1
|
Mozhui K, O’Callaghan JP, Ashbrook DG, Prins P, Zhao W, Lu L, Jones BC. Epigenetic analysis in a murine genetic model of Gulf War illness. FRONTIERS IN TOXICOLOGY 2023; 5:1162749. [PMID: 37389175 PMCID: PMC10300436 DOI: 10.3389/ftox.2023.1162749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 05/22/2023] [Indexed: 07/01/2023] Open
Abstract
Of the nearly 1 million military personnel who participated in the 1990-1991 Gulf War, between 25% and 35% became ill with what now is referred to as Gulf War Illness (GWI) by the Department of Defense. Symptoms varied from gastrointestinal distress to lethargy, memory loss, inability to concentrate, depression, respiratory, and reproductive problems. The symptoms have persisted for 30 years in those afflicted but the basis of the illness remains largely unknown. Nerve agents and other chemical exposures in the war zone have been implicated but the long-term effects of these acute exposures have left few if any identifiable signatures. The major aim of this study is to elucidate the possible genomic basis for the persistence of symptoms, especially of the neurological and behavioral effects. To address this, we performed a whole genome epigenetic analysis of the proposed cause of GWI, viz., exposure to organophosphate neurotoxicants combined with high circulating glucocorticoids in two inbred mouse strains, C57BL/6J and DBA/2J. The animals received corticosterone in their drinking water for 7 days followed by injection of diisopropylfluorophosphate, a nerve agent surrogate. Six weeks after DFP injection, the animals were euthanized and medial prefrontal cortex harvested for genome-wide DNA methylation analysis using high-throughput sequencing. We observed 67 differentially methylated genes, notably among them, Ttll7, Akr1c14, Slc44a4, and Rusc2, all related to different symptoms of GWI. Our results support proof of principle of genetic differences in the chronic effects of GWI-related exposures and may reveal why the disease has persisted in many of the now aging Gulf War veterans.
Collapse
Affiliation(s)
- Khyobeni Mozhui
- Department of Preventive Medicine, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
- Department of Genetics, Genomics and Informatics, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
| | - James P. O’Callaghan
- Molecular Neurotoxicology Laboratory, Toxicology, and Molecular Biology Branch, Health Effects Laboratory Division, U. S. Centers for Disease Control and Prevention, NIOSH, Morgantown, WV, United States
| | - David G. Ashbrook
- Department of Genetics, Genomics and Informatics, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Pjotr Prins
- Department of Genetics, Genomics and Informatics, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Wenyuan Zhao
- Department of Genetics, Genomics and Informatics, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Lu Lu
- Department of Genetics, Genomics and Informatics, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Byron C. Jones
- Department of Genetics, Genomics and Informatics, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
- Department of Pharmacology, Addiction Science, and Toxicology, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
| |
Collapse
|
2
|
Yasmin A, Ambreen S, Shabir S. Biotransformation of dimethoate into novel metabolites by bacterial isolate Pseudomonas kilonensis MB490. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART. B, PESTICIDES, FOOD CONTAMINANTS, AND AGRICULTURAL WASTES 2022; 57:13-22. [PMID: 34978268 DOI: 10.1080/03601234.2021.2017723] [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] [Indexed: 06/14/2023]
Abstract
Bacterial strain (Pseudomonas kilonensis MB490) isolated from agricultural fields of Mianwali, was selected to check its potential to degrade Organophosphate insecticide dimethoate (DM). Strain MB490 was able to degrade dimethoate equally well at given pH range (6.0, 7.0 and 8.0), thus showing its pH independence for dimethoate degradation. Optimum temperature for dimethoate degradation varied from 25-30 °C. There was more dimethoate degradation under shaking conditions with optimum growth. Strain MB490 showed 90% dimethoate degradation in M-9 broth and 90.6% in soil slurry, while exhibited 81.5% dimethoate degradation in soil microcosm within 9 days, based on HPLC analysis of bacterial samples supplemented with 200 mg/L dimethoate. The average half-life (t 1/2) of dimethoate after bacterial degradation ranged from 1.95 days in 1st phase to 5 days in 2nd phase in M-9 broth, soil slurry and soil microcosm, while in control media without bacteria, it ranged from 30 to 64.3 days. GCMS investigation revealed the transformation of dimethoate into 5 metabolic products namely Methyl diethanol amine, Aspartylglycine ethyl ester, Phosphonothioic acid propyl-O, S-dimethyl ester, O, O, O-Trimethyl thiophosphate and omethoate which were ultimately mineralized by the strain MB490, providing energy for its growth.
Collapse
Affiliation(s)
- Azra Yasmin
- Microbiology & Biotechnology Research Lab, Department of Biotechnology, Fatima Jinnah Women University, The Mall, Rawalpindi, Pakistan
| | - Samina Ambreen
- Microbiology & Biotechnology Research Lab, Department of Biotechnology, Fatima Jinnah Women University, The Mall, Rawalpindi, Pakistan
| | - Sumera Shabir
- Department of Botany, PMAS Arid Agricultural University, Rawalpindi, Pakistan
| |
Collapse
|
5
|
Vyas M, Fisher TW, He R, Nelson W, Yin G, Cicero JM, Willer M, Kim R, Kramer R, May GA, Crow JA, Soderlund CA, Gang DR, Brown JK. Asian Citrus Psyllid Expression Profiles Suggest Candidatus Liberibacter Asiaticus-Mediated Alteration of Adult Nutrition and Metabolism, and of Nymphal Development and Immunity. PLoS One 2015; 10:e0130328. [PMID: 26091106 PMCID: PMC4474670 DOI: 10.1371/journal.pone.0130328] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 05/19/2015] [Indexed: 11/29/2022] Open
Abstract
The Asian citrus psyllid (ACP) Diaphorina citri Kuwayama (Hemiptera: Psyllidae) is the insect vector of the fastidious bacterium Candidatus Liberibacter asiaticus (CLas), the causal agent of citrus greening disease, or Huanglongbing (HLB). The widespread invasiveness of the psyllid vector and HLB in citrus trees worldwide has underscored the need for non-traditional approaches to manage the disease. One tenable solution is through the deployment of RNA interference technology to silence protein-protein interactions essential for ACP-mediated CLas invasion and transmission. To identify psyllid interactor-bacterial effector combinations associated with psyllid-CLas interactions, cDNA libraries were constructed from CLas-infected and CLas-free ACP adults and nymphs, and analyzed for differential expression. Library assemblies comprised 24,039,255 reads and yielded 45,976 consensus contigs. They were annotated (UniProt), classified using Gene Ontology, and subjected to in silico expression analyses using the Transcriptome Computational Workbench (TCW) (http://www.sohomoptera.org/ACPPoP/). Functional-biological pathway interpretations were carried out using the Kyoto Encyclopedia of Genes and Genomes databases. Differentially expressed contigs in adults and/or nymphs represented genes and/or metabolic/pathogenesis pathways involved in adhesion, biofilm formation, development-related, immunity, nutrition, stress, and virulence. Notably, contigs involved in gene silencing and transposon-related responses were documented in a psyllid for the first time. This is the first comparative transcriptomic analysis of ACP adults and nymphs infected and uninfected with CLas. The results provide key initial insights into host-parasite interactions involving CLas effectors that contribute to invasion-virulence, and to host nutritional exploitation and immune-related responses that appear to be essential for successful ACP-mediated circulative, propagative CLas transmission.
Collapse
Affiliation(s)
- Meenal Vyas
- School of Plant Sciences, The University of Arizona, Tucson, Arizona, United States of America
| | - Tonja W. Fisher
- School of Plant Sciences, The University of Arizona, Tucson, Arizona, United States of America
| | - Ruifeng He
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, United States of America
| | - William Nelson
- BIO5, The University of Arizona, Tucson, Arizona, United States of America
| | - Guohua Yin
- School of Plant Sciences, The University of Arizona, Tucson, Arizona, United States of America
| | - Joseph M. Cicero
- School of Plant Sciences, The University of Arizona, Tucson, Arizona, United States of America
| | - Mark Willer
- BIO5, The University of Arizona, Tucson, Arizona, United States of America
| | - Ryan Kim
- National Center for Genome Resources, Santa Fe, New Mexico, United States of America
| | - Robin Kramer
- National Center for Genome Resources, Santa Fe, New Mexico, United States of America
| | - Greg A. May
- National Center for Genome Resources, Santa Fe, New Mexico, United States of America
| | - John A. Crow
- National Center for Genome Resources, Santa Fe, New Mexico, United States of America
| | - Carol A. Soderlund
- BIO5, The University of Arizona, Tucson, Arizona, United States of America
| | - David R. Gang
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, United States of America
| | - Judith K. Brown
- School of Plant Sciences, The University of Arizona, Tucson, Arizona, United States of America
| |
Collapse
|
8
|
Touchon M, Hoede C, Tenaillon O, Barbe V, Baeriswyl S, Bidet P, Bingen E, Bonacorsi S, Bouchier C, Bouvet O, Calteau A, Chiapello H, Clermont O, Cruveiller S, Danchin A, Diard M, Dossat C, Karoui ME, Frapy E, Garry L, Ghigo JM, Gilles AM, Johnson J, Le Bouguénec C, Lescat M, Mangenot S, Martinez-Jéhanne V, Matic I, Nassif X, Oztas S, Petit MA, Pichon C, Rouy Z, Ruf CS, Schneider D, Tourret J, Vacherie B, Vallenet D, Médigue C, Rocha EPC, Denamur E. Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. PLoS Genet 2009; 5:e1000344. [PMID: 19165319 PMCID: PMC2617782 DOI: 10.1371/journal.pgen.1000344] [Citation(s) in RCA: 775] [Impact Index Per Article: 51.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2008] [Accepted: 12/16/2008] [Indexed: 01/01/2023] Open
Abstract
The Escherichia coli species represents one of the best-studied model organisms, but also encompasses a variety of commensal and pathogenic strains that diversify by high rates of genetic change. We uniformly (re-) annotated the genomes of 20 commensal and pathogenic E. coli strains and one strain of E. fergusonii (the closest E. coli related species), including seven that we sequenced to completion. Within the ∼18,000 families of orthologous genes, we found ∼2,000 common to all strains. Although recombination rates are much higher than mutation rates, we show, both theoretically and using phylogenetic inference, that this does not obscure the phylogenetic signal, which places the B2 phylogenetic group and one group D strain at the basal position. Based on this phylogeny, we inferred past evolutionary events of gain and loss of genes, identifying functional classes under opposite selection pressures. We found an important adaptive role for metabolism diversification within group B2 and Shigella strains, but identified few or no extraintestinal virulence-specific genes, which could render difficult the development of a vaccine against extraintestinal infections. Genome flux in E. coli is confined to a small number of conserved positions in the chromosome, which most often are not associated with integrases or tRNA genes. Core genes flanking some of these regions show higher rates of recombination, suggesting that a gene, once acquired by a strain, spreads within the species by homologous recombination at the flanking genes. Finally, the genome's long-scale structure of recombination indicates lower recombination rates, but not higher mutation rates, at the terminus of replication. The ensuing effect of background selection and biased gene conversion may thus explain why this region is A+T-rich and shows high sequence divergence but low sequence polymorphism. Overall, despite a very high gene flow, genes co-exist in an organised genome. Although abundant knowledge has been accumulated regarding the E. coli laboratory strain K-12, little is known about the evolutionary trajectories that have driven the high diversity observed among natural isolates of the species, which encompass both commensal and highly virulent intestinal and extraintestinal pathogenic strains. We have annotated or re-annotated the genomes of 20 commensal and pathogenic E. coli strains and one strain of E. fergusonii (the closest E. coli related species), including seven that we sequenced to completion. Although recombination rates are much higher than mutation rates, we were able to reconstruct a robust phylogeny based on the ∼2,000 genes common to all strains. Based on this phylogeny, we established the evolutionary scenario of gains and losses of thousands of specific genes, identifying functional classes under opposite selection pressures. This genome flux is confined to very few positions in the chromosome, which are the same for every genome. Notably, we identified few or no extraintestinal virulence-specific genes. We also defined a long-scale structure of recombination in the genome with lower recombination rates at the terminus of replication. These findings demonstrate that, despite a very high gene flow, genes can co-exist in an organised genome.
Collapse
Affiliation(s)
- Marie Touchon
- Atelier de BioInformatique, Université Pierre et Marie Curie - Paris 6 (UPMC), Paris, France
- Microbial Evolutionary Genomics, Institut Pasteur, CNRS URA2171, Paris, France
| | - Claire Hoede
- Faculté de Médecine, Université Paris 7 Denis Diderot, INSERM U722, Site Xavier Bichat, Paris, France
| | - Olivier Tenaillon
- Faculté de Médecine, Université Paris 7 Denis Diderot, INSERM U722, Site Xavier Bichat, Paris, France
| | | | - Simon Baeriswyl
- Faculté de Médecine, Université Paris 5 René Descartes, INSERM U571, Paris, France
| | - Philippe Bidet
- Université Paris 7 Denis Diderot, Hôpital Robert Debré (APHP), EA 3105, Paris, France
| | - Edouard Bingen
- Université Paris 7 Denis Diderot, Hôpital Robert Debré (APHP), EA 3105, Paris, France
| | - Stéphane Bonacorsi
- Université Paris 7 Denis Diderot, Hôpital Robert Debré (APHP), EA 3105, Paris, France
| | | | - Odile Bouvet
- Faculté de Médecine, Université Paris 7 Denis Diderot, INSERM U722, Site Xavier Bichat, Paris, France
| | - Alexandra Calteau
- Laboratoire de Génomique Comparative, CNRS UMR8030, Institut de Génomique, CEA, Génoscope, Evry, France
| | - Hélène Chiapello
- UR1077 Mathématique, Informatique, et Génome, INRA, Jouy en Josas, France
| | - Olivier Clermont
- Faculté de Médecine, Université Paris 7 Denis Diderot, INSERM U722, Site Xavier Bichat, Paris, France
| | - Stéphane Cruveiller
- Laboratoire de Génomique Comparative, CNRS UMR8030, Institut de Génomique, CEA, Génoscope, Evry, France
| | - Antoine Danchin
- Unité de Génétique des Génomes Bactériens, Institut Pasteur, CNRS URA2171, Paris, France
| | - Médéric Diard
- Faculté de Médecine, Université Paris 5 René Descartes, INSERM U571, Paris, France
| | | | - Meriem El Karoui
- UR888 Unité des Bactéries Lactiques et Pathogènes Opportunistes, INRA, Jouy en Josas, France
| | - Eric Frapy
- Faculté de Médecine, Université Paris 5 René Descartes, INSERM U570, Paris, France
| | - Louis Garry
- Faculté de Médecine, Université Paris 7 Denis Diderot, INSERM U722, Site Xavier Bichat, Paris, France
| | - Jean Marc Ghigo
- Unité de Génétique des Biofilms, Institut Pasteur, CNRS URA2172, Paris, France
| | - Anne Marie Gilles
- Unité de Génétique des Génomes Bactériens, Institut Pasteur, CNRS URA2171, Paris, France
| | - James Johnson
- Veterans Affairs Medical Center, Minneapolis, Minnesota, United States of America
- Department of Medicine, University of Minnesota, Minneapolis, Minnesota, United States of America
| | | | - Mathilde Lescat
- Faculté de Médecine, Université Paris 7 Denis Diderot, INSERM U722, Site Xavier Bichat, Paris, France
| | | | | | - Ivan Matic
- Faculté de Médecine, Université Paris 5 René Descartes, INSERM U571, Paris, France
| | - Xavier Nassif
- Faculté de Médecine, Université Paris 5 René Descartes, INSERM U570, Paris, France
| | - Sophie Oztas
- Génoscope, Institut de Génomique, CEA, Evry, France
| | - Marie Agnès Petit
- UR888 Unité des Bactéries Lactiques et Pathogènes Opportunistes, INRA, Jouy en Josas, France
| | - Christophe Pichon
- Pathogénie Bactérienne des Muqueuses, Institut Pasteur, Paris, France
| | - Zoé Rouy
- Laboratoire de Génomique Comparative, CNRS UMR8030, Institut de Génomique, CEA, Génoscope, Evry, France
| | - Claude Saint Ruf
- Faculté de Médecine, Université Paris 5 René Descartes, INSERM U571, Paris, France
| | | | - Jérôme Tourret
- Faculté de Médecine, Université Paris 7 Denis Diderot, INSERM U722, Site Xavier Bichat, Paris, France
| | | | - David Vallenet
- Laboratoire de Génomique Comparative, CNRS UMR8030, Institut de Génomique, CEA, Génoscope, Evry, France
| | - Claudine Médigue
- Laboratoire de Génomique Comparative, CNRS UMR8030, Institut de Génomique, CEA, Génoscope, Evry, France
- * E-mail: (CM); (EPCR); (ED)
| | - Eduardo P. C. Rocha
- Atelier de BioInformatique, Université Pierre et Marie Curie - Paris 6 (UPMC), Paris, France
- Microbial Evolutionary Genomics, Institut Pasteur, CNRS URA2171, Paris, France
- * E-mail: (CM); (EPCR); (ED)
| | - Erick Denamur
- Faculté de Médecine, Université Paris 7 Denis Diderot, INSERM U722, Site Xavier Bichat, Paris, France
- * E-mail: (CM); (EPCR); (ED)
| |
Collapse
|