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Dingsdag SA, Clay OK, Quintero GA. COVID-19 severity, miR-21 targets, and common human genetic variation. Letter regarding the article 'Circulating cardiovascular microRNAs in critically ill COVID-19 patients'. Eur J Heart Fail 2021; 23:1986-1987. [PMID: 34318976 PMCID: PMC8427028 DOI: 10.1002/ejhf.2317] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/19/2021] [Accepted: 07/22/2021] [Indexed: 01/01/2023] Open
Affiliation(s)
- Simon A Dingsdag
- Translational Microbiology and Emerging Diseases (MICROS), Universidad del Rosario, Bogotá, Colombia
| | - Oliver K Clay
- Translational Microbiology and Emerging Diseases (MICROS), Universidad del Rosario, Bogotá, Colombia
| | - Gustavo A Quintero
- Translational Microbiology and Emerging Diseases (MICROS), Universidad del Rosario, Bogotá, Colombia
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Gallo JE, Ochoa JE, Warren HR, Misas E, Correa MM, Gallo-Villegas JA, Bedoya G, Aristizábal D, McEwen JG, Caulfield MJ, Parati G, Clay OK. Hypertension and the roles of the 9p21.3 risk locus: Classic findings and new association data. Int J Cardiol Hypertens 2020; 7:100050. [PMID: 33330845 PMCID: PMC7491459 DOI: 10.1016/j.ijchy.2020.100050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 09/10/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The band 9p21.3 contains an established genomic risk zone for cardiovascular disease (CVD). Since the initial 2007 Wellcome Trust Case Control Consortium study (WTCCC), the increased CVD risk associated with 9p21.3 has been confirmed by multiple studies in different continents. However, many years later there was still no confirmed report of a corresponding association of 9p21.3 with hypertension, a major CV risk factor, nor with blood pressure (BP). THEORY In this contribution, we review the bipartite haplotype structure of the 9p21.3 risk locus: one block is devoid of protein-coding genes but contains the lead CVD risk SNPs, while the other block contains the first exon and regulatory DNA of the gene for the cell cycle inhibitor p15. We consider how findings from molecular biology offer possibilities of an involvement of p15 in hypertension etiology, with expression of the p15 gene modulated by genetic variation from within the 9p21.3 risk locus. RESULTS We present original results from a Colombian study revealing moderate but persistent association signals for BP and hypertension within the classic 9p21.3 CVD risk locus. These SNPs are mostly confined to a 'hypertension island' that spans less than 60 kb and coincides with the p15 haplotype block. We find confirmation in data originating from much larger, recent European BP studies, albeit with opposite effect directions. CONCLUSION Although more work will be needed to elucidate possible mechanisms, previous findings and new data prompt reconsidering the question of how variation in 9p21.3 might influence hypertension components of cardiovascular risk.
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Key Words
- 1 KG, 1000 Genomes Project
- BP, blood pressure
- Blood pressure levels
- CVD, cardiovascular disease
- DBP, diastolic blood pressure
- EGFR, epidermal growth factor receptor
- GWAS, genome wide association studi(es)
- Genotype-phenotype associations
- Haplotypes
- MAF, minor allele frequency
- RAS, renin angiotensin system
- SBP, systolic blood pressure
- SNP, single nucleotide polymorphism
- TGF-β, transforming growth factor beta
- VSMC, vascular smooth muscle cell(s)
- bp, base pair
- kb, kilobase pair
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Affiliation(s)
- Juan E. Gallo
- Cellular & Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia
- Doctoral Program in Biomedical Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Juan E. Ochoa
- Cellular & Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia
- Istituto Auxologico Italiano, IRCCS, Department of Cardiovascular Neural and Metabolic Sciences, San Luca Hospital, Milan, Italy
- Department of Medicine and Surgery, University of Milano-Bicocca, Milan, Italy
| | - Helen R. Warren
- Clinical Pharmacology Department, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- National Institute for Health Research, Barts Cardiovascular Biomedical Research Center, Queen Mary University of London, London, UK
| | - Elizabeth Misas
- Cellular & Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia
- Institute of Biology, Universidad de Antioquia, Medellín, Colombia
| | | | | | - Gabriel Bedoya
- Institute of Biology, Universidad de Antioquia, Medellín, Colombia
| | - Dagnóvar Aristizábal
- Cellular & Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia
- SICOR, Medellín, Colombia
| | - Juan G. McEwen
- Cellular & Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia
- School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | - Mark J. Caulfield
- Clinical Pharmacology Department, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- National Institute for Health Research, Barts Cardiovascular Biomedical Research Center, Queen Mary University of London, London, UK
| | - Gianfranco Parati
- Istituto Auxologico Italiano, IRCCS, Department of Cardiovascular Neural and Metabolic Sciences, San Luca Hospital, Milan, Italy
- Department of Medicine and Surgery, University of Milano-Bicocca, Milan, Italy
| | - Oliver K. Clay
- Cellular & Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia
- Translational Microbiology and Emerging Diseases (MICROS), School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
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Misas E, Chow NA, Gómez OM, Muñoz JF, McEwen JG, Litvintseva AP, Clay OK. Mitochondrial Genome Sequences of the Emerging Fungal Pathogen Candida auris. Front Microbiol 2020; 11:560332. [PMID: 33193142 PMCID: PMC7652928 DOI: 10.3389/fmicb.2020.560332] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 09/30/2020] [Indexed: 11/25/2022] Open
Abstract
Candida auris is an emerging fungal pathogen capable of causing invasive infections in humans. Since its first appearance around 1996, it has been isolated in countries spanning five continents. C. auris is a yeast that has the potential to cause outbreaks in hospitals, can survive in adverse conditions, including dry surfaces and high temperatures, and has been frequently misidentified by traditional methods. Furthermore, strains have been identified that are resistant to two and even all three of the main classes of antifungals currently in use. Several nuclear genome assemblies of C. auris have been published representing different clades and continents, yet until recently, the mitochondrial genomes (mtDNA chromosomes) of this species and the closely related species of C. haemulonii, C. duobushaemulonii, and C. pseudohaemulonii had not been analyzed in depth. We used reads from PacBio and Illumina sequencing to obtain a de novo reference assembly of the mitochondrial genome of the C. auris clade I isolate B8441 from Pakistan. This assembly has a total size of 28.2 kb and contains 13 core protein-coding genes, 25 tRNAs and the 12S and 16S ribosomal subunits. We then performed a comparative analysis by aligning Illumina reads of 129 other isolates from South Asia, Japan, South Africa, and South America with the B8441 reference. The clades of the phylogenetic tree we obtained from the aligned mtDNA sequences were consistent with those derived from the nuclear genome. The mitochondrial genome revealed a generally low genetic variation within clades, although the South Asian clade displayed two sub-branches including strains from both Pakistan and India. In particular, the 86 isolates from Colombia and Venezuela had mtDNA sequences that were all identical at the base level, i.e., a single conserved haplotype or mitochondrial background that exhibited characteristic differences from the Pakistan reference isolate B8441, such as a unique 25-nt insert that may affect function.
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Affiliation(s)
- Elizabeth Misas
- Cellular and Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia
- Wisconsin One Health Consortium, Universidad Nacional de Colombia, Medellín, Colombia
| | - Nancy A. Chow
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Oscar M. Gómez
- Cellular and Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia
- School of Microbiology, Universidad de Antioquia, Medellín, Colombia
- Genoma CES, Universidad CES, Medellín, Colombia
| | - José F. Muñoz
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Juan G. McEwen
- Cellular and Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia
- School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | | | - Oliver K. Clay
- Cellular and Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia
- Translational Microbiology and Emerging Diseases, School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
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Misas E, Gómez OM, Botero V, Muñoz JF, Teixeira MM, Gallo JE, Clay OK, McEwen JG. Updates and Comparative Analysis of the Mitochondrial Genomes of Paracoccidioides spp. Using Oxford Nanopore MinION Sequencing. Front Microbiol 2020; 11:1751. [PMID: 32849380 PMCID: PMC7417371 DOI: 10.3389/fmicb.2020.01751] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 07/06/2020] [Indexed: 02/03/2023] Open
Abstract
The mitochondrial genome of the Paracoccidioides brasiliensis reference isolate Pb18 was first sequenced and described by Cardoso et al. (2007), as a circular genome with a size of 71.3 kb and containing 14 protein coding genes, 25 tRNAs, and the large and small subunits of ribosomal RNA. Later in 2011, Desjardins et al. (2011) obtained partial assemblies of mitochondrial genomes of P. lutzii (Pb01), P. americana (Pb03), and P. brasiliensis sensu stricto (Pb18), although with a size of only 43.1 kb for Pb18. Sequencing errors or other limitations resulting from earlier technologies, and the advantages of NGS (short and long reads), prompted us to improve and update the mtDNA sequences and annotations of two Paracoccidioides species. Using Oxford Nanopore and Illumina read sequencing, we generated high-quality complete de novo mitochondrial genome assemblies and annotations for P. brasiliensis (Pb18) and P. americana (Pb03). Both assemblies were characterized by an unusually long spacer or intron region (>50 kb) between exons 2 and 3 of the nad5 gene, which was moderately conserved between Pb03 and Pb18 but not similar to other reported sequences, except for an unassigned contig in the 2011 assembly of Pb03. The reliability of the insert missing from previous mtDNA genome assemblies was confirmed by inspection of the individual Nanopore read sequences containing nad5 coding DNA, and experimentally by PCR for Pb18. We propose that the insert may aid replication initiation and may be excised to produce a smaller structural variant. The updated mtDNA genomes should enable more accurate SNP and other comparative or evolutionary analyses and primer/probe designs. A comparative analysis of the mtDNA from 32 isolates of Paracoccidioides spp., using the SNPs of the aligned mitochondrial genomes, showed groupings within the brasiliensis species complex that were largely consistent with previous findings from only five mitochondrial loci.
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Affiliation(s)
- Elizabeth Misas
- Cellular and Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia
- Colombia Wisconsin One Health Consortium, Universidad Nacional de Colombia, Medellín, Colombia
| | - Oscar M. Gómez
- Cellular and Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia
- Genoma CES, Universidad CES, Medellín, Colombia
| | - Vanessa Botero
- Cellular and Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia
| | - José F. Muñoz
- Cellular and Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | | | - Juan E. Gallo
- Cellular and Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia
- Genoma CES, Universidad CES, Medellín, Colombia
| | - Oliver K. Clay
- Translational Microbiology and Emerging Diseases (MICROS), School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Juan G. McEwen
- Cellular and Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia
- School of Medicine, Universidad de Antioquia, Medellín, Colombia
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Misas E, Escandón P, McEwen JG, Clay OK. The LUFS domain, its transcriptional regulator proteins, and drug resistance in the fungal pathogen Candida auris. Protein Sci 2020; 28:2024-2029. [PMID: 31503375 DOI: 10.1002/pro.3727] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 06/29/2019] [Revised: 09/06/2019] [Accepted: 09/09/2019] [Indexed: 01/08/2023]
Abstract
The LUFS domain (LUG/LUH, Flo8, single-strand DNA-binding protein [SSBP]) is a well-conserved and apparently ancient region found in diverse proteins and taxa. This domain, which has as its most obvious structural feature a series of three helices, has been identified in transcriptional regulator proteins of animals, plants, and fungi. Recently, in these pages (Wang et al., Protein Sci., 2019, 28:788-793), the first crystal structure of a LUFS domain was reported, for the human SSBP2, a transcriptional repressor. We briefly address how the new insights into LUFS structures might contribute to a better understanding of an important transcriptional activator of yeasts that contains the LUFS domain, Flo8, and consider how a focus on the LUFS domain and its variation could help us to understand etiologies of drug resistance in a recently emerged pathogenic fungus, Candida auris.
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Affiliation(s)
- Elizabeth Misas
- Cellular & Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia.,Institute of Biology, Universidad de Antioquia, Medellín, Colombia
| | - Patricia Escandón
- Grupo de Microbiología, Instituto Nacional de Salud, Bogotá, Colombia
| | - Juan G McEwen
- Cellular & Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia.,School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | - Oliver K Clay
- Cellular & Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia.,Translational Microbiology and Emerging Diseases (MICROS), School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
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Gallo JE, Misas E, McEwen JG, Clay OK. Toward Multiple SNP Motif Analyses of Loci Associated With Phenotypic Traits. J Am Coll Cardiol 2019; 70:1539-1540. [PMID: 28911523 DOI: 10.1016/j.jacc.2017.05.080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 05/30/2017] [Indexed: 11/17/2022]
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Dukik K, Muñoz JF, Jiang Y, Feng P, Sigler L, Stielow JB, Freeke J, Jamalian A, van den Ende BG, McEwen JG, Clay OK, Schwartz IS, Govender NP, Maphanga TG, Cuomo CA, Moreno L, Kenyon C, Borman AM, de Hoog S. Novel taxa of thermally dimorphic systemic pathogens in the Ajellomycetaceae (Onygenales). Mycoses 2017; 60:296-309. [PMID: 28176377 PMCID: PMC5775888 DOI: 10.1111/myc.12601] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 12/30/2016] [Accepted: 12/30/2016] [Indexed: 12/11/2022]
Abstract
Recent discoveries of novel systemic fungal pathogens with thermally dimorphic yeast-like phases have challenged the current taxonomy of the Ajellomycetaceae, a family currently comprising the genera Blastomyces, Emmonsia, Emmonsiellopsis, Helicocarpus, Histoplasma, Lacazia and Paracoccidioides. Our morphological, phylogenetic and phylogenomic analyses demonstrated species relationships and their specific phenotypes, clarified generic boundaries and provided the first annotated genome assemblies to support the description of two new species. A new genus, Emergomyces, accommodates Emmonsia pasteuriana as type species, and the new species Emergomyces africanus, the aetiological agent of case series of disseminated infections in South Africa. Both species produce small yeast cells that bud at a narrow base at 37°C and lack adiaspores, classically associated with the genus Emmonsia. Another novel dimorphic pathogen, producing broad-based budding cells at 37°C and occurring outside North America, proved to belong to the genus Blastomyces, and is described as Blastomyces percursus.
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Affiliation(s)
- Karolina Dukik
- CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, the Netherlands
| | - Jose F. Muñoz
- Broad Institute of MIT and Harvard, Cambridge, MA, U.S.A
- Cellular and Molecular Biology Unit, Corporación para Investigaciones Biológicas (CIB), Medellín, Colombia
- Institute of Biology, Universidad de Antioquia, Medellín, Colombia
| | - Yanping Jiang
- CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands
- Department of Dermatology, The Affiliated Hospital, Guizhou Medical University, Guiyang, China
| | - Peiying Feng
- CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands
- Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Lynne Sigler
- University of Alberta Microfungus Collection and Herbarium and Biological Sciences, Edmonton, Alberta, Canada
| | - J. Benjamin Stielow
- CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands
- Thermo Fisher Scientific, Landsmeer, The Netherlands
| | - Joanna Freeke
- CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands
- Thermo Fisher Scientific, Landsmeer, The Netherlands
| | - Azadeh Jamalian
- CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands
- Thermo Fisher Scientific, Landsmeer, The Netherlands
| | | | - Juan G. McEwen
- Cellular and Molecular Biology Unit, Corporación para Investigaciones Biológicas (CIB), Medellín, Colombia
- School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | - Oliver K. Clay
- Cellular and Molecular Biology Unit, Corporación para Investigaciones Biológicas (CIB), Medellín, Colombia
- School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Ilan S. Schwartz
- Epidemiology for Global Health Institute, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
- Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Nelesh P. Govender
- University of Cape Town, Cape Town, South Africa
- National Institute for Communicable Diseases, Johannesburg, South Africa
| | | | | | - Leandro Moreno
- CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, the Netherlands
- Basic Pathology Department, Federal University of Paraná, Curitiba, Paraná, Brazil
| | - Chris Kenyon
- University of Cape Town, Cape Town, South Africa
- Sexually Transmitted Infection Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | | | - Sybren de Hoog
- CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, the Netherlands
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Muñoz JF, Farrer RA, Desjardins CA, Gallo JE, Sykes S, Sakthikumar S, Misas E, Whiston EA, Bagagli E, Soares CMA, Teixeira MDM, Taylor JW, Clay OK, McEwen JG, Cuomo CA. Genome Diversity, Recombination, and Virulence across the Major Lineages of Paracoccidioides. mSphere 2016; 1:e00213-16. [PMID: 27704050 PMCID: PMC5040785 DOI: 10.1128/msphere.00213-16] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 09/06/2016] [Indexed: 12/29/2022] Open
Abstract
The Paracoccidioides genus includes two species of thermally dimorphic fungi that cause paracoccidioidomycosis, a neglected health-threatening human systemic mycosis endemic to Latin America. To examine the genome evolution and the diversity of Paracoccidioides spp., we conducted whole-genome sequencing of 31 isolates representing the phylogenetic, geographic, and ecological breadth of the genus. These samples included clinical, environmental and laboratory reference strains of the S1, PS2, PS3, and PS4 lineages of P. brasiliensis and also isolates of Paracoccidioides lutzii species. We completed the first annotated genome assemblies for the PS3 and PS4 lineages and found that gene order was highly conserved across the major lineages, with only a few chromosomal rearrangements. Comparing whole-genome assemblies of the major lineages with single-nucleotide polymorphisms (SNPs) predicted from the remaining 26 isolates, we identified a deep split of the S1 lineage into two clades we named S1a and S1b. We found evidence for greater genetic exchange between the S1b lineage and all other lineages; this may reflect the broad geographic range of S1b, which is often sympatric with the remaining, largely geographically isolated lineages. In addition, we found evidence of positive selection for the GP43 and PGA1 antigen genes and genes coding for other secreted proteins and proteases and lineage-specific loss-of-function mutations in cell wall and protease genes; these together may contribute to virulence and host immune response variation among natural isolates of Paracoccidioides spp. These insights into the recent evolutionary events highlight important differences between the lineages that could impact the distribution, pathogenicity, and ecology of Paracoccidioides. IMPORTANCE Characterization of genetic differences between lineages of the dimorphic human-pathogenic fungus Paracoccidioides can identify changes linked to important phenotypes and guide the development of new diagnostics and treatments. In this article, we compared genomes of 31 diverse isolates representing the major lineages of Paracoccidioides spp. and completed the first annotated genome sequences for the PS3 and PS4 lineages. We analyzed the population structure and characterized the genetic diversity among the lineages of Paracoccidioides, including a deep split of S1 into two lineages (S1a and S1b), and differentiated S1b, associated with most clinical cases, as the more highly recombining and diverse lineage. In addition, we found patterns of positive selection in surface proteins and secreted enzymes among the lineages, suggesting diversifying mechanisms of pathogenicity and adaptation across this species complex. These genetic differences suggest associations with the geographic range, pathogenicity, and ecological niches of Paracoccidioides lineages.
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Affiliation(s)
- José F. Muñoz
- Cellular and Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia
- Institute of Biology, Universidad de Antioquia, Medellín, Colombia
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Rhys A. Farrer
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | | | - Juan E. Gallo
- Cellular and Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia
- Doctoral Program in Biomedical Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Sean Sykes
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | | | - Elizabeth Misas
- Cellular and Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia
- Institute of Biology, Universidad de Antioquia, Medellín, Colombia
| | - Emily A. Whiston
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA
| | - Eduardo Bagagli
- Instituto de Biociências, Universidade Estadual Paulista, Botucatu, São Paulo, Brazil
| | - Celia M. A. Soares
- Laboratório de Biología Molecular, Instituto de Ciências Biológicas, ICBII, Goiânia, Brazil
| | - Marcus de M. Teixeira
- Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, Distrito Federal, Brazil
- Division of Pathogen Genomics, Translational Genomics Research Institute North, Flagstaff, Arizona, USA
| | - John W. Taylor
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA
| | - Oliver K. Clay
- Cellular and Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia
- School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Juan G. McEwen
- Cellular and Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia
- School of Medicine, Universidad de Antioquia, Medellín, Colombia
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Muñoz JF, Gauthier GM, Desjardins CA, Gallo JE, Holder J, Sullivan TD, Marty AJ, Carmen JC, Chen Z, Ding L, Gujja S, Magrini V, Misas E, Mitreva M, Priest M, Saif S, Whiston EA, Young S, Zeng Q, Goldman WE, Mardis ER, Taylor JW, McEwen JG, Clay OK, Klein BS, Cuomo CA. The Dynamic Genome and Transcriptome of the Human Fungal Pathogen Blastomyces and Close Relative Emmonsia. PLoS Genet 2015; 11:e1005493. [PMID: 26439490 PMCID: PMC4595289 DOI: 10.1371/journal.pgen.1005493] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 08/11/2015] [Indexed: 12/05/2022] Open
Abstract
Three closely related thermally dimorphic pathogens are causal agents of major fungal diseases affecting humans in the Americas: blastomycosis, histoplasmosis and paracoccidioidomycosis. Here we report the genome sequence and analysis of four strains of the etiological agent of blastomycosis, Blastomyces, and two species of the related genus Emmonsia, typically pathogens of small mammals. Compared to related species, Blastomyces genomes are highly expanded, with long, often sharply demarcated tracts of low GC-content sequence. These GC-poor isochore-like regions are enriched for gypsy elements, are variable in total size between isolates, and are least expanded in the avirulent B. dermatitidis strain ER-3 as compared with the virulent B. gilchristii strain SLH14081. The lack of similar regions in related species suggests these isochore-like regions originated recently in the ancestor of the Blastomyces lineage. While gene content is highly conserved between Blastomyces and related fungi, we identified changes in copy number of genes potentially involved in host interaction, including proteases and characterized antigens. In addition, we studied gene expression changes of B. dermatitidis during the interaction of the infectious yeast form with macrophages and in a mouse model. Both experiments highlight a strong antioxidant defense response in Blastomyces, and upregulation of dioxygenases in vivo suggests that dioxide produced by antioxidants may be further utilized for amino acid metabolism. We identify a number of functional categories upregulated exclusively in vivo, such as secreted proteins, zinc acquisition proteins, and cysteine and tryptophan metabolism, which may include critical virulence factors missed before in in vitro studies. Across the dimorphic fungi, loss of certain zinc acquisition genes and differences in amino acid metabolism suggest unique adaptations of Blastomyces to its host environment. These results reveal the dynamics of genome evolution and of factors contributing to virulence in Blastomyces. Dimorphic fungal pathogens including Blastomyces are the cause of major fungal diseases in North and South America. The genus Emmonsia includes species infecting small mammals as well as a newly emerging pathogenic species recently reported in HIV-positive patients in South Africa. Here, we synthesize both genome sequencing of four isolates of Blastomyces and two species of Emmonsia as well as deep sequencing of Blastomyces RNA to draw major new insights into the evolution of this group and the pathogen response to infection. We investigate the trajectory of genome evolution of this group, characterizing the phylogenetic relationships of these species, a remarkable genome expansion that formed large isochore-like regions of low GC content in Blastomyces, and variation of gene content, related to host interaction, among the dimorphic fungal pathogens. Using RNA-Seq, we profile the response of Blastomyces to macrophage and mouse pulmonary infection, identifying key pathways and novel virulence factors. The identification of key fungal genes involved in adaptation to the host suggests targets for further study and therapeutic intervention in Blastomyces and related dimorphic fungal pathogens.
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Affiliation(s)
- José F. Muñoz
- Cellular and Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia
- Institute of Biology, Universidad de Antioquia, Medellín, Colombia
| | - Gregory M. Gauthier
- Department of Medicine, University of Wisconsin, Madison, Madison, Wisconsin, United States of America
| | | | - Juan E. Gallo
- Cellular and Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia
- Doctoral Program in Biomedical Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Jason Holder
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Thomas D. Sullivan
- Department of Pediatrics, University of Wisconsin, Madison, Madison, Wisconsin, United States of America
| | - Amber J. Marty
- Department of Medicine, University of Wisconsin, Madison, Madison, Wisconsin, United States of America
| | - John C. Carmen
- Department of Pediatrics, University of Wisconsin, Madison, Madison, Wisconsin, United States of America
| | - Zehua Chen
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Li Ding
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Sharvari Gujja
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Vincent Magrini
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Elizabeth Misas
- Cellular and Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia
- Institute of Biology, Universidad de Antioquia, Medellín, Colombia
| | - Makedonka Mitreva
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Margaret Priest
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Sakina Saif
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Emily A. Whiston
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, United States of America
| | - Sarah Young
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Qiandong Zeng
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - William E. Goldman
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Elaine R. Mardis
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - John W. Taylor
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, United States of America
| | - Juan G. McEwen
- Cellular and Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia
- School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | - Oliver K. Clay
- Cellular and Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia
- School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Bruce S. Klein
- Department of Medicine, University of Wisconsin, Madison, Madison, Wisconsin, United States of America
- Department of Pediatrics, University of Wisconsin, Madison, Madison, Wisconsin, United States of America
- Department of Medical Microbiology & Immunology, University of Wisconsin, Madison, Madison, Wisconsin, United States of America
| | - Christina A. Cuomo
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- * E-mail:
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10
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Muñoz JF, Gallo JE, Misas E, Priest M, Imamovic A, Young S, Zeng Q, Clay OK, McEwen JG, Cuomo CA. Genome update of the dimorphic human pathogenic fungi causing paracoccidioidomycosis. PLoS Negl Trop Dis 2014; 8:e3348. [PMID: 25474325 PMCID: PMC4256289 DOI: 10.1371/journal.pntd.0003348] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 10/14/2014] [Indexed: 11/19/2022] Open
Abstract
Paracoccidiodomycosis (PCM) is a clinically important fungal disease that can acquire serious systemic forms and is caused by the thermodimorphic fungal Paracoccidioides spp. PCM is a tropical disease that is endemic in Latin America, where up to ten million people are infected; 80% of reported cases occur in Brazil, followed by Colombia and Venezuela. To enable genomic studies and to better characterize the pathogenesis of this dimorphic fungus, two reference strains of P. brasiliensis (Pb03, Pb18) and one strain of P. lutzii (Pb01) were sequenced [1]. While the initial draft assemblies were accurate in large scale structure and had high overall base quality, the sequences had frequent small scale defects such as poor quality stretches, unknown bases (N's), and artifactual deletions or nucleotide duplications, all of which caused larger scale errors in predicted gene structures. Since assembly consensus errors can now be addressed using next generation sequencing (NGS) in combination with recent methods allowing systematic assembly improvement, we re-sequenced the three reference strains of Paracoccidioides spp. using Illumina technology. We utilized the high sequencing depth to re-evaluate and improve the original assemblies generated from Sanger sequence reads, and obtained more complete and accurate reference assemblies. The new assemblies led to improved transcript predictions for the vast majority of genes of these reference strains, and often substantially corrected gene structures. These include several genes that are central to virulence or expressed during the pathogenic yeast stage in Paracoccidioides and other fungi, such as HSP90, RYP1-3, BAD1, catalase B, alpha-1,3-glucan synthase and the beta glucan synthase target gene FKS1. The improvement and validation of these reference sequences will now allow more accurate genome-based analyses. To our knowledge, this is one of the first reports of a fully automated and quality-assessed upgrade of a genome assembly and annotation for a non-model fungus. The fungal genus Paracoccidioides is the causal agent of paracoccidioidomycosis (PCM), a neglected tropical disease that is endemic in several countries of South America. Paracoccidioides is a pathogenic dimorphic fungus that is capable of converting to a virulent yeast form after inhalation by the host. Therefore the molecular biology of the switch to the yeast phase is of particular interest for understanding the virulence of this and other human pathogenic fungi, and ultimately for reducing the morbidity and mortality caused by such fungal infections. We here present the strategy and methods we used to update and improve accuracy of three reference genome sequences of Paracoccidioides spp. utilizing state-of-the-art Illumina re-sequencing, assembly improvement, re-annotation, and quality assessment. The resulting improved genome resource should be of wide use not solely for advancing research on the genetics and molecular biology of Paracoccidioides and the closely related pathogenic species Histoplasma and Blastomyces, but also for fungal diagnostics based on sequencing or molecular assays, characterizing rapidly changing proteins that may be involved in virulence, SNP-based population analyses and other tasks that require high sequence accuracy. The genome update and underlying strategy and methods also serve as a proof of principle that could encourage similar improvements of other draft genomes.
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Affiliation(s)
- José F. Muñoz
- Cellular and Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia
- Institute of Biology, Universidad de Antioquia, Medellín, Colombia
| | - Juan E. Gallo
- Cellular and Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia
- Doctoral Program in Biomedical Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Elizabeth Misas
- Cellular and Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia
- Institute of Biology, Universidad de Antioquia, Medellín, Colombia
| | - Margaret Priest
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Alma Imamovic
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Sarah Young
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Qiandong Zeng
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Oliver K. Clay
- Cellular and Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia
- School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Juan G. McEwen
- Cellular and Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia
- School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | - Christina A. Cuomo
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- * E-mail:
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11
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Ahmed S, Clay OK, Schaffner W. Proto-oncogenes, unlike 'harmless' genes, tend to be dispersed in the human genome: selection against out-of-register recombination? Biol Chem 1999; 380:3-5. [PMID: 10064131 DOI: 10.1515/bc.1999.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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12
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Rother KI, Clay OK, Bourquin JP, Silke J, Schaffner W. Long non-stop reading frames on the antisense strand of heat shock protein 70 genes and prion protein (PrP) genes are conserved between species. Biol Chem 1997; 378:1521-30. [PMID: 9461351 DOI: 10.1515/bchm.1997.378.12.1521] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [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
Several mammalian genes, including heat shock protein (Hsp70) and prion protein (PrP) genes, have been reported to have long open reading frames (ORFs) or non-stop reading frames (NRFs) in the antisense direction. A simple explanation would be that these long antisense reading frames, which are usually in the same triplet frame as the coding strand, are the fortuitous byproduct of a high overall [G+C] content with concomitant preference for G/C over A/T in the third codon position, a preference for RNY type codons (purine/any nucleotide/pyrimidine), and/or a bias against serine and leucine, the only amino acids with codons that can be read as stop codons in the antisense direction. The PrP genes and most heat shock genes with long antisense NRFs (aNRFs) are indeed relatively [G+C] rich but do not show a bias against serine and leucine. In several vertebrates investigated, at least one of the Hsp70 genes has a long antisense reading frame, and we found that some, though not all, putative stop codons in long Hsp70 antisense reading frames were due to sequencing errors. The PrP gene contains an extended antisense open reading frame in all 45 eutherian mammals tested, but not in a marsupial and in a bird. In the PrP gene, the long, protein-coding exon also harbors the antisense nonstop reading frame. In both Hsp70 and PrP genes, the putative antisense protein sequence is well conserved. Even though there is no clear evidence in Hsp70 or PrP genes for the existence of the respective antisense proteins, we speculate that such antisense proteins serve to regulate the genuine Hsp and PrP proteins under special circumstances. Alternatively, regulation might occur at the RNA level, and the antisense RNA would merely lack stop codons to prevent its rapid degradation by an mRNA quality control mechanism that is triggered by premature stop codons. We note that both Hsp and PrP are involved in physiological or pathological protein aggregation phenomena, that scrapie prions have been reported to modify the expression or localization of heat shock proteins, and that in yeast, propagation of a prion-like state (PSI+) depends on a heat shock (Hsp104) protein.
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Affiliation(s)
- K I Rother
- Institut für Molekularbiologie II, Universität Zürich, Switzerland
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