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Meier CS, Pagni M, Richard S, Mühlethaler K, Almeida JMGCF, Nevez G, Cushion MT, Calderón EJ, Hauser PM. Fungal antigenic variation using mosaicism and reassortment of subtelomeric genes' repertoires. Nat Commun 2023; 14:7026. [PMID: 37919276 PMCID: PMC10622565 DOI: 10.1038/s41467-023-42685-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 10/18/2023] [Indexed: 11/04/2023] Open
Abstract
Surface antigenic variation is crucial for major pathogens that infect humans. To escape the immune system, they exploit various mechanisms. Understanding these mechanisms is important to better prevent and fight the deadly diseases caused. Those used by the fungus Pneumocystis jirovecii that causes life-threatening pneumonia in immunocompromised individuals remain poorly understood. Here, though this fungus is currently not cultivable, our detailed analysis of the subtelomeric sequence motifs and genes encoding surface proteins suggests that the system involves the reassortment of the repertoire of ca. 80 non-expressed genes present in each strain, from which single genes are retrieved for mutually exclusive expression. Dispersion of the new repertoires, supposedly by healthy carrier individuals, appears very efficient because identical alleles are observed in patients from different countries. Our observations reveal a unique strategy of antigenic variation. They also highlight the possible role in genome rearrangements of small imperfect mirror sequences forming DNA triplexes.
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Affiliation(s)
- Caroline S Meier
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Marco Pagni
- Vital-IT Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Sophie Richard
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Konrad Mühlethaler
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - João M G C F Almeida
- UCIBIO, Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal
| | - Gilles Nevez
- Laboratoire de Parasitologie et Mycologie, Hôpital de La Cavale Blanche, CHU de Brest, Brest, France
- Infections respiratoires fongiques (IFR), Université d'Angers, Université de Brest, Brest, France
| | - Melanie T Cushion
- Department of Internal Medicine, Division of Infectious Diseases, College of Medicine, University of Cincinnati, Cincinnati, OH, 45267, USA
- Cincinnati VAMC, Medical Research Service, Cincinnati, OH, 45220, USA
| | - Enrique J Calderón
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocίo/Consejo Superior de Investigaciones Cientίficas/Universidad de Sevilla, Seville, Spain
- Centro de Investigación Biomédica en Red de Epidemiologίa y Salud Pública, Servicio de Medicina Interna, Hospital Universitario Virgen del Rocίo, Departamento de Medicina, Facultad de Medicina, Seville, Spain
| | - Philippe M Hauser
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland.
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Priyashantha AKH, Dai DQ, Bhat DJ, Stephenson SL, Promputtha I, Kaushik P, Tibpromma S, Karunarathna SC. Plant-Fungi Interactions: Where It Goes? BIOLOGY 2023; 12:809. [PMID: 37372094 PMCID: PMC10295453 DOI: 10.3390/biology12060809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 05/29/2023] [Accepted: 05/30/2023] [Indexed: 06/29/2023]
Abstract
Fungi live different lifestyles-including pathogenic and symbiotic-by interacting with living plants. Recently, there has been a substantial increase in the study of phytopathogenic fungi and their interactions with plants. Symbiotic relationships with plants appear to be lagging behind, although progressive. Phytopathogenic fungi cause diseases in plants and put pressure on survival. Plants fight back against such pathogens through complicated self-defense mechanisms. However, phytopathogenic fungi develop virulent responses to overcome plant defense reactions, thus continuing their deteriorative impacts. Symbiotic relationships positively influence both plants and fungi. More interestingly, they also help plants protect themselves from pathogens. In light of the nonstop discovery of novel fungi and their strains, it is imperative to pay more attention to plant-fungi interactions. Both plants and fungi are responsive to environmental changes, therefore construction of their interaction effects has emerged as a new field of study. In this review, we first attempt to highlight the evolutionary aspect of plant-fungi interactions, then the mechanism of plants to avoid the negative impact of pathogenic fungi, and fungal strategies to overcome the plant defensive responses once they have been invaded, and finally the changes of such interactions under the different environmental conditions.
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Affiliation(s)
- A. K. Hasith Priyashantha
- Center for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing 655011, China; (A.K.H.P.); (D.-Q.D.)
| | - Dong-Qin Dai
- Center for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing 655011, China; (A.K.H.P.); (D.-Q.D.)
| | - Darbhe J. Bhat
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia;
- Biology Division, Vishnugupta Vishwavidyapeetam, Gokarna 581326, India
| | - Steven L. Stephenson
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA;
| | - Itthayakorn Promputtha
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand;
| | | | - Saowaluck Tibpromma
- Center for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing 655011, China; (A.K.H.P.); (D.-Q.D.)
| | - Samantha C. Karunarathna
- Center for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing 655011, China; (A.K.H.P.); (D.-Q.D.)
- National Institute of Fundamental Studies (NIFS), Hantana Road, Kandy 20000, Sri Lanka
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Ametrano CG, Lumbsch HT, Di Stefano I, Sangvichien E, Muggia L, Grewe F. Should we hail the Red King? Evolutionary consequences of a mutualistic lifestyle in genomes of lichenized ascomycetes. Ecol Evol 2022; 12:e8471. [PMID: 35136549 PMCID: PMC8809443 DOI: 10.1002/ece3.8471] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 11/18/2021] [Accepted: 11/19/2021] [Indexed: 11/17/2022] Open
Abstract
The Red Queen dynamic is often brought into play for antagonistic relationships. However, the coevolutionary effects of mutualistic interactions, which predict slower evolution for interacting organisms (Red King), have been investigated to a lesser extent. Lichens are a stable, mutualistic relationship of fungi and cyanobacteria and/or algae, which originated several times independently during the evolution of fungi. Therefore, they represent a suitable system to investigate the coevolutionary effect of mutualism on the fungal genome. We measured substitution rates and selective pressure of about 2000 protein-coding genes (plus the rDNA region) in two different classes of Ascomycota, each consisting of closely related lineages of lichenized and non-lichenized fungi. Our results show that independent lichenized clades are characterized by significantly slower rates for both synonymous and non-synonymous substitutions. We hypothesize that this evolutionary pattern is connected to the lichen life cycle (longer generation time of lichenized fungi) rather than a result of different selection strengths, which is described as the main driver for the Red Kind dynamic. This first empirical evidence of slower evolution in lichens provides an important insight on how biotic cooperative interactions are able to shape the evolution of symbiotic organisms.
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Affiliation(s)
- Claudio G. Ametrano
- Grainger Bioinformatics Center and Negaunee Integrative Research Center, Science and EducationField Museum of Natural HistoryChicagoIllinoisUSA
| | - H. Thorsten Lumbsch
- Grainger Bioinformatics Center and Negaunee Integrative Research Center, Science and EducationField Museum of Natural HistoryChicagoIllinoisUSA
| | - Isabel Di Stefano
- Grainger Bioinformatics Center and Negaunee Integrative Research Center, Science and EducationField Museum of Natural HistoryChicagoIllinoisUSA
| | - Ek Sangvichien
- Department of BiologyFaculty of ScienceRamkhamhaeng UniversityBangkokThailand
| | | | - Felix Grewe
- Grainger Bioinformatics Center and Negaunee Integrative Research Center, Science and EducationField Museum of Natural HistoryChicagoIllinoisUSA
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Ma L, Chen Z, Huang DW, Cissé OH, Rothenburger JL, Latinne A, Bishop L, Blair R, Brenchley JM, Chabé M, Deng X, Hirsch V, Keesler R, Kutty G, Liu Y, Margolis D, Morand S, Pahar B, Peng L, Van Rompay KKA, Song X, Song J, Sukura A, Thapar S, Wang H, Weissenbacher-Lang C, Xu J, Lee CH, Jardine C, Lempicki RA, Cushion MT, Cuomo CA, Kovacs JA. Diversity and Complexity of the Large Surface Protein Family in the Compacted Genomes of Multiple Pneumocystis Species. mBio 2020; 11:e02878-19. [PMID: 32127451 PMCID: PMC7064768 DOI: 10.1128/mbio.02878-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 01/16/2020] [Indexed: 12/23/2022] Open
Abstract
Pneumocystis, a major opportunistic pathogen in patients with a broad range of immunodeficiencies, contains abundant surface proteins encoded by a multicopy gene family, termed the major surface glycoprotein (Msg) gene superfamily. This superfamily has been identified in all Pneumocystis species characterized to date, highlighting its important role in Pneumocystis biology. In this report, through a comprehensive and in-depth characterization of 459 msg genes from 7 Pneumocystis species, we demonstrate, for the first time, the phylogeny and evolution of conserved domains in Msg proteins and provide a detailed description of the classification, unique characteristics, and phylogenetic relatedness of five Msg families. We further describe, for the first time, the relative expression levels of individual msg families in two rodent Pneumocystis species, the substantial variability of the msg repertoires in P. carinii from laboratory and wild rats, and the distinct features of the expression site for the classic msg genes in Pneumocystis from 8 mammalian host species. Our analysis suggests multiple functions for this superfamily rather than just conferring antigenic variation to allow immune evasion as previously believed. This study provides a rich source of information that lays the foundation for the continued experimental exploration of the functions of the Msg superfamily in Pneumocystis biology.IMPORTANCEPneumocystis continues to be a major cause of disease in humans with immunodeficiency, especially those with HIV/AIDS and organ transplants, and is being seen with increasing frequency worldwide in patients treated with immunodepleting monoclonal antibodies. Annual health care associated with Pneumocystis pneumonia costs ∼$475 million dollars in the United States alone. In addition to causing overt disease in immunodeficient individuals, Pneumocystis can cause subclinical infection or colonization in healthy individuals, which may play an important role in species preservation and disease transmission. Our work sheds new light on the diversity and complexity of the msg superfamily and strongly suggests that the versatility of this superfamily reflects multiple functions, including antigenic variation to allow immune evasion and optimal adaptation to host environmental conditions to promote efficient infection and transmission. These findings are essential to consider in developing new diagnostic and therapeutic strategies.
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Affiliation(s)
- Liang Ma
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Zehua Chen
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Da Wei Huang
- Leidos BioMedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Ousmane H Cissé
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Jamie L Rothenburger
- Department of Pathobiology, Canadian Wildlife Health Cooperative, Ontario Veterinary College, University of Guelph, Ontario, Canada
| | | | - Lisa Bishop
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Robert Blair
- Tulane National Primate Research Center, Tulane University, New Orleans, Louisiana, USA
| | - Jason M Brenchley
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Magali Chabé
- Université Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 8204-CIIL-Centre d'Infection et d'Immunité de Lille, Lille, France
| | - Xilong Deng
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Vanessa Hirsch
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Rebekah Keesler
- California National Primate Research Center, University of California, Davis, Davis, California, USA
| | - Geetha Kutty
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Yueqin Liu
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Daniel Margolis
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Serge Morand
- Institut des Sciences de l'Evolution, Université de Montpellier 2, Montpellier, France
| | - Bapi Pahar
- Tulane National Primate Research Center, Tulane University, New Orleans, Louisiana, USA
| | - Li Peng
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Koen K A Van Rompay
- California National Primate Research Center, University of California, Davis, Davis, California, USA
| | - Xiaohong Song
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Jun Song
- Center for Advanced Models for Translational Sciences and Therapeutics, University of Michigan Medical Center, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Antti Sukura
- Department of Veterinary Pathology, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Sabrina Thapar
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Honghui Wang
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | | | - Jie Xu
- Center for Advanced Models for Translational Sciences and Therapeutics, University of Michigan Medical Center, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Chao-Hung Lee
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Claire Jardine
- Department of Pathobiology, Canadian Wildlife Health Cooperative, Ontario Veterinary College, University of Guelph, Ontario, Canada
| | - Richard A Lempicki
- Leidos BioMedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Melanie T Cushion
- Department of Internal Medicine, College of Medicine, University of Cincinnati, Cincinnati, Ohio, USA
| | - Christina A Cuomo
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Joseph A Kovacs
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
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Fillinger RJ, Anderson MZ. Seasons of change: Mechanisms of genome evolution in human fungal pathogens. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2019; 70:165-174. [PMID: 30826447 DOI: 10.1016/j.meegid.2019.02.031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 02/23/2019] [Accepted: 02/26/2019] [Indexed: 06/09/2023]
Abstract
Fungi are a diverse kingdom of organisms capable of thriving in various niches across the world including those in close association with multicellular eukaryotes. Fungal pathogens that contribute to human disease reside both within the host as commensal organisms of the microbiota and the environment. Their niche of origin dictates how infection initiates but also places specific selective pressures on the fungal pathogen that contributes to its genome organization and genetic repertoire. Recent efforts to catalogue genomic variation among major human fungal pathogens have unveiled evolutionary themes that shape the fungal genome. Mechanisms ranging from large scale changes such as aneuploidy and ploidy cycling as well as more targeted mutations like base substitutions and gene copy number variations contribute to the evolution of these species, which are often under multiple competing selective pressures with their host, environment, and other microbes. Here, we provide an overview of the major selective pressures and mechanisms acting to evolve the genome of clinically important fungal pathogens of humans.
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Affiliation(s)
- Robert J Fillinger
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210, USA
| | - Matthew Z Anderson
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210, USA; Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.
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