an over-expression of this DNA ligase E following X-ray exposure. We also provide evidence that A. vaga ligase E is a major contributor of DNA breaks ligation activity, which is a common step of all important DNA repair pathways. Consistently, its heterologous expression in human cell lines significantly improves their radio-tolerance. Overall, this study highlights the potential of horizontal gene transfers in eukaryotes, and their contribution to the adaptation to extreme conditions.
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Affiliation(s)
- Emilien Nicolas
- Université Libre de Bruxelles, Molecular Biology and Evolution, Brussels, 1050, Belgium.
| | - Paul Simion
- Université de Namur, Laboratory of Evolutionary Genetics and Ecology, Namur, 5000, Belgium
- Université de Rennes, Ecosystèmes, biodiversité, évolution (ECOBIO UMR 6553), CNRS, Rennes, France
| | - Marc Guérineau
- Université Libre de Bruxelles, Molecular Biology and Evolution, Brussels, 1050, Belgium
| | - Matthieu Terwagne
- Université de Namur, Laboratory of Evolutionary Genetics and Ecology, Namur, 5000, Belgium
| | - Mathilde Colinet
- Université de Namur, Laboratory of Evolutionary Genetics and Ecology, Namur, 5000, Belgium
| | - Julie Virgo
- Université de Namur, Laboratory of Evolutionary Genetics and Ecology, Namur, 5000, Belgium
| | - Maxime Lingurski
- Université Libre de Bruxelles, Molecular Biology and Evolution, Brussels, 1050, Belgium
| | - Anaïs Boutsen
- Université de Namur, Laboratory of Evolutionary Genetics and Ecology, Namur, 5000, Belgium
| | - Marc Dieu
- Université de Namur, MaSUN-mass spectrometry facility, Namur, 5000, Belgium
| | - Bernard Hallet
- Université Catholique de Louvain, Louvain Institute of Biomolecular Science and Technology, Louvain-la-Neuve, 1348, Belgium.
| | - Karine Van Doninck
- Université Libre de Bruxelles, Molecular Biology and Evolution, Brussels, 1050, Belgium.
- Université de Namur, Laboratory of Evolutionary Genetics and Ecology, Namur, 5000, Belgium.
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6
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Ribes-Navarro A, Kabeya N, Castro LFC, Gomes-dos-Santos A, Fonseca MM, Alberts-Hubatsch H, Hontoria F, Navarro JC, Monroig Ó. Examination of gammarid transcriptomes reveals a widespread occurrence of key metabolic genes from epibiont bdelloid rotifers in freshwater species. Open Biol 2023; 13:230196. [PMID: 37875161 PMCID: PMC10597677 DOI: 10.1098/rsob.230196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 09/19/2023] [Indexed: 10/26/2023] Open
Abstract
Previous data revealed the unexpected presence of genes encoding for long-chain polyunsaturated fatty acid (LC-PUFA) biosynthetic enzymes in transcriptomes from freshwater gammarids but not in marine species, even though closely related species were compared. This study aimed to clarify the origin and occurrence of selected LC-PUFA biosynthesis gene markers across all published gammarid transcriptomes. Through systematic searches, we confirmed the widespread occurrence of sequences from seven elongases and desaturases involved in LC-PUFA biosynthesis, in transcriptomes from freshwater gammarids but not marine species, and clarified that such occurrence is independent from the gammarid species and geographical origin. The phylogenetic analysis established that the retrieved elongase and desaturase sequences were closely related to bdelloid rotifers, confirming that multiple transcriptomes from freshwater gammarids contain contaminating rotifers' genetic material. Using the Adineta steineri genome, we investigated the genomic location and exon-intron organization of the elongase and desaturase genes, establishing they are all genome-anchored and, importantly, identifying instances of horizontal gene transfer. Finally, we provide compelling evidence demonstrating Bdelloidea desaturases and elongases enable these organisms to perform all the reactions for de novo biosynthesis of PUFA and, from them, LC-PUFA, an advantageous trait when considering the low abundance of these essential nutrients in freshwater environments.
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Affiliation(s)
- Alberto Ribes-Navarro
- Instituto de Acuicultura Torre de la Sal (IATS), CSIC, 12595 Ribera de Cabanes, Castellón, Spain
| | - Naoki Kabeya
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Konan 4-5-7, Minato, Tokyo, Japan
| | - L. Filipe C. Castro
- CIMAR/CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal
- Department of Biology, Faculty of Sciences, University of Porto (U. Porto), Rua do Campo Alegre S/N, 4169-007 Porto, Portugal
| | - André Gomes-dos-Santos
- CIMAR/CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal
| | - Miguel M. Fonseca
- CIMAR/CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal
| | - Hilke Alberts-Hubatsch
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Francisco Hontoria
- Instituto de Acuicultura Torre de la Sal (IATS), CSIC, 12595 Ribera de Cabanes, Castellón, Spain
| | - Juan C. Navarro
- Instituto de Acuicultura Torre de la Sal (IATS), CSIC, 12595 Ribera de Cabanes, Castellón, Spain
| | - Óscar Monroig
- Instituto de Acuicultura Torre de la Sal (IATS), CSIC, 12595 Ribera de Cabanes, Castellón, Spain
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7
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Hespeels B, Fontaneto D, Cornet V, Penninckx S, Berthe J, Bruneau L, Larrick JW, Rapport E, Bailly J, Debortoli N, Iakovenko N, Janko K, Heuskin AC, Lucas S, Hallet B, Van Doninck K. Back to the roots, desiccation and radiation resistances are ancestral characters in bdelloid rotifers. BMC Biol 2023; 21:72. [PMID: 37024917 PMCID: PMC10080820 DOI: 10.1186/s12915-023-01554-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 02/27/2023] [Indexed: 04/08/2023] Open
Abstract
BACKGROUND Bdelloid rotifers are micro-invertebrates distributed worldwide, from temperate latitudes to the most extreme areas of the planet like Antarctica or the Atacama Desert. They have colonized any habitat where liquid water is temporarily available, including terrestrial environments such as soils, mosses, and lichens, tolerating desiccation and other types of stress such as high doses of ionizing radiation (IR). It was hypothesized that bdelloid desiccation and radiation resistance may be attributed to their potential ability to repair DNA double-strand breaks (DSBs). Here, these properties are investigated and compared among nine bdelloid species collected from both mild and harsh habitats, addressing the correlation between the ability of bdelloid rotifers to survive desiccation and their capacity to repair massive DNA breakage in a phylogenetically explicit context. Our research includes both specimens isolated from habitats that experience frequent desiccation (at least 1 time per generation), and individuals sampled from habitats that rarely or never experienced desiccation. RESULTS Our analysis reveals that DNA repair prevails in somatic cells of both desiccation-tolerant and desiccation-sensitive bdelloid species after exposure to X-ray radiation. Species belonging to both categories are able to withstand high doses of ionizing radiation, up to 1000 Gy, without experiencing any negative effects on their survival. However, the fertility of two desiccation-sensitive species, Rotaria macrura and Rotaria rotatoria, was more severely impacted by low doses of radiation than that of desiccation-resistant species. Surprisingly, the radioresistance of desiccation-resistant species is not related to features of their original habitat. Indeed, bdelloids isolated from Atacama Desert or Antarctica were not characterized by a higher radioresistance than species found in more temperate environments. CONCLUSIONS Tolerance to desiccation and radiation are supported as ancestral features of bdelloid rotifers, with a group of species of the genus Rotaria having lost this trait after colonizing permanent water habitats. Together, our results provide a comprehensive overview of the evolution of desiccation and radiation resistance among bdelloid rotifers.
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Affiliation(s)
- Boris Hespeels
- Research Unit in Environmental and Evolutionary Biology (URBE), Laboratory of Evolutionary Genetics and Ecology (LEGE), NAmur Research Institute for Life Sciences (NARILIS), University of Namur, Namur, Belgium.
- Research Unit in Environmental and Evolutionary Biology (URBE), Institute of Life, Earth & Environment (ILEE), University of Namur, Namur, Belgium.
| | - Diego Fontaneto
- Molecular Ecology Group (MEG), Water Research Institute (IRSA), National Research Council of Italy (CNR), Verbania Pallanza, Italy
- Laboratory of Non-Mendelian Evolution, Institute of Animal Physiology and Genetics AS CR, Rumburská 89, Liběchov, 277 21, Czech Republic
| | - Valérie Cornet
- Research Unit in Environmental and Evolutionary Biology (URBE), Institute of Life, Earth & Environment (ILEE), University of Namur, Namur, Belgium
| | - Sébastien Penninckx
- Medical Physics Department, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium
| | - Jérémy Berthe
- Research Unit in Environmental and Evolutionary Biology (URBE), Laboratory of Evolutionary Genetics and Ecology (LEGE), NAmur Research Institute for Life Sciences (NARILIS), University of Namur, Namur, Belgium
- Research Unit in Molecular Biology and Evolution, DBO, Université libre de Bruxelles (ULB), 1050, Brussels, Belgium
| | - Lucie Bruneau
- Research Unit in Environmental and Evolutionary Biology (URBE), Laboratory of Evolutionary Genetics and Ecology (LEGE), NAmur Research Institute for Life Sciences (NARILIS), University of Namur, Namur, Belgium
| | - James W Larrick
- Panorama Research Institute, Sunnyvale, CA, USA
- SETI Institute, Mountain View, CA, USA
| | - Eloïse Rapport
- Research Unit in Environmental and Evolutionary Biology (URBE), Laboratory of Evolutionary Genetics and Ecology (LEGE), NAmur Research Institute for Life Sciences (NARILIS), University of Namur, Namur, Belgium
| | - Jérémie Bailly
- Research Unit in Environmental and Evolutionary Biology (URBE), Laboratory of Evolutionary Genetics and Ecology (LEGE), NAmur Research Institute for Life Sciences (NARILIS), University of Namur, Namur, Belgium
| | - Nicolas Debortoli
- Research Unit in Environmental and Evolutionary Biology (URBE), Laboratory of Evolutionary Genetics and Ecology (LEGE), NAmur Research Institute for Life Sciences (NARILIS), University of Namur, Namur, Belgium
| | - Nataliia Iakovenko
- Laboratory of Non-Mendelian Evolution, Institute of Animal Physiology and Genetics AS CR, Rumburská 89, Liběchov, 277 21, Czech Republic
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Kamýcká 129, CZ - 165 21 Praha 6, Suchdol, Czech Republic
- Faculty of Science, University of Ostrava, Chittussiho 10, 71000, Ostrava, Czech Republic
| | - Karel Janko
- Laboratory of Non-Mendelian Evolution, Institute of Animal Physiology and Genetics AS CR, Rumburská 89, Liběchov, 277 21, Czech Republic
- Faculty of Science, University of Ostrava, Chittussiho 10, 71000, Ostrava, Czech Republic
| | - Anne-Catherine Heuskin
- Laboratory of Analysis by Nuclear Reactions (LARN), Namur Research Institute for Life Sciences (Narilis), University of Namur, Namur, Belgium
| | - Stéphane Lucas
- Laboratory of Analysis by Nuclear Reactions (LARN), Namur Research Institute for Life Sciences (Narilis), University of Namur, Namur, Belgium
| | - Bernard Hallet
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, B-1348, Louvain-la-Neuve, Belgium
| | - Karine Van Doninck
- Research Unit in Environmental and Evolutionary Biology (URBE), Laboratory of Evolutionary Genetics and Ecology (LEGE), NAmur Research Institute for Life Sciences (NARILIS), University of Namur, Namur, Belgium.
- Research Unit in Environmental and Evolutionary Biology (URBE), Institute of Life, Earth & Environment (ILEE), University of Namur, Namur, Belgium.
- Research Unit in Molecular Biology and Evolution, DBO, Université libre de Bruxelles (ULB), 1050, Brussels, Belgium.
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8
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Dong LF, Rohlena J, Zobalova R, Nahacka Z, Rodriguez AM, Berridge MV, Neuzil J. Mitochondria on the move: Horizontal mitochondrial transfer in disease and health. J Cell Biol 2023; 222:213873. [PMID: 36795453 PMCID: PMC9960264 DOI: 10.1083/jcb.202211044] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 01/12/2023] [Accepted: 02/01/2023] [Indexed: 02/17/2023] Open
Abstract
Mammalian genes were long thought to be constrained within somatic cells in most cell types. This concept was challenged recently when cellular organelles including mitochondria were shown to move between mammalian cells in culture via cytoplasmic bridges. Recent research in animals indicates transfer of mitochondria in cancer and during lung injury in vivo, with considerable functional consequences. Since these pioneering discoveries, many studies have confirmed horizontal mitochondrial transfer (HMT) in vivo, and its functional characteristics and consequences have been described. Additional support for this phenomenon has come from phylogenetic studies. Apparently, mitochondrial trafficking between cells occurs more frequently than previously thought and contributes to diverse processes including bioenergetic crosstalk and homeostasis, disease treatment and recovery, and development of resistance to cancer therapy. Here we highlight current knowledge of HMT between cells, focusing primarily on in vivo systems, and contend that this process is not only (patho)physiologically relevant, but also can be exploited for the design of novel therapeutic approaches.
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Affiliation(s)
- Lan-Feng Dong
- https://ror.org/02sc3r913School of Pharmacy and Medical Sciences, Griffith University, Southport, Australia,Lan-Feng Dong:
| | - Jakub Rohlena
- https://ror.org/00wzqmx94Institute of Biotechnology, Academy of Sciences of the Czech Republic, Prague-West, Czech Republic
| | - Renata Zobalova
- https://ror.org/00wzqmx94Institute of Biotechnology, Academy of Sciences of the Czech Republic, Prague-West, Czech Republic
| | - Zuzana Nahacka
- https://ror.org/00wzqmx94Institute of Biotechnology, Academy of Sciences of the Czech Republic, Prague-West, Czech Republic
| | | | | | - Jiri Neuzil
- https://ror.org/02sc3r913School of Pharmacy and Medical Sciences, Griffith University, Southport, Australia,https://ror.org/00wzqmx94Institute of Biotechnology, Academy of Sciences of the Czech Republic, Prague-West, Czech Republic,Faculty of Science, Charles University, Prague, Czech Republic,First Faculty of Medicine, Charles University, Prague, Czech Republic,Correspondence to Jiri Neuzil: ,
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9
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Wang Y, Shahid MQ. Genome sequencing and resequencing identified three horizontal gene transfers and uncovered the genetic mechanism on the intraspecies adaptive evolution of Gastrodia elata Blume. FRONTIERS IN PLANT SCIENCE 2023; 13:1035157. [PMID: 36684780 PMCID: PMC9848658 DOI: 10.3389/fpls.2022.1035157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 12/13/2022] [Indexed: 06/17/2023]
Abstract
Horizontal gene transfer is a rare and useful genetic mechanism in higher plants. Gastrodia elata Blume (GE) (Orchidaceae), well known as traditional medicinal material in East Asia, adopts a heterotrophic lifestyle, thus being considered to be more prone to horizontal gene transfer (HGT). GE is a "polytypic species" that currently comprised of five recognized forms according to the plant morphology. G. elata Blume forma elata (GEE) and G. elata Bl.f.glauca (GEG) are two common forms that naturally grow in different habitats with difference in altitude and latitude. G. elata Bl.f.viridis (GEV) often occurs sporadically in cultivated populations of GEE and GEG. However, the genetic relationships and genetic mechanism underpinned the divergent ecological adaptations of GEE and GEG have not been revealed. Here, we assembled a chromosome-level draft genome of GEE with 1.04 Gb. Among predicted 17,895 protein coding genes, we identified three HGTs. Meanwhile, we resequenced 10 GEE accessions, nine GEG accessions, and 10 GEV accessions, and identified two independent genetic lineages: GEG_pedigree (GEG individuals and GEV individuals collected from GEG populations) and GEE_pedigree (GEE individuals and GEV individuals collected from GEE populations), which strongly support the taxonomic status of GEE and GEG as subspecies, not as different forms. In highly differentiated genomic regions of GEE_pedigree and GEG_pedigree, three chalcone synthase-encoding genes and one Phox/Bem1p (PB1) domain of encoding Auxin (AUX)/Indoleacetic acid (IAA) were identified in selection sweeping genome regions, which suggested that differentiation between GEE_pedigree and GEG_pedigree was promoted by the selection of genes related to photoresponse and growth and development. Overall, this new genome would be helpful for breeding and utilization of GE and the new findings would deepen the understanding about ecological adaptation and evolution of GE.
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Affiliation(s)
- Yunsheng Wang
- School of Health and Life Science, Kaili University, Kaili, Guizhou, China
| | - Muhammad Qasim Shahid
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
- College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
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10
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Koutsovoulos GD, Granjeon Noriot S, Bailly-Bechet M, Danchin EGJ, Rancurel C. AvP: A software package for automatic phylogenetic detection of candidate horizontal gene transfers. PLoS Comput Biol 2022; 18:e1010686. [PMID: 36350852 PMCID: PMC9678320 DOI: 10.1371/journal.pcbi.1010686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 11/21/2022] [Accepted: 10/26/2022] [Indexed: 11/10/2022] Open
Abstract
Horizontal gene transfer (HGT) is the transfer of genes between species outside the transmission from parent to offspring. Due to their impact on the genome and biology of various species, HGTs have gained broader attention, but high-throughput methods to robustly identify them are lacking. One rapid method to identify HGT candidates is to calculate the difference in similarity between the most similar gene in closely related species and the most similar gene in distantly related species. Although metrics on similarity associated with taxonomic information can rapidly detect putative HGTs, these methods are hampered by false positives that are difficult to track. Furthermore, they do not inform on the evolutionary trajectory and events such as duplications. Hence, phylogenetic analysis is necessary to confirm HGT candidates and provide a more comprehensive view of their origin and evolutionary history. However, phylogenetic reconstruction requires several time-consuming manual steps to retrieve the homologous sequences, produce a multiple alignment, construct the phylogeny and analyze the topology to assess whether it supports the HGT hypothesis. Here, we present AvP which automatically performs all these steps and detects candidate HGTs within a phylogenetic framework.
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Affiliation(s)
- Georgios D. Koutsovoulos
- Institut Sophia Agrobiotech, Université Côte d’Azur, INRAE, CNRS, Sophia Antipolis, France
- * E-mail:
| | - Solène Granjeon Noriot
- Institut Sophia Agrobiotech, Université Côte d’Azur, INRAE, CNRS, Sophia Antipolis, France
| | - Marc Bailly-Bechet
- Institut Sophia Agrobiotech, Université Côte d’Azur, INRAE, CNRS, Sophia Antipolis, France
| | - Etienne G. J. Danchin
- Institut Sophia Agrobiotech, Université Côte d’Azur, INRAE, CNRS, Sophia Antipolis, France
| | - Corinne Rancurel
- Institut Sophia Agrobiotech, Université Côte d’Azur, INRAE, CNRS, Sophia Antipolis, France
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11
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Abstract
Gene-by-environment interactions play a crucial role in horizontal gene transfer by affecting how the transferred genes alter host fitness. However, how the environment modulates the fitness effect of transferred genes has not been tested systematically in an experimental study. We adapted a high-throughput technique for obtaining very precise estimates of bacterial fitness, in order to measure the fitness effects of 44 orthologs transferred from Salmonella Typhimurium to Escherichia coli in six physiologically relevant environments. We found that the fitness effects of individual genes were highly dependent on the environment, while the distributions of fitness effects across genes were not, with all tested environments resulting in distributions of same shape and spread. Furthermore, the extent to which the fitness effects of a gene varied between environments depended on the average fitness effect of that gene across all environments, with nearly neutral and nearly lethal genes having more consistent fitness effects across all environments compared to deleterious genes. Put together, our results reveal the unpredictable nature of how environmental conditions impact the fitness effects of each individual gene. At the same time, distributions of fitness effects across environments exhibit consistent features, pointing to the generalizability of factors that shape horizontal gene transfer of orthologous genes.
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Affiliation(s)
- Hande Acar Kirit
- Veterinary and Ecological Sciences, Institute of Infection, University of Liverpool, Liverpool, Merseyside, United Kingdom
- Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, OK
- Department of Anthropology, University of Oklahoma, Norman, OK
| | - Jonathan P Bollback
- Veterinary and Ecological Sciences, Institute of Infection, University of Liverpool, Liverpool, Merseyside, United Kingdom
| | - Mato Lagator
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
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12
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Benites LF, Stephens TG, Bhattacharya D. Multiple waves of viral invasions in Symbiodiniaceae algal genomes. Virus Evol 2022; 8:veac101. [PMID: 36381231 PMCID: PMC9651163 DOI: 10.1093/ve/veac101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 08/29/2022] [Accepted: 10/25/2022] [Indexed: 08/13/2023] Open
Abstract
Dinoflagellates from the family Symbiodiniaceae are phototrophic marine protists that engage in symbiosis with diverse hosts. Their large and distinct genomes are characterized by pervasive gene duplication and large-scale retroposition events. However, little is known about the role and scale of horizontal gene transfer (HGT) in the evolution of this algal family. In other dinoflagellates, high levels of HGTs have been observed, linked to major genomic transitions, such as the appearance of a viral-acquired nucleoprotein that originated via HGT from a large DNA algal virus. Previous work showed that Symbiodiniaceae from different hosts are actively infected by viral groups, such as giant DNA viruses and ssRNA viruses, that may play an important role in coral health. Latent viral infections may also occur, whereby viruses could persist in the cytoplasm or integrate into the host genome as a provirus. This hypothesis received experimental support; however, the cellular localization of putative latent viruses and their taxonomic affiliation are still unknown. In addition, despite the finding of viral sequences in some genomes of Symbiodiniaceae, viral origin, taxonomic breadth, and metabolic potential have not been explored. To address these questions, we searched for putative viral-derived proteins in thirteen Symbiodiniaceae genomes. We found fifty-nine candidate viral-derived HGTs that gave rise to twelve phylogenies across ten genomes. We also describe the taxonomic affiliation of these virus-related sequences, their structure, and their genomic context. These results lead us to propose a model to explain the origin and fate of Symbiodiniaceae viral acquisitions.
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Affiliation(s)
- L Felipe Benites
- Department of Biochemistry and Microbiology, Rutgers University, 102 Foran Hall, 59 Dudley Road, New Brunswick, NJ 08901-8520, USA
| | - Timothy G Stephens
- Department of Biochemistry and Microbiology, Rutgers University, 102 Foran Hall, 59 Dudley Road, New Brunswick, NJ 08901-8520, USA
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, 102 Foran Hall, 59 Dudley Road, New Brunswick, NJ 08901-8520, USA
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13
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Deciphering the Biological Enigma-Genomic Evolution Underlying Anhydrobiosis in the Phylum Tardigrada and the Chironomid Polypedilum vanderplanki. INSECTS 2022; 13:insects13060557. [PMID: 35735894 PMCID: PMC9224920 DOI: 10.3390/insects13060557] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/13/2022] [Accepted: 06/17/2022] [Indexed: 02/04/2023]
Abstract
Anhydrobiosis, an ametabolic dehydrated state triggered by water loss, is observed in several invertebrate lineages. Anhydrobiotes revive when rehydrated, and seem not to suffer the ultimately lethal cell damage that results from severe loss of water in other organisms. Here, we review the biochemical and genomic evidence that has revealed the protectant molecules, repair systems, and maintenance pathways associated with anhydrobiosis. We then introduce two lineages in which anhydrobiosis has evolved independently: Tardigrada, where anhydrobiosis characterizes many species within the phylum, and the genus Polypedilum, where anhydrobiosis occurs in only two species. Finally, we discuss the complexity of the evolution of anhydrobiosis within invertebrates based on current knowledge, and propose perspectives to enhance the understanding of anhydrobiosis.
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14
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Nakamura-Gouvea N, Alves-Lima C, Benites LF, Iha C, Maracaja-Coutinho V, Aliaga-Tobar V, Araujo Amaral Carneiro M, Yokoya NS, Marinho-Soriano E, Graminha MAS, Collén J, Oliveira MC, Setubal JC, Colepicolo P. Insights into agar and secondary metabolite pathways from the genome of the red alga Gracilaria domingensis (Rhodophyta, Gracilariales). JOURNAL OF PHYCOLOGY 2022; 58:406-423. [PMID: 35090189 DOI: 10.1111/jpy.13238] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 11/24/2021] [Indexed: 06/14/2023]
Abstract
Gracilariales is a clade of florideophycean red macroalgae known for being the main source of agar. We present a de novo genome assembly and annotation of Gracilaria domingensis, an agarophyte alga with flattened thallus widely distributed along Central and South American Atlantic intertidal zones. In addition to structural analysis, an organizational comparison was done with other Rhodophyta genomes. The nuclear genome has 78 Mbp, with 11,437 predicted coding genes, 4,075 of which did not have hits in sequence databases. We also predicted 1,567 noncoding RNAs, distributed in 14 classes. The plastid and mitochondrion genome structures were also obtained. Genes related to agar synthesis were identified. Genes for type II galactose sulfurylases could not be found. Genes related to ascorbate synthesis were found. These results suggest an intricate connection of cell wall polysaccharide synthesis and the redox systems through the use of L-galactose in Rhodophyta. The genome of G. domingensis should be valuable to phycological and aquacultural research, as it is the first tropical and Western Atlantic red macroalgal genome to be sequenced.
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Affiliation(s)
- Natalia Nakamura-Gouvea
- Laboratory of Algal Biochemistry and Molecular Biology, Department of Biochemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu, Prestes, 748, São Paulo, SP, 05508-000, Brazil
| | - Cicero Alves-Lima
- Laboratory of Algal Biochemistry and Molecular Biology, Department of Biochemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu, Prestes, 748, São Paulo, SP, 05508-000, Brazil
| | - Luiz Felipe Benites
- CNRS, UMR 7232 Biologie Intégrative des Organismes Marins (BIOM), Sorbonne Université, Observatoire Océanologique - F-66650, Banyuls-sur-Mer, France
| | - Cintia Iha
- Department of Botany, Institute of Biosciences, University of São Paulo, R Matão 277, São Paulo, SP, 05508-090, Brazil
| | - Vinicius Maracaja-Coutinho
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Universidad de Chile - Independencia, Santiago, 8380492, Chile
| | - Victor Aliaga-Tobar
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Universidad de Chile - Independencia, Santiago, 8380492, Chile
| | - Marcella Araujo Amaral Carneiro
- Department of Oceanography and Limnology, Federal University of Rio Grande do Norte - Via Costeira, Praia de Mãe Luiza, s/n, Natal, RN, 59014-002, Brazil
| | - Nair S Yokoya
- Phycology Research Center, Institute of Botany, Secretary of Infrastructure and Environment of São Paulo State, Brazil - Av. Miguel Estefano, 3687, Água Funda, São Paulo, SP, 04301-012, Brazil
| | - Eliane Marinho-Soriano
- Department of Oceanography and Limnology, Federal University of Rio Grande do Norte - Via Costeira, Praia de Mãe Luiza, s/n, Natal, RN, 59014-002, Brazil
| | - Marcia A S Graminha
- School of Pharmaceutical Sciences, São Paulo State University (UNESP), Rod. Araraquara-Jaú km 1, Campus Ville, Araraquara, SP, 14800-903, Brazil
| | - Jonas Collén
- Station Biologique de Roscoff, UMR 8227, Integrative Biology of Marine Models - CS 90074, Roscoff cedex, 29688, France
| | - Mariana C Oliveira
- Department of Botany, Institute of Biosciences, University of São Paulo, R Matão 277, São Paulo, SP, 05508-090, Brazil
| | - Joao C Setubal
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo, SP, 05508-000, Brazil
| | - Pio Colepicolo
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo, SP, 05508-000, Brazil
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15
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Bacterial N4-methylcytosine as an epigenetic mark in eukaryotic DNA. Nat Commun 2022; 13:1072. [PMID: 35228526 PMCID: PMC8885841 DOI: 10.1038/s41467-022-28471-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 01/21/2022] [Indexed: 01/04/2023] Open
Abstract
DNA modifications are used to regulate gene expression and defend against invading genetic elements. In eukaryotes, modifications predominantly involve C5-methylcytosine (5mC) and occasionally N6-methyladenine (6mA), while bacteria frequently use N4-methylcytosine (4mC) in addition to 5mC and 6mA. Here we report that 4mC can serve as an epigenetic mark in eukaryotes. Bdelloid rotifers, tiny freshwater invertebrates with transposon-poor genomes rich in foreign genes, lack canonical eukaryotic C5-methyltransferases for 5mC addition, but encode an amino-methyltransferase, N4CMT, captured from bacteria >60 Mya. N4CMT deposits 4mC at active transposons and certain tandem repeats, and fusion to a chromodomain shapes its “histone-read-DNA-write” architecture recognizing silent chromatin marks. Furthermore, amplification of SETDB1 H3K9me3 histone methyltransferases yields variants preferentially binding 4mC-DNA, suggesting “DNA-read-histone-write” partnership to maintain chromatin-based silencing. Our results show how non-native DNA methyl groups can reshape epigenetic systems to silence transposons and demonstrate the potential of horizontal gene transfer to drive regulatory innovation in eukaryotes. Eukaryotic DNA can be methylated as 5-methylcytosine and N6-methyladenine, but whether other forms of DNA methylation occur has been controversial. Here the authors show that a bacterial DNA methyltransferase was acquired >60 Mya in bdelloid rotifers that catalyzes N4-methylcytosine addition and is involved in suppression of transposon proliferation.
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16
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Lin D, Xiang S, Sanogo B, Liang Y, Sun X, Wu Z. Molecular Characterization of Rotifers and Their Potential Use in the Biological Control of Biomphalaria. Front Cell Infect Microbiol 2021; 11:744352. [PMID: 34621694 PMCID: PMC8491568 DOI: 10.3389/fcimb.2021.744352] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 08/11/2021] [Indexed: 11/13/2022] Open
Abstract
Background Schistosomiasis is one of the most important tropical parasitic diseases worldwide. Biomphalaria straminea, the intermediate host of Schistosoma mansoni, has invaded and spread to Southern China since 1974 and may pose enormous threats to public health. Controlling intermediate host snails is an effective strategy in schistosomiasis intervention. However, the only effective chemical molluscicide, niclosamide, currently recommended by WHO may cause environmental pollution, loss of biodiversity, and high costs. Thus, to counter intermediate hosts, a sustainable and environmentally friendly tool is urgently needed. Here, we conducted field investigations to collect and identify a potential snail competitor rotifer and evaluated its molluscicide effect. Results In this study, we collected two samples of rotifers from Shenzhen. We found both red and black phenotypic B. straminea snails at the sampling sites. We identified the rotifer population as a species of the genus Philodina according to the amplification and phylogenetic analysis results of coxI gene. We found that rotifer exposure did not significantly affect the hatching rate of B. straminea eggs but promoted the killing of juvenile snails. Meanwhile, rotifer exposure did not significantly alter the fecundity of B. straminea quantified by the number of eggs per egg mass, the number of egg masses per snail, and the number of eggs per snail; but the snails exposed to rotifers showed lower fecundity performance than the control snails. Importantly, rotifer exposure could significantly affect the development of juvenile B. straminea, showing a smaller shell diameter of the exposed snails than that of the control snails. In addition, rotifer exposure affected the life span of B. straminea snails, showing a 16.61% decline in the average life span. After rotifer exposure, the S. mansoni-infected B. straminea snails died significantly faster than those without rotifer exposure. Similar findings were observed in S. mansoni-infected Biomphalaria glabrata snails. These results implied that rotifer exposure significantly promoted the mortality of S. mansoni-infected B. straminea and B. glabrata. Conclusions Our study demonstrated the potential molluscicide effect of rotifers on intermediate hosts under laboratory conditions. Our findings may provide new insights into the development of biocontrol strategies for snail-borne disease transmission.
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Affiliation(s)
- Datao Lin
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China.,Provincial Engineering Technology Research Center for Diseases-Vectors Control, Key Laboratory of Tropical Disease Control, Ministry of Education, Guangzhou, China
| | - Suoyu Xiang
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China.,Provincial Engineering Technology Research Center for Diseases-Vectors Control, Key Laboratory of Tropical Disease Control, Ministry of Education, Guangzhou, China
| | - Benjamin Sanogo
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China.,Provincial Engineering Technology Research Center for Diseases-Vectors Control, Key Laboratory of Tropical Disease Control, Ministry of Education, Guangzhou, China
| | - Yousheng Liang
- Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, China
| | - Xi Sun
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China.,Provincial Engineering Technology Research Center for Diseases-Vectors Control, Key Laboratory of Tropical Disease Control, Ministry of Education, Guangzhou, China
| | - Zhongdao Wu
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China.,Provincial Engineering Technology Research Center for Diseases-Vectors Control, Key Laboratory of Tropical Disease Control, Ministry of Education, Guangzhou, China
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17
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Simion P, Narayan J, Houtain A, Derzelle A, Baudry L, Nicolas E, Arora R, Cariou M, Cruaud C, Gaudray FR, Gilbert C, Guiglielmoni N, Hespeels B, Kozlowski DKL, Labadie K, Limasset A, Llirós M, Marbouty M, Terwagne M, Virgo J, Cordaux R, Danchin EGJ, Hallet B, Koszul R, Lenormand T, Flot JF, Van Doninck K. Chromosome-level genome assembly reveals homologous chromosomes and recombination in asexual rotifer Adineta vaga. SCIENCE ADVANCES 2021; 7:eabg4216. [PMID: 34613768 PMCID: PMC8494291 DOI: 10.1126/sciadv.abg4216] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Bdelloid rotifers are notorious as a speciose ancient clade comprising only asexual lineages. Thanks to their ability to repair highly fragmented DNA, most bdelloid species also withstand complete desiccation and ionizing radiation. Producing a well-assembled reference genome is a critical step to developing an understanding of the effects of long-term asexuality and DNA breakage on genome evolution. To this end, we present the first high-quality chromosome-level genome assemblies for the bdelloid Adineta vaga, composed of six pairs of homologous (diploid) chromosomes with a footprint of paleotetraploidy. The observed large-scale losses of heterozygosity are signatures of recombination between homologous chromosomes, either during mitotic DNA double-strand break repair or when resolving programmed DNA breaks during a modified meiosis. Dynamic subtelomeric regions harbor more structural diversity (e.g., chromosome rearrangements, transposable elements, and haplotypic divergence). Our results trigger the reappraisal of potential meiotic processes in bdelloid rotifers and help unravel the factors underlying their long-term asexual evolutionary success.
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Affiliation(s)
- Paul Simion
- Research Unit in Environmental and Evolutionary Biology, Université de Namur, Namur 5000, Belgium
- Corresponding author. (K.V.D.); (J.-F.F.); (P.S.)
| | - Jitendra Narayan
- Research Unit in Environmental and Evolutionary Biology, Université de Namur, Namur 5000, Belgium
| | - Antoine Houtain
- Research Unit in Environmental and Evolutionary Biology, Université de Namur, Namur 5000, Belgium
| | - Alessandro Derzelle
- Research Unit in Environmental and Evolutionary Biology, Université de Namur, Namur 5000, Belgium
| | - Lyam Baudry
- Institut Pasteur, Unité Régulation Spatiale des Génomes, UMR 3525, CNRS, Paris F-75015, France
- Collège Doctoral, Sorbonne Université, F-75005 Paris, France
| | - Emilien Nicolas
- Research Unit in Environmental and Evolutionary Biology, Université de Namur, Namur 5000, Belgium
- Molecular Biology and Evolution, Université libre de Bruxelles (ULB), Brussels 1050, Belgium
| | - Rohan Arora
- Research Unit in Environmental and Evolutionary Biology, Université de Namur, Namur 5000, Belgium
- Molecular Biology and Evolution, Université libre de Bruxelles (ULB), Brussels 1050, Belgium
| | - Marie Cariou
- Research Unit in Environmental and Evolutionary Biology, Université de Namur, Namur 5000, Belgium
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France
| | - Corinne Cruaud
- Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
| | | | - Clément Gilbert
- Évolution, Génomes, Comportement et Écologie, Université Paris-Saclay, CNRS, IRD, UMR, 91198 Gif-sur-Yvette, France
| | - Nadège Guiglielmoni
- Evolutionary Biology and Ecology, Université libre de Bruxelles (ULB), Brussels 1050, Belgium
| | - Boris Hespeels
- Research Unit in Environmental and Evolutionary Biology, Université de Namur, Namur 5000, Belgium
| | - Djampa K. L. Kozlowski
- INRAE, Université Côte-d’Azur, CNRS, Institut Sophia Agrobiotech, Sophia Antipolis 06903, France
| | - Karine Labadie
- Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
| | - Antoine Limasset
- Université de Lille, CNRS, UMR 9189 - CRIStAL, 59655 Villeneuve-d’Ascq, France
| | - Marc Llirós
- Research Unit in Environmental and Evolutionary Biology, Université de Namur, Namur 5000, Belgium
- Institut d’Investigació Biomédica de Girona, Malalties Digestives i Microbiota, 17190 Salt, Spain
| | - Martial Marbouty
- Institut Pasteur, Unité Régulation Spatiale des Génomes, UMR 3525, CNRS, Paris F-75015, France
| | - Matthieu Terwagne
- Research Unit in Environmental and Evolutionary Biology, Université de Namur, Namur 5000, Belgium
| | - Julie Virgo
- Research Unit in Environmental and Evolutionary Biology, Université de Namur, Namur 5000, Belgium
| | - Richard Cordaux
- Ecologie et Biologie des interactions, Université de Poitiers, UMR CNRS 7267, 5 rue Albert Turpain, 86073 Poitiers, France
| | - Etienne G. J. Danchin
- INRAE, Université Côte-d’Azur, CNRS, Institut Sophia Agrobiotech, Sophia Antipolis 06903, France
| | - Bernard Hallet
- LIBST, Université Catholique de Louvain (UCLouvain), Croix du Sud 4/5, Louvain-la-Neuve 1348, Belgium
| | - Romain Koszul
- Institut Pasteur, Unité Régulation Spatiale des Génomes, UMR 3525, CNRS, Paris F-75015, France
| | - Thomas Lenormand
- CEFE, Univ Montpellier, CNRS, Univ Paul Valéry Montpellier 3, EPHE, IRD, Montpellier, France
| | - Jean-Francois Flot
- Evolutionary Biology and Ecology, Université libre de Bruxelles (ULB), Brussels 1050, Belgium
- Interuniversity Institute of Bioinformatics in Brussels - (IB), Brussels 1050, Belgium
- Corresponding author. (K.V.D.); (J.-F.F.); (P.S.)
| | - Karine Van Doninck
- Research Unit in Environmental and Evolutionary Biology, Université de Namur, Namur 5000, Belgium
- Molecular Biology and Evolution, Université libre de Bruxelles (ULB), Brussels 1050, Belgium
- Corresponding author. (K.V.D.); (J.-F.F.); (P.S.)
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18
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Hara Y, Shibahara R, Kondo K, Abe W, Kunieda T. Parallel evolution of trehalose production machinery in anhydrobiotic animals via recurrent gene loss and horizontal transfer. Open Biol 2021; 11:200413. [PMID: 34255978 PMCID: PMC8277472 DOI: 10.1098/rsob.200413] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Trehalose is a versatile non-reducing sugar. In some animal groups possessing its intrinsic production machinery, it is used as a potent protectant against environmental stresses, as well as blood sugar. However, the trehalose biosynthesis genes remain unidentified in the large majority of metazoan phyla, including vertebrates. To uncover the evolutionary history of trehalose production machinery in metazoans, we scrutinized the available genome resources and identified bifunctional trehalose-6-phosphate synthase-trehalose-6-phosphate phosphatase (TPS–TPP) genes in various taxa. The scan included our newly sequenced genome assembly of a desiccation-tolerant tardigrade Paramacrobiotus sp. TYO, revealing that this species retains TPS–TPP genes activated upon desiccation. Phylogenetic analyses identified a monophyletic group of the many of the metazoan TPS–TPP genes, namely ‘pan-metazoan’ genes, that were acquired in the early ancestors of metazoans. Furthermore, coordination of our results with the previous horizontal gene transfer studies illuminated that the two tardigrade lineages, nematodes and bdelloid rotifers, all of which include desiccation-tolerant species, independently acquired the TPS–TPP homologues via horizontal transfer accompanied with loss of the ‘pan-metazoan’ genes. Our results indicate that the parallel evolution of trehalose synthesis via recurrent loss and horizontal transfer of the biosynthesis genes resulted in the acquisition and/or augmentation of anhydrobiotic lives in animals.
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Affiliation(s)
- Yuichiro Hara
- Research Center for Genome and Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Reira Shibahara
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Koyuki Kondo
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Wataru Abe
- Department of Biology, Dokkyo Medical University, Tochigi, Japan
| | - Takekazu Kunieda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
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19
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Maeda T, Takahashi S, Yoshida T, Shimamura S, Takaki Y, Nagai Y, Toyoda A, Suzuki Y, Arimoto A, Ishii H, Satoh N, Nishiyama T, Hasebe M, Maruyama T, Minagawa J, Obokata J, Shigenobu S. Chloroplast acquisition without the gene transfer in kleptoplastic sea slugs, Plakobranchus ocellatus. eLife 2021; 10:60176. [PMID: 33902812 PMCID: PMC8079154 DOI: 10.7554/elife.60176] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 04/01/2021] [Indexed: 12/14/2022] Open
Abstract
Some sea slugs sequester chloroplasts from algal food in their intestinal cells and photosynthesize for months. This phenomenon, kleptoplasty, poses a question of how the chloroplast retains its activity without the algal nucleus. There have been debates on the horizontal transfer of algal genes to the animal nucleus. To settle the arguments, this study reported the genome of a kleptoplastic sea slug, Plakobranchus ocellatus, and found no evidence of photosynthetic genes encoded on the nucleus. Nevertheless, it was confirmed that light illumination prolongs the life of mollusk under starvation. These data presented a paradigm that a complex adaptive trait, as typified by photosynthesis, can be transferred between eukaryotic kingdoms by a unique organelle transmission without nuclear gene transfer. Our phylogenomic analysis showed that genes for proteolysis and immunity undergo gene expansion and are up-regulated in chloroplast-enriched tissue, suggesting that these molluskan genes are involved in the phenotype acquisition without horizontal gene transfer.
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Affiliation(s)
- Taro Maeda
- National Institute for Basic Biology, Okazaki, Japan
| | - Shunichi Takahashi
- Sesoko Station, Tropical Biosphere Research Center, University of the Ryukyu, Okinawa, Japan
| | - Takao Yoshida
- Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Shigeru Shimamura
- Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Yoshihiro Takaki
- Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Yukiko Nagai
- Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | | | | | - Asuka Arimoto
- Marine Biological Laboratory, Hiroshima University, Hiroshima, Japan
| | | | - Nori Satoh
- Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Tomoaki Nishiyama
- Research Center for Experimental Modeling of Human Disease, Kanazawa University, Kanazawa, Japan
| | - Mitsuyasu Hasebe
- National Institute for Basic Biology, Okazaki, Japan.,SOKENDAI, the Graduate University for Advanced Studies, Okazaki, Japan
| | | | - Jun Minagawa
- National Institute for Basic Biology, Okazaki, Japan.,SOKENDAI, the Graduate University for Advanced Studies, Okazaki, Japan
| | - Junichi Obokata
- Kyoto Prefectural University, Kyoto, Japan.,Setsunan Universiy, Hirakata, Japan
| | - Shuji Shigenobu
- National Institute for Basic Biology, Okazaki, Japan.,SOKENDAI, the Graduate University for Advanced Studies, Okazaki, Japan
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20
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Tran Van P, Anselmetti Y, Bast J, Dumas Z, Galtier N, Jaron KS, Martens K, Parker DJ, Robinson-Rechavi M, Schwander T, Simion P, Schön I. First annotated draft genomes of nonmarine ostracods (Ostracoda, Crustacea) with different reproductive modes. G3 (BETHESDA, MD.) 2021; 11:jkab043. [PMID: 33591306 PMCID: PMC8049415 DOI: 10.1093/g3journal/jkab043] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 02/05/2021] [Indexed: 11/14/2022]
Abstract
Ostracods are one of the oldest crustacean groups with an excellent fossil record and high importance for phylogenetic analyses but genome resources for this class are still lacking. We have successfully assembled and annotated the first reference genomes for three species of nonmarine ostracods; two with obligate sexual reproduction (Cyprideis torosa and Notodromas monacha) and the putative ancient asexual Darwinula stevensoni. This kind of genomic research has so far been impeded by the small size of most ostracods and the absence of genetic resources such as linkage maps or BAC libraries that were available for other crustaceans. For genome assembly, we used an Illumina-based sequencing technology, resulting in assemblies of similar sizes for the three species (335-382 Mb) and with scaffold numbers and their N50 (19-56 kb) in the same orders of magnitude. Gene annotations were guided by transcriptome data from each species. The three assemblies are relatively complete with BUSCO scores of 92-96. The number of predicted genes (13,771-17,776) is in the same range as Branchiopoda genomes but lower than in most malacostracan genomes. These three reference genomes from nonmarine ostracods provide the urgently needed basis to further develop ostracods as models for evolutionary and ecological research.
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Affiliation(s)
- Patrick Tran Van
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Yoann Anselmetti
- ISEM—Institut des Sciences de l’Evolution, Montpellier 34090, France
| | - Jens Bast
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
| | - Zoé Dumas
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
| | - Nicolas Galtier
- ISEM—Institut des Sciences de l’Evolution, Montpellier 34090, France
| | - Kamil S Jaron
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
| | - Koen Martens
- Royal Belgian Institute of Natural Sciences, OD Nature, Freshwater Biology, Brussels 1000, Belgium
- Department of Biology, University of Ghent, Ghent 9000, Belgium
| | - Darren J Parker
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Marc Robinson-Rechavi
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Tanja Schwander
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
| | - Paul Simion
- ISEM—Institut des Sciences de l’Evolution, Montpellier 34090, France
- Université de Namur, LEGE, URBE, Namur 5000, Belgium
| | - Isa Schön
- Royal Belgian Institute of Natural Sciences, OD Nature, Freshwater Biology, Brussels 1000, Belgium
- University of Hasselt, Research Group Zoology, Diepenbeek 3590, Belgium
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21
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Ali SA, Mittal D, Kaur G. In-situ monitoring of xenobiotics using genetically engineered whole-cell-based microbial biosensors: recent advances and outlook. World J Microbiol Biotechnol 2021; 37:81. [PMID: 33843020 DOI: 10.1007/s11274-021-03024-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 02/25/2021] [Indexed: 02/07/2023]
Abstract
Industrialisation, directly or indirectly, exposes humans to various xenobiotics. The increased magnitude of chemical pesticides and toxic heavy metals in the environment, as well as their intrusion into the food chain, seriously threatens human health. Therefore, the surveillance of xenobiotics is crucial for social safety and security. Online investigation by traditional methods is not sufficient for the detection and identification of such compounds because of the high costs and their complexity. Advancement in the field of genetic engineering provides a potential opportunity to use genetically modified microorganisms. In this regard, whole-cell-based microbial biosensors (WCBMB) represent an essential tool that couples genetically engineered organisms with an operator/promoter derived from a heavy metal-resistant operon combined with a regulatory protein in the gene circuit. The plasmid controls the expression of the reporter gene, such as gfp, luc, lux and lacZ, to an inducible gene promoter and has been widely applied to assay toxicity and bioavailability. This review summarises the recent trends in the development and application of microbial biosensors and the use of mobile genes for biomedical and environmental safety concerns.
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Affiliation(s)
- Syed Azmal Ali
- Proteomics and Cell Biology Lab, Animal Biotechnology Center, National Dairy Research Institute, Karnal, Haryana, India. .,Proteomics and Cell Biology Lab, Animal Biotechnology Center, ICAR-National Dairy Research Institute, 132001, Karnal, Haryana, India.
| | - Deepti Mittal
- Animal Biochemistry Division, National Dairy Research Institute, Karnal, Haryana, India
| | - Gurjeet Kaur
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, 2052, Sydney, NSW, Australia
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22
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Matriano DM, Alegado RA, Conaco C. Detection of horizontal gene transfer in the genome of the choanoflagellate Salpingoeca rosetta. Sci Rep 2021; 11:5993. [PMID: 33727612 PMCID: PMC7971027 DOI: 10.1038/s41598-021-85259-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 02/28/2021] [Indexed: 01/31/2023] Open
Abstract
Horizontal gene transfer (HGT), the movement of heritable materials between distantly related organisms, is crucial in eukaryotic evolution. However, the scale of HGT in choanoflagellates, the closest unicellular relatives of metazoans, and its possible roles in the evolution of animal multicellularity remains unexplored. We identified at least 175 candidate HGTs in the genome of the colonial choanoflagellate Salpingoeca rosetta using sequence-based tests. The majority of these were orthologous to genes in bacterial and microalgal lineages, yet displayed genomic features consistent with the rest of the S. rosetta genome-evidence of ancient acquisition events. Putative functions include enzymes involved in amino acid and carbohydrate metabolism, cell signaling, and the synthesis of extracellular matrix components. Functions of candidate HGTs may have contributed to the ability of choanoflagellates to assimilate novel metabolites, thereby supporting adaptation, survival in diverse ecological niches, and response to external cues that are possibly critical in the evolution of multicellularity in choanoflagellates.
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Affiliation(s)
- Danielle M Matriano
- Marine Science Institute, University of the Philippines, Diliman, Quezon City, Philippines
| | - Rosanna A Alegado
- Department of Oceanography, Hawai'i Sea Grant, Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawai'i at Manoa, Honolulu, USA
| | - Cecilia Conaco
- Marine Science Institute, University of the Philippines, Diliman, Quezon City, Philippines.
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23
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Jaron KS, Bast J, Nowell RW, Ranallo-Benavidez TR, Robinson-Rechavi M, Schwander T. Genomic Features of Parthenogenetic Animals. J Hered 2021; 112:19-33. [PMID: 32985658 PMCID: PMC7953838 DOI: 10.1093/jhered/esaa031] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 08/17/2020] [Indexed: 12/21/2022] Open
Abstract
Evolution without sex is predicted to impact genomes in numerous ways. Case studies of individual parthenogenetic animals have reported peculiar genomic features that were suggested to be caused by their mode of reproduction, including high heterozygosity, a high abundance of horizontally acquired genes, a low transposable element load, or the presence of palindromes. We systematically characterized these genomic features in published genomes of 26 parthenogenetic animals representing at least 18 independent transitions to asexuality. Surprisingly, not a single feature was systematically replicated across a majority of these transitions, suggesting that previously reported patterns were lineage-specific rather than illustrating the general consequences of parthenogenesis. We found that only parthenogens of hybrid origin were characterized by high heterozygosity levels. Parthenogens that were not of hybrid origin appeared to be largely homozygous, independent of the cellular mechanism underlying parthenogenesis. Overall, despite the importance of recombination rate variation for the evolution of sexual animal genomes, the genome-wide absence of recombination does not appear to have had the dramatic effects which are expected from classical theoretical models. The reasons for this are probably a combination of lineage-specific patterns, the impact of the origin of parthenogenesis, and a survivorship bias of parthenogenetic lineages.
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Affiliation(s)
- Kamil S Jaron
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Jens Bast
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Reuben W Nowell
- Department of Life Sciences, Imperial College London, Ascot, Berkshire, UK
- Reuben W. Nowell is now at the Department of Zoology, University of Oxford, Oxford, UK
| | | | - Marc Robinson-Rechavi
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Tanja Schwander
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
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24
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Nowell RW, Wilson CG, Almeida P, Schiffer PH, Fontaneto D, Becks L, Rodriguez F, Arkhipova IR, Barraclough TG. Evolutionary dynamics of transposable elements in bdelloid rotifers. eLife 2021; 10:e63194. [PMID: 33543711 PMCID: PMC7943196 DOI: 10.7554/elife.63194] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 02/04/2021] [Indexed: 12/17/2022] Open
Abstract
Transposable elements (TEs) are selfish genomic parasites whose ability to spread autonomously is facilitated by sexual reproduction in their hosts. If hosts become obligately asexual, TE frequencies and dynamics are predicted to change dramatically, but the long-term outcome is unclear. Here, we test current theory using whole-genome sequence data from eight species of bdelloid rotifers, a class of invertebrates in which males are thus far unknown. Contrary to expectations, we find a variety of active TEs in bdelloid genomes, at an overall frequency within the range seen in sexual species. We find no evidence that TEs are spread by cryptic recombination or restrained by unusual DNA repair mechanisms. Instead, we find that that TE content evolves relatively slowly in bdelloids and that gene families involved in RNAi-mediated TE suppression have undergone significant expansion, which might mitigate the deleterious effects of active TEs and compensate for the consequences of long-term asexuality.
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Affiliation(s)
- Reuben W Nowell
- Department of Zoology, University of OxfordOxfordUnited Kingdom
- Department of Life Sciences, Imperial College London, Silwood Park CampusAscot, BerkshireUnited Kingdom
| | - Christopher G Wilson
- Department of Zoology, University of OxfordOxfordUnited Kingdom
- Department of Life Sciences, Imperial College London, Silwood Park CampusAscot, BerkshireUnited Kingdom
| | - Pedro Almeida
- Department of Life Sciences, Imperial College London, Silwood Park CampusAscot, BerkshireUnited Kingdom
- Division of Biosciences, University College LondonLondonUnited Kingdom
| | - Philipp H Schiffer
- Institute of Zoology, Section Developmental Biology, University of Cologne, KölnWormlabGermany
| | - Diego Fontaneto
- National Research Council of Italy, Water Research InstituteVerbania PallanzaItaly
| | - Lutz Becks
- Community Dynamics Group, Department of Evolutionary Ecology, Max Planck Institute for Evolutionary BiologyPlönGermany
- Aquatic Ecology and Evolution, University of KonstanzKonstanzGermany
| | - Fernando Rodriguez
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological LaboratoryWoods Hole, MAUnited States
| | - Irina R Arkhipova
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological LaboratoryWoods Hole, MAUnited States
| | - Timothy G Barraclough
- Department of Zoology, University of OxfordOxfordUnited Kingdom
- Department of Life Sciences, Imperial College London, Silwood Park CampusAscot, BerkshireUnited Kingdom
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25
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Lyall R, Nikoloski Z, Gechev T. Comparative Analysis of ROS Network Genes in Extremophile Eukaryotes. Int J Mol Sci 2020; 21:E9131. [PMID: 33266251 PMCID: PMC7730656 DOI: 10.3390/ijms21239131] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 11/27/2020] [Accepted: 11/29/2020] [Indexed: 12/12/2022] Open
Abstract
The reactive oxygen species (ROS) gene network, consisting of both ROS-generating and detoxifying enzymes, adjusts ROS levels in response to various stimuli. We performed a cross-kingdom comparison of ROS gene networks to investigate how they have evolved across all Eukaryotes, including protists, fungi, plants and animals. We included the genomes of 16 extremotolerant Eukaryotes to gain insight into ROS gene evolution in organisms that experience extreme stress conditions. Our analysis focused on ROS genes found in all Eukaryotes (such as catalases, superoxide dismutases, glutathione reductases, peroxidases and glutathione peroxidase/peroxiredoxins) as well as those specific to certain groups, such as ascorbate peroxidases, dehydroascorbate/monodehydroascorbate reductases in plants and other photosynthetic organisms. ROS-producing NADPH oxidases (NOX) were found in most multicellular organisms, although several NOX-like genes were identified in unicellular or filamentous species. However, despite the extreme conditions experienced by extremophile species, we found no evidence for expansion of ROS-related gene families in these species compared to other Eukaryotes. Tardigrades and rotifers do show ROS gene expansions that could be related to their extreme lifestyles, although a high rate of lineage-specific horizontal gene transfer events, coupled with recent tetraploidy in rotifers, could explain this observation. This suggests that the basal Eukaryotic ROS scavenging systems are sufficient to maintain ROS homeostasis even under the most extreme conditions.
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Affiliation(s)
- Rafe Lyall
- Department Bioinformatics and Mathematical Modelling, Center of Plant Systems Biology and Biotechnology, 139 Ruski Blvd., 4000 Plovdiv, Bulgaria; (Z.N.); (T.G.)
| | - Zoran Nikoloski
- Department Bioinformatics and Mathematical Modelling, Center of Plant Systems Biology and Biotechnology, 139 Ruski Blvd., 4000 Plovdiv, Bulgaria; (Z.N.); (T.G.)
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam-Golm, Germany
- Systems Biology and Mathematical Modelling Group, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Tsanko Gechev
- Department Bioinformatics and Mathematical Modelling, Center of Plant Systems Biology and Biotechnology, 139 Ruski Blvd., 4000 Plovdiv, Bulgaria; (Z.N.); (T.G.)
- Department of Plant Physiology and Molecular Biology, Plovdiv University, 24 Tsar Assen str., 4000 Plovdiv, Bulgaria
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26
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Li X, Fang C, Zhao JP, Zhou XY, Ni Z, Niu DK. Desiccation does not drastically increase the accessibility of exogenous DNA to nuclear genomes: evidence from the frequency of endosymbiotic DNA transfer. BMC Genomics 2020; 21:452. [PMID: 32611311 PMCID: PMC7329468 DOI: 10.1186/s12864-020-06865-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 06/23/2020] [Indexed: 12/04/2022] Open
Abstract
Background Although horizontal gene transfer (HGT) is a widely accepted force in the evolution of prokaryotic genomes, its role in the evolution of eukaryotic genomes remains hotly debated. Some bdelloid rotifers that are resistant to extreme desiccation and radiation undergo a very high level of HGT, whereas in another desiccation-resistant invertebrate, the tardigrade, the pattern does not exist. Overall, the DNA double-strand breaks (DSBs) induced by prolonged desiccation have been postulated to open a gateway to the nuclear genome for exogenous DNA integration and thus to facilitate the HGT process, thereby enhancing the rate of endosymbiotic DNA transfer (EDT). Results We first surveyed the abundance of nuclear mitochondrial DNAs (NUMTs) and nuclear plastid DNAs (NUPTs) in five eukaryotes that are highly resistant to desiccation: the bdelloid rotifers Adineta vaga and Adineta ricciae, the tardigrade Ramazzottius varieornatus, and the resurrection plants Dorcoceras hygrometricum and Selaginella tamariscina. Excessive NUMTs or NUPTs were not detected. Furthermore, we compared 24 groups of desiccation-tolerant organisms with their relatively less desiccation-tolerant relatives but did not find a significant difference in NUMT/NUPT contents. Conclusions Desiccation may induce DSBs, but it is unlikely to dramatically increase the frequency of exogenous sequence integration in most eukaryotes. The capture of exogenous DNA sequences is possible only when DSBs are repaired through a subtype of non-homologous end joining, named alternative end joining (alt-EJ). Due to the deleterious effects of the resulting insertion mutations, alt-EJ is less frequently initiated than other mechanisms.
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Affiliation(s)
- Xixi Li
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Cheng Fang
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Jun-Peng Zhao
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Xiao-Yu Zhou
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Zhihua Ni
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China.,College of Life Sciences, Hebei University, Baoding, 071002, China
| | - Deng-Ke Niu
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China.
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27
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Mauer K, Hellmann SL, Groth M, Fröbius AC, Zischler H, Hankeln T, Herlyn H. The genome, transcriptome, and proteome of the fish parasite Pomphorhynchus laevis (Acanthocephala). PLoS One 2020; 15:e0232973. [PMID: 32574180 PMCID: PMC7310846 DOI: 10.1371/journal.pone.0232973] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 04/24/2020] [Indexed: 01/05/2023] Open
Abstract
Thorny-headed worms (Acanthocephala) are endoparasites exploiting Mandibulata (Arthropoda) and Gnathostomata (Vertebrata). Despite their world-wide occurrence and economic relevance as a pest, genome and transcriptome assemblies have not been published before. However, such data might hold clues for a sustainable control of acanthocephalans in animal production. For this reason, we present the first draft of an acanthocephalan nuclear genome, besides the mitochondrial one, using the fish parasite Pomphorhynchus laevis (Palaeacanthocephala) as a model. Additionally, we have assembled and annotated the transcriptome of this species and the proteins encoded. A hybrid assembly of long and short reads resulted in a near-complete P. laevis draft genome of ca. 260 Mb, comprising a large repetitive portion of ca. 63%. Numbers of transcripts and translated proteins (35,683) were within the range of other members of the Rotifera-Acanthocephala clade. Our data additionally demonstrate a significant reorganization of the acanthocephalan gene repertoire. Thus, more than 20% of the usually conserved metazoan genes were lacking in P. laevis. Ontology analysis of the retained genes revealed many connections to the incorporation of carotinoids. These are probably taken up via the surface together with lipids, thus accounting for the orange coloration of P. laevis. Furthermore, we found transcripts and protein sequences to be more derived in P. laevis than in rotifers from Monogononta and Bdelloidea. This was especially the case in genes involved in energy metabolism, which might reflect the acanthocephalan ability to use the scarce oxygen in the host intestine for respiration and simultaneously carry out fermentation. Increased plasticity of the gene repertoire through the integration of foreign DNA into the nuclear genome seems to be another underpinning factor of the evolutionary success of acanthocephalans. In any case, energy-related genes and their proteins may be considered as candidate targets for the acanthocephalan control.
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Affiliation(s)
- Katharina Mauer
- Anthropology, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg University Mainz, Mainz, Germany
| | - Sören Lukas Hellmann
- Molecular Genetics and Genomic Analysis Group, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg University Mainz, Mainz, Germany
| | - Marco Groth
- CF DNA sequencing, Leibniz Institute on Aging–Fritz Lipmann Institute, Jena, Germany
| | - Andreas C. Fröbius
- Molecular Andrology, Biomedical Research Center Seltersberg (BFS), Justus Liebig University Gießen, Gießen, Germany
| | - Hans Zischler
- Anthropology, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg University Mainz, Mainz, Germany
| | - Thomas Hankeln
- Molecular Genetics and Genomic Analysis Group, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg University Mainz, Mainz, Germany
| | - Holger Herlyn
- Anthropology, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg University Mainz, Mainz, Germany
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28
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Emamalipour M, Seidi K, Zununi Vahed S, Jahanban-Esfahlan A, Jaymand M, Majdi H, Amoozgar Z, Chitkushev LT, Javaheri T, Jahanban-Esfahlan R, Zare P. Horizontal Gene Transfer: From Evolutionary Flexibility to Disease Progression. Front Cell Dev Biol 2020; 8:229. [PMID: 32509768 PMCID: PMC7248198 DOI: 10.3389/fcell.2020.00229] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 03/17/2020] [Indexed: 12/11/2022] Open
Abstract
Flexibility in the exchange of genetic material takes place between different organisms of the same or different species. This phenomenon is known to play a key role in the genetic, physiological, and ecological performance of the host. Exchange of genetic materials can cause both beneficial and/or adverse biological consequences. Horizontal gene transfer (HGT) or lateral gene transfer (LGT) as a general mechanism leads to biodiversity and biological innovations in nature. HGT mediators are one of the genetic engineering tools used for selective introduction of desired changes in the genome for gene/cell therapy purposes. HGT, however, is crucial in development, emergence, and recurrence of various human-related diseases, such as cancer, genetic-, metabolic-, and neurodegenerative disorders and can negatively affect the therapeutic outcome by promoting resistant forms or disrupting the performance of genome editing toolkits. Because of the importance of HGT and its vital physio- and pathological roles, here the variety of HGT mechanisms are reviewed, ranging from extracellular vesicles (EVs) and nanotubes in prokaryotes to cell-free DNA and apoptotic bodies in eukaryotes. Next, we argue that HGT plays a role both in the development of useful features and in pathological states associated with emerging and recurrent forms of the disease. A better understanding of the different HGT mediators and their genome-altering effects/potentials may pave the way for the development of more effective therapeutic and diagnostic regimes.
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Affiliation(s)
- Melissa Emamalipour
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Khaled Seidi
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | | | - Mehdi Jaymand
- Nano Drug Delivery Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Hasan Majdi
- Department of Medical Nanotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Zohreh Amoozgar
- Edwin L. Steele Laboratories, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
| | - L T Chitkushev
- Department of Computer Science, Metropolitan College, Boston University, Boston, MA, United States.,Health Informatics Lab, Metropolitan College, Boston University, Boston, MA, United States
| | - Tahereh Javaheri
- Health Informatics Lab, Metropolitan College, Boston University, Boston, MA, United States
| | - Rana Jahanban-Esfahlan
- Department of Medical Biotechnology, School of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Peyman Zare
- Faculty of Medicine, Cardinal Stefan Wyszyński University in Warsaw, Warsaw, Poland.,Dioscuri Center of Chromatin Biology and Epigenomics, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
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Zolfaghari Emameh R, Masoori L, Taheri RA, Falak R. Identification and characterization of parvalbumin-like protein in Trichophyton violaceum. Fungal Biol 2020; 124:592-600. [PMID: 32448450 DOI: 10.1016/j.funbio.2020.02.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 01/15/2020] [Accepted: 02/23/2020] [Indexed: 01/08/2023]
Abstract
Parvalbumins play crucial physiological roles in neuromuscular systems of vertebrates, such as cell-cycle, development of neurons, contraction of muscles, and regulation of intracellular calcium. To perform these neuromuscular functions, parvalbumin may be in associated with other proteins including calbindin, carbonic anhydrase, and cytochrome oxidase. Humans may show an IgE-specific hypersensitivity to parvalbumins after consumption of some distinct fish species. While this protein is abundant in fish muscles, literature review of publications related to fish parvalbumins, do not point to the presence of parvalbumins in eukaryotic microbes. In this study, we propose that distantly related parvalbumins may be found in some non-fish species. Bioinformatics studies such as multiple sequence alignment (MSA), phylogenetic analysis as well as molecular-based experiments indicate that, at least two parvalbumins sequences (UniProt IDs: A0A178F775 and A0A178F7E4) with EF-hand domains and Ca2+-binding sites could be identified in Trichophyton violaceum, a pathogenic fungal species. It was determined that both genes consisted of a single exon and encoded for parvalbumin proteins possessing conserved amino acid motifs. Antigenicity prediction revealed antigenic sites located in both sides of the Ca2+-binding site of the first EF-hand domain. Our phylogenetic analysis revealed that one of parvalbumins (UniProt ID: 0A178F775) can be evolved to other parvalbumins in T. violaceum (UniProt ID: A0A178F7E4) and fish species through evolutionary phenomenon. To confirm our in-silico findings, we designed three primer pairs to detect one of the T. violaceum parvalbumins (UniProt ID: A0A178F7E4) by polymerase chain reaction (PCR); one primer pair showed a strong and specific band in agarose gel electrophoresis. To evaluate the specificity of the method, the primers were tested on extracted DNA from Trichophyton rubrum and T. mentagrophytes. The results demonstrated that the evaluated parvalbumin gene (UniProt ID: A0A178F7E4) was T. violaceum-specific and this pathogenic fungus can be differentiated from T. rubrum and T. mentagrophytes through identification of parvalbumin genes. Further studies are necessary to unravel the biochemical and physiological functions of parvalbumins in T. violaceum.
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Affiliation(s)
- Reza Zolfaghari Emameh
- Department of Energy and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), 14965/161, Tehran, Iran.
| | - Leila Masoori
- Department of Laboratory Sciences, Lorestan University of Medical Sciences, Khorramabad, Iran
| | - Ramezan Ali Taheri
- Nanobiotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Reza Falak
- Immunology Research Center, Iran University of Medical Sciences, Tehran, Iran
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Boothby TC. Mechanisms and evolution of resistance to environmental extremes in animals. EvoDevo 2019; 10:30. [PMID: 31827759 PMCID: PMC6862762 DOI: 10.1186/s13227-019-0143-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 11/02/2019] [Indexed: 11/25/2022] Open
Abstract
When animals are exposed to an extreme environmental stress, one of three possible outcomes takes place: the animal dies, the animal avoids the environmental stress and survives, or the animal tolerates the environmental stress and survives. This review is concerned with the third possibility, and will look at mechanisms that rare animals use to survive extreme environmental stresses including freezing, desiccation, intense heat, irradiation, and low-oxygen conditions (hypoxia). In addition, an increasing understanding of the molecular mechanisms involved in environmental stress tolerance allows us to speculate on how these tolerances arose. Uncovering the mechanisms of extreme environmental stress tolerance and how they evolve has broad implications for our understanding of the evolution of early life on this planet, colonization of new environments, and the search for novel forms of life both on Earth and elsewhere, as well as a number of agricultural and health-related applications.
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Affiliation(s)
- Thomas C Boothby
- Department of Molecular Biology, University of Wyoming, Laramie, WY USA
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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: 52] [Impact Index Per Article: 10.4] [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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Features of a novel protein, rusticalin, from the ascidian Styela rustica reveal ancestral horizontal gene transfer event. Mob DNA 2019; 10:4. [PMID: 30675192 PMCID: PMC6339383 DOI: 10.1186/s13100-019-0146-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 01/02/2019] [Indexed: 12/18/2022] Open
Abstract
Background The transfer of genetic material from non-parent organisms is called horizontal gene transfer (HGT). One of the most conclusive cases of HGT in metazoans was previously described for the cellulose synthase gene in ascidians. Results In this study we identified a new protein, rusticalin, from the ascidian Styela rustica and presented evidence for its likely origin by HGT. Discernible homologues of rusticalin were found in placozoans, coral, and basal Chordates. Rusticalin was predicted to consist of two distinct regions, an N-terminal domain and a C-terminal domain. The N-terminal domain comprises two cysteine-rich repeats and shows remote similarity to the tick carboxypeptidase inhibitor. The C-terminal domain shares significant sequence similarity with bacterial MD peptidases and bacteriophage A500 L-alanyl-D-glutamate peptidase. A possible transfer of the C-terminal domain by bacteriophage was confirmed by an analysis of noncoding sequences of C. intestinalis rusticalin-like gene, which was found to contain a sequence similar to the bacteriophage A500 recombination site. Moreover, a sequence similar to the bacteriophage recombination site was found to be adjacent to the cellulose synthase catalytic subunit gene in the genome of Streptomices sp., the donor of ascidian cellulose synthase. Conclusions The C-terminal domain of rusticalin and rusticalin-like proteins is likely to be horizontally transferred by the bacteriophage A500. A common mechanism involving bacteriophage mediated gene transfer can be proposed for at least two HGT events in ascidians.
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Hand SC, Moore DS, Patil Y. Challenges during diapause and anhydrobiosis: Mitochondrial bioenergetics and desiccation tolerance. IUBMB Life 2018; 70:1251-1259. [PMID: 30369011 DOI: 10.1002/iub.1953] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 09/10/2018] [Accepted: 09/11/2018] [Indexed: 11/11/2022]
Abstract
In preparation for the onset of environmental challenges like overwintering, food limitation, anoxia, or water stress, many invertebrates and certain killifish enter diapause. Diapause is a developmentally-programed dormancy characterized by suppression of development and metabolism. For embryos of Artemia franciscana (brine shrimp), the metabolic arrest is profound. These gastrula-stage embryos depress oxidative metabolism by ~99% during diapause and survive years of severe desiccation in a state termed anhydrobiosis. Trehalose is the sole fuel source for this developmental stage. Mitochondrial function during diapause is downregulated primarily by restricting substrate supply, as a result of inhibiting key enzymes of carbohydrate metabolism. Because proton conductance across the inner membrane is not decreased during diapause, the inference is that membrane potential must be compromised. In the absence of any intervention, the possibility exists that the F1 Fo ATP synthase and the adenine nucleotide translocator may reverse, leading to wholesale hydrolysis of cellular ATP. Studies with anhydrobiotes like A. franciscana are revealing multiple traits useful for improving desiccation tolerance that include the expression and accumulation late embryogenesis abundant (LEA) proteins and trehalose. LEA proteins are intrinsically disordered in aqueous solution but gain secondary structure (predominantly α-helix) as water is removed. These protective agents stabilize biological structures including lipid bilayers and mitochondria during severe water stress. © 2018 IUBMB Life, 70(12):1251-1259, 2018.
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Affiliation(s)
- Steven C Hand
- Department of Biological Sciences, Division of Cellular Developmental and Integrative Biology, Louisiana State University, LA, USA
| | - Daniel S Moore
- Department of Biological Sciences, Division of Cellular Developmental and Integrative Biology, Louisiana State University, LA, USA
| | - Yuvraj Patil
- Department of Biological Sciences, Division of Cellular Developmental and Integrative Biology, Louisiana State University, LA, USA
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Cross-Contamination Explains "Inter and Intraspecific Horizontal Genetic Transfers" between Asexual Bdelloid Rotifers. Curr Biol 2018; 28:2436-2444.e14. [PMID: 30017483 DOI: 10.1016/j.cub.2018.05.070] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 12/07/2017] [Accepted: 05/23/2018] [Indexed: 11/22/2022]
Abstract
A few metazoan lineages are thought to have persisted for millions of years without sexual reproduction. If so, they would offer important clues to the evolutionary paradox of sex itself [1, 2]. Most "ancient asexuals" are subject to ongoing doubt because extant populations continue to invest in males [3-9]. However, males are famously unknown in bdelloid rotifers, a class of microscopic invertebrates comprising hundreds of species [10-12]. Bdelloid genomes have acquired an unusually high proportion of genes from non-metazoans via horizontal transfer [13-17]. This well-substantiated finding has invited speculation [13] that homologous horizontal transfer between bdelloid individuals also may occur, perhaps even "replacing" sex [14]. In 2016, Current Biology published an article claiming to supply evidence for this idea. Debortoli et al. [18] sampled rotifers from natural populations and sequenced one mitochondrial and four nuclear loci. Species assignments were incongruent among loci for several samples, which was interpreted as evidence of "interspecific horizontal genetic transfers." Here, we use sequencing chromatograms supplied by the authors to demonstrate that samples treated as individuals actually contained two or more highly divergent mitochondrial and ribosomal sequences, revealing cross-contamination with DNA from multiple animals of different species. Other chromatograms indicate contamination with DNA from conspecific animals, explaining genetic and genomic evidence for "intraspecific horizontal exchanges" reported in the same study. Given the clear evidence of contamination, the data and findings of Debortoli et al. [18] provide no reliable support for their conclusions that DNA is transferred horizontally between or within bdelloid species.
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Denton RD, Morales AE, Gibbs HL. Genome-specific histories of divergence and introgression between an allopolyploid unisexual salamander lineage and two ancestral sexual species. Evolution 2018; 72:1689-1700. [PMID: 29926914 DOI: 10.1111/evo.13528] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 06/07/2018] [Accepted: 06/14/2018] [Indexed: 02/06/2023]
Abstract
Quantifying introgression between sexual species and polyploid lineages traditionally thought to be asexual is an important step in understanding what drives the longevity of putatively asexual groups. Here, we capitalize on three recent innovations-ultraconserved element (UCE) sequencing, bioinformatic techniques for identifying genome-specific variation in polyploids, and model-based methods for evaluating historical gene flow-to measure the extent and tempo of introgression over the evolutionary history of an allopolyploid lineage of all-female salamanders and two ancestral sexual species. Our analyses support a scenario in which the genomes sampled in unisexual salamanders last shared a common ancestor with genomes in their parental species ∼3.4 million years ago, followed by a period of divergence between homologous genomes. Recently, secondary introgression has occurred at different times with each sexual species during the last 500,000 years. Sustained introgression of sexual genomes into the unisexual lineage is the defining characteristic of their reproductive mode, but this study provides the first evidence that unisexual genomes have undergone long periods of divergence without introgression. Unlike other sperm-dependent taxa in which introgression is rare, the alternating periods of divergence and introgression between unisexual salamanders and their sexual relatives could explain why these salamanders are among the oldest described unisexual animals.
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Affiliation(s)
- Robert D Denton
- Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus, Ohio 43210
- Ohio Biodiversity Conservation Partnership, Columbus, Ohio 43210
- Current Address: Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269
| | - Ariadna E Morales
- Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus, Ohio 43210
| | - H Lisle Gibbs
- Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus, Ohio 43210
- Ohio Biodiversity Conservation Partnership, Columbus, Ohio 43210
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Hernandez AM, Ryan JF. Horizontally transferred genes in the ctenophore Mnemiopsis leidyi. PeerJ 2018; 6:e5067. [PMID: 29922518 PMCID: PMC6005172 DOI: 10.7717/peerj.5067] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 06/04/2018] [Indexed: 12/16/2022] Open
Abstract
Horizontal gene transfer (HGT) has had major impacts on the biology of a wide range of organisms from antibiotic resistance in bacteria to adaptations to herbivory in arthropods. A growing body of literature shows that HGT between non-animals and animals is more commonplace than previously thought. In this study, we present a thorough investigation of HGT in the ctenophore Mnemiopsis leidyi. We applied tests of phylogenetic incongruence to identify nine genes that were likely transferred horizontally early in ctenophore evolution from bacteria and non-metazoan eukaryotes. All but one of these HGTs (an uncharacterized protein) are homologous to characterized enzymes, supporting previous observations that genes encoding enzymes are more likely to be retained after HGT events. We found that the majority of these nine horizontally transferred genes were expressed during development, suggesting that they are active and play a role in the biology of M. leidyi. This is the first report of HGT in ctenophores, and contributes to an ever-growing literature on the prevalence of genetic information flowing between non-animals and animals.
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Affiliation(s)
- Alexandra M Hernandez
- Whitney Laboratory for Marine Bioscience, St. Augustine, FL, USA.,Department of Biology, University of Florida, Gainesville, FL, USA
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, St. Augustine, FL, USA.,Department of Biology, University of Florida, Gainesville, FL, USA
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Wybouw N, Van Leeuwen T, Dermauw W. A massive incorporation of microbial genes into the genome of Tetranychus urticae, a polyphagous arthropod herbivore. INSECT MOLECULAR BIOLOGY 2018; 27:333-351. [PMID: 29377385 DOI: 10.1111/imb.12374] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
A number of horizontal gene transfers (HGTs) have been identified in the spider mite Tetranychus urticae, a chelicerate herbivore. However, the genome of this mite species has at present not been thoroughly mined for the presence of HGT genes. Here, we performed a systematic screen for HGT genes in the T. urticae genome using the h-index metric. Our results not only validated previously identified HGT genes but also uncovered 25 novel HGT genes. In addition to HGT genes with a predicted biochemical function in carbohydrate, lipid and folate metabolism, we also identified the horizontal transfer of a ketopantoate hydroxymethyltransferase and a pantoate β-alanine ligase gene. In plants and bacteria, both genes are essential for vitamin B5 biosynthesis and their presence in the mite genome strongly suggests that spider mites, similar to Bemisia tabaci and nematodes, can synthesize their own vitamin B5. We further show that HGT genes were physically embedded within the mite genome and were expressed in different life stages. By screening chelicerate genomes and transcriptomes, we were able to estimate the evolutionary histories of these HGTs during chelicerate evolution. Our study suggests that HGT has made a significant and underestimated impact on the metabolic repertoire of plant-feeding spider mites.
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Affiliation(s)
- N Wybouw
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, the Netherlands
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - T Van Leeuwen
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, the Netherlands
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - W Dermauw
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
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Li M, Zhao J, Tang N, Sun H, Huang J. Horizontal Gene Transfer From Bacteria and Plants to the Arbuscular Mycorrhizal Fungus Rhizophagus irregularis. FRONTIERS IN PLANT SCIENCE 2018; 9:701. [PMID: 29887874 PMCID: PMC5982333 DOI: 10.3389/fpls.2018.00701] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 05/07/2018] [Indexed: 05/28/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) belong to Glomeromycotina, and are mutualistic symbionts of many land plants. Associated bacteria accompany AMF during their lifecycle to establish a robust tripartite association consisting of fungi, plants and bacteria. Physical association among this trinity provides possibilities for the exchange of genetic materials. However, very few horizontal gene transfer (HGT) from bacteria or plants to AMF has been reported yet. In this study, we complement existing algorithms by developing a new pipeline, Blast2hgt, to efficiently screen for putative horizontally derived genes from a whole genome. Genome analyses of the glomeromycete Rhizophagus irregularis identified 19 fungal genes that had been transferred between fungi and bacteria/plants, of which seven were obtained from bacteria. Another 18 R. irregularis genes were found to be recently acquired from either plants or bacteria. In the R. irregularis genome, gene duplication has contributed to the expansion of three foreign genes. Importantly, more than half of the R. irregularis foreign genes were expressed in various transcriptomic experiments, suggesting that these genes are functional in R. irregularis. Functional annotation and available evidence showed that these acquired genes may participate in diverse but fundamental biological processes such as regulation of gene expression, mitosis and signal transduction. Our study suggests that horizontal gene influx through endosymbiosis is a source of new functions for R. irregularis, and HGT might have played a role in the evolution and symbiotic adaptation of this arbuscular mycorrhizal fungus.
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Affiliation(s)
- Meng Li
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jinjie Zhao
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Nianwu Tang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Hang Sun
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Jinling Huang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Henan University, Kaifeng, China
- Department of Biology, East Carolina University, Greenville, NC, United States
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Clasen FJ, Pierneef RE, Slippers B, Reva O. EuGI: a novel resource for studying genomic islands to facilitate horizontal gene transfer detection in eukaryotes. BMC Genomics 2018; 19:323. [PMID: 29724163 PMCID: PMC5934851 DOI: 10.1186/s12864-018-4724-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 04/25/2018] [Indexed: 11/17/2022] Open
Abstract
Background Genomic islands (GIs) are inserts of foreign DNA that have potentially arisen through horizontal gene transfer (HGT). There are evidences that GIs can contribute significantly to the evolution of prokaryotes. The acquisition of GIs through HGT in eukaryotes has, however, been largely unexplored. In this study, the previously developed GI prediction tool, SeqWord Gene Island Sniffer (SWGIS), is modified to predict GIs in eukaryotic chromosomes. Artificial simulations are used to estimate ratios of predicting false positive and false negative GIs by inserting GIs into different test chromosomes and performing the SWGIS v2.0 algorithm. Using SWGIS v2.0, GIs are then identified in 36 fungal, 22 protozoan and 8 invertebrate genomes. Results SWGIS v2.0 predicts GIs in large eukaryotic chromosomes based on the atypical nucleotide composition of these regions. Averages for predicting false negative and false positive GIs were 20.1% and 11.01% respectively. A total of 10,550 GIs were identified in 66 eukaryotic species with 5299 of these GIs coding for at least one functional protein. The EuGI web-resource, freely accessible at http://eugi.bi.up.ac.za, was developed that allows browsing the database created from identified GIs and genes within GIs through an interactive and visual interface. Conclusions SWGIS v2.0 along with the EuGI database, which houses GIs identified in 66 different eukaryotic species, and the EuGI web-resource, provide the first comprehensive resource for studying HGT in eukaryotes. Electronic supplementary material The online version of this article (10.1186/s12864-018-4724-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Frederick Johannes Clasen
- Centre for Bioinformatics and Computational Biology; Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, Private Bag X20, Hatfield, 0028, South Africa. .,Forestry and Agricultural Biotechnology Institute; Department of Biochemistry , Genetics and Microbiology, University of Pretoria, Pretoria, 0002, South Africa.
| | - Rian Ewald Pierneef
- Centre for Bioinformatics and Computational Biology; Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, Private Bag X20, Hatfield, 0028, South Africa
| | - Bernard Slippers
- Forestry and Agricultural Biotechnology Institute; Department of Biochemistry , Genetics and Microbiology, University of Pretoria, Pretoria, 0002, South Africa
| | - Oleg Reva
- Centre for Bioinformatics and Computational Biology; Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, Private Bag X20, Hatfield, 0028, South Africa
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40
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Nowell RW, Almeida P, Wilson CG, Smith TP, Fontaneto D, Crisp A, Micklem G, Tunnacliffe A, Boschetti C, Barraclough TG. Comparative genomics of bdelloid rotifers: Insights from desiccating and nondesiccating species. PLoS Biol 2018; 16:e2004830. [PMID: 29689044 PMCID: PMC5916493 DOI: 10.1371/journal.pbio.2004830] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Accepted: 03/19/2018] [Indexed: 12/22/2022] Open
Abstract
Bdelloid rotifers are a class of microscopic invertebrates that have existed for millions of years apparently without sex or meiosis. They inhabit a variety of temporary and permanent freshwater habitats globally, and many species are remarkably tolerant of desiccation. Bdelloids offer an opportunity to better understand the evolution of sex and recombination, but previous work has emphasised desiccation as the cause of several unusual genomic features in this group. Here, we present high-quality whole-genome sequences of 3 bdelloid species: Rotaria macrura and R. magnacalcarata, which are both desiccation intolerant, and Adineta ricciae, which is desiccation tolerant. In combination with the published assembly of A. vaga, which is also desiccation tolerant, we apply a comparative genomics approach to evaluate the potential effects of desiccation tolerance and asexuality on genome evolution in bdelloids. We find that ancestral tetraploidy is conserved among all 4 bdelloid species, but homologous divergence in obligately aquatic Rotaria genomes is unexpectedly low. This finding is contrary to current models regarding the role of desiccation in shaping bdelloid genomes. In addition, we find that homologous regions in A. ricciae are largely collinear and do not form palindromic repeats as observed in the published A. vaga assembly. Consequently, several features interpreted as genomic evidence for long-term ameiotic evolution are not general to all bdelloid species, even within the same genus. Finally, we substantiate previous findings of high levels of horizontally transferred nonmetazoan genes in both desiccating and nondesiccating bdelloid species and show that this unusual feature is not shared by other animal phyla, even those with desiccation-tolerant representatives. These comparisons call into question the proposed role of desiccation in mediating horizontal genetic transfer.
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Affiliation(s)
- Reuben W. Nowell
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire, United Kingdom
| | - Pedro Almeida
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire, United Kingdom
| | - Christopher G. Wilson
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire, United Kingdom
| | - Thomas P. Smith
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire, United Kingdom
| | - Diego Fontaneto
- National Research Council of Italy, Institute of Ecosystem Study, Verbania Pallanza, Italy
| | - Alastair Crisp
- Department of Chemical Engineering and Biotechnology, West Cambridge Site, University of Cambridge, Cambridge, United Kingdom
| | - Gos Micklem
- Department of Genetics, Cambridge Systems Biology Centre, Downing Site, University of Cambridge, Cambridge, United Kingdom
| | - Alan Tunnacliffe
- Department of Chemical Engineering and Biotechnology, West Cambridge Site, University of Cambridge, Cambridge, United Kingdom
| | - Chiara Boschetti
- Department of Chemical Engineering and Biotechnology, West Cambridge Site, University of Cambridge, Cambridge, United Kingdom
- School of Biological and Marine Sciences, Plymouth University, Portland Square Building, Plymouth, United Kingdom
| | - Timothy G. Barraclough
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire, United Kingdom
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41
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Fierst JL, Murdock DA. Decontaminating eukaryotic genome assemblies with machine learning. BMC Bioinformatics 2017; 18:533. [PMID: 29191179 PMCID: PMC5709863 DOI: 10.1186/s12859-017-1941-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 11/14/2017] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND High-throughput sequencing has made it theoretically possible to obtain high-quality de novo assembled genome sequences but in practice DNA extracts are often contaminated with sequences from other organisms. Currently, there are few existing methods for rigorously decontaminating eukaryotic assemblies. Those that do exist filter sequences based on nucleotide similarity to contaminants and risk eliminating sequences from the target organism. RESULTS We introduce a novel application of an established machine learning method, a decision tree, that can rigorously classify sequences. The major strength of the decision tree is that it can take any measured feature as input and does not require a priori identification of significant descriptors. We use the decision tree to classify de novo assembled sequences and compare the method to published protocols. CONCLUSIONS A decision tree performs better than existing methods when classifying sequences in eukaryotic de novo assemblies. It is efficient, readily implemented, and accurately identifies target and contaminant sequences. Importantly, a decision tree can be used to classify sequences according to measured descriptors and has potentially many uses in distilling biological datasets.
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Affiliation(s)
- Janna L Fierst
- Department of Biological Sciences, University of Alabama, Tuscaloosa, 35487, AL, USA.
| | - Duncan A Murdock
- Department of Biological Sciences, University of Alabama, Tuscaloosa, 35487, AL, USA
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42
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43
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Evangelista CCS, Guidelli GV, Borges G, Araujo TF, Souza TAJD, Neves UPDC, Tunnacliffe A, Pereira TC. Multiple genes contribute to anhydrobiosis (tolerance to extreme desiccation) in the nematode Panagrolaimus superbus. Genet Mol Biol 2017; 40:790-802. [PMID: 29111563 PMCID: PMC5738622 DOI: 10.1590/1678-4685-gmb-2017-0030] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 07/20/2017] [Indexed: 11/21/2022] Open
Abstract
The molecular basis of anhydrobiosis, the state of suspended animation entered by some species during extreme desiccation, is still poorly understood despite a number of transcriptome and proteome studies. We therefore conducted functional screening by RNA interference (RNAi) for genes involved in anhydrobiosis in the holo-anhydrobiotic nematode Panagrolaimus superbus. A new method of survival analysis, based on staining, and proof-of-principle RNAi experiments confirmed a role for genes involved in oxidative stress tolerance, while a novel medium-scale RNAi workflow identified a further 40 anhydrobiosis-associated genes, including several involved in proteostasis, DNA repair and signal transduction pathways. This suggests that multiple genes contribute to anhydrobiosis in P. superbus.
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Affiliation(s)
- Cláudia Carolina Silva Evangelista
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto, SP, Brazil.,Programa de Pós-Graduação em Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto, SP, Brazil
| | - Giovanna Vieira Guidelli
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto, SP, Brazil
| | - Gustavo Borges
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto, SP, Brazil
| | - Thais Fenz Araujo
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto, SP, Brazil
| | - Tiago Alves Jorge de Souza
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto, SP, Brazil.,Programa de Pós-Graduação em Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto, SP, Brazil
| | - Ubiraci Pereira da Costa Neves
- Departamento de Física, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto, SP, Brazil
| | - Alan Tunnacliffe
- Deptartment of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Tiago Campos Pereira
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto, SP, Brazil.,Programa de Pós-Graduação em Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto, SP, Brazil
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44
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Rancurel C, Legrand L, Danchin EGJ. Alienness: Rapid Detection of Candidate Horizontal Gene Transfers across the Tree of Life. Genes (Basel) 2017; 8:E248. [PMID: 28961181 PMCID: PMC5664098 DOI: 10.3390/genes8100248] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 09/22/2017] [Accepted: 09/22/2017] [Indexed: 11/22/2022] Open
Abstract
Horizontal gene transfer (HGT) is the transmission of genes between organisms by other means than parental to offspring inheritance. While it is prevalent in prokaryotes, HGT is less frequent in eukaryotes and particularly in Metazoa. Here, we propose Alienness, a taxonomy-aware web application available at http://alienness.sophia.inra.fr. Alienness parses BLAST results against public libraries to rapidly identify candidate HGT in any genome of interest. Alienness takes as input the result of a BLAST of a whole proteome of interest against any National Center for Biotechnology Information (NCBI) protein library. The user defines recipient (e.g., Metazoa) and donor (e.g., bacteria, fungi) branches of interest in the NCBI taxonomy. Based on the best BLAST E-values of candidate donor and recipient taxa, Alienness calculates an Alien Index (AI) for each query protein. An AI > 0 indicates a better hit to candidate donor than recipient taxa and a possible HGT. Higher AI represent higher gap of E-values between candidate donor and recipient and a more likely HGT. We confirmed the accuracy of Alienness on phylogenetically confirmed HGT of non-metazoan origin in plant-parasitic nematodes. Alienness scans whole proteomes to rapidly identify possible HGT in any species of interest and thus fosters exploration of HGT more easily and largely across the tree of life.
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Affiliation(s)
- Corinne Rancurel
- INRA, CNRS, ISA, Université Côte d'Azur, 06903 Sophia Antipolis Cedex, France.
| | - Ludovic Legrand
- LIPM, INRA, CNRS, Université de Toulouse, 31326 Castanet-Tolosan Cedex, France.
| | - Etienne G J Danchin
- INRA, CNRS, ISA, Université Côte d'Azur, 06903 Sophia Antipolis Cedex, France.
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45
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Yoshida Y, Koutsovoulos G, Laetsch DR, Stevens L, Kumar S, Horikawa DD, Ishino K, Komine S, Kunieda T, Tomita M, Blaxter M, Arakawa K. Comparative genomics of the tardigrades Hypsibius dujardini and Ramazzottius varieornatus. PLoS Biol 2017; 15:e2002266. [PMID: 28749982 PMCID: PMC5531438 DOI: 10.1371/journal.pbio.2002266] [Citation(s) in RCA: 132] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 06/23/2017] [Indexed: 01/27/2023] Open
Abstract
Tardigrada, a phylum of meiofaunal organisms, have been at the center of discussions of the evolution of Metazoa, the biology of survival in extreme environments, and the role of horizontal gene transfer in animal evolution. Tardigrada are placed as sisters to Arthropoda and Onychophora (velvet worms) in the superphylum Panarthropoda by morphological analyses, but many molecular phylogenies fail to recover this relationship. This tension between molecular and morphological understanding may be very revealing of the mode and patterns of evolution of major groups. Limnoterrestrial tardigrades display extreme cryptobiotic abilities, including anhydrobiosis and cryobiosis, as do bdelloid rotifers, nematodes, and other animals of the water film. These extremophile behaviors challenge understanding of normal, aqueous physiology: how does a multicellular organism avoid lethal cellular collapse in the absence of liquid water? Meiofaunal species have been reported to have elevated levels of horizontal gene transfer (HGT) events, but how important this is in evolution, and particularly in the evolution of extremophile physiology, is unclear. To address these questions, we resequenced and reassembled the genome of H. dujardini, a limnoterrestrial tardigrade that can undergo anhydrobiosis only after extensive pre-exposure to drying conditions, and compared it to the genome of R. varieornatus, a related species with tolerance to rapid desiccation. The 2 species had contrasting gene expression responses to anhydrobiosis, with major transcriptional change in H. dujardini but limited regulation in R. varieornatus. We identified few horizontally transferred genes, but some of these were shown to be involved in entry into anhydrobiosis. Whole-genome molecular phylogenies supported a Tardigrada+Nematoda relationship over Tardigrada+Arthropoda, but rare genomic changes tended to support Tardigrada+Arthropoda.
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Affiliation(s)
- Yuki Yoshida
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Kanagawa, Japan
| | - Georgios Koutsovoulos
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Dominik R. Laetsch
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
- The James Hutton Institute, Dundee, United Kingdom
| | - Lewis Stevens
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Sujai Kumar
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Daiki D. Horikawa
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Kanagawa, Japan
| | - Kyoko Ishino
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Shiori Komine
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Takekazu Kunieda
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Kanagawa, Japan
| | - Mark Blaxter
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Kazuharu Arakawa
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Kanagawa, Japan
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46
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Dong LF, Kovarova J, Bajzikova M, Bezawork-Geleta A, Svec D, Endaya B, Sachaphibulkij K, Coelho AR, Sebkova N, Ruzickova A, Tan AS, Kluckova K, Judasova K, Zamecnikova K, Rychtarcikova Z, Gopalan V, Andera L, Sobol M, Yan B, Pattnaik B, Bhatraju N, Truksa J, Stopka P, Hozak P, Lam AK, Sedlacek R, Oliveira PJ, Kubista M, Agrawal A, Dvorakova-Hortova K, Rohlena J, Berridge MV, Neuzil J. Horizontal transfer of whole mitochondria restores tumorigenic potential in mitochondrial DNA-deficient cancer cells. eLife 2017; 6. [PMID: 28195532 PMCID: PMC5367896 DOI: 10.7554/elife.22187] [Citation(s) in RCA: 187] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Accepted: 02/13/2017] [Indexed: 12/12/2022] Open
Abstract
Recently, we showed that generation of tumours in syngeneic mice by cells devoid of mitochondrial (mt) DNA (ρ0 cells) is linked to the acquisition of the host mtDNA. However, the mechanism of mtDNA movement between cells remains unresolved. To determine whether the transfer of mtDNA involves whole mitochondria, we injected B16ρ0 mouse melanoma cells into syngeneic C57BL/6Nsu9-DsRed2 mice that express red fluorescent protein in their mitochondria. We document that mtDNA is acquired by transfer of whole mitochondria from the host animal, leading to normalisation of mitochondrial respiration. Additionally, knockdown of key mitochondrial complex I (NDUFV1) and complex II (SDHC) subunits by shRNA in B16ρ0 cells abolished or significantly retarded their ability to form tumours. Collectively, these results show that intact mitochondria with their mtDNA payload are transferred in the developing tumour, and provide functional evidence for an essential role of oxidative phosphorylation in cancer. DOI:http://dx.doi.org/10.7554/eLife.22187.001
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Affiliation(s)
- Lan-Feng Dong
- School of Medical Science, Griffith University, Southport, Australia
| | - Jaromira Kovarova
- Institute of Biotechnology, Czech Academy of Sciences, Prague, Czech Republic
| | - Martina Bajzikova
- Institute of Biotechnology, Czech Academy of Sciences, Prague, Czech Republic
| | | | - David Svec
- Institute of Biotechnology, Czech Academy of Sciences, Prague, Czech Republic
| | - Berwini Endaya
- School of Medical Science, Griffith University, Southport, Australia
| | | | - Ana R Coelho
- Institute of Biotechnology, Czech Academy of Sciences, Prague, Czech Republic.,CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Cantanhede, Portugal
| | - Natasa Sebkova
- Institute of Biotechnology, Czech Academy of Sciences, Prague, Czech Republic.,Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Anna Ruzickova
- Institute of Biotechnology, Czech Academy of Sciences, Prague, Czech Republic
| | - An S Tan
- Malaghan Institute of Medical Research, Wellington, New Zealand
| | - Katarina Kluckova
- Institute of Biotechnology, Czech Academy of Sciences, Prague, Czech Republic
| | - Kristyna Judasova
- Institute of Biotechnology, Czech Academy of Sciences, Prague, Czech Republic
| | - Katerina Zamecnikova
- Institute of Biotechnology, Czech Academy of Sciences, Prague, Czech Republic.,Zittau/Goerlitz University of Applied Sciences, Zittau, Germany
| | - Zuzana Rychtarcikova
- Institute of Biotechnology, Czech Academy of Sciences, Prague, Czech Republic.,Faculty of Pharmacy, Charles University, Hradec Kralove, Czech Republic
| | - Vinod Gopalan
- School of Medical Science, Griffith University, Southport, Australia.,School of Medicine, Griffith University, Southport, Australia
| | - Ladislav Andera
- Institute of Biotechnology, Czech Academy of Sciences, Prague, Czech Republic
| | - Margarita Sobol
- Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czech Republic
| | - Bing Yan
- School of Medical Science, Griffith University, Southport, Australia
| | - Bijay Pattnaik
- CSIR Institute of Genomics and Integrative Biology, New Delhi, India
| | - Naveen Bhatraju
- CSIR Institute of Genomics and Integrative Biology, New Delhi, India
| | - Jaroslav Truksa
- Institute of Biotechnology, Czech Academy of Sciences, Prague, Czech Republic
| | - Pavel Stopka
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Pavel Hozak
- Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czech Republic
| | - Alfred K Lam
- School of Medicine, Griffith University, Southport, Australia
| | - Radislav Sedlacek
- Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czech Republic
| | - Paulo J Oliveira
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Cantanhede, Portugal
| | - Mikael Kubista
- Institute of Biotechnology, Czech Academy of Sciences, Prague, Czech Republic.,TATAA Biocenter, Gothenburg, Sweden
| | - Anurag Agrawal
- CSIR Institute of Genomics and Integrative Biology, New Delhi, India
| | - Katerina Dvorakova-Hortova
- Institute of Biotechnology, Czech Academy of Sciences, Prague, Czech Republic.,Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jakub Rohlena
- Institute of Biotechnology, Czech Academy of Sciences, Prague, Czech Republic
| | | | - Jiri Neuzil
- School of Medical Science, Griffith University, Southport, Australia.,Institute of Biotechnology, Czech Academy of Sciences, Prague, Czech Republic
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47
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García-Fontana C, Narváez-Reinaldo JJ, Castillo F, González-López J, Luque I, Manzanera M. A New Physiological Role for the DNA Molecule as a Protector against Drying Stress in Desiccation-Tolerant Microorganisms. Front Microbiol 2016; 7:2066. [PMID: 28066383 PMCID: PMC5177630 DOI: 10.3389/fmicb.2016.02066] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 12/07/2016] [Indexed: 11/13/2022] Open
Abstract
The DNA molecule is associated with the role of encoding information required to produce RNA which is translated into proteins needed by the cell. This encoding involves information transmission to offspring or to other organisms by horizontal transfer. However, despite the abundance of this molecule in both the cell and the environment, its physiological role seems to be restricted mainly to that of a coding and inheritance molecule. In this paper, we report a new physiological role for the DNA molecule as involved in protection against desiccation, in addition to its well-established main information transfer and other recently reported functions such as bio-film formation in eDNA form. Desiccation-tolerant microorganisms such as Microbacterium sp. 3J1 significantly upregulate genes involved in DNA synthesis to produce DNA as part of their defensive mechanisms to protect protein structures and functions from drying according to RNA-seq analysis. We have observed the intracellular overproduction of DNA in two desiccation-tolerant microorganisms, Microbacterium sp. 3J1 and Arthrobacter siccitolerans 4J27, in response to desiccation signals. In addition, this conclusion can be made from our observations that synthetic DNA protects two proteins from drying and when part of a xeroprotectant preparation, DNA from various organisms including desiccation-sensitive species, does the same. Removal of DNA by nuclease treatment results in absence of this additive protective effect. We validated this role in biochemical and biophysical assays in proteins and occurs in trans even with short, single chains of synthetically produced DNA.
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Affiliation(s)
- Cristina García-Fontana
- Institute for Water Research, Department of Microbiology, University of Granada Granada, Spain
| | - Juan J Narváez-Reinaldo
- Institute for Water Research, Department of Microbiology, University of Granada Granada, Spain
| | - Francisco Castillo
- Institute of Biotechnology, Department of Physical Chemistry, University of Granada Granada, Spain
| | - Jesús González-López
- Institute for Water Research, Department of Microbiology, University of Granada Granada, Spain
| | - Irene Luque
- Institute of Biotechnology, Department of Physical Chemistry, University of Granada Granada, Spain
| | - Maximino Manzanera
- Institute for Water Research, Department of Microbiology, University of Granada Granada, Spain
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48
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Suring W, Mariën J, Broekman R, van Straalen NM, Roelofs D. Biochemical pathways supporting beta-lactam biosynthesis in the springtail Folsomia candida. Biol Open 2016; 5:1784-1789. [PMID: 27793835 PMCID: PMC5200902 DOI: 10.1242/bio.019620] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Recently, an active set of beta-lactam biosynthesis genes was reported in the genome of the arthropod springtail Folsomia candida (Collembola). Evidence was provided that these genes were acquired through horizontal gene transfer. However, successful integration of fungal- or bacterial-derived beta-lactam biosynthesis into the metabolism of an animal requires the beta-lactam precursor L-α-aminoadipic acid and a phosphopantetheinyl transferase for activation of the first enzyme of the pathway, δ-(L-α-aminoadipoyl)-L-cysteinyl-D-valine synthetase (ACVS). In this study, we characterized these supporting pathways and their transcriptional regulation in F. candida. We identified one phosphopantetheinyl transferase and three pathways for L-α-aminoadipic acid production, distinct from the pathways utilized by microorganisms. We found that after heat shock, the phosphopantetheinyl transferase was co-regulated with ACVS, confirming its role in activating ACVS. Two of the three L-α-aminoadipic acid production pathways were downregulated, while PIPOX, an enzyme participating in the pipecolate pathway, was slightly co-regulated with ACVS. This indicates that L-α-aminoadipic acid may not be a limiting factor in beta-lactam biosynthesis in F. candida, in contrast to microorganisms. In conclusion, we show that all components for L-α-aminoadipic acid synthesis are present and transcriptionally active in F. candida. This demonstrates how springtails could have recruited native enzymes to integrate a beta-lactam biosynthesis pathway into their metabolism after horizontal gene transfer. Summary: Analysis of phosphopantetheinyl transferases and metabolic pathways for L-α-aminoadipic acid that are required for beta-lactam biosynthesis in the arthropod Folsomia candida.
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Affiliation(s)
- Wouter Suring
- Department of Ecological Science, Vrije Universiteit Amsterdam, De Boelelaan 1085-1087, Amsterdam 1081 HV, The Netherlands
| | - Janine Mariën
- Department of Ecological Science, Vrije Universiteit Amsterdam, De Boelelaan 1085-1087, Amsterdam 1081 HV, The Netherlands
| | - Rhody Broekman
- Department of Ecological Science, Vrije Universiteit Amsterdam, De Boelelaan 1085-1087, Amsterdam 1081 HV, The Netherlands
| | - Nico M van Straalen
- Department of Ecological Science, Vrije Universiteit Amsterdam, De Boelelaan 1085-1087, Amsterdam 1081 HV, The Netherlands
| | - Dick Roelofs
- Department of Ecological Science, Vrije Universiteit Amsterdam, De Boelelaan 1085-1087, Amsterdam 1081 HV, The Netherlands
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49
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Levin RA, Voolstra CR, Weynberg KD, van Oppen MJH. Evidence for a role of viruses in the thermal sensitivity of coral photosymbionts. ISME JOURNAL 2016; 11:808-812. [PMID: 27911439 DOI: 10.1038/ismej.2016.154] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 09/04/2016] [Accepted: 09/18/2016] [Indexed: 11/10/2022]
Abstract
Symbiodinium, the dinoflagellate photosymbiont of corals, is posited to become more susceptible to viral infections when heat-stressed. To investigate this hypothesis, we mined transcriptome data of a thermosensitive and a thermotolerant type C1 Symbiodinium population at ambient (27 °C) and elevated (32°C) temperatures. We uncovered hundreds of transcripts from nucleocytoplasmic large double-stranded DNA viruses (NCLDVs) and the genome of a novel positive-sense single-stranded RNA virus (+ssRNAV). In the transcriptome of the thermosensitive population only, +ssRNAV transcripts had remarkable expression levels in the top 0.03% of all transcripts at 27 °C, but at 32 °C, expression levels of +ssRNAV transcripts decreased, while expression levels of anti-viral transcripts increased. In both transcriptomes, expression of NCLDV transcripts increased at 32 °C, but thermal induction of NCLDV transcripts involved in DNA manipulation was restricted to the thermosensitive population. Our findings reveal that viruses infecting Symbiodinium are affected by heat stress and may contribute to Symbiodinium thermal sensitivity.
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Affiliation(s)
- Rachel Ashley Levin
- Centre for Marine Bio-Innovation, The University of New South Wales (UNSW), Sydney, NSW, Australia.,School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW, Australia.,Climate Change Cluster, University of Technology Sydney, Sydney, NSW, Australia
| | - Christian Robert Voolstra
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, 4700 King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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50
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Ku C, Martin WF. A natural barrier to lateral gene transfer from prokaryotes to eukaryotes revealed from genomes: the 70 % rule. BMC Biol 2016; 14:89. [PMID: 27751184 PMCID: PMC5067920 DOI: 10.1186/s12915-016-0315-9] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 09/28/2016] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The literature harbors many claims for lateral gene transfer (LGT) from prokaryotes to eukaryotes. Such claims are typically founded in analyses of genome sequences. It is undisputed that many genes entered the eukaryotic lineage via the origin of mitochondria and the origin of plastids. Claims for lineage-specific LGT to eukaryotes outside the context of organelle origins and claims of continuous LGT to eukaryotic lineages are more problematic. If eukaryotes acquire genes from prokaryotes continuously during evolution, then sequenced eukaryote genomes should harbor evidence for recent LGT, like prokaryotic genomes do. RESULTS Here we devise an approach to investigate 30,358 eukaryotic sequences in the context of 1,035,375 prokaryotic homologs among 2585 phylogenetic trees containing homologs from prokaryotes and eukaryotes. Prokaryote genomes reflect a continuous process of gene acquisition and inheritance, with abundant recent acquisitions showing 80-100 % amino acid sequence identity to their phylogenetic sister-group homologs from other phyla. By contrast, eukaryote genomes show no evidence for either continuous or recent gene acquisitions from prokaryotes. We find that, in general, genes in eukaryotic genomes that share ≥70 % amino acid identity to prokaryotic homologs are genome-specific; that is, they are not found outside individual genome assemblies. CONCLUSIONS Our analyses indicate that eukaryotes do not acquire genes through continual LGT like prokaryotes do. We propose a 70 % rule: Coding sequences in eukaryotic genomes that share more than 70 % amino acid sequence identity to prokaryotic homologs are most likely assembly or annotation artifacts. The findings further uncover that the role of differential loss in eukaryote genome evolution has been vastly underestimated.
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Affiliation(s)
- Chuan Ku
- Institute of Molecular Evolution, Heinrich-Heine University, Düsseldorf, Germany.
| | - William F Martin
- Institute of Molecular Evolution, Heinrich-Heine University, Düsseldorf, Germany.
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