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Tisza MJ, Smith DDN, Clark AE, Youn JH, Khil PP, Dekker JP. Roving methyltransferases generate a mosaic epigenetic landscape and influence evolution in Bacteroides fragilis group. Nat Commun 2023; 14:4082. [PMID: 37429841 DOI: 10.1038/s41467-023-39892-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 06/29/2023] [Indexed: 07/12/2023] Open
Abstract
Three types of DNA methyl modifications have been detected in bacterial genomes, and mechanistic studies have demonstrated roles for DNA methylation in physiological functions ranging from phage defense to transcriptional control of virulence and host-pathogen interactions. Despite the ubiquity of methyltransferases and the immense variety of possible methylation patterns, epigenomic diversity remains unexplored for most bacterial species. Members of the Bacteroides fragilis group (BFG) reside in the human gastrointestinal tract as key players in symbiotic communities but also can establish anaerobic infections that are increasingly multi-drug resistant. In this work, we utilize long-read sequencing technologies to perform pangenomic (n = 383) and panepigenomic (n = 268) analysis of clinical BFG isolates cultured from infections seen at the NIH Clinical Center over four decades. Our analysis reveals that single BFG species harbor hundreds of DNA methylation motifs, with most individual motif combinations occurring uniquely in single isolates, implying immense unsampled methylation diversity within BFG epigenomes. Mining of BFG genomes identified more than 6000 methyltransferase genes, approximately 1000 of which were associated with intact prophages. Network analysis revealed substantial gene flow among disparate phage genomes, implying a role for genetic exchange between BFG phages as one of the ultimate sources driving BFG epigenome diversity.
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Affiliation(s)
- Michael J Tisza
- Bacterial Pathogenesis and Antimicrobial Resistance Unit, LCIM, NIAID, NIH, Bethesda, MD, USA
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiol, Baylor College of Medicine, Houston, TX, USA
| | - Derek D N Smith
- Bacterial Pathogenesis and Antimicrobial Resistance Unit, LCIM, NIAID, NIH, Bethesda, MD, USA
- Environment and Climate Change Canada, Ecotoxicology and Wildlife Health Division, Wildlife Toxicology Research Section, Ottawa, ON, Canada
| | - Andrew E Clark
- National Institutes of Health Clinical Center, NIH, Bethesda, MD, USA
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jung-Ho Youn
- National Institutes of Health Clinical Center, NIH, Bethesda, MD, USA
| | - Pavel P Khil
- Bacterial Pathogenesis and Antimicrobial Resistance Unit, LCIM, NIAID, NIH, Bethesda, MD, USA
- National Institutes of Health Clinical Center, NIH, Bethesda, MD, USA
| | - John P Dekker
- Bacterial Pathogenesis and Antimicrobial Resistance Unit, LCIM, NIAID, NIH, Bethesda, MD, USA.
- National Institutes of Health Clinical Center, NIH, Bethesda, MD, USA.
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2
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Cissé OH, Curran S, Folco HD, Liu Y, Bishop L, Wang H, Fischer ER, Davis AS, Babb-Biernacki S, Doyle VP, Richards JK, Hassan SA, Dekker JP, Khil PP, Brenchley JM, Grewal S, Cushion M, Ma L, Kovacs JA. The Host Adapted Fungal Pathogens of Pneumocystis Genus Utilize Genic Regional Centromeres. bioRxiv 2023:2023.05.12.540427. [PMID: 37425787 PMCID: PMC10327204 DOI: 10.1101/2023.05.12.540427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Centromeres are genomic regions that coordinate accurate chromosomal segregation during mitosis and meiosis. Yet, despite their essential function, centromeres evolve rapidly across eukaryotes. Centromeres are often the sites of chromosomal breaks which contribute to genome shuffling and promote speciation by inhibiting gene flow. How centromeres form in strongly host-adapted fungal pathogens has yet to be investigated. Here, we characterized the centromere structures in closely related species of mammalian-specific pathogens of the fungal phylum of Ascomycota. Methods allowing reliable continuous culture of Pneumocystis species do not currently exist, precluding genetic manipulation. CENP-A, a variant of histone H3, is the epigenetic marker that defines centromeres in most eukaryotes. Using heterologous complementation, we show that the Pneumocystis CENP-A ortholog is functionally equivalent to CENP-ACnp1 of Schizosaccharomyces pombe. Using organisms from a short-term in vitro culture or infected animal models and ChIP-seq, we identified centromeres in three Pneumocystis species that diverged ~100 million years ago. Each species has a unique short regional centromere (< 10kb) flanked by heterochromatin in 16-17 monocentric chromosomes. They span active genes and lack conserved DNA sequence motifs and repeats. CENP-C, a scaffold protein that links the inner centromere to the kinetochore appears dispensable in one species, suggesting a kinetochore rewiring. Despite the loss of DNA methyltransferases, 5-methylcytosine DNA methylation occurs in these species, though not related to centromere function. These features suggest an epigenetic specification of centromere function.
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Affiliation(s)
- Ousmane H Cissé
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Shelly Curran
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - H Diego Folco
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Yueqin Liu
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Lisa Bishop
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Honghui Wang
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Elizabeth R Fischer
- Microscopy Unit, Research Technologies Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - A Sally Davis
- Diagnostic Medicine/Pathobiology, Kansas State University College of Veterinary Medicine, Manhattan, USA
| | - Spenser Babb-Biernacki
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Vinson P Doyle
- Department of Plant Pathology and Crop Physiology, Lousiana State University AgCenter, Baton Rouge, Louisiana, USA
| | - Jonathan K Richards
- Department of Plant Pathology and Crop Physiology, Lousiana State University AgCenter, Baton Rouge, Louisiana, USA
| | - Sergio A Hassan
- Bioinformatics and Computational Biosciences Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - John P Dekker
- Bacterial Pathogenesis and Antimicrobial Resistance Unit, National Institute of Allergy, and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Pavel P Khil
- Bacterial Pathogenesis and Antimicrobial Resistance Unit, National Institute of Allergy, and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Jason M Brenchley
- Laboratory of Viral Diseases, National Institute of Allergy, and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Shiv Grewal
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Melanie Cushion
- Department of Internal Medicine, College of Medicine, University of Cincinnati, Cincinnati, Ohio, USA
| | - Liang Ma
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Joseph A Kovacs
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
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Dulanto Chiang A, Patil PP, Beka L, Youn JH, Launay A, Bonomo RA, Khil PP, Dekker JP. Hypermutator strains of Pseudomonas aeruginosa reveal novel pathways of resistance to combinations of cephalosporin antibiotics and beta-lactamase inhibitors. PLoS Biol 2022; 20:e3001878. [PMID: 36399436 PMCID: PMC9718400 DOI: 10.1371/journal.pbio.3001878] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 12/02/2022] [Accepted: 10/13/2022] [Indexed: 11/19/2022] Open
Abstract
Hypermutation due to DNA mismatch repair (MMR) deficiencies can accelerate the development of antibiotic resistance in Pseudomonas aeruginosa. Whether hypermutators generate resistance through predominantly similar molecular mechanisms to wild-type (WT) strains is not fully understood. Here, we show that MMR-deficient P. aeruginosa can evolve resistance to important broad-spectrum cephalosporin/beta-lactamase inhibitor combination antibiotics through novel mechanisms not commonly observed in WT lineages. Using whole-genome sequencing (WGS) and transcriptional profiling of isolates that underwent in vitro adaptation to ceftazidime/avibactam (CZA), we characterized the detailed sequence of mutational and transcriptional changes underlying the development of resistance. Surprisingly, MMR-deficient lineages rapidly developed high-level resistance (>256 μg/mL) largely without corresponding fixed mutations or transcriptional changes in well-established resistance genes. Further investigation revealed that these isolates had paradoxically generated an early inactivating mutation in the mexB gene of the MexAB-OprM efflux pump, a primary mediator of CZA resistance in P. aeruginosa, potentially driving an evolutionary search for alternative resistance mechanisms. In addition to alterations in a number of genes not known to be associated with resistance, 2 mutations were observed in the operon encoding the RND efflux pump MexVW. These mutations resulted in a 4- to 6-fold increase in resistance to ceftazidime, CZA, cefepime, and ceftolozane-tazobactam when engineered into a WT strain, demonstrating a potentially important and previously unappreciated mechanism of resistance to these antibiotics in P. aeruginosa. Our results suggest that MMR-deficient isolates may rapidly evolve novel resistance mechanisms, sometimes with complex dynamics that reflect gene inactivation that occurs with hypermutation. The apparent ease with which hypermutators may switch to alternative resistance mechanisms for which antibiotics have not been developed may carry important clinical implications.
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Affiliation(s)
- Augusto Dulanto Chiang
- Bacterial Pathogenesis and Antimicrobial Resistance Unit, LCIM, NIAID, NIH, Bethesda, Maryland, United States of America
| | - Prashant P. Patil
- Bacterial Pathogenesis and Antimicrobial Resistance Unit, LCIM, NIAID, NIH, Bethesda, Maryland, United States of America
| | - Lidia Beka
- Bacterial Pathogenesis and Antimicrobial Resistance Unit, LCIM, NIAID, NIH, Bethesda, Maryland, United States of America
| | - Jung-Ho Youn
- Dept. Laboratory Medicine, NIH Clinical Center, NIH, Bethesda, Maryland, United States of America
| | - Adrien Launay
- Bacterial Pathogenesis and Antimicrobial Resistance Unit, LCIM, NIAID, NIH, Bethesda, Maryland, United States of America
| | - Robert A. Bonomo
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, United States of America
- Departments of Pharmacology, Molecular Biology and Microbiology, Biochemistry, and Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES) Cleveland, Ohio, United States of America
| | - Pavel P. Khil
- Bacterial Pathogenesis and Antimicrobial Resistance Unit, LCIM, NIAID, NIH, Bethesda, Maryland, United States of America
- Dept. Laboratory Medicine, NIH Clinical Center, NIH, Bethesda, Maryland, United States of America
| | - John P. Dekker
- Bacterial Pathogenesis and Antimicrobial Resistance Unit, LCIM, NIAID, NIH, Bethesda, Maryland, United States of America
- Dept. Laboratory Medicine, NIH Clinical Center, NIH, Bethesda, Maryland, United States of America
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4
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Totten AH, Uzel G, Khil PP, Youn JH, Treat J, Soutar CD, Holland SM, Dekker JP, Zerbe CS. Disseminated Mycoplasma orale infection in patients with Phosphoinositide-3-Kinase Regulatory Subunit 1 Mutations. Open Forum Infect Dis 2022; 9:ofac472. [DOI: 10.1093/ofid/ofac472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 09/09/2022] [Indexed: 11/14/2022] Open
Abstract
Abstract
Mycoplasma orale is a rare cause of invasive infection in immunodeficient hosts. Phosphatidylinositol 3-Kinase, Regulatory Subunit 1 (PI3KR1) mutations predispose patients to sinopulmonary infections, alongside bronchiectasis autoimmunity and lymphoproliferation. We report the two cases of PI3KR1 deficiency with invasive M. orale and effective treatment options.
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Affiliation(s)
- Arthur H Totten
- Clinical Center, National Institutes of Health , Bethesda, MD , USA
| | - Gulbu Uzel
- National Institute of Allergy and Infectious Diseases, National Institutes of Health , Bethesda, MD , USA
| | - Pavel P Khil
- Clinical Center, National Institutes of Health , Bethesda, MD , USA
| | - Jung Ho Youn
- Clinical Center, National Institutes of Health , Bethesda, MD , USA
| | - Jennifer Treat
- National Institute of Allergy and Infectious Diseases, National Institutes of Health , Bethesda, MD , USA
| | - Craig D Soutar
- Clinical Center, National Institutes of Health , Bethesda, MD , USA
| | - Steven M Holland
- National Institute of Allergy and Infectious Diseases, National Institutes of Health , Bethesda, MD , USA
| | - John P Dekker
- National Institute of Allergy and Infectious Diseases, National Institutes of Health , Bethesda, MD , USA
| | - Christa S Zerbe
- National Institute of Allergy and Infectious Diseases, National Institutes of Health , Bethesda, MD , USA
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5
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Cissé OH, Ma L, Dekker JP, Khil PP, Youn JH, Brenchley JM, Blair R, Pahar B, Chabé M, Van Rompay KKA, Keesler R, Sukura A, Hirsch V, Kutty G, Liu Y, Peng L, Chen J, Song J, Weissenbacher-Lang C, Xu J, Upham NS, Stajich JE, Cuomo CA, Cushion MT, Kovacs JA. Genomic insights into the host specific adaptation of the Pneumocystis genus. Commun Biol 2021; 4:305. [PMID: 33686174 PMCID: PMC7940399 DOI: 10.1038/s42003-021-01799-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 02/04/2021] [Indexed: 11/21/2022] Open
Abstract
Pneumocystis jirovecii, the fungal agent of human Pneumocystis pneumonia, is closely related to macaque Pneumocystis. Little is known about other Pneumocystis species in distantly related mammals, none of which are capable of establishing infection in humans. The molecular basis of host specificity in Pneumocystis remains unknown as experiments are limited due to an inability to culture any species in vitro. To explore Pneumocystis evolutionary adaptations, we have sequenced the genomes of species infecting macaques, rabbits, dogs and rats and compared them to available genomes of species infecting humans, mice and rats. Complete whole genome sequence data enables analysis and robust phylogeny, identification of important genetic features of the host adaptation, and estimation of speciation timing relative to the rise of their mammalian hosts. Our data reveals insights into the evolution of P. jirovecii, the sole member of the genus able to infect humans. Cissé, Ma et al. utilize genomic data from Pneumocystis species infecting macaques, rabbit, dogs and rats to investigate the molecular basis of host specificity in Pneumocystis. Their analyses provide insight to the specific adaptations enabling the infection of humans by P. jirovecii.
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Affiliation(s)
- Ousmane H Cissé
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health (NIH), Bethesda, MD, USA.
| | - Liang Ma
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health (NIH), Bethesda, MD, USA.
| | - John P Dekker
- Bacterial Pathogenesis and Antimicrobial Resistance Unit, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD, USA.,Department of Laboratory Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Pavel P Khil
- Bacterial Pathogenesis and Antimicrobial Resistance Unit, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD, USA.,Department of Laboratory Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Jung-Ho Youn
- Department of Laboratory Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | | | - Robert Blair
- Tulane National Primate Research Center, Tulane University, New Orleans, LA, USA
| | - Bapi Pahar
- Tulane National Primate Research Center, Tulane University, New Orleans, LA, USA
| | - Magali Chabé
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 9017-CIIL-Centre d'Infection et d'Immunité de Lille, Lille, France
| | - Koen K A Van Rompay
- California National Primate Research Center, University of California, Davis, CA, USA
| | - Rebekah Keesler
- California National Primate Research Center, University of California, Davis, CA, USA
| | - Antti Sukura
- Department of Veterinary Pathology, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Vanessa Hirsch
- Laboratory of Molecular Microbiology, NIAID, NIH, Bethesda, MD, USA
| | - Geetha Kutty
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Yueqin Liu
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Li Peng
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jie Chen
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jun Song
- Center for Advanced Models for Translational Sciences and Therapeutics, University of Michigan Medical Center, University of Michigan Medical School, Ann Arbor, MI, USA
| | | | - Jie Xu
- Center for Advanced Models for Translational Sciences and Therapeutics, University of Michigan Medical Center, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Nathan S Upham
- Arizona State University, School of Life Sciences, Tempe, ARI, USA
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology and Institute for Integrative Genome Biology, University of California, Riverside, Riverside-California, Riverside, CA, USA
| | - Christina A Cuomo
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Melanie T Cushion
- Department of Internal Medicine, College of Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Joseph A Kovacs
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health (NIH), Bethesda, MD, USA.
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Das S, Lau AF, Youn JH, Khil PP, Zelazny AM, Frank KM. Pooled Testing for Surveillance of SARS-CoV-2 in Asymptomatic Individuals. J Clin Virol 2020; 132:104619. [PMID: 32920431 PMCID: PMC7470739 DOI: 10.1016/j.jcv.2020.104619] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 09/02/2020] [Indexed: 12/23/2022]
Affiliation(s)
- Sanchita Das
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA.
| | - Anna F Lau
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Jung-Ho Youn
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Pavel P Khil
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Adrian M Zelazny
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Karen M Frank
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
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Srivastava K, Khil PP, Sippert E, Volkova E, Dekker JP, Rios M, Flegel WA. ACKR1 Alleles at 5.6 kb in a Well-Characterized Renewable US Food and Drug Administration (FDA) Reference Panel for Standardization of Blood Group Genotyping. J Mol Diagn 2020; 22:1272-1279. [PMID: 32688055 DOI: 10.1016/j.jmoldx.2020.06.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 06/17/2020] [Accepted: 06/26/2020] [Indexed: 12/18/2022] Open
Abstract
The glycoprotein encoded by the ACKR1 gene expresses the Duffy blood group antigens and is a receptor for malaria parasites. We recently described 18 long-range ACKR1 alleles in an autochthonous population of a malaria endemic region. Extending this work, we sequenced the gene in a 53-sample repository established by the US Food and Drug Administration (FDA) as reference reagents for blood group genotyping. The FDA samples have been characterized for 19 genes; however, long-range haplotype information for these genes, including ACKR1, was lacking. We used a hybrid approach, novel for this type of gene, to characterize ACKR1 by combining two next-generation sequencing technologies, the short-read massively parallel sequencing and the long-read nanopore sequencing. The expedient integration of data from both next-generation sequencing systems were necessary and sufficient to allow determination of all 25 long-range ACKR1 alleles found in the 53 samples accurately. All 25 alleles identified in our current FDA cohort were novel and, unexpectedly, none had been observed among the 18 alleles in our previous study. The alleles will be useful for validation, calibration, and proficiency testing of red cell genotyping. The lack of any overlap between the ACKR1 alleles in the two studies documents differences in mutation rate and recombination frequency among populations. The exact haplotype and their interethnic or interpopulation dissimilarities can influence disease susceptibility and therapy.
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Affiliation(s)
- Kshitij Srivastava
- Department of Transfusion Medicine, NIH Clinical Center, NIH, Bethesda, Maryland
| | - Pavel P Khil
- Laboratory Medicine, NIH Clinical Center, NIH, Bethesda, Maryland
| | - Emilia Sippert
- Office of Blood Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland
| | - Evgeniya Volkova
- Office of Blood Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland
| | - John P Dekker
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland
| | - Maria Rios
- Office of Blood Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland
| | - Willy A Flegel
- Department of Transfusion Medicine, NIH Clinical Center, NIH, Bethesda, Maryland.
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Dulanto Chiang A, Khil PP, Manion M, Sereti I, Zelazny A, Dekker JP. 232. Genomic Evidence for Dissemination of Mycobacterium marinum in an HIV Patient with Multifocal Cutaneous Disease. Open Forum Infect Dis 2019. [PMCID: PMC6810534 DOI: 10.1093/ofid/ofz360.307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Background
Hematogenous dissemination has been proposed to explain multifocal cutaneous disease caused by Mycobacterium marinum in certain patients. Treatment duration for disseminated disease is often months longer than for skin infection alone. However, distinguishing multiple independent inoculation events from dissemination has relied primarily on clinical judgement. Additionally, whether temperature-sensitive non-tuberculous mycobacteria such as M. marinum are indeed capable of invading the vascular space at core body temperature is debated. Here we used whole-genome sequencing (WGS) of serial isolates from a single patient with multifocal cutaneous M. marinum infection to distinguish dissemination of a clonal strain from multiple inoculation events.
Methods
A 35-year-old male with HIV (CD4 of 66 cells/µL) presented with a two-month history of a non-healing M. marinum wound on his left elbow (isolate MM0). This was followed a month later after initiation of antiretroviral therapy by a second M. marinum lesion on the right heel (MM1) without history of repeat inoculation, and increased swelling and erythema of the wound on the left arm (MM2) consistent with paradoxical immune reconstitution inflammatory syndrome. A PacBio genome was generated for MM0 and short read Illumina genomes were generated for MM1 and MM2.
Results
All isolates were found to be closely related, with MM1 and MM2 distinguished from MM0 by one and five single-nucleotide variants (SNVs), respectively. Given the substantial genetic heterogeneity among environmental M. marinum strains, such close relatedness of these isolates suggests common origin, and provides strong evidence for dissemination of a clonal strain in this patient. The SNVs included a frameshift mutation in the purT gene, which encodes a formate-dependent phosphoribosylglycinamide formyltransferase involved in de novo purine synthesis, and missense mutations in atsA and the DNA methylase hsdM. All isolates grew at 35°C, compared with the optimal growth temperature of 30°C typically observed for M. marinum, suggesting thermotolerance permissive for dissemination.
Conclusion
These results demonstrate the potential role of WGS for providing supportive evidence of disseminated infection with M. marinum.
Disclosures
All authors: No reported disclosures.
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Affiliation(s)
| | | | - Maura Manion
- Division of Clinical Research, NIAID, Bethesda, Maryland
| | - Irini Sereti
- Laboratory of Immunoregulation, NIAID, Bethesda, Maryland
| | | | - John P Dekker
- National Institute of Allergy and Infectious Diseases, Bethesda, Maryland
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9
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Khil PP, Dulanto Chiang A, Ho J, Youn JH, Lemon JK, Gea-Banacloche J, Frank KM, Parta M, Bonomo RA, Dekker JP. Dynamic Emergence of Mismatch Repair Deficiency Facilitates Rapid Evolution of Ceftazidime-Avibactam Resistance in Pseudomonas aeruginosa Acute Infection. mBio 2019; 10:e01822-19. [PMID: 31530672 PMCID: PMC6751058 DOI: 10.1128/mbio.01822-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 08/22/2019] [Indexed: 01/09/2023] Open
Abstract
Strains of Pseudomonas aeruginosa with deficiencies in DNA mismatch repair have been studied in the context of chronic infection, where elevated mutational rates ("hypermutation") may facilitate the acquisition of antimicrobial resistance. Whether P. aeruginosa hypermutation can also play an adaptive role in the more dynamic context of acute infection remains unclear. In this work, we demonstrate that evolved mismatch repair deficiencies may be exploited by P. aeruginosa to facilitate rapid acquisition of antimicrobial resistance in acute infection, and we directly document rapid clonal succession by such a hypermutating lineage in a patient. Whole-genome sequencing (WGS) was performed on nine serially cultured blood and respiratory isolates from a patient in whom ceftazidime-avibactam (CZA) resistance emerged in vivo over the course of days. The CZA-resistant clone was differentiated by 14 mutations, including a gain-of-function G183D substitution in the PDC-5 chromosomal AmpC cephalosporinase conferring CZA resistance. This lineage also contained a substitution (R656H) at a conserved position in the ATPase domain of the MutS mismatch repair (MMR) protein, and elevated mutational rates were confirmed by mutational accumulation experiments with WGS of evolved lineages in conjunction with rifampin resistance assays. To test whether MMR-deficient hypermutation could facilitate rapid acquisition of CZA resistance, in vitro adaptive evolution experiments were performed with a mutS-deficient strain. These experiments demonstrated rapid hypermutation-facilitated acquisition of CZA resistance compared with the isogenic wild-type strain. Our results suggest a possibly underappreciated role for evolved MMR deficiency in facilitating rapid adaptive evolution of P. aeruginosa in the context of acute infection.IMPORTANCE Antimicrobial resistance in bacteria represents one of the most consequential problems in modern medicine, and its emergence and spread threaten to compromise central advances in the treatment of infectious diseases. Ceftazidime-avibactam (CZA) belongs to a new class of broad-spectrum beta-lactam/beta-lactamase inhibitor combinations designed to treat infections caused by multidrug-resistant bacteria. Understanding the emergence of resistance to this important new drug class is of critical importance. In this work, we demonstrate that evolved mismatch repair deficiency in P. aeruginosa, an important pathogen responsible for significant morbidity and mortality among hospitalized patients, may facilitate rapid acquisition of resistance to CZA in the context of acute infection. These findings are relevant for both diagnosis and treatment of antimicrobial resistance emerging in acute infection in the hypermutator background and additionally have implications for the emergence of more virulent phenotypes.
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Affiliation(s)
- Pavel P Khil
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, Fredrick, Maryland, USA
| | - Augusto Dulanto Chiang
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, Fredrick, Maryland, USA
| | - Jonathan Ho
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Jung-Ho Youn
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Jamie K Lemon
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Juan Gea-Banacloche
- Experimental Transplantation and Immunology Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Karen M Frank
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Mark Parta
- Clinical Research Directorate, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Fredrick, Maryland, USA
| | - Robert A Bonomo
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, Ohio, USA
- Medical Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
- GRECC, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Case Center for Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - John P Dekker
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, Fredrick, Maryland, USA
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10
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Lerner AM, Bennett JE, Pittaluga S, Khil PP, Youn JH, Fahle GA, Frank KM, Dekker JP, Jerussi TD, Sun C, Wiestner A, Gea-Banacloche J. Protracted course of disseminated adenovirus disease with necrotizing granulomas in the liver. Diagn Microbiol Infect Dis 2019; 94:180-182. [PMID: 30679057 DOI: 10.1016/j.diagmicrobio.2018.12.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 11/23/2018] [Accepted: 12/26/2018] [Indexed: 02/06/2023]
Abstract
A 52- year-old male with chronic lymphocytic leukemia was hospitalized with disseminated adenovirus disease. More than a month following recovery, hepatic necrotizing granulomas secondary to adenovirus were found. This case illustrates the protracted course that adenovirus disease may take and emphasizes an unusual presentation with hepatic necrotizing granulomas.
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Affiliation(s)
- Andrea M Lerner
- Division of Clinical Research, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), 9000 Center Drive, Bethesda, MD 20892, USA.
| | - John E Bennett
- Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, 9000 Center Drive, Bethesda, MD 20892, USA
| | - Stefania Pittaluga
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute (NCI), NIH, 9000 Center Drive, Bethesda, MD 20892, USA
| | - Pavel P Khil
- Microbiology Service, Department of Laboratory Medicine, NIH, 9000 Center Drive, Bethesda, MD 20892, USA
| | - J H Youn
- Microbiology Service, Department of Laboratory Medicine, NIH, 9000 Center Drive, Bethesda, MD 20892, USA
| | - Gary A Fahle
- Microbiology Service, Department of Laboratory Medicine, NIH, 9000 Center Drive, Bethesda, MD 20892, USA
| | - Karen M Frank
- Microbiology Service, Department of Laboratory Medicine, NIH, 9000 Center Drive, Bethesda, MD 20892, USA
| | - John P Dekker
- Microbiology Service, Department of Laboratory Medicine, NIH, 9000 Center Drive, Bethesda, MD 20892, USA
| | - Theresa D Jerussi
- Office of Patient Safety and Clinical Quality, Clinical Center, NIH, 9000 Center Drive, Bethesda, MD, 20892, USA
| | - Clare Sun
- Hematology Branch, National Heart, Lung, and Blood Institute (NHLBI), NIH, 9000 Center Drive, Bethesda, MD 20892, USA
| | - Adrian Wiestner
- Hematology Branch, National Heart, Lung, and Blood Institute (NHLBI), NIH, 9000 Center Drive, Bethesda, MD 20892, USA
| | - Juan Gea-Banacloche
- Division of Infectious Diseases, Mayo Clinic Hospital, 5777 East Mayo Boulevard, Phoenix, AZ 85054, USA
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11
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Esteve-Sole A, Sánchez-Dávila SP, Deyà-Martínez A, Freeman AF, Zelazny AM, Dekker JP, Khil PP, Holland SM, Noguera-Julian A, Bustamante J, Casanova JL, Juan M, Cordova W, Alsina L. Severe BCG-osis Misdiagnosed as Multidrug-Resistant Tuberculosis in an IL-12Rβ1-Deficient Peruvian Girl. J Clin Immunol 2018; 38:712-716. [PMID: 30039354 DOI: 10.1007/s10875-018-0535-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 07/09/2018] [Indexed: 12/16/2022]
Abstract
PURPOSE Mendelian suceptibility to mycobacterial disease (MSMD) is a rare primary immunodeficiency predisposing to severe disease caused by mycobacteria and other intracellular pathogens. Delay in diagnosis can have an impact on the patient's prognosis. METHODS We evaluated the IFN-γ circuit by studying IFN-γ production after mycobacterial challenge as well as IL-12Rβ1 expression and STAT4 phosphorylation in response to IL-12p70 stimulation in whole blood of a 6-year-old Peruvian girl with disseminated recurrent mycobacterial infection diagnosed as multidrug-resistant tuberculosis. Genetic studies with Sanger sequencing were used to identify the causative mutation. Microbiological studies based on PCR reactions were used to diagnose the specific mycobacterial species. RESULTS We identified a homozygous mutation in the IL12RB1 gene (p. Arg211*) causing abolished expression of IL-12Rβ1 and IL-12 response. MSMD diagnosis led to a microbiological reevaluation of the patient, revealing a BCG vaccine-related infection instead of tuberculosis. Treatment was then adjusted, with good response. CONCLUSIONS We report the first Peruvian patient with IL-12Rβ1 deficiency. Specific mycobacterial species diagnosis within Mycobacterium tuberculosis complex is still challenging in countries with limited access to PCR-based microbiological diagnostic techniques. Awareness of MSMD warning signs and accurate microbiological diagnosis of mycobacterial infections are of the utmost importance for optimal diagnosis and management of affected patients.
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Affiliation(s)
- Ana Esteve-Sole
- Functional Unit of Clinical Immunology and Primary Immunodeficiencies, Hospital Sant Joan de Déu, University of Barcelona, Pediatric Research Institute Sant Joan de Déu, Barcelona, Spain
- Functional Unit of Clinical Immunology, Hospital Sant Joan de Déu-Hospital Clinic, Barcelona, Spain
| | - Suly P Sánchez-Dávila
- National reference center Allergy Asthma Immunology, National Institute of Child Health, Lima, Peru
| | - Angela Deyà-Martínez
- Functional Unit of Clinical Immunology and Primary Immunodeficiencies, Hospital Sant Joan de Déu, University of Barcelona, Pediatric Research Institute Sant Joan de Déu, Barcelona, Spain
- Functional Unit of Clinical Immunology, Hospital Sant Joan de Déu-Hospital Clinic, Barcelona, Spain
| | - Alexandra F Freeman
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Adrian M Zelazny
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - John P Dekker
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Pavel P Khil
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Steven M Holland
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Antoni Noguera-Julian
- Infectious Diseases and Systemic Inflammatory Response in Pediatrics, Infectious Diseases Unit, Pediatrics Department, Pediatric Research Institute Sant Joan de Déu, Barcelona, Spain
- Department of Pediatrics, University of Barcelona, Barcelona, Spain
- CIBER of Epidemiology and Public Health, CIBERESP, Madrid, Spain
- Translational Research Network in Pediatric Infectious Diseases (RITIP), Madrid, Spain
| | - Jacinta Bustamante
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM-U1163, Paris, France
- Imagine Institute, Paris Descartes University, Paris, France
- Center for the Study of Primary Immunodeficiencies, Necker Hospital for Sick Children, AP-HP, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller branch, The Rockefeller University, New York, NY, USA
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM-U1163, Paris, France
- Imagine Institute, Paris Descartes University, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller branch, The Rockefeller University, New York, NY, USA
- Pediatric Hematology-Immunology Unit, Necker Hospital for Sick Children, Paris, France
- Howard Hughes Medical Institute, New York, NY, USA
| | - Manel Juan
- Functional Unit of Clinical Immunology, Hospital Sant Joan de Déu-Hospital Clinic, Barcelona, Spain
- Immunology Department, Biomedical Diagnostics Center, Hospital Clinic-IDIBAPS, Barcelona, Spain
| | - Wilmer Cordova
- National reference center Allergy Asthma Immunology, National Institute of Child Health, Lima, Peru
| | - Laia Alsina
- Functional Unit of Clinical Immunology and Primary Immunodeficiencies, Hospital Sant Joan de Déu, University of Barcelona, Pediatric Research Institute Sant Joan de Déu, Barcelona, Spain.
- Functional Unit of Clinical Immunology, Hospital Sant Joan de Déu-Hospital Clinic, Barcelona, Spain.
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12
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Lemon JK, Khil PP, Frank KM, Dekker JP. Rapid Nanopore Sequencing of Plasmids and Resistance Gene Detection in Clinical Isolates. J Clin Microbiol 2017; 55:3530-3543. [PMID: 29021151 PMCID: PMC5703817 DOI: 10.1128/jcm.01069-17] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 10/03/2017] [Indexed: 11/20/2022] Open
Abstract
Recent advances in nanopore sequencing technology have led to a substantial increase in throughput and sequence quality. Together, these improvements may permit real-time benchtop genomic sequencing and antimicrobial resistance gene detection in clinical isolates. In this study, we evaluated workflows and turnaround times for a benchtop long-read sequencing approach in the clinical microbiology laboratory using the Oxford Nanopore Technologies MinION sequencer. We performed genomic and plasmid sequencing of three clinical isolates with both MinION and Illumina MiSeq, using different library preparation methods (2D and rapid 1D) with the goal of antimicrobial resistance gene detection. We specifically evaluated the advantages of using plasmid DNA for sequencing and the value of supplementing MinION sequences with MiSeq reads for increasing assembly accuracy. Resequencing of three plasmids in a reference Klebsiella pneumoniae isolate demonstrated ∼99% accuracy of draft MinION-only assembly and >99.9% accuracy of assembly polished with MiSeq reads. Plasmid DNA sequencing of previously uncharacterized clinical extended-spectrum β-lactamase (ESBL)-producing Escherichia coli and K. pneumoniae isolates using MinION allowed successful identification of antimicrobial resistance genes in the draft assembly corresponding to all classes of observed plasmid-based phenotypic resistance. Importantly, use of plasmid DNA enabled lower depth sequencing, and assemblies sufficient for full antimicrobial resistance gene annotation were obtained with as few as 2,000 to 5,000 reads, which could be acquired in 20 min of sequencing. With a MinION-only workflow that balances accuracy against turnaround time, full annotation of plasmid resistance gene content could be obtained in under 6 h from a subcultured isolate, less time than traditional phenotypic susceptibility testing.
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Affiliation(s)
- Jamie K Lemon
- Microbiology Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Pavel P Khil
- Microbiology Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Karen M Frank
- Microbiology Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - John P Dekker
- Microbiology Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
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13
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Abstract
BACKGROUND Differentiation of primordial germ cells into mature spermatozoa proceeds through multiple stages, one of the most important of which is meiosis. Meiotic recombination is in turn a key part of meiosis. To achieve the highly specialized and diverse functions necessary for the successful completion of meiosis and the generation of spermatozoa thousands of genes are coordinately regulated through spermatogenesis. A complete and unbiased characterization of the transcriptome dynamics of spermatogenesis is, however, still lacking. RESULTS In order to characterize gene expression during spermatogenesis we sequenced eight mRNA samples from testes of juvenile mice from 6 to 38 days post partum. Using gene expression clustering we defined over 1,000 novel meiotically-expressed genes. We also developed a computational de-convolution approach and used it to estimate cell type-specific gene expression in pre-meiotic, meiotic and post-meiotic cells. In addition, we detected 13,000 novel alternative splicing events around 40% of which preserve an open reading frame, and found experimental support for 159 computational gene predictions. A comparison of RNA polymerase II (Pol II) ChIP-Seq signals with RNA-Seq coverage shows that gene expression correlates well with Pol II signals, both at promoters and along the gene body. However, we observe numerous instances of non-canonical promoter usage, as well as intergenic Pol II peaks that potentially delineate unannotated promoters, enhancers or small RNA clusters. CONCLUSIONS Here we provide a comprehensive analysis of gene expression throughout mouse meiosis and spermatogenesis. Importantly, we find over a thousand of novel meiotic genes and over 5,000 novel potentially coding isoforms. These data should be a valuable resource for future studies of meiosis and spermatogenesis in mammals.
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Affiliation(s)
- Gennady Margolin
- Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health (NIH), Building 5, Room 205A, Bethesda, MD 20892, USA
| | - Pavel P Khil
- Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health (NIH), Building 5, Room 205A, Bethesda, MD 20892, USA
| | - Joongbaek Kim
- Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health (NIH), Building 5, Room 205A, Bethesda, MD 20892, USA
| | - Marina A Bellani
- National Institute of Aging, National Institutes of Health (NIH), Baltimore, MD 21224, USA
| | - R Daniel Camerini-Otero
- Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health (NIH), Building 5, Room 205A, Bethesda, MD 20892, USA
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14
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Abstract
Meiotic DNA double-stranded breaks (DSBs) initiate genetic recombination in discrete areas of the genome called recombination hotspots. DSBs can be directly mapped using chromatin immunoprecipitation followed by sequencing (ChIP-seq). Nevertheless, the genome-wide mapping of recombination hotspots in mammals is still a challenge due to the low frequency of recombination, high heterogeneity of the germ cell population, and the relatively low efficiency of ChIP. To overcome these limitations we have developed a novel method—single-stranded DNA (ssDNA) sequencing (SSDS)—that specifically detects protein-bound single-stranded DNA at DSB ends. SSDS comprises a computational framework for the specific detection of ssDNA-derived reads in a sequencing library and a new library preparation procedure for the enrichment of fragments originating from ssDNA. The use of our technique reduces the nonspecific double-stranded DNA (dsDNA) background >10-fold. Our method can be extended to other systems where the identification of ssDNA or DSBs is desired.
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Affiliation(s)
- Pavel P Khil
- Genetics and Biochemistry Branch, National Institute of Diabetes, Digestive and Kidney Diseases, NIH, Bethesda, MD 20892, USA
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15
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Abstract
Hotspots of meiotic recombination can change rapidly over time. This instability and the reported high level of inter-individual variation in meiotic recombination puts in question the accuracy of the calculated hotspot map, which is based on the summation of past genetic crossovers. To estimate the accuracy of the computed recombination rate map, we have mapped genetic crossovers to a median resolution of 70 Kb in 10 CEPH pedigrees. We then compared the positions of crossovers with the hotspots computed from HapMap data and performed extensive computer simulations to compare the observed distributions of crossovers with the distributions expected from the calculated recombination rate maps. Here we show that a population-averaged hotspot map computed from linkage disequilibrium data predicts well present-day genetic crossovers. We find that computed hotspot maps accurately estimate both the strength and the position of meiotic hotspots. An in-depth examination of not-predicted crossovers shows that they are preferentially located in regions where hotspots are found in other populations. In summary, we find that by combining several computed population-specific maps we can capture the variation in individual hotspots to generate a hotspot map that can predict almost all present-day genetic crossovers. In eukaryotes genetic crossovers are responsible for generating genetic diversity and ensuring the proper segregation of chromosomes. Genetic crossovers are tightly clustered in hotspots. Although the existence of hotspots in humans is clearly proven, mechanisms of their formation and the regulation of meiotic recombination in general remain poorly understood. An additional complication in studies of meiotic recombination is the fact that the direct experimental mapping of human hotspots on a genome-wide scale is not feasible with current methods. The best available indirect methods compute the position of hotspots from patterns of historic associations between genetic markers in population samples. In this study we determined the positions of genetic crossovers in ten pedigrees of European origin and then compared the positions of crossovers with the hotspots computed from HapMap data. Importantly, we find that the population-averaged computed map is in close agreement with the observed distribution of genetic crossovers. We also find that cryptic hotspots that are not easily detected in the computed European map can be more effectively identified if other populations are included in the analysis. Our analysis shows that high-resolution recombination profiles are highly similar between distantly related populations and that by including computed hotspots from several populations we can predict nearly all crossovers.
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Affiliation(s)
- Pavel P. Khil
- Genetics and Biochemistry Branch, The National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - R. Daniel Camerini-Otero
- Genetics and Biochemistry Branch, The National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
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16
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Abstract
Recent advances in genomic sequencing of multiple organisms have fostered significant advances in our understanding of the evolution of the sex chromosomes. The integration of this newly available sequence information with functional data has facilitated a considerable refinement of our conceptual framework of the forces driving this evolution. Here we address multiple functional constraints that were encountered in the evolution of the X chromosome and the impact that this evolutionary history has had on its modern behavior.
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Affiliation(s)
- Pavel P Khil
- Genetics and Biochemistry Branch, National Institutes of Health, Bethesda, MD 20892, USA
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17
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Abstract
In the last 30 years it has become evident that patterns of meiotic recombination can be highly variable among individuals. The evidence comes from both low and high resolution analyses of hotspots of recombination in human and other species. In addition, a comparison of the recombination profiles in closely related species such as human and chimpanzee reveals essentially no correlation in the position of hotspots. Although the variation in hotspots of meiotic recombination is clearly documented, the mechanisms responsible for such variation are far from being understood. Here we will review the available evidence of natural variation in meiotic recombination and will discuss potential implications of this variation on the functional mechanisms of crossover formation and control.
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Affiliation(s)
- P P Khil
- Genetics and Biochemistry Branch, NIDDK, National Institutes of Health, Bethesda, Md., USA
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18
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Smirnova NA, Romanienko PJ, Khil PP, Camerini-Otero RD. Gene expression profiles of Spo11-/- mouse testes with spermatocytes arrested in meiotic prophase I. Reproduction 2006; 132:67-77. [PMID: 16816334 DOI: 10.1530/rep.1.00997] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Spo11, a meiosis-specific protein, introduces double-strand breaks on chromosomal DNA and initiates meiotic recombination in a wide variety of organisms. Mouse null Spo11 spermatocytes fail to synapse chromosomes and progress beyond the zygotene stage of meiosis. We analyzed gene expression profiles in Spo11(-/ -)adult and juvenile wild-type testis to describe genes expressed before and after the meiotic arrest resulting from the knocking out of Spo11. These genes were characterized using the Gene Ontology data base. To focus on genes involved in meiosis, we performed comparative gene expression analysis of Spo11(-/ -)and wild-type testes from 15-day mice, when spermatocytes have just entered pachytene. We found that the knockout of Spo11 causes dramatic changes in the level of expression of genes that participate in meiotic recombination (Hop2, Brca2, Mnd1, FancG) and in the meiotic checkpoint (cyclin B2, Cks2), but does not affect genes encoding protein components of the synaptonemal complex. Finally, we discovered unknown genes that are affected by the disruption of the Spo11 gene and therefore may be specifically involved in meiosis and spermatogenesis.
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Affiliation(s)
- Natalya A Smirnova
- Genetics and Biochemistry Branch, NIDDK, National Institutes of Health, 5 Memorial Drive, Bethesda, Maryland 20892, USA
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19
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Abstract
As the heteromorphic sex chromosomes evolved from a pair of autosomes, the sex chromosomes became increasingly different in gene content and structure from each other and from the autosomes. Although recently there has been progress in documenting and understanding these differences, the molecular mechanisms that have fashioned some of these changes remain unclear. A new study addresses the differential distribution of retroposed genes in human and mouse genomes. Surprisingly, chromosome X is a major source and a preferred target for retrotransposition.
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Affiliation(s)
- Pavel P Khil
- Genetics and Biochemistry Branch and Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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20
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Khil PP, Camerini-Otero RD. Reply to: Explaining the X-linkage bias of placentally expressed genes. Nat Genet 2005. [DOI: 10.1038/ng0105-3b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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21
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Khil PP, Smirnova NA, Romanienko PJ, Camerini-Otero RD. The mouse X chromosome is enriched for sex-biased genes not subject to selection by meiotic sex chromosome inactivation. Nat Genet 2004; 36:642-6. [PMID: 15156144 DOI: 10.1038/ng1368] [Citation(s) in RCA: 264] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2003] [Accepted: 03/25/2004] [Indexed: 11/09/2022]
Abstract
Sex chromosomes are subject to sex-specific selective evolutionary forces. One model predicts that genes with sex-biased expression should be enriched on the X chromosome. In agreement with Rice's hypothesis, spermatogonial genes are over-represented on the X chromosome of mice and sex- and reproduction-related genes are over-represented on the human X chromosome. Male-biased genes are under-represented on the X chromosome in worms and flies, however. Here we show that mouse spermatogenesis genes are relatively under-represented on the X chromosome and female-biased genes are enriched on it. We used Spo11(-/-) mice blocked in spermatogenesis early in meiosis to evaluate the temporal pattern of gene expression in sperm development. Genes expressed before the Spo11 block are enriched on the X chromosome, whereas those expressed later in spermatogenesis are depleted. Inactivation of the X chromosome in male meiosis may be a universal driving force for X-chromosome demasculinization.
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Affiliation(s)
- Pavel P Khil
- Genetics and Biochemistry Branch, NIDDK, National Institutes of Health, 5 Memorial Drive, Bethesda, Maryland 20892, USA
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22
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Khil PP, Obmolova G, Teplyakov A, Howard AJ, Gilliland GL, Camerini-Otero RD. Crystal structure of the Escherichia coli YjiA protein suggests a GTP-dependent regulatory function. Proteins 2004; 54:371-4. [PMID: 14696199 DOI: 10.1002/prot.10430] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Pavel P Khil
- Genetics and Biochemistry Branch, NIDDK, National Institutes of Health, Bethesda, Maryland 20892, USA.
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23
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Ladner JE, Obmolova G, Teplyakov A, Howard AJ, Khil PP, Camerini-Otero RD, Gilliland GL. Crystal structure of Escherichia coli protein ybgI, a toroidal structure with a dinuclear metal site. BMC Struct Biol 2003; 3:7. [PMID: 14519207 PMCID: PMC239858 DOI: 10.1186/1472-6807-3-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2003] [Accepted: 09/30/2003] [Indexed: 11/22/2022]
Abstract
BACKGROUND The protein encoded by the gene ybgI was chosen as a target for a structural genomics project emphasizing the relation of protein structure to function. RESULTS The structure of the ybgI protein is a toroid composed of six polypeptide chains forming a trimer of dimers. Each polypeptide chain binds two metal ions on the inside of the toroid. CONCLUSION The toroidal structure is comparable to that of some proteins that are involved in DNA metabolism. The di-nuclear metal site could imply that the specific function of this protein is as a hydrolase-oxidase enzyme.
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Affiliation(s)
- Jane E Ladner
- Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute and the National Institute of Standards and Technology, 9600 Gudelsky Drive, Rockville, MD 20850, U.S.A
| | - Galina Obmolova
- Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute and the National Institute of Standards and Technology, 9600 Gudelsky Drive, Rockville, MD 20850, U.S.A
| | - Alexey Teplyakov
- Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute and the National Institute of Standards and Technology, 9600 Gudelsky Drive, Rockville, MD 20850, U.S.A
| | - Andrew J Howard
- Physical Sciences Department, Illinois Institute of Technology, Chicago, Illinois 60616, U.S.A
| | - Pavel P Khil
- Genetics and Biochemistry Branch, NIDDK, National Institutes of Health, 10 Center Drive, Bethesda, MD 20892, U.S.A
| | - R Daniel Camerini-Otero
- Genetics and Biochemistry Branch, NIDDK, National Institutes of Health, 10 Center Drive, Bethesda, MD 20892, U.S.A
| | - Gary L Gilliland
- Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute and the National Institute of Standards and Technology, 9600 Gudelsky Drive, Rockville, MD 20850, U.S.A
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24
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Obmolova G, Teplyakov A, Khil PP, Howard AJ, Camerini-Otero RD, Gilliland GL. Crystal structure of theEscherichia coli Tas protein, an NADP(H)-dependent aldo-keto reductase. Proteins 2003; 53:323-5. [PMID: 14517983 DOI: 10.1002/prot.10367] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Galina Obmolova
- Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute and the National Institute of Standards and Technology, Rockville, Maryland 20850, USA
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25
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Abstract
The dinG promoter was first isolated in a genetic screen scoring for damage-inducible loci in Escherichia coli (Lewis, L. K., Jenkins, M. E., and Mount, D. W. (1992) J. Bacteriol. 174, 3377-3385). Sequence analysis suggests that the dinG gene encodes a putative helicase related to a group of eukaryotic helicases that includes mammalian XPD (Koonin, E. V. (1993) Nucleic Acids Res. 21, 1497), an enzyme involved in transcription-coupled nucleotide excision repair and basal transcription. We have characterized the dinG gene product from E. coli using genetic and biochemical approaches. Deletion of dinG has no severe phenotype, indicating that it is non-essential for cell viability. Both dinG deletion and over-expression of the DinG protein from a multicopy plasmid result in a slight reduction of UV resistance. DinG, purified as a fusion protein from E. coli cells, behaves as a monomer in solution, as judged from gel filtration experiments. DinG is an ATP-hydrolyzing enzyme; single-stranded (ss) DNA stimulates the ATPase activity 15-fold. Kinetic data yield a Hill coefficient of 1, consistent with one ATP-hydrolyzing site per DinG molecule. DinG possesses a DNA helicase activity; it translocates along ssDNA in a 5' --> 3' direction, as revealed in experiments with substrates containing non-natural 5'-5' and 3'-3' linkages. The ATP-dependent DNA helicase activity of DinG requires divalent cations (Mg2+, Ca2+, and Mn2+) but is not observed in the presence of Zn2+. The DinG helicase does not discriminate between ribonucleotide and deoxyribonucleotide triphosphates, and it unwinds duplex DNA with similar efficiency in the presence of ATP or dATP. We discuss the possible involvement of the DinG helicase in DNA replication and repair processes.
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Affiliation(s)
- Oleg N Voloshin
- Genetics and Biochemistry Branch, NIDDK, National Institutes of Health, Bethesda, Maryland 20892, USA
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Teplyakov A, Obmolova G, Khil PP, Howard AJ, Camerini-Otero RD, Gilliland GL. Crystal structure of the Escherichia coli YcdX protein reveals a trinuclear zinc active site. Proteins 2003; 51:315-8. [PMID: 12661000 DOI: 10.1002/prot.10352] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Alexey Teplyakov
- Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute and the National Institute of Standards and Technology, Rockville, Maryland 20850, USA
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27
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Abstract
Changes in gene expression after treatment of Escherichia coli cultures with mitomycin C were assessed using gene array technology. Unexpectedly, a large number of genes (nearly 30% of all genes) displayed significant changes in their expression level. Analysis and classification of expression profiles of the corresponding genes allowed us to assign this large number of genes into one or two dozen small clusters of genes with similar expression profiles. This assignment allowed us to describe systematically the changes in the level of gene expression in response to DNA damage. Among the damage-induced genes, more than 100 are novel. From those genes involved in DNA metabolism that have not previously been shown to be induced by DNA damage, the mutS gene involved in mismatch repair is especially noteworthy. In addition to the SOS response, we observed the induction of other stress response pathways, such as those of oxidative stress and osmotic protection. Among the genes that are downregulated in response to DNA damage are numerous protein biosynthesis genes. Analysis of the gene expression data highlighted the essential involvement of sigma(s)-regulated genes and the general stress response network in the response to DNA damage.
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Affiliation(s)
- Pavel P Khil
- Genetics and Biochemistry Branch, NIDDK, National Institutes of Health, 10 Center Drive, Bethesda, MD 20892, USA
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28
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Lebedev YB, Belonovitch OS, Zybrova NV, Khil PP, Kurdyukov SG, Vinogradova TV, Hunsmann G, Sverdlov ED. Differences in HERV-K LTR insertions in orthologous loci of humans and great apes. Gene 2000; 247:265-77. [PMID: 10773466 DOI: 10.1016/s0378-1119(00)00062-7] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The classification of the long terminal repeats (LTRs) of the human endogenous retrovirus HERV-K (HML-2) family was refined according to diagnostic differences between the LTR sequences. The mutation rate was estimated to be approximately equal for LTRs belonging to different families and branches of human endogenous retroviruses (HERVs). An average mutation rate value was calculated based on differences between LTRs of the same HERV and was found to be 0.13% per million years (Myr). Using this value, the ages of different LTR groups belonging to the LTR HML-2 subfamily were found to vary from 3 to 50Myr. Orthologous potential LTR-containing loci from different primate species were PCR amplified using primers corresponding to the genomic sequences flanking LTR integration sites. This allowed us to calculate the phylogenetic times of LTR integrations in primate lineages in the course of the evolution and to demonstrate that they are in good agreement with the LTR ages calculated from the mutation rates. Human-specific integrations for some very young LTRs were demonstrated. The possibility of LTRs and HERVs involvement in the evolution of primates is discussed.
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Affiliation(s)
- Y B Lebedev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya St., Moscow, Russia.
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29
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Lapuk AV, Khil PP, Lavrentieva IV, Lebedev YB, Sverdlov ED. A human endogenous retrovirus-like (HERV) LTR formed more than 10 million years ago due to an insertion of HERV-H LTR into the 5' LTR of HERV-K is situated on human chromosomes 10, 19 and Y. J Gen Virol 1999; 80 ( Pt 4):835-839. [PMID: 10211950 DOI: 10.1099/0022-1317-80-4-835] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A chimeric long terminal repeat (LTR) containing the whole LTR of a human endogenous retrovirus-like element of the H family (HERV-H) inserted downstream of the core enhancer region of the 5' LTR of a HERV-K retroelement was detected and sequenced in the human 19p12 locus, known to be enriched with genes encoding zinc finger proteins. Similar chimeras were also detected in human chromosomes 10 and Y in human-hamster hybrid cells containing individual human chromosomes. This finding was interpreted as evidence of transpositions of the chimera in the genome. PCR analyses detected the chimera in the genomes of chimpanzee and gorilla, but not in that of orangutan. These data demonstrate that the chimera appeared in the primate germ cells more than 10 million years ago, before divergence of the human/chimpanzee and the gorilla lineages. The combination of the two LTRs forms a new regulatory system that can be involved in nearby gene expression.
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Klinov DV, Lagutina IV, Prokhorov VV, Neretina T, Khil PP, Lebedev YB, Cherny DI, Demin VV, Sverdlov ED. High resolution mapping DNAs by R-loop atomic force microscopy. Nucleic Acids Res 1998; 26:4603-10. [PMID: 9753727 PMCID: PMC147898 DOI: 10.1093/nar/26.20.4603] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
R-loops formed by short RNA transcripts have been imaged by atomic force microscopy (AFM) at a constant force in the height mode. The technique was applied to mapping the human endogenous retrovirus K10 family (HERV-K10) long terminal repeats (LTR) within individual plasmids and cosmids. RNA probes specific for the U3 (384 nt) and U5 (375 nt) LTR regions separated by a span of 200 bp were used for R-loop formation with LTRs located within plasmid (3.8 kb) or cosmid ( approximately 40 kb) DNAs. R-loops stabilized by glyoxal treatment and adsorbed onto the mica surface in the presence of magnesium ions looked like looped out segments of RNA:DNA hybrids. The total yield of R-loops was usually approximately 95%. The RNA:DNA hybrids were found to be 12-15% shorter than the corresponding DNA:DNA duplex. The two regions of the LTR could be easily discerned in the AFM images as clearly separated loops. R-loop positions determined on cosmids by AFM were accurate to approximately 0.5% of the cosmid length. This technique might be easily adapted for mapping various sequences such as gene exons or regulatory regions and for detecting insertions, deletions and rearrangements that cause human genetic diseases.
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Affiliation(s)
- D V Klinov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry and Institute of Molecular Genetics,Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117871, Russia
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31
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Khil PP, Lebedev IB, Sverdlov ED. [Long terminal repeat of the human endogenous retrovirus HERV-K in the intron of the ZNF91 gene]. Bioorg Khim 1998; 24:126-31. [PMID: 10335408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
The relative positions of the ZNF91 gene (exon-intron organization) and the HERV-K human endogenous virus long terminal repeat (LTR), which was earlier found to be located in the ZNF91 gene locus, on the EcoRI restriction metric map of the human chromosome 19 were determined with a high resolution. The direction of the ZNF91 gene transcription relative to the chromosome 19 telomeres was determined. The HERV-K LTR was localized to the ZNF91 gene intron 19. The role of retroviral sequences in the evolution of the ZNF91 gene family is discussed.
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Affiliation(s)
- P P Khil
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
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32
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Akopov SB, Nikolaev LG, Khil PP, Lebedev YB, Sverdlov ED. Long terminal repeats of human endogenous retrovirus K family (HERV-K) specifically bind host cell nuclear proteins. FEBS Lett 1998; 421:229-33. [PMID: 9468312 DOI: 10.1016/s0014-5793(97)01569-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Solitary long terminal repeats (LTRs) of the human endogenous retroviruses, scattered in several thousand copies throughout the human genome, are potentially capable of affecting the expression of closely located genes. To assess their regulatory potential, the LTR sequences of one of the most abundant HERV families (HERV-K) were screened for the presence of binding sites for the host cell nuclear factors using mobility shift and UV-crosslinking assays. It was shown that the LTR sequences of two subfamilies harbor a specific binding site for a complex consisting of at least three proteins, ERF1, ERF2 and ERF3 of 98, 91 and 88 kDa apparent molecular mass, respectively. This binding site is located in the 5' region of the LTR U3 element. The preservation of the specific protein binding site in different HERV-K LTR sequences suggests their possible role in regulation of nearby located genes.
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Affiliation(s)
- S B Akopov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow.
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