1
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Dallagnol LC, Cônsoli FL. Evolutionary and phylogenetic insights from the mitochondrial genomic analysis of Diceraeus melacanthus and D. furcatus (Hemiptera: Pentatomidae). Sci Rep 2024; 14:12861. [PMID: 38834792 DOI: 10.1038/s41598-024-63584-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 05/30/2024] [Indexed: 06/06/2024] Open
Abstract
The mitochondrial genomes of D. melacanthus and D. furcatus were sequenced and used to investigate the phylogenetic relationships with 54 species of Pentatomidae. Their mitogenomes are 17,197 and 15,444 bp-long, respectively, including 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, and 22/21 transfer RNA genes, with conserved gene arrangement. Leu, Lys, and Ser were the most common amino acids in their PCGs. PCGs evolutionary analysis indicated their mitogenomes are under purifying selection, and the most conserved genes are from the cytochrome complex, reinforcing their suitability as markers for molecular taxonomy. We identified 490 mtSSRs in 56 Pentatomidae species, with large variation and a positive correlation between mtSSR number and genome size. Three mtSSRs were identified in each Diceraeus species. Only the mtSSR in the nad6 (D. melacanthus) and nad4 (D. furcatus) appear to have application as molecular markers for species characterization. Phylogenetic analysis confirmed the monophyly of Pentatomidae. However, our analysis challenged the monophyly of Pentatominae and Podopinae. We also detected unexpected relationships among some tribes and genera, highlighting the complexity of the internal taxonomic structure of Pentatomidae. Both Diceraeus species were grouped in the same clade with the remaining Carpocorini analyzed.
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Affiliation(s)
- Lilian Cris Dallagnol
- Insect Interactions Laboratory, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, SP, Brazil
| | - Fernando Luís Cônsoli
- Insect Interactions Laboratory, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, SP, Brazil.
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2
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Earle K, Valero C, Conn DP, Vere G, Cook PC, Bromley MJ, Bowyer P, Gago S. Pathogenicity and virulence of Aspergillus fumigatus. Virulence 2023; 14:2172264. [PMID: 36752587 PMCID: PMC10732619 DOI: 10.1080/21505594.2023.2172264] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 12/16/2022] [Indexed: 02/09/2023] Open
Abstract
Pulmonary infections caused by the mould pathogen Aspergillus fumigatus are a major cause of morbidity and mortality globally. Compromised lung defences arising from immunosuppression, chronic respiratory conditions or more recently, concomitant viral or bacterial pulmonary infections are recognised risks factors for the development of pulmonary aspergillosis. In this review, we will summarise our current knowledge of the mechanistic basis of pulmonary aspergillosis with a focus on emerging at-risk populations.
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Affiliation(s)
- Kayleigh Earle
- Manchester Fungal Infection Group, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Clara Valero
- Manchester Fungal Infection Group, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Daniel P. Conn
- MRC Centre for Medical Mycology, University of Exeter, Exeter, UK
| | - George Vere
- MRC Centre for Medical Mycology, University of Exeter, Exeter, UK
| | - Peter C. Cook
- MRC Centre for Medical Mycology, University of Exeter, Exeter, UK
| | - Michael J. Bromley
- Manchester Fungal Infection Group, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Paul Bowyer
- Manchester Fungal Infection Group, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Sara Gago
- Manchester Fungal Infection Group, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
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3
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Barac A, Vujovic A, Drazic A, Stevanovic G, Paglietti B, Lukic K, Stojanovic M, Stjepanovic M. Diagnosis of Chronic Pulmonary Aspergillosis: Clinical, Radiological or Laboratory? J Fungi (Basel) 2023; 9:1084. [PMID: 37998889 PMCID: PMC10672318 DOI: 10.3390/jof9111084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 10/27/2023] [Accepted: 11/03/2023] [Indexed: 11/25/2023] Open
Abstract
Chronic pulmonary aspergillosis (CPA) is a chronic progressive lung disease associated with a poor prognosis and a 5-year mortality rate of approximately 40-50%. The disease is characterized by slowly progressive destruction of the lung parenchyma, in the form of multiple cavities, nodules, infiltrates or fibrosis. CPA can be challenging to diagnose due to its non-specific symptoms and similarities with other respiratory conditions combined with the poor awareness of the medical community about the disease. This can result in delayed treatment even for years and worsening of the patient's condition. Serological tests certainly play a significant role in diagnosing CPA but cannot be interpreted without radiological confirmation of CPA. Although many data are published on this hot topic, there is yet no single definitive test for diagnosing CPA, and a multidisciplinary approach which involves a combination of clinical picture, radiological findings, microbiological results and exclusion of other mimicking diseases, is essential for the accurate diagnosis of CPA.
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Affiliation(s)
- Aleksandra Barac
- Clinic for Infectious and Tropical Diseases, University Clinical Center of Serbia, 11000 Belgrade, Serbia; (A.V.); (G.S.)
- Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia; (A.D.); (M.S.); (M.S.)
| | - Ankica Vujovic
- Clinic for Infectious and Tropical Diseases, University Clinical Center of Serbia, 11000 Belgrade, Serbia; (A.V.); (G.S.)
- Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia; (A.D.); (M.S.); (M.S.)
| | - Ana Drazic
- Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia; (A.D.); (M.S.); (M.S.)
| | - Goran Stevanovic
- Clinic for Infectious and Tropical Diseases, University Clinical Center of Serbia, 11000 Belgrade, Serbia; (A.V.); (G.S.)
- Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia; (A.D.); (M.S.); (M.S.)
| | - Bianca Paglietti
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy;
| | - Katarina Lukic
- Center for Radiology and MRI, University Clinical Center of Serbia, 11000 Belgrade, Serbia;
| | - Maja Stojanovic
- Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia; (A.D.); (M.S.); (M.S.)
- Clinic of Allergy and Immunology, University Clinical Center of Serbia, 11000 Belgrade, Serbia
| | - Mihailo Stjepanovic
- Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia; (A.D.); (M.S.); (M.S.)
- Clinic for Pulmonology, University Clinical Center of Serbia, 11000 Belgrade, Serbia
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4
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Hu Y, Gong H, Lu Z, Zhang P, Zheng S, Wang J, Tian B, Fang A, Yang Y, Bi C, Cheng J, Yu Y. Variable Tandem Glycine-Rich Repeats Contribute to Cell Death-Inducing Activity of a Glycosylphosphatidylinositol-Anchored Cell Wall Protein That Is Associated with the Pathogenicity of Sclerotinia sclerotiorum. Microbiol Spectr 2023; 11:e0098623. [PMID: 37140432 PMCID: PMC10269696 DOI: 10.1128/spectrum.00986-23] [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: 03/06/2023] [Accepted: 04/07/2023] [Indexed: 05/05/2023] Open
Abstract
Glycosylphosphatidylinositol (GPI) anchoring of proteins is a conserved posttranslational modification in eukaryotes. GPI-anchored proteins are widely distributed in fungal plant pathogens, but the specific roles of the GPI-anchored proteins in the pathogenicity of Sclerotinia sclerotiorum, a devastating necrotrophic plant pathogen with a worldwide distribution, remain largely unknown. This research addresses SsGSR1, which encodes an S. sclerotiorum glycine- and serine-rich protein named SsGsr1 with an N-terminal secretory signal and a C-terminal GPI-anchor signal. SsGsr1 is located at the cell wall of hyphae, and deletion of SsGSR1 leads to abnormal cell wall architecture and impaired cell wall integrity of hyphae. The transcription levels of SsGSR1 were maximal in the initial stage of infection, and SsGSR1-deletion strains showed impaired virulence in multiple hosts, indicating that SsGSR1 is critical for the pathogenicity. Interestingly, SsGsr1 targeted the apoplast of host plants to induce cell death that relies on the glycine-rich 11-amino-acid repeats arranged in tandem. The homologs of SsGsr1 in Sclerotinia, Botrytis, and Monilinia species contain fewer repeat units and have lost their cell death activity. Moreover, allelic variants of SsGSR1 exist in field isolates of S. sclerotiorum from rapeseed, and one of the variants lacking one repeat unit results in a protein that exhibits loss of function relative to the cell death-inducing activity and the virulence of S. sclerotiorum. Taken together, our results demonstrate that a variation in tandem repeats provides the functional diversity of GPI-anchored cell wall protein that, in S. sclerotiorum and other necrotrophic pathogens, allows successful colonization of the host plants. IMPORTANCE Sclerotinia sclerotiorum is an economically important necrotrophic plant pathogen and mainly applies cell wall-degrading enzymes and oxalic acid to kill plant cells before colonization. In this research, we characterized a glycosylphosphatidylinositol (GPI)-anchored cell wall protein named SsGsr1, which is critical for the cell wall architecture and the pathogenicity of S. sclerotiorum. Additionally, SsGsr1 induces rapid cell death of host plants that is dependent on glycine-rich tandem repeats. Interestingly, the number of repeat units varies among homologs and alleles of SsGsr1, and such a variation creates alterations in the cell death-inducing activity and the role in pathogenicity. This work advances our understanding of the variation of tandem repeats in accelerating the evolution of a GPI-anchored cell wall protein associated with the pathogenicity of necrotrophic fungal pathogens and prepares the way toward a fuller understanding of the interaction between S. sclerotiorum and host plants.
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Affiliation(s)
- Yawen Hu
- College of Plant Protection, Southwest University, Chongqing City, China
| | - Hang Gong
- College of Plant Protection, Southwest University, Chongqing City, China
| | - Ziyang Lu
- College of Plant Protection, Southwest University, Chongqing City, China
| | - Pengpeng Zhang
- College of Plant Protection, Southwest University, Chongqing City, China
| | - Sinian Zheng
- College of Plant Protection, Southwest University, Chongqing City, China
| | - Jing Wang
- College of Plant Protection, Southwest University, Chongqing City, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River, Ministry of Education, Southwest University, Chongqing City, China
| | - Binnian Tian
- College of Plant Protection, Southwest University, Chongqing City, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River, Ministry of Education, Southwest University, Chongqing City, China
| | - Anfei Fang
- College of Plant Protection, Southwest University, Chongqing City, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River, Ministry of Education, Southwest University, Chongqing City, China
| | - Yuheng Yang
- College of Plant Protection, Southwest University, Chongqing City, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River, Ministry of Education, Southwest University, Chongqing City, China
| | - Chaowei Bi
- College of Plant Protection, Southwest University, Chongqing City, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River, Ministry of Education, Southwest University, Chongqing City, China
| | - Jiasen Cheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan City, China
| | - Yang Yu
- College of Plant Protection, Southwest University, Chongqing City, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River, Ministry of Education, Southwest University, Chongqing City, China
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5
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Zhu X, Guo L, Zhu R, Zhou X, Zhang J, Li D, He S, Qiao Y. Phytophthora sojae effector PsAvh113 associates with the soybean transcription factor GmDPB to inhibit catalase-mediated immunity. PLANT BIOTECHNOLOGY JOURNAL 2023. [PMID: 36972124 DOI: 10.1111/pbi.14043] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/17/2023] [Accepted: 02/28/2023] [Indexed: 06/18/2023]
Abstract
Phytophthora species are the most destructive plant pathogens worldwide and the main threat to agricultural and natural ecosystems; however, their pathogenic mechanism remains largely unknown. Here, we show that Avh113 effector is required for the virulence of Phytophthora sojae and is important for development of Phytophthora root and stem rot (PRSR) in soybean (Glycine max). Ectopic expression of PsAvh113 enhanced viral and Phytophthora infection in Nicotiana benthamiana. PsAvh113 directly associated with the soybean transcription factor GmDPB, inducing its degradation by the 26S proteasome. The internal repeat 2 (IR2) motif of PsAvh113 was important for its virulence and interaction with GmDPB, while silencing and overexpression of GmDPB in soybean hairy roots altered the resistance to P. sojae. Upon binding to GmDPB, PsAvh113 decreased the transcription of the downstream gene GmCAT1, which acts as a positive regulator of plant immunity. Furthermore, we revealed that PsAvh113 suppressed the GmCAT1-induced cell death by associating with GmDPB, thereby enhancing plant susceptibility to Phytophthora. Together, our findings reveal a vital role of PsAvh113 in inducing PRSR in soybean and offer a novel insight into the interplay between defence and counter-defence during the P. sojae infection of soybean.
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Affiliation(s)
- Xiaoguo Zhu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Liang Guo
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Ruiqing Zhu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Xiaoyi Zhou
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Jianing Zhang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Die Li
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Shidan He
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Yongli Qiao
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
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6
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Wright SE, Todd PK. Native functions of short tandem repeats. eLife 2023; 12:e84043. [PMID: 36940239 PMCID: PMC10027321 DOI: 10.7554/elife.84043] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 03/08/2023] [Indexed: 03/21/2023] Open
Abstract
Over a third of the human genome is comprised of repetitive sequences, including more than a million short tandem repeats (STRs). While studies of the pathologic consequences of repeat expansions that cause syndromic human diseases are extensive, the potential native functions of STRs are often ignored. Here, we summarize a growing body of research into the normal biological functions for repetitive elements across the genome, with a particular focus on the roles of STRs in regulating gene expression. We propose reconceptualizing the pathogenic consequences of repeat expansions as aberrancies in normal gene regulation. From this altered viewpoint, we predict that future work will reveal broader roles for STRs in neuronal function and as risk alleles for more common human neurological diseases.
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Affiliation(s)
- Shannon E Wright
- Department of Neurology, University of Michigan–Ann ArborAnn ArborUnited States
- Neuroscience Graduate Program, University of Michigan–Ann ArborAnn ArborUnited States
- Department of Neuroscience, Picower InstituteCambridgeUnited States
| | - Peter K Todd
- Department of Neurology, University of Michigan–Ann ArborAnn ArborUnited States
- VA Ann Arbor Healthcare SystemAnn ArborUnited States
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7
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Descorps-Declère S, Richard GF. Megasatellite formation and evolution in vertebrate genes. Cell Rep 2022; 40:111347. [PMID: 36103826 DOI: 10.1016/j.celrep.2022.111347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 04/28/2022] [Accepted: 08/23/2022] [Indexed: 11/03/2022] Open
Abstract
Since formation of the first proto-eukaryotes, gene repertoire and genome complexity have significantly increased. Among genetic elements responsible for this increase are tandem repeats. Here we describe a genome-wide analysis of large tandem repeats, called megasatellites, in 58 vertebrate genomes. Two bursts occurred, one after the radiation between Agnatha and Gnathostomata fishes and the second one in therian mammals. Megasatellites are enriched in subtelomeric regions and frequently encoded in genes involved in transcription regulation, intracellular trafficking, and cell membrane metabolism, reminiscent of what is observed in fungus genomes. The presence of many introns within young megasatellites suggests that an exon-intron DNA segment is first duplicated and amplified before accumulation of mutations in intronic parts partially erases the megasatellite in such a way that it becomes detectable only in exons. Our results suggest that megasatellite formation and evolution is a dynamic and still ongoing process in vertebrate genomes.
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Affiliation(s)
- Stéphane Descorps-Declère
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, 25 rue du Dr Roux, 75015 Paris, France.
| | - Guy-Franck Richard
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Natural & Synthetic Genome Instabilities, 25 rue du Dr Roux, 75015 Paris, France.
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8
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Subroto E, van Neer J, Valdes I, de Cock H. Growth of Aspergillus fumigatus in Biofilms in Comparison to Candida albicans. J Fungi (Basel) 2022; 8:48. [PMID: 35049988 PMCID: PMC8779434 DOI: 10.3390/jof8010048] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 12/29/2021] [Accepted: 12/31/2021] [Indexed: 12/18/2022] Open
Abstract
Biofilm formation during infections with the opportunistic pathogen Aspergillus fumigatus can be very problematic in clinical settings, since it provides the fungal cells with a protective environment. Resistance against drug treatments, immune recognition as well as adaptation to the host environment allows fungal survival in the host. The exact molecular mechanisms behind most processes in the formation of biofilms are unclear. In general, the formation of biofilms can be categorized roughly in a few stages; adhesion, conidial germination and development of hyphae, biofilm maturation and cell dispersion. Fungi in biofilms can adapt to the in-host environment. These adaptations can occur on a level of phenotypic plasticity via gene regulation. However, also more substantial genetic changes of the genome can result in increased resistance and adaptation in the host, enhancing the survival chances of fungi in biofilms. Most research has focused on the development of biofilms. However, to tackle developing microbial resistance and adaptation in biofilms, more insight in mechanisms behind genetic adaptations is required to predict which defense mechanisms can be expected. This can be helpful in the development of novel and more targeted antifungal treatments to combat fungal infections.
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Affiliation(s)
| | | | | | - Hans de Cock
- Molecular Microbiology Laboratory, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; (E.S.); (J.v.N.); (I.V.)
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9
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Arastehfar A, Carvalho A, Houbraken J, Lombardi L, Garcia-Rubio R, Jenks J, Rivero-Menendez O, Aljohani R, Jacobsen I, Berman J, Osherov N, Hedayati M, Ilkit M, Armstrong-James D, Gabaldón T, Meletiadis J, Kostrzewa M, Pan W, Lass-Flörl C, Perlin D, Hoenigl M. Aspergillus fumigatus and aspergillosis: From basics to clinics. Stud Mycol 2021; 100:100115. [PMID: 34035866 PMCID: PMC8131930 DOI: 10.1016/j.simyco.2021.100115] [Citation(s) in RCA: 99] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The airborne fungus Aspergillus fumigatus poses a serious health threat to humans by causing numerous invasive infections and a notable mortality in humans, especially in immunocompromised patients. Mould-active azoles are the frontline therapeutics employed to treat aspergillosis. The global emergence of azole-resistant A. fumigatus isolates in clinic and environment, however, notoriously limits the therapeutic options of mould-active antifungals and potentially can be attributed to a mortality rate reaching up to 100 %. Although specific mutations in CYP 51A are the main cause of azole resistance, there is a new wave of azole-resistant isolates with wild-type CYP 51A genotype challenging the efficacy of the current diagnostic tools. Therefore, applications of whole-genome sequencing are increasingly gaining popularity to overcome such challenges. Prominent echinocandin tolerance, as well as liver and kidney toxicity posed by amphotericin B, necessitate a continuous quest for novel antifungal drugs to combat emerging azole-resistant A. fumigatus isolates. Animal models and the tools used for genetic engineering require further refinement to facilitate a better understanding about the resistance mechanisms, virulence, and immune reactions orchestrated against A. fumigatus. This review paper comprehensively discusses the current clinical challenges caused by A. fumigatus and provides insights on how to address them.
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Affiliation(s)
- A. Arastehfar
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, 07110, USA
| | - A. Carvalho
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's - PT Government Associate Laboratory, Guimarães/Braga, Portugal
| | - J. Houbraken
- Westerdijk Fungal Biodiversity Institute, Utrecht, the Netherlands
| | - L. Lombardi
- UCD Conway Institute and School of Medicine, University College Dublin, Dublin 4, Ireland
| | - R. Garcia-Rubio
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, 07110, USA
| | - J.D. Jenks
- Department of Medicine, University of California San Diego, San Diego, CA, 92103, USA
- Clinical and Translational Fungal-Working Group, University of California San Diego, La Jolla, CA, 92093, USA
| | - O. Rivero-Menendez
- Medical Mycology Reference Laboratory, National Center for Microbiology, Instituto de Salud Carlos III, Madrid, 28222, Spain
| | - R. Aljohani
- Department of Infectious Diseases, Imperial College London, London, UK
| | - I.D. Jacobsen
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology—Hans Knöll Institute, Jena, Germany
- Institute for Microbiology, Friedrich Schiller University, Jena, Germany
| | - J. Berman
- Research Group Microbial Immunology, Leibniz Institute for Natural Product Research and Infection Biology—Hans Knöll Institute, Jena, Germany
| | - N. Osherov
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine Ramat-Aviv, Tel-Aviv, 69978, Israel
| | - M.T. Hedayati
- Invasive Fungi Research Center/Department of Medical Mycology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - M. Ilkit
- Division of Mycology, Department of Microbiology, Faculty of Medicine, Çukurova University, 01330, Adana, Turkey
| | | | - T. Gabaldón
- Life Sciences Programme, Supercomputing Center (BSC-CNS), Jordi Girona, Barcelona, 08034, Spain
- Mechanisms of Disease Programme, Institute for Research in Biomedicine (IRB), Barcelona, Spain
- ICREA, Pg. Lluís Companys 23, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010, Barcelona, Spain
| | - J. Meletiadis
- Clinical Microbiology Laboratory, Attikon University Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | | | - W. Pan
- Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, 200003, China
| | - C. Lass-Flörl
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - D.S. Perlin
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, 07110, USA
| | - M. Hoenigl
- Department of Medicine, University of California San Diego, San Diego, CA, 92103, USA
- Section of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Medical University of Graz, 8036, Graz, Austria
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, San Diego, CA 92093, USA
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10
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Schiefermeier-Mach N, Perkhofer S, Heinrich L, Haller T. Stimulation of surfactant exocytosis in primary alveolar type II cells by A. fumigatus. Med Mycol 2021; 59:168-179. [PMID: 32459847 DOI: 10.1093/mmy/myaa042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 04/06/2020] [Accepted: 04/30/2020] [Indexed: 02/06/2023] Open
Abstract
Aspergillus fumigatus is an opportunistic fungal pathogen with small airborne spores (conidia) that may escape clearance by upper airways and directly impact the alveolar epithelium. Consequently, innate alveolar defense mechanisms are being activated, including professional phagocytosis by alveolar macrophages, recruitment of circulating neutrophils and probably enhanced secretion of pulmonary surfactant by the alveolar type II (AT II) cells. However, no data are available in support of the latter hypothesis. We therefore used a coculture model of GFP-Aspergillus conidia with primary rat AT II cells and studied fungal growth, cellular Ca2+ homeostasis, and pulmonary surfactant exocytosis by live cell video microscopy. We observed all stages of fungal development, including reversible attachment, binding and internalization of conidia as well as conidial swelling, formation of germ tubes and outgrowth of hyphae. In contrast to resting conidia, which did not provoke immediate cellular effects, metabolically active conidia, fungal cellular extracts (CE) and fungal culture filtrates (CF) prepared from swollen conidia caused a Ca2+-independent exocytosis. Ca2+ signals of greatly varying delays, durations and amplitudes were observed by applying CE or CF obtained from hyphae of A. fumigatus, suggesting compounds secreted by filamentous A. fumigatus that severely interfere with AT II cell Ca2+ homeostasis. The mechanisms underlying the stimulatory effects, with respect to exocytosis and Ca2+ signaling, are unclear and need to be identified.
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Affiliation(s)
| | - Susanne Perkhofer
- FH Gesundheit, Health University of Applied Sciences Tyrol, Innrain 98, A-6020 Innsbruck, Austria
| | - Lea Heinrich
- FH Gesundheit, Health University of Applied Sciences Tyrol, Innrain 98, A-6020 Innsbruck, Austria.,Department of Physiology and Medical Physics, Institute of Physiology, Medical University of Innsbruck, Schöpfstrasse 41, A-6020 Innsbruck, Austria
| | - Thomas Haller
- Department of Physiology and Medical Physics, Institute of Physiology, Medical University of Innsbruck, Schöpfstrasse 41, A-6020 Innsbruck, Austria
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11
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Warner EF, Bohálová N, Brázda V, Waller ZAE, Bidula S. Analysis of putative quadruplex-forming sequences in fungal genomes: novel antifungal targets? Microb Genom 2021; 7:000570. [PMID: 33956596 PMCID: PMC8209732 DOI: 10.1099/mgen.0.000570] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 03/26/2021] [Indexed: 12/26/2022] Open
Abstract
Fungal infections cause >1 million deaths annually and the emergence of antifungal resistance has prompted the exploration for novel antifungal targets. Quadruplexes are four-stranded nucleic acid secondary structures, which can regulate processes such as transcription, translation, replication and recombination. They are also found in genes linked to virulence in microbes, and ligands that bind to quadruplexes can eliminate drug-resistant pathogens. Using a computational approach, we quantified putative quadruplex-forming sequences (PQS) in 1359 genomes across the fungal kingdom and explored their presence in genes related to virulence, drug resistance and biological processes associated with pathogenicity in Aspergillus fumigatus. Here we present the largest analysis of PQS in fungi and identify significant heterogeneity of these sequences throughout phyla, genera and species. PQS were genetically conserved in Aspergillus spp. and frequently pathogenic species appeared to contain fewer PQS than their lesser/non-pathogenic counterparts. GO-term analysis identified that PQS-containing genes were involved in processes linked with virulence such as zinc ion binding, the biosynthesis of secondary metabolites and regulation of transcription in A. fumigatus. Although the genome frequency of PQS was lower in A. fumigatus, PQS could be found enriched in genes involved in virulence, and genes upregulated during germination and hypoxia. Moreover, PQS were found in genes involved in drug resistance. Quadruplexes could have important roles within fungal biology and virulence, but their roles require further elucidation.
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Affiliation(s)
- Emily F. Warner
- School of Clinical Medicine, University of Cambridge, Cambridge, UK
- Present address: Ikarovec Limited, Norwich Research Park Innovation Centre, Norwich, UK
| | - Natália Bohálová
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czechia
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Václav Brázda
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czechia
| | | | - Stefan Bidula
- School of Biological Sciences, University of East Anglia, Norwich, UK
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12
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van der Torre MH, Shen H, Rautemaa-Richardson R, Richardson MD, Novak-Frazer L. Molecular Epidemiology of Aspergillus fumigatus in Chronic Pulmonary Aspergillosis Patients. J Fungi (Basel) 2021; 7:jof7020152. [PMID: 33672698 PMCID: PMC7924367 DOI: 10.3390/jof7020152] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 02/15/2021] [Accepted: 02/17/2021] [Indexed: 12/17/2022] Open
Abstract
Molecular fungal genotyping techniques developed and employed for epidemiological studies have understandably concentrated on establishing the genetic diversity of Aspergillus fumigatus in invasive aspergillosis due to its severity, the urgency for treatment, and the need to demonstrate possible sources. Some early studies suggested that these strains were phenotypically, if not genotypically, different from others. However, with improved discrimination and evaluations, incorporating environmental as well as clinical isolates from other Aspergillus conditions (e.g., chronic pulmonary aspergillosis and cystic fibrosis), this premise is no longer upheld. Moreover, with the onset of increased global triazole resistance, there has been a concerted effort to incorporate resistance profiling into genotyping studies and the realisation that the wider population of non-immunocompromised aspergillosis patients are at risk. This review summarises the developments in molecular genotyping studies that incorporate resistance profiling with attention to chronic pulmonary aspergillosis and an example of our UK experience.
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Affiliation(s)
- Mireille H. van der Torre
- Mycology Reference Centre Manchester, ECMM Centre of Excellence in Clinical and Laboratory Mycology and Clinical Studies, Manchester University NHS Foundation Trust, Wythenshawe Hospital, Manchester M23 9LT, UK; (M.H.v.d.T.); (R.R.-R.); (M.D.R.)
- Division of Infection, Inflammation and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK;
| | - Hongwei Shen
- Division of Infection, Inflammation and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK;
| | - Riina Rautemaa-Richardson
- Mycology Reference Centre Manchester, ECMM Centre of Excellence in Clinical and Laboratory Mycology and Clinical Studies, Manchester University NHS Foundation Trust, Wythenshawe Hospital, Manchester M23 9LT, UK; (M.H.v.d.T.); (R.R.-R.); (M.D.R.)
- Division of Infection, Inflammation and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK;
- Department of Infectious Diseases, Manchester University NHS Foundation Trust, Wythenshawe Hospital, Manchester M23 9LT, UK
| | - Malcolm D. Richardson
- Mycology Reference Centre Manchester, ECMM Centre of Excellence in Clinical and Laboratory Mycology and Clinical Studies, Manchester University NHS Foundation Trust, Wythenshawe Hospital, Manchester M23 9LT, UK; (M.H.v.d.T.); (R.R.-R.); (M.D.R.)
- Division of Infection, Inflammation and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK;
| | - Lilyann Novak-Frazer
- Mycology Reference Centre Manchester, ECMM Centre of Excellence in Clinical and Laboratory Mycology and Clinical Studies, Manchester University NHS Foundation Trust, Wythenshawe Hospital, Manchester M23 9LT, UK; (M.H.v.d.T.); (R.R.-R.); (M.D.R.)
- Division of Infection, Inflammation and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK;
- Correspondence: ; Tel.: +44-161-2915856
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13
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Besnard F, Picao-Osorio J, Dubois C, Félix MA. A broad mutational target explains a fast rate of phenotypic evolution. eLife 2020; 9:54928. [PMID: 32851977 PMCID: PMC7556874 DOI: 10.7554/elife.54928] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 08/27/2020] [Indexed: 12/30/2022] Open
Abstract
The rapid evolution of a trait in a clade of organisms can be explained by the sustained action of natural selection or by a high mutational variance, that is the propensity to change under spontaneous mutation. The causes for a high mutational variance are still elusive. In some cases, fast evolution depends on the high mutation rate of one or few loci with short tandem repeats. Here, we report on the fastest evolving cell fate among vulva precursor cells in Caenorhabditis nematodes, that of P3.p. We identify and validate causal mutations underlying P3.p's high mutational variance. We find that these positions do not present any characteristics of a high mutation rate, are scattered across the genome and the corresponding genes belong to distinct biological pathways. Our data indicate that a broad mutational target size is the cause of the high mutational variance and of the corresponding fast phenotypic evolutionary rate. Heritable characteristics or traits of a group of organisms, for example the large brain size of primates or the hooves of a horse, are determined by genes, the environment, and by the interactions between them. Traits can change over time and generations when enough mutations in these genes have spread in a species to result in visible differences. However, some traits, such as the large brain of primates, evolve faster than others, but why this is the case has been unclear. It could be that a few specific genes important for that trait in question mutate at a high rate, or, that many genes affect the trait, creating a lot of variation for natural selection to choose from. Here, Besnard, Picao-Osorio et al. studied the roundworm Caenorhabditis elegans to better understand the causes underlying the different rates of trait evolution. These worms have a short life cycle and evolve quickly over many generations, making them an ideal candidate for studying mutation rates in different traits. Previous studies have shown that one of C. elegans’ six cells of the reproductive system evolves faster than the others. To investigate this further, Besnard, Picao-Osorio et al. analysed the genetic mutations driving change in this cell in 250 worm generations. The results showed that five mutations in five different genes – all responsible for different processes in the cells – were behind the supercharged evolution of this particular cell. This suggests that fast evolution results from natural selection acting upon a collection of genes, rather than one gene, and that many genes and pathways shape this trait. In conclusion, these results demonstrate that how traits are coded at the molecular level, in one gene or many, can influence the rate at which they evolve.
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Affiliation(s)
- Fabrice Besnard
- Institut de Biologie de l'École Normale Supérieure, CNRS, Inserm, Paris, France.,Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Inria, Lyon, France
| | - Joao Picao-Osorio
- Institut de Biologie de l'École Normale Supérieure, CNRS, Inserm, Paris, France
| | - Clément Dubois
- Institut de Biologie de l'École Normale Supérieure, CNRS, Inserm, Paris, France
| | - Marie-Anne Félix
- Institut de Biologie de l'École Normale Supérieure, CNRS, Inserm, Paris, France
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14
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Wang Y, Geng L, Xu J, Jiang P, An Q, Pu Y, Jiang Y, He S, Tao X, Luo J, Pan G. Expression and Identification of a Novel Spore Wall Protein in Microsporidian Nosema bombycis. J Eukaryot Microbiol 2020; 67:671-677. [PMID: 32702183 DOI: 10.1111/jeu.12820] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 07/07/2020] [Accepted: 07/14/2020] [Indexed: 01/09/2023]
Abstract
Microsporidia are a group of obligate intracellular parasites causing significant disease in human beings and economically important animals. Though a few spore wall proteins (SWPs) have now been identified in these intriguing species, the information on SWPs remains too little to elucidate the spore wall formation mechanisms of microsporidia. It has been well described that numerous proteins with tandem repeats tend to be localized on the cell wall of fungi and parasites. Previously, by scanning the proteins with tandem repeats in microsporidian Nosema bombycis, we obtained 83 candidate SWPs based on whether those proteins possess a signal peptide and/or transmembrane domain. Here, we further characterized a candidate protein (EOB13250) with three tandem repeats in the N-terminal region and a transmembrane domain in C-terminus of N. bombycis. Sequence analysis showed that the tandem repeat domain of EOB13250 was species-specific for this parasite. RT-PCR indicated that the expression of the gene encoding this protein started on the fourth day postinfection. After cloned and expressed in Escherichia coli, a polyclone antibody against the recombinant EOB13250 protein was prepared. Western blotting demonstrated this protein exist in N. bombycis. Immunofluorescence analysis (IFA) and immunoelectron microscopy analysis (IEM) further provided evidence that EOB13250 was an endospore wall protein. These results together suggested that EOB13250 was a novel spore wall protein of N. bombycis. This study provides a further enrichment of the number of identified spore wall proteins in microsporidia and advances our understanding of the spore wall formation mechanism in these obligate unicellular parasites.
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Affiliation(s)
- Ying Wang
- Department of Pathogenic Biology, School of Basic Medicine, Southwest Medical University, Luzhou, 646000, China.,The State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400716, China
| | - Lixia Geng
- Department of Childcare, Shandong Provincial Third Hospital, Jinan, 250000, China
| | - Jinzhi Xu
- The State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400716, China
| | - Ping Jiang
- School of Clinical Medicine, Southwest Medical University, Luzhou, 646000, China
| | - Qin An
- School of Clinical Medicine, Southwest Medical University, Luzhou, 646000, China
| | - Yaojia Pu
- School of Clinical Medicine, Southwest Medical University, Luzhou, 646000, China
| | - Yu Jiang
- School of Clinical Medicine, Southwest Medical University, Luzhou, 646000, China
| | - Siyi He
- School of Clinical Medicine, Southwest Medical University, Luzhou, 646000, China
| | - Xuemei Tao
- School of Clinical Medicine, Southwest Medical University, Luzhou, 646000, China
| | - Jie Luo
- School of Medicine, Chongqing University of Arts and Sciences, Chongqing, 402160, China
| | - Guoqing Pan
- The State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400716, China
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15
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Blango MG, Pschibul A, Rivieccio F, Krüger T, Rafiq M, Jia LJ, Zheng T, Goldmann M, Voltersen V, Li J, Panagiotou G, Kniemeyer O, Brakhage AA. Dynamic Surface Proteomes of Allergenic Fungal Conidia. J Proteome Res 2020; 19:2092-2104. [PMID: 32233371 DOI: 10.1021/acs.jproteome.0c00013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Fungal spores and hyphal fragments play an important role as allergens in respiratory diseases. In this study, we performed trypsin shaving and secretome analyses to identify the surface-exposed proteins and secreted/shed proteins of Aspergillus fumigatus conidia, respectively. We investigated the surface proteome under different conditions, including temperature variation and germination. We found that the surface proteome of resting A. fumigatus conidia is not static but instead unexpectedly dynamic, as evidenced by drastically different surface proteomes under different growth conditions. Knockouts of two abundant A. fumigatus surface proteins, ScwA and CweA, were found to function only in fine-tuning the cell wall stress response, implying that the conidial surface is very robust against perturbations. We then compared the surface proteome of A. fumigatus to other allergy-inducing molds, including Alternaria alternata, Penicillium rubens, and Cladosporium herbarum, and performed comparative proteomics on resting and swollen conidia, as well as secreted proteins from germinating conidia. We detected 125 protein ortholog groups, including 80 with putative catalytic activity, in the extracellular region of all four molds, and 42 nonorthologous proteins produced solely by A. fumigatus. Ultimately, this study highlights the dynamic nature of the A. fumigatus conidial surface and provides targets for future diagnostics and immunotherapy.
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Affiliation(s)
- Matthew G Blango
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (Leibniz-HKI), Jena 07745, Germany
| | - Annica Pschibul
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (Leibniz-HKI), Jena 07745, Germany.,Department of Microbiology and Molecular Biology, Institute of Microbiology, Friedrich Schiller University, Jena 07745, Germany
| | - Flora Rivieccio
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (Leibniz-HKI), Jena 07745, Germany.,Department of Microbiology and Molecular Biology, Institute of Microbiology, Friedrich Schiller University, Jena 07745, Germany
| | - Thomas Krüger
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (Leibniz-HKI), Jena 07745, Germany
| | - Muhammad Rafiq
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (Leibniz-HKI), Jena 07745, Germany.,Department of Microbiology and Molecular Biology, Institute of Microbiology, Friedrich Schiller University, Jena 07745, Germany
| | - Lei-Jie Jia
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (Leibniz-HKI), Jena 07745, Germany
| | - Tingting Zheng
- Department of Systems Biology and Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (Leibniz-HKI), Jena 07745, Germany
| | - Marie Goldmann
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (Leibniz-HKI), Jena 07745, Germany.,Department of Microbiology and Molecular Biology, Institute of Microbiology, Friedrich Schiller University, Jena 07745, Germany
| | - Vera Voltersen
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (Leibniz-HKI), Jena 07745, Germany
| | - Jun Li
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong S.A.R., China.,School of Data Science, City University of Hong Kong, Kowloon, Hong Kong S.A.R., China
| | - Gianni Panagiotou
- Department of Systems Biology and Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (Leibniz-HKI), Jena 07745, Germany
| | - Olaf Kniemeyer
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (Leibniz-HKI), Jena 07745, Germany.,Department of Microbiology and Molecular Biology, Institute of Microbiology, Friedrich Schiller University, Jena 07745, Germany
| | - Axel A Brakhage
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (Leibniz-HKI), Jena 07745, Germany.,Department of Microbiology and Molecular Biology, Institute of Microbiology, Friedrich Schiller University, Jena 07745, Germany
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16
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Affiliation(s)
- Matthew G. Blango
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
- * E-mail:
| | - Olaf Kniemeyer
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
- Department of Microbiology and Molecular Biology, Institute for Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Axel A. Brakhage
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
- Department of Microbiology and Molecular Biology, Institute for Microbiology, Friedrich Schiller University Jena, Jena, Germany
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17
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Xiong J, Yang W, Chen K, Jiang C, Ma Y, Chai X, Yan G, Wang G, Yuan D, Liu Y, Bidwell SL, Zafar N, Hadjithomas M, Krishnakumar V, Coyne RS, Orias E, Miao W. Hidden genomic evolution in a morphospecies-The landscape of rapidly evolving genes in Tetrahymena. PLoS Biol 2019; 17:e3000294. [PMID: 31158217 PMCID: PMC6564038 DOI: 10.1371/journal.pbio.3000294] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 06/13/2019] [Accepted: 05/13/2019] [Indexed: 01/08/2023] Open
Abstract
A morphospecies is defined as a taxonomic species based wholly on morphology, but often morphospecies consist of clusters of cryptic species that can be identified genetically or molecularly. The nature of the evolutionary novelty that accompanies speciation in a morphospecies is an intriguing question. Morphospecies are particularly common among ciliates, a group of unicellular eukaryotes that separates 2 kinds of nuclei—the silenced germline nucleus (micronucleus [MIC]) and the actively expressed somatic nucleus (macronucleus [MAC])—within a common cytoplasm. Because of their very similar morphologies, members of the Tetrahymena genus are considered a morphospecies. We explored the hidden genomic evolution within this genus by performing a comprehensive comparative analysis of the somatic genomes of 10 species and the germline genomes of 2 species of Tetrahymena. These species show high genetic divergence; phylogenomic analysis suggests that the genus originated about 300 million years ago (Mya). Seven universal protein domains are preferentially included among the species-specific (i.e., the youngest) Tetrahymena genes. In particular, leucine-rich repeat (LRR) genes make the largest contribution to the high level of genome divergence of the 10 species. LRR genes can be sorted into 3 different age groups. Parallel evolutionary trajectories have independently occurred among LRR genes in the different Tetrahymena species. Thousands of young LRR genes contain tandem arrays of exactly 90-bp exons. The introns separating these exons show a unique, extreme phase 2 bias, suggesting a clonal origin and successive expansions of 90-bp–exon LRR genes. Identifying LRR gene age groups allowed us to document a Tetrahymena intron length cycle. The youngest 90-bp exon LRR genes in T. thermophila are concentrated in pericentromeric and subtelomeric regions of the 5 micronuclear chromosomes, suggesting that these regions act as genome innovation centers. Copies of a Tetrahymena Long interspersed element (LINE)-like retrotransposon are very frequently found physically adjacent to 90-bp exon/intron repeat units of the youngest LRR genes. We propose that Tetrahymena species have used a massive exon-shuffling mechanism, involving unequal crossing over possibly in concert with retrotransposition, to create the unique 90-bp exon array LRR genes. Genomic comparison of ten morphologically very similar species of ciliate from the genus Tetrahymena reveals how parallel microevolutionary processes have shaped their genomes and created unique genes through retrotransposition.
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Affiliation(s)
- Jie Xiong
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wentao Yang
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Kai Chen
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chuanqi Jiang
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yang Ma
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaocui Chai
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Guanxiong Yan
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Guangying Wang
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Dongxia Yuan
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Yifan Liu
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Shelby L. Bidwell
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Nikhat Zafar
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | | | - Vivek Krishnakumar
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Robert S. Coyne
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Eduardo Orias
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, California, United States of America
| | - Wei Miao
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Animal Evolution and Genetics, Kunming, China
- State Key Laboratory of Freshwater Ecology and Biotechnology of China, Wuhan, China
- * E-mail:
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18
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de Groot T, Meis JF. Microsatellite Stability in STR Analysis Aspergillus fumigatus Depends on Number of Repeat Units. Front Cell Infect Microbiol 2019; 9:82. [PMID: 30984630 PMCID: PMC6449440 DOI: 10.3389/fcimb.2019.00082] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 03/11/2019] [Indexed: 01/02/2023] Open
Abstract
More than a decade ago a short tandem repeat-based typing method was developed for the fungus Aspergillus fumigatus. This STRAf assay is based on the analysis of nine short tandem repeat markers. Interpretation of this STRAf assay is complicated when there are only one or two differences in tandem repeat markers between isolates, as the stability of these markers is unknown. To determine the stability of these nine markers, a STRAf assay was performed on 73–100 successive generations of five clonally expanded A. fumigatus isolates. In a total of 473 generations we found five times an increase of one tandem repeat unit. Three changes were found in the trinucleotide repeat marker STRAf 3A, while the other two were found in the trinucleotide repeat marker STRAf 3C. The di- or tetranucleotide repeats were not altered. The altered STRAf markers 3A and 3C demonstrated the highest number of repeat units (≥50) as compared to the other markers (≤26). Altogether, we demonstrated that 7 of 9 STRAf markers remain stable for 473 generations and that the frequency of alterations in tandem repeats is positively correlated with the number of repeats. The potential low level instability of STRAf markers 3A and 3C should be taken into account when interpreting STRAf data during an outbreak.
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Affiliation(s)
- Theun de Groot
- Department of Medical Microbiology and Infectious Diseases, Canisius Wilhelmina Hospital (CWZ), Nijmegen, Netherlands
| | - Jacques F Meis
- Department of Medical Microbiology and Infectious Diseases, Canisius Wilhelmina Hospital (CWZ), Nijmegen, Netherlands.,Centre of Expertise in Mycology, Radboudumc/CWZ, Nijmegen, Netherlands.,Department of Medical Microbiology, Radboudumc, Nijmegen, Netherlands
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19
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Gago S, Denning DW, Bowyer P. Pathophysiological aspects of Aspergillus colonization in disease. Med Mycol 2019; 57:S219-S227. [PMID: 30239804 DOI: 10.1093/mmy/myy076] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 07/20/2018] [Accepted: 08/24/2018] [Indexed: 12/31/2022] Open
Abstract
Aspergillus colonization of the lower respiratory airways is common in normal people, and of little clinical significance. However, in some patients, colonization is associated with severe disease including poorly controlled asthma, allergic bronchopulmonary aspergillosis (ABPA) with sputum plugs, worse lung function in chronic obstructive pulmonary aspergillosis (COPD), invasive aspergillosis, and active infection in patients with chronic pulmonary aspergillosis (CPA). Therefore, understanding the pathophysiological mechanisms of fungal colonization in disease is essential to develop strategies to avert or minimise disease. Aspergillus cell components promoting fungal adherence to the host surface, extracellular matrix, or basal lamina are indispensable for pathogen persistence. However, our understanding of individual differences in clearance of A. fumigatus from the lung in susceptible patients is close to zero.
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Affiliation(s)
- Sara Gago
- Manchester Fungal Infection Group, Division of Infection, Immunity and Respiratory Medicine, University of Manchester, CTF Building, 46 Grafton, Street, Manchester M13 9NT, United Kingdom
| | - David W Denning
- Manchester Fungal Infection Group, Division of Infection, Immunity and Respiratory Medicine, University of Manchester, CTF Building, 46 Grafton, Street, Manchester M13 9NT, United Kingdom.,National Aspergillosis Centre, University Hospital of South Manchester NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Paul Bowyer
- Manchester Fungal Infection Group, Division of Infection, Immunity and Respiratory Medicine, University of Manchester, CTF Building, 46 Grafton, Street, Manchester M13 9NT, United Kingdom
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20
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Ma LS, Pellegrin C, Kahmann R. Repeat-containing effectors of filamentous pathogens and symbionts. Curr Opin Microbiol 2018; 46:123-130. [PMID: 29929732 DOI: 10.1016/j.mib.2018.01.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 01/05/2018] [Accepted: 01/11/2018] [Indexed: 11/26/2022]
Abstract
Pathogenic and symbiotic filamentous microbes secrete effectors which suppress host immune responses and promote a successful colonization. Pathogen effectors are engaged in the arms race with their hosts and because of this they are subject to intense evolutionary pressure. Effectors particularly prone to rapid evolution display repeat-containing domains which can easily expand or contract and accumulate point mutations without altering their original function. In this review we address the diversity of function in such repeat-containing effectors, focus on new findings and point out avenues for future work.
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21
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Ma LS, Wang L, Trippel C, Mendoza-Mendoza A, Ullmann S, Moretti M, Carsten A, Kahnt J, Reissmann S, Zechmann B, Bange G, Kahmann R. The Ustilago maydis repetitive effector Rsp3 blocks the antifungal activity of mannose-binding maize proteins. Nat Commun 2018; 9:1711. [PMID: 29703884 PMCID: PMC5923269 DOI: 10.1038/s41467-018-04149-0] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 04/06/2018] [Indexed: 12/22/2022] Open
Abstract
To cause disease in maize, the biotrophic fungus Ustilago maydis secretes a large arsenal of effector proteins. Here, we functionally characterize the repetitive effector Rsp3 (repetitive secreted protein 3), which shows length polymorphisms in field isolates and is highly expressed during biotrophic stages. Rsp3 is required for virulence and anthocyanin accumulation. During biotrophic growth, Rsp3 decorates the hyphal surface and interacts with at least two secreted maize DUF26-domain family proteins (designated AFP1 and AFP2). AFP1 binds mannose and displays antifungal activity against the rsp3 mutant but not against a strain constitutively expressing rsp3. Maize plants silenced for AFP1 and AFP2 partially rescue the virulence defect of rsp3 mutants, suggesting that blocking the antifungal activity of AFP1 and AFP2 by the Rsp3 effector is an important virulence function. Rsp3 orthologs are present in all sequenced smut fungi, and the ortholog from Sporisorium reilianum can complement the rsp3 mutant of U. maydis, suggesting a novel widespread fungal protection mechanism. The fungus Ustilago maydis secretes many effector proteins to cause disease in maize. Here, Ma et al. show that the repetitive effector Rsp3 is required for virulence by inhibiting the antifungal activity of two mannose-binding proteins that are secreted by the plant cells.
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Affiliation(s)
- Lay-Sun Ma
- Department of Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany
| | - Lei Wang
- Department of Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany.,Department of Pharmacology, Max Planck Institute for Heart and Lung Research, 61231, Bad Nauheim, Germany
| | - Christine Trippel
- Department of Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany.,Department of Plant Cell Biology, Albrecht-von-Haller-Institute, Georg-August-University-Göttingen, 37077, Göttingen, Germany
| | - Artemio Mendoza-Mendoza
- Department of Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany.,Bio-Protection Research Centre, Lincoln University, PO Box 64, Lincoln, 7647, New Zealand
| | - Steffen Ullmann
- Department of Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany.,, Düsseldorfer Straße 177, 45481, Mülheim an der Ruhr, Germany
| | - Marino Moretti
- Department of Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany
| | - Alexander Carsten
- Department of Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany
| | - Jörg Kahnt
- Mass Spectroscopy Facility, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Stefanie Reissmann
- Department of Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany
| | - Bernd Zechmann
- Center for Microscopy and Imaging (CMI), Baylor University, Waco, Texas, 76798-7046, USA
| | - Gert Bange
- LOEWE Center for Synthetic Microbiology and Faculty of Chemistry, Philipps-Universität Marburg, 35032 Marburg, Germany
| | - Regine Kahmann
- Department of Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany.
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22
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Azole Resistance of Environmental and Clinical Aspergillus fumigatus Isolates from Switzerland. Antimicrob Agents Chemother 2018; 62:AAC.02088-17. [PMID: 29437612 PMCID: PMC5913999 DOI: 10.1128/aac.02088-17] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 01/22/2018] [Indexed: 11/21/2022] Open
Abstract
Aspergillus fumigatus is a ubiquitous opportunistic pathogen. This fungus can acquire resistance to azole antifungals due to mutations in the azole target (cyp51A). Recently, cyp51A mutations typical for environmental azole resistance acquisition (for example, TR34/L98H) have been reported. These mutations can also be found in isolates recovered from patients. Environmental azole resistance acquisition has been reported on several continents. Here we describe, for the first time, the occurrence of azole-resistant A. fumigatus isolates of environmental origin in Switzerland with cyp51A mutations, and we show that these isolates can also be recovered from a few patients. While the TR34/L98H mutation was dominant, a single azole-resistant isolate exhibited a cyp51A mutation (G54R) that was reported only for clinical isolates. In conclusion, our study demonstrates that azole resistance with an environmental signature is present in environments and patients of Swiss origin and that mutations believed to be unique to clinical settings are now also observed in the environment.
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23
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Franco ME, Bitencourt TA, Marins M, Fachin AL. In silico characterization of tandem repeats in Trichophyton rubrum and related dermatophytes provides new insights into their role in pathogenesis. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2018; 2017:3866792. [PMID: 29220431 PMCID: PMC5502367 DOI: 10.1093/database/bax035] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 03/28/2017] [Indexed: 01/01/2023]
Abstract
Trichophyton rubrum is the most common etiological agent of dermatophytoses worldwide, which is able to degrade keratinized tissues. The sequencing of the genome of different dermatophyte species has provided a large amount of data, including tandem repeats that may play a role in genetic variability and in the pathogenesis of these fungi. Tandem repeats are adjacent DNA sequences of 2–200 nucleotides in length, which exert regulatory and adaptive functions. These repetitive DNA sequences are found in different classes of fungal proteins, especially those involved in cell adhesion, a determinant factor for the establishment of fungal infection. The objective of this study was to develop a Dermatophyte Tandem Repeat Database (DTRDB) for the storage and identification of tandem repeats in T. rubrum and six other dermatophyte species. The current version of the database contains 35 577 tandem repeats detected in 16 173 coding sequences. The repeats can be searched using entry parameters such as repeat unit length (nt—nucleotide), repeat number, variability score, and repeat sequence motif. These data were used to study the relative frequency and distribution of repeats in the sequences, as well as their possible functions in dermatophytes. A search of the database revealed that these repeats occur in 22–33% of genes transcribed in dermatophytes where they could be involved in the success of adaptation to the host tissue and establishment of infection. The repeats were detected in transcripts that are mainly related to three biological processes: regulation, adhesion, and metabolism. The database developed enables users to identify and analyse tandem repeat regions in target genes related to pathogenicity and fungal–host interactions in dermatophytes and may contribute to the discovery of new targets for the development of antifungal agents. Database URL:http://comp.mch.ifsuldeminas.edu.br/dtrdb/
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Affiliation(s)
- Matheus Eloy Franco
- Unidade de Biotecnologia, Universidade de Ribeirão Preto, Av: Costabile Romano 2201, 14096-900, Ribeirao Preto SP, Brazil.,Federal Institute of Education, Science and Technology of South of Minas Gerais - IFSULDEMINAS, 37750-000, Brazil
| | - Tamires Aparecida Bitencourt
- Unidade de Biotecnologia, Universidade de Ribeirão Preto, Av: Costabile Romano 2201, 14096-900, Ribeirao Preto SP, Brazil.,Departamento de Genetica, 049-900, FMRP-USP, SP, Brazil
| | - Mozart Marins
- Unidade de Biotecnologia, Universidade de Ribeirão Preto, Av: Costabile Romano 2201, 14096-900, Ribeirao Preto SP, Brazil.,Curso de Medicina, Universidade de Ribeirão Preto, SP, Brazil
| | - Ana Lúcia Fachin
- Unidade de Biotecnologia, Universidade de Ribeirão Preto, Av: Costabile Romano 2201, 14096-900, Ribeirao Preto SP, Brazil.,Curso de Medicina, Universidade de Ribeirão Preto, SP, Brazil
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24
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Bertuzzi M, Hayes GE, Icheoku UJ, van Rhijn N, Denning DW, Osherov N, Bignell EM. Anti-Aspergillus Activities of the Respiratory Epithelium in Health and Disease. J Fungi (Basel) 2018; 4:E8. [PMID: 29371501 PMCID: PMC5872311 DOI: 10.3390/jof4010008] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 01/03/2018] [Accepted: 01/05/2018] [Indexed: 02/06/2023] Open
Abstract
Respiratory epithelia fulfil multiple roles beyond that of gaseous exchange, also acting as primary custodians of lung sterility and inflammatory homeostasis. Inhaled fungal spores pose a continual antigenic, and potentially pathogenic, challenge to lung integrity against which the human respiratory mucosa has developed various tolerance and defence strategies. However, respiratory disease and immune dysfunction frequently render the human lung susceptible to fungal diseases, the most common of which are the aspergilloses, a group of syndromes caused by inhaled spores of Aspergillus fumigatus. Inhaled Aspergillus spores enter into a multiplicity of interactions with respiratory epithelia, the mechanistic bases of which are only just becoming recognized as important drivers of disease, as well as possible therapeutic targets. In this mini-review we examine current understanding of Aspergillus-epithelial interactions and, based upon the very latest developments in the field, we explore two apparently opposing schools of thought which view epithelial uptake of Aspergillus spores as either a curative or disease-exacerbating event.
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Affiliation(s)
- Margherita Bertuzzi
- Manchester Fungal Infection Group, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9NT, UK.
| | - Gemma E Hayes
- Northern Devon Healthcare NHS Trust, North Devon District Hospital, Raleigh Park, Barnstaple EX31 4JB, UK.
| | - Uju J Icheoku
- Manchester Fungal Infection Group, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9NT, UK.
| | - Norman van Rhijn
- Manchester Fungal Infection Group, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9NT, UK.
| | - David W Denning
- The National Aspergillosis Centre, Education and Research Centre, Wythenshawe Hospital, Manchester University NHS Foundation Trust, Manchester M23 9LT, UK.
| | - Nir Osherov
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
| | - Elaine M Bignell
- Manchester Fungal Infection Group, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9NT, UK.
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25
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Takahashi-Nakaguchi A, Sakai K, Takahashi H, Hagiwara D, Toyotome T, Chibana H, Watanabe A, Yaguchi T, Yamaguchi M, Kamei K, Gonoi T. Aspergillus fumigatus adhesion factors in dormant conidia revealed through comparative phenotypic and transcriptomic analyses. Cell Microbiol 2017; 20. [PMID: 29113011 PMCID: PMC5838799 DOI: 10.1111/cmi.12802] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 07/11/2017] [Accepted: 10/30/2017] [Indexed: 01/29/2023]
Abstract
Aspergillus fumigatus is an important fungal pathogen of humans. Inhaled conidia of A. fumigatus adhere to pulmonary epithelial cells, causing opportunistic infection. However, little is known about the molecular mechanism of the adherence of resting conidia. Fungal molecules adhesive to host cells are presumed to be displayed on the conidial surface during conidial formation as a result of changes in gene expression. Therefore, we exhaustively searched for adhesion molecules by comparing the phenotypes and the gene expression profiles of A. fumigatus strains that have conidia showing either high or low adherence to human pulmonary A549 cells. Morphological observation suggested that strains that produce conidia of reduced size, hydrophobicity, or number show decreased adherence to A549 cells. K-means cluster analyses of gene expression revealed 31 genes that were differentially expressed in the high-adherence strains during conidial formation. We knocked out three of these genes and showed that the conidia of AFUA_4G01030 (encoding a hypothetical protein) and AFUA_4G08805 (encoding a haemolysin-like protein) knockout strains had significantly reduced adherence to host cells. Furthermore, the conidia of these knockout strains had lower hydrophobicity and fewer surface spikes compared to the control strain. We suggest that the selectively expressed gene products, including those we identified experimentally, have composite synergistic roles in the adhesion of conidia to pulmonary epithelial cells.
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Affiliation(s)
| | - Kanae Sakai
- Medical Mycology Research Center, Chiba University, Chiba, Japan
| | - Hiroki Takahashi
- Medical Mycology Research Center, Chiba University, Chiba, Japan
| | - Daisuke Hagiwara
- Medical Mycology Research Center, Chiba University, Chiba, Japan
| | | | - Hiroji Chibana
- Medical Mycology Research Center, Chiba University, Chiba, Japan
| | - Akira Watanabe
- Medical Mycology Research Center, Chiba University, Chiba, Japan
| | - Takashi Yaguchi
- Medical Mycology Research Center, Chiba University, Chiba, Japan
| | | | - Katsuhiko Kamei
- Medical Mycology Research Center, Chiba University, Chiba, Japan
| | - Tohru Gonoi
- Medical Mycology Research Center, Chiba University, Chiba, Japan
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26
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Valsecchi I, Sarikaya-Bayram Ö, Wong Sak Hoi J, Muszkieta L, Gibbons J, Prevost MC, Mallet A, Krijnse-Locker J, Ibrahim-Granet O, Mouyna I, Carr P, Bromley M, Aimanianda V, Yu JH, Rokas A, Braus GH, Saveanu C, Bayram Ö, Latgé JP. MybA, a transcription factor involved in conidiation and conidial viability of the human pathogenAspergillus fumigatus. Mol Microbiol 2017; 105:880-900. [DOI: 10.1111/mmi.13744] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/04/2017] [Indexed: 11/28/2022]
Affiliation(s)
| | | | | | | | - John Gibbons
- Department of Biological Sciences; Vanderbilt University; Nashville TN 37235 USA
| | | | - Adeline Mallet
- Plate-Forme de Microscopie Ultrastructurale; Institut Pasteur; Paris 75015 France
| | | | | | | | - Paul Carr
- Manchester Fungal Infection Group; Institute of Inflammation and Repair, University of Manchester; Manchester UK
| | - Michael Bromley
- Manchester Fungal Infection Group; Institute of Inflammation and Repair, University of Manchester; Manchester UK
| | | | - Jae-Hyuk Yu
- Department of Bacteriology and Genetics; University of Wisconsin; Madison WI 53706 USA
| | - Antonis Rokas
- Department of Biological Sciences; Vanderbilt University; Nashville TN 37235 USA
| | - Gerhard H Braus
- Department of Molecular Microbiology and Genetics; Georg August University; Göttingen 37077 Germany
| | - Cosmin Saveanu
- Unité de Génétique des Interactions Macromoléculaires; CNRS UMR3525, Institut Pasteur; Paris France
| | - Özgür Bayram
- Department of Biology; Maynooth University; Maynooth Co. Kildare Ireland
- Department of Molecular Microbiology and Genetics; Georg August University; Göttingen 37077 Germany
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27
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Evaluation and assessment of read-mapping by multiple next-generation sequencing aligners based on genome-wide characteristics. Genomics 2017; 109:186-191. [PMID: 28286147 DOI: 10.1016/j.ygeno.2017.03.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 03/07/2017] [Accepted: 03/08/2017] [Indexed: 01/18/2023]
Abstract
Massive data produced due to the advent of next-generation sequencing (NGS) technology is widely used for biological researches and medical diagnosis. The crucial step in NGS analysis is read alignment or mapping which is computationally intensive and complex. The mapping bias tends to affect the downstream analysis, including detection of polymorphisms. In order to provide guidelines to the biologist for suitable selection of aligners; we have evaluated and benchmarked 5 different aligners (BWA, Bowtie2, NovoAlign, Smalt and Stampy) and their mapping bias based on characteristics of 5 microbial genomes. Two million simulated read pairs of various sizes (36bp, 50bp, 72bp, 100bp, 125bp, 150bp, 200bp, 250bp and 300bp) were aligned. Specific alignment features such as sensitivity of mapping, percentage of properly paired reads, alignment time and effect of tandem repeats on incorrectly mapped reads were evaluated. BWA showed faster alignment followed by Bowtie2 and Smalt. NovoAlign and Stampy were comparatively slower. Most of the aligners showed high sensitivity towards long reads (>100bp) mapping. On the other hand NovoAlign showed higher sensitivity towards both short reads (36bp, 50bp, 72bp) and long reads (>100bp) mappings; It also showed higher sensitivity towards mapping a complex genome like Plasmodium falciparum. The percentage of properly paired reads aligned by NovoAlign, BWA and Stampy were markedly higher. None of the aligners outperforms the others in the benchmark, however the aligners perform differently with genome characteristics. We expect that the results from this study will be useful for the end user to choose aligner, thus enhance the accuracy of read mapping.
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28
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A New Aspergillus fumigatus Typing Method Based on Hypervariable Tandem Repeats Located within Exons of Surface Protein Coding Genes (TRESP). PLoS One 2016; 11:e0163869. [PMID: 27701437 PMCID: PMC5049851 DOI: 10.1371/journal.pone.0163869] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 09/15/2016] [Indexed: 11/19/2022] Open
Abstract
Aspergillus fumigatus is a saprotrophic mold fungus ubiquitously found in the environment and is the most common species causing invasive aspergillosis in immunocompromised individuals. For A. fumigatus genotyping, the short tandem repeat method (STRAf) is widely accepted as the first choice. However, difficulties associated with PCR product size and required technology have encouraged the development of novel typing techniques. In this study, a new genotyping method based on hypervariable tandem repeats within exons of surface protein coding genes (TRESP) was designed. A. fumigatus isolates were characterized by PCR amplification and sequencing with a panel of three TRESP encoding genes: cell surface protein A; MP-2 antigenic galactomannan protein; and hypothetical protein with a CFEM domain. The allele sequence repeats of each of the three targets were combined to assign a specific genotype. For the evaluation of this method, 126 unrelated A. fumigatus strains were analyzed and 96 different genotypes were identified, showing a high level of discrimination [Simpson’s index of diversity (D) 0.994]. In addition, 49 azole resistant strains were analyzed identifying 26 genotypes and showing a lower D value (0.890) among them. This value could indicate that these resistant strains are closely related and share a common origin, although more studies are needed to confirm this hypothesis. In summary, a novel genotyping method for A. fumigatus has been developed which is reproducible, easy to perform, highly discriminatory and could be especially useful for studying outbreaks.
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29
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Tabib A, Vishwanathan S, Seleznev A, McKeown PC, Downing T, Dent C, Sanchez-Bermejo E, Colling L, Spillane C, Balasubramanian S. A Polynucleotide Repeat Expansion Causing Temperature-Sensitivity Persists in Wild Irish Accessions of Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2016; 7:1311. [PMID: 27630650 PMCID: PMC5006647 DOI: 10.3389/fpls.2016.01311] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 08/16/2016] [Indexed: 05/15/2023]
Abstract
Triplet repeat expansions underlie several human genetic diseases such as Huntington's disease and Friedreich's ataxia. Although such mutations are primarily known from humans, a triplet expansion associated genetic defect has also been reported at the IIL1 locus in the Bur-0 accession of the model plant Arabidopsis thaliana. The IIL1 triplet expansion is an example of cryptic genetic variation as its phenotypic effects are seen only under genetic or environmental perturbation, with high temperatures resulting in a growth defect. Here we demonstrate that the IIL1 triplet expansion associated growth defect is not a general stress response and is specific to particular environmental perturbations. We also confirm and map genetic modifiers that suppress the effect of IIL1 triplet repeat expansion. By collecting and analyzing accessions from the island of Ireland, we recover the repeat expansion in wild populations suggesting that the repeat expansion has persisted at least 60 years in Ireland. Through genome-wide genotyping, we show that the repeat expansion is present in diverse Irish populations. Our findings indicate that even deleterious alleles can persist in populations if their effect is conditional. Our study demonstrates that analysis of groups of wild populations is a powerful tool for understanding the dynamics of cryptic genetic variation.
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Affiliation(s)
- Amanda Tabib
- School of Biological Sciences, Monash UniversityMelbourne, VIC, Australia
| | | | - Andrei Seleznev
- School of Biological Sciences, Monash UniversityMelbourne, VIC, Australia
| | - Peter C. McKeown
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre, School of Natural Sciences, National University of IrelandGalway, Ireland
| | - Tim Downing
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre, School of Natural Sciences, National University of IrelandGalway, Ireland
- School of Biotechnology, Dublin City UniversityDublin, Ireland
| | - Craig Dent
- School of Biological Sciences, Monash UniversityMelbourne, VIC, Australia
| | | | - Luana Colling
- School of Biological Sciences, Monash UniversityMelbourne, VIC, Australia
| | - Charles Spillane
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre, School of Natural Sciences, National University of IrelandGalway, Ireland
| | - Sureshkumar Balasubramanian
- School of Biological Sciences, Monash UniversityMelbourne, VIC, Australia
- *Correspondence: Sureshkumar Balasubramanian
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30
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Schaper E, Anisimova M. The evolution and function of protein tandem repeats in plants. THE NEW PHYTOLOGIST 2015; 206:397-410. [PMID: 25420631 DOI: 10.1111/nph.13184] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 10/18/2014] [Indexed: 05/27/2023]
Abstract
Sequence tandem repeats (TRs) are abundant in proteomes across all domains of life. For plants, little is known about their distribution or contribution to protein function. We exhaustively annotated TRs and studied the evolution of TR unit variations for all Ensembl plants. Using phylogenetic patterns of TR units, we detected conserved TRs with unit number and order preserved during evolution, and those TRs that have diverged via recent TR unit gains/losses. We correlated the mode of evolution of TRs to protein function. TR number was strongly correlated with proteome size, with about one-half of all TRs recognized as common protein domains. The majority of TRs have been highly conserved over long evolutionary distances, some since the separation of red algae and green plants c. 1.6 billion yr ago. Conversely, recurrent recent TR unit mutations were rare. Our results suggest that the first TRs by far predate the first plants, and that TR appearance is an ongoing process with similar rates across the plant kingdom. Interestingly, the few detected highly mutable TRs might provide a source of variation for rapid adaptation. In particular, such TRs are enriched in leucine-rich repeats (LRRs) commonly found in R genes, where TR unit gain/loss may facilitate resistance to emerging pathogens.
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Affiliation(s)
- Elke Schaper
- Department of Computer Science, ETH Zürich, Zürich, 8092, Switzerland
- Institute of Integrative Biology, ETH Zürich, Zürich, 8092, Switzerland
- Vital-IT Competency Center, Swiss Institute for Bioinformatics (SIB), Lausanne, 1015, Switzerland
| | - Maria Anisimova
- Institute of Applied Simulation (IAS), School of Life Sciences and Facility Management, Zürich University of Applied Sciences (ZHAW), Wädenswil, 8820, Switzerland
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31
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Frascella A, Bettini PP, Kolařík M, Comparini C, Pazzagli L, Luti S, Scala F, Scala A. Interspecific variability of class II hydrophobin GEO1 in the genus Geosmithia. Fungal Biol 2014; 118:862-71. [PMID: 25442290 DOI: 10.1016/j.funbio.2014.07.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2013] [Revised: 07/04/2014] [Accepted: 07/28/2014] [Indexed: 11/24/2022]
Abstract
The genus Geosmithia Pitt (Ascomycota: Hypocreales) comprises cosmopolite fungi living in the galleries built by phloeophagous insects. Following the characterization in Geosmithia species 5 of the class II hydrophobin GEO1 and of the corresponding gene, the presence of the geo1 gene was investigated in 26 strains derived from different host plants and geographic locations and representing the whole phylogenetic diversity of the genus. The geo1 gene was detected in all the species tested where it maintained the general organization shown in Geosmithia species 5, comprising three exons and two introns. Size variations were found in both introns and in the first exon, the latter being due to the presence of an intragenic tandem repeat sequence corresponding to a stretch of glycine residues in the deduced proteins. At the amino acid level the deduced proteins had 44.6 % identity and no major differences in the biochemical parameters (pI, GRAVY index, hydropathy plots) were found. GEO1 release in the fungal culture medium was also assessed by turbidimetric assay and SDS-PAGE, and showed high variability between species. The phylogeny based on the geo1 sequences did not correspond to that generated from a neutral marker (ITS rDNA), suggesting that sequence similarities could be influenced by other factors than phylogenetic relatedness, such as the intimacy of the symbiosis with insect vectors. The hypothesis of a strong selection pressure on the geo1 gene was sustained by the low values (<1) of non synonymous to synonymous nucleotide substitutions ratios (Ka/Ks), which suggest that purifying selection might act on this gene. These results are compatible with either a birth-and-death evolution scenario or horizontal transfer of the gene between Geosmithia species.
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Affiliation(s)
- Arcangela Frascella
- Dipartimento di Biologia, Università di Firenze, via Madonna del Piano 6, 50019 Sesto Fiorentino, FI, Italy; Dipartimento di Scienze delle Produzioni Agroalimentari e dell'Ambiente (DISPAA), Università di Firenze, via della Lastruccia 10, 50019 Sesto Fiorentino, FI, Italy.
| | - Priscilla P Bettini
- Dipartimento di Biologia, Università di Firenze, via Madonna del Piano 6, 50019 Sesto Fiorentino, FI, Italy.
| | - Miroslav Kolařík
- Institute of Microbiology of the ASCR, v.v.i, Videnská 1083, 142 20 Praha 4, Czech Republic.
| | - Cecilia Comparini
- Dipartimento di Scienze delle Produzioni Agroalimentari e dell'Ambiente (DISPAA), Università di Firenze, via della Lastruccia 10, 50019 Sesto Fiorentino, FI, Italy.
| | - Luigia Pazzagli
- Dipartimento di Scienze Biomediche, Sperimentali e Cliniche, Università di Firenze, Viale Morgagni 50, 50134 Florence, Italy.
| | - Simone Luti
- Dipartimento di Scienze Biomediche, Sperimentali e Cliniche, Università di Firenze, Viale Morgagni 50, 50134 Florence, Italy.
| | - Felice Scala
- Dipartimento di Arboricoltura, Botanica e Patologia Vegetale, Sezione di Patologia Vegetale, Università di Napoli "Federico II", via Università 100, 80055 Portici, NA, Italy.
| | - Aniello Scala
- Dipartimento di Scienze delle Produzioni Agroalimentari e dell'Ambiente (DISPAA), Università di Firenze, via della Lastruccia 10, 50019 Sesto Fiorentino, FI, Italy.
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32
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Identification of hypoxia-inducible target genes of Aspergillus fumigatus by transcriptome analysis reveals cellular respiration as an important contributor to hypoxic survival. EUKARYOTIC CELL 2014; 13:1241-53. [PMID: 25084861 DOI: 10.1128/ec.00084-14] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Aspergillus fumigatus is an opportunistic, airborne pathogen that causes invasive aspergillosis in immunocompromised patients. During the infection process, A. fumigatus is challenged by hypoxic microenvironments occurring in inflammatory, necrotic tissue. To gain further insights into the adaptation mechanism, A. fumigatus was cultivated in an oxygen-controlled chemostat under hypoxic and normoxic conditions. Transcriptome analysis revealed a significant increase in transcripts associated with cell wall polysaccharide metabolism, amino acid and metal ion transport, nitrogen metabolism, and glycolysis. A concomitant reduction in transcript levels was observed with cellular trafficking and G-protein-coupled signaling. To learn more about the functional roles of hypoxia-induced transcripts, we deleted A. fumigatus genes putatively involved in reactive nitrogen species detoxification (fhpA), NAD(+) regeneration (frdA and osmA), nitrogen metabolism (niaD and niiA), and respiration (rcfB). We show that the nitric oxygen (NO)-detoxifying flavohemoprotein gene fhpA is strongly induced by hypoxia independent of the nitrogen source but is dispensable for hypoxic survival. By deleting the nitrate reductase gene niaD, the nitrite reductase gene niiA, and the two fumarate reductase genes frdA and osmA, we found that alternative electron acceptors, such as nitrate and fumarate, do not have a significant impact on growth of A. fumigatus during hypoxia, but functional mitochondrial respiratory chain complexes are essential under these conditions. Inhibition studies indicated that primarily complexes III and IV play a crucial role in the hypoxic growth of A. fumigatus.
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Schaper E, Gascuel O, Anisimova M. Deep conservation of human protein tandem repeats within the eukaryotes. Mol Biol Evol 2014; 31:1132-48. [PMID: 24497029 PMCID: PMC3995336 DOI: 10.1093/molbev/msu062] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Tandem repeats (TRs) are a major element of protein sequences in all domains of life. They are particularly abundant in mammals, where by conservative estimates one in three proteins contain a TR. High generation-scale duplication and deletion rates were reported for nucleic TR units. However, it is not known whether protein TR units can also be frequently lost or gained providing a source of variation for rapid adaptation of protein function, or alternatively, tend to have conserved TR unit configurations over long evolutionary times. To obtain a systematic picture, we performed a proteome-wide analysis of the mode of evolution for human protein TRs. For this purpose, we propose a novel method for the detection of orthologous TRs based on circular profile hidden Markov models. For all detected TRs, we reconstructed bispecies TR unit phylogenies across 61 eukaryotes ranging from human to yeast. Moreover, we performed additional analyses to correlate functional and structural annotations of human TRs with their mode of evolution. Surprisingly, we find that the vast majority of human TRs are ancient, with TR unit number and order preserved intact since distant speciation events. For example, ≥61% of all human TRs have been strongly conserved at least since the root of all mammals, approximately 300 Ma. Further, we find no human protein TR that shows evidence for strong recent duplications and deletions. The results are in contrast to the high generation-scale mutability of nucleic TRs. Presumably, most protein TRs fold into stable and conserved structures that are indispensable for the function of the TR-containing protein. All of our data and results are available for download from http://www.atgc-montpellier.fr/TRE.
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Affiliation(s)
- Elke Schaper
- Department of Computer Science, ETH Zürich, Zürich, Switzerland
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Vaknin Y, Shadkchan Y, Levdansky E, Morozov M, Romano J, Osherov N. The three Aspergillus fumigatus CFEM-domain GPI-anchored proteins (CfmA-C) affect cell-wall stability but do not play a role in fungal virulence. Fungal Genet Biol 2013; 63:55-64. [PMID: 24361821 DOI: 10.1016/j.fgb.2013.12.005] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 12/10/2013] [Accepted: 12/11/2013] [Indexed: 10/25/2022]
Abstract
Fungal cell-wall proteins containing the conserved fungal CFEM domain have been implicated in host-pathogen interactions and virulence. To determine the role of these proteins in the mold pathogen Aspergillus fumigatus, we deleted the entire family of three CFEM-containing genes (CfmA-C), singly and in all combinations. We found an additive increase in the susceptibility of the single, double and triple ΔCfm mutants towards the chitin/β-glucan-microfibril destabilizing compounds Congo Red (CR) and Calcofluor White (CFW), indicating that the A. fumigatus CFEM proteins are involved in stabilizing the cell wall. No defects in growth or germination were observed, indicating that CFEM proteins do not have an essential role in the morphogenesis of A. fumigatus. Unlike in Candida albicans, the A. fumigatus CFEM proteins were not implicated in heme uptake or biofilm formation. The ΔTriple-Cfm deletion strain did not exhibit altered virulence in either insect or murine models of infection, suggesting that cell-wall proteins containing the conserved fungal CFEM domain are not a significant virulence factor in A. fumigatus.
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Affiliation(s)
- Yakir Vaknin
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Ramat-Aviv, Tel-Aviv, Israel
| | - Yana Shadkchan
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Ramat-Aviv, Tel-Aviv, Israel
| | - Emma Levdansky
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Ramat-Aviv, Tel-Aviv, Israel
| | - Michael Morozov
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Ramat-Aviv, Tel-Aviv, Israel
| | - Jacob Romano
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Ramat-Aviv, Tel-Aviv, Israel
| | - Nir Osherov
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Ramat-Aviv, Tel-Aviv, Israel.
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Tuntevski K, Durney BC, Snyder AK, LaSala PR, Nayak AP, Green BJ, Beezhold DH, Rio RVM, Holland LA, Lukomski S. Aspergillus collagen-like genes (acl): identification, sequence polymorphism, and assessment for PCR-based pathogen detection. Appl Environ Microbiol 2013; 79:7882-95. [PMID: 24123732 PMCID: PMC3837832 DOI: 10.1128/aem.02835-13] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Accepted: 10/02/2013] [Indexed: 12/16/2022] Open
Abstract
The genus Aspergillus is a burden to public health due to its ubiquitous presence in the environment, its production of allergens, and wide demographic susceptibility among cystic fibrosis, asthmatic, and immunosuppressed patients. Current methods of detection of Aspergillus colonization and infection rely on lengthy morphological characterization or nonstandardized serological assays that are restricted to identifying a fungal etiology. Collagen-like genes have been shown to exhibit species-specific conservation across the noncollagenous regions as well as strain-specific polymorphism in the collagen-like regions. Here we assess the conserved region of the Aspergillus collagen-like (acl) genes and explore the application of PCR amplicon size-based discrimination among the five most common etiologic species of the Aspergillus genus, including Aspergillus fumigatus, A. flavus, A. nidulans, A. niger, and A. terreus. Genetic polymorphism and phylogenetic analysis of the aclF1 gene were additionally examined among the available strains. Furthermore, the applicability of the PCR-based assay to identification of these five species in cultures derived from sputum and bronchoalveolar fluid from 19 clinical samples was explored. Application of capillary electrophoresis on nanogels was additionally demonstrated to improve the discrimination between Aspergillus species. Overall, this study demonstrated that Aspergillus acl genes could be used as PCR targets to discriminate between clinically relevant Aspergillus species. Future studies aim to utilize the detection of Aspergillus acl genes in PCR and microfluidic applications to determine the sensitivity and specificity for the identification of Aspergillus colonization and invasive aspergillosis in immunocompromised subjects.
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Affiliation(s)
| | | | | | - P. Rocco LaSala
- Department of Pathology, West Virginia University
- Clinical Laboratory, West Virginia University Healthcare, Morgantown, West Virginia, USA
| | - Ajay P. Nayak
- Allergy and Clinical Immunology Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health (NIOSH), Centers for Disease Control and Prevention, Morgantown, West Virginia, USA
| | - Brett J. Green
- Allergy and Clinical Immunology Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health (NIOSH), Centers for Disease Control and Prevention, Morgantown, West Virginia, USA
| | - Donald H. Beezhold
- Allergy and Clinical Immunology Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health (NIOSH), Centers for Disease Control and Prevention, Morgantown, West Virginia, USA
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Glycosylphosphatidylinositol-anchored proteins in Fusarium graminearum: inventory, variability, and virulence. PLoS One 2013; 8:e81603. [PMID: 24312325 PMCID: PMC3843709 DOI: 10.1371/journal.pone.0081603] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 10/14/2013] [Indexed: 11/24/2022] Open
Abstract
The contribution of cell surface proteins to plant pathogenicity of fungi is not well understood. As such, the objective of this study was to investigate the functions and importance of glycosylphosphatidylinositol-anchored proteins (GPI-APs) in the wheat pathogen F. graminearum. GPI-APs are surface proteins that are attached to either the membrane or cell wall. In order to simultaneously disrupt several GPI-APs, a phosphoethanolamine transferase-encoding gene gpi7 was deleted and the resultant mutant characterized in terms of growth, development, and virulence. The Δgpi7 mutants exhibited slower radial growth rates and aberrantly shaped macroconidia. Furthermore, virulence tests and microscopic analyses indicated that Gpi7 is required for ramification of the fungus throughout the rachis of wheat heads. In parallel, bioinformatics tools were utilized to predict and inventory GPI-APs within the proteome of F. graminearum. Two of the genes identified in this screen (FGSG_01588 and FGSG_08844) displayed isolate-specific length variability as observed for other fungal cell wall adhesion genes. Nevertheless, deletion of these genes failed to reveal obvious defects in growth, development, or virulence. This research demonstrates the global importance of GPI-APs to in planta proliferation in F. graminearum, and also highlights the potential of individual GPI-APs as diagnostic markers.
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Sun L, Li X, Fu Y, Zhu Z, Tan L, Liu F, Sun X, Sun X, Sun C. GS6, a member of the GRAS gene family, negatively regulates grain size in rice. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2013; 55:938-49. [PMID: 23650998 DOI: 10.1111/jipb.12062] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 05/01/2013] [Indexed: 05/07/2023]
Abstract
Grain size is an important yield-related trait in rice. Intensive artificial selection for grain size during domestication is evidenced by the larger grains of most of today's cultivars compared with their wild relatives. However, the molecular genetic control of rice grain size is still not well characterized. Here, we report the identification and cloning of Grain Size 6 (GS6), which plays an important role in reducing grain size in rice. A premature stop at the +348 position in the coding sequence (CDS) of GS6 increased grain width and weight significantly. Alignment of the CDS regions of GS6 in 90 rice materials revealed three GS6 alleles. Most japonica varieties (95%) harbor the Type I haplotype, and 62.9% of indica varieties harbor the Type II haplotype. Association analysis revealed that the Type I haplotype tends to increase the width and weight of grains more than either of the Type II or Type III haplotypes. Further investigation of genetic diversity and the evolutionary mechanisms of GS6 showed that the GS6 gene was strongly selected in japonica cultivars. In addition, a "ggc" repeat region identified in the region that encodes the GRAS domain of GS6 played an important historic role in the domestication of grain size in rice. Knowledge of the function of GS6 might aid efforts to elucidate the molecular mechanisms that control grain development and evolution in rice plants, and could facilitate the genetic improvement of rice yield.
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Affiliation(s)
- Lianjun Sun
- State Key Laboratory of Plant Physiology and Biochemistry, National Center for Evaluation of Agricultural Wild Plants (Rice), MOE Key Laboratory of Crop Heterosis and Utilization, Beijing 100193, China; Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
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Detection and characterization of megasatellites in orthologous and nonorthologous genes of 21 fungal genomes. EUKARYOTIC CELL 2013; 12:794-803. [PMID: 23543670 DOI: 10.1128/ec.00001-13] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Megasatellites are large DNA tandem repeats, originally described in Candida glabrata, in protein-coding genes. Most of the genes in which megasatellites are found are of unknown function. In this work, we extended the search for megasatellites to 20 additional completely sequenced fungal genomes and extracted 216 megasatellites in 203 out of 142,121 genes, corresponding to the most exhaustive description of such genetic elements available today. We show that half of the megasatellites detected encode threonine-rich peptides predicted to be intrinsically disordered, suggesting that they may interact with several partners or serve as flexible linkers. Megasatellite motifs were clustered into several families. Their distribution in fungal genes shows that different motifs are found in orthologous genes and similar motifs are found in unrelated genes, suggesting that megasatellite formation or spreading does not necessarily track the evolution of their host genes. Altogether, these results suggest that megasatellites are created and lost during evolution of fungal genomes, probably sharing similar functions, although their primary sequences are not necessarily conserved.
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Shi J, Huang S, Fu D, Yu J, Wang X, Hua W, Liu S, Liu G, Wang H. Evolutionary dynamics of microsatellite distribution in plants: insight from the comparison of sequenced brassica, Arabidopsis and other angiosperm species. PLoS One 2013; 8:e59988. [PMID: 23555856 PMCID: PMC3610691 DOI: 10.1371/journal.pone.0059988] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Accepted: 02/24/2013] [Indexed: 11/19/2022] Open
Abstract
Despite their ubiquity and functional importance, microsatellites have been largely ignored in comparative genomics, mostly due to the lack of genomic information. In the current study, microsatellite distribution was characterized and compared in the whole genomes and both the coding and non-coding DNA sequences of the sequenced Brassica, Arabidopsis and other angiosperm species to investigate their evolutionary dynamics in plants. The variation in the microsatellite frequencies of these angiosperm species was much smaller than those for their microsatellite numbers and genome sizes, suggesting that microsatellite frequency may be relatively stable in plants. The microsatellite frequencies of these angiosperm species were significantly negatively correlated with both their genome sizes and transposable elements contents. The pattern of microsatellite distribution may differ according to the different genomic regions (such as coding and non-coding sequences). The observed differences in many important microsatellite characteristics (especially the distribution with respect to motif length, type and repeat number) of these angiosperm species were generally accordant with their phylogenetic distance, which suggested that the evolutionary dynamics of microsatellite distribution may be generally consistent with plant divergence/evolution. Importantly, by comparing these microsatellite characteristics (especially the distribution with respect to motif type) the angiosperm species (aside from a few species) all clustered into two obviously different groups that were largely represented by monocots and dicots, suggesting a complex and generally dichotomous evolutionary pattern of microsatellite distribution in angiosperms. Polyploidy may lead to a slight increase in microsatellite frequency in the coding sequences and a significant decrease in microsatellite frequency in the whole genome/non-coding sequences, but have little effect on the microsatellite distribution with respect to motif length, type and repeat number. Interestingly, several microsatellite characteristics seemed to be constant in plant evolution, which can be well explained by the general biological rules.
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Affiliation(s)
- Jiaqin Shi
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Shunmou Huang
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Donghui Fu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang, China
| | - Jinyin Yu
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Xinfa Wang
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Wei Hua
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Shengyi Liu
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Guihua Liu
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Hanzhong Wang
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
- * E-mail:
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Chin BL, Ryan O, Lewitter F, Boone C, Fink GR. Genetic variation in Saccharomyces cerevisiae: circuit diversification in a signal transduction network. Genetics 2012; 192:1523-32. [PMID: 23051644 PMCID: PMC3512157 DOI: 10.1534/genetics.112.145573] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Accepted: 10/01/2012] [Indexed: 01/07/2023] Open
Abstract
The connection between genotype and phenotype was assessed by determining the adhesion phenotype for the same mutation in two closely related yeast strains, S288c and Sigma, using two identical deletion libraries. Previous studies, all in Sigma, had shown that the adhesion phenotype was controlled by the filamentation mitogen-activated kinase (fMAPK) pathway, which activates a set of transcription factors required for the transcription of the structural gene FLO11. Unexpectedly, the fMAPK pathway is not required for FLO11 transcription in S288c despite the fact that the fMAPK genes are present and active in other pathways. Using transformation and a sensitized reporter, it was possible to isolate RPI1, one of the modifiers that permits the bypass of the fMAPK pathway in S288c. RPI1 encodes a transcription factor with allelic differences between the two strains: The RPI1 allele from S288c but not the one from Sigma can confer fMAPK pathway-independent transcription of FLO11. Biochemical analysis reveals differences in phosphorylation between the alleles. At the nucleotide level the two alleles differ in the number of tandem repeats in the ORF. A comparison of genomes between the two strains shows that many genes differ in size due to variation in repeat length.
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Affiliation(s)
- Brian L. Chin
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142
| | - Owen Ryan
- Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1 Canada
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Fran Lewitter
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142
| | - Charles Boone
- Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1 Canada
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Gerald R. Fink
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142
- Broad Institute of MIT and Harvard, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142
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Brown NA, Antoniw J, Hammond-Kosack KE. The predicted secretome of the plant pathogenic fungus Fusarium graminearum: a refined comparative analysis. PLoS One 2012; 7:e33731. [PMID: 22493673 PMCID: PMC3320895 DOI: 10.1371/journal.pone.0033731] [Citation(s) in RCA: 125] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Accepted: 02/16/2012] [Indexed: 11/18/2022] Open
Abstract
The fungus Fusarium graminearum forms an intimate association with the host species wheat whilst infecting the floral tissues at anthesis. During the prolonged latent period of infection, extracellular communication between live pathogen and host cells must occur, implying a role for secreted fungal proteins. The wheat cells in contact with fungal hyphae subsequently die and intracellular hyphal colonisation results in the development of visible disease symptoms. Since the original genome annotation analysis was done in 2007, which predicted the secretome using TargetP, the F. graminearum gene call has changed considerably through the combined efforts of the BROAD and MIPS institutes. As a result of the modifications to the genome and the recent findings that suggested a role for secreted proteins in virulence, the F. graminearum secretome was revisited. In the current study, a refined F. graminearum secretome was predicted by combining several bioinformatic approaches. This strategy increased the probability of identifying truly secreted proteins. A secretome of 574 proteins was predicted of which 99% was supported by transcriptional evidence. The function of the annotated and unannotated secreted proteins was explored. The potential role(s) of the annotated proteins including, putative enzymes, phytotoxins and antifungals are discussed. Characterisation of the unannotated proteins included the analysis of Pfam domains and features associated with known fungal effectors, for example, small size, cysteine-rich and containing internal amino acid repeats. A comprehensive comparative genomic analysis involving 57 fungal and oomycete genomes revealed that only a small number of the predicted F. graminearum secreted proteins can be considered to be either species or sequenced strain specific.
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Affiliation(s)
- Neil A Brown
- Centre for Sustainable Pest and Disease Management, Department of Plant Pathology and Microbiology, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
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Zhou L, Powell CA, Hoffman MT, Li W, Fan G, Liu B, Lin H, Duan Y. Diversity and plasticity of the intracellular plant pathogen and insect symbiont "Candidatus Liberibacter asiaticus" as revealed by hypervariable prophage genes with intragenic tandem repeats. Appl Environ Microbiol 2011; 77:6663-73. [PMID: 21784907 PMCID: PMC3187138 DOI: 10.1128/aem.05111-11] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Accepted: 07/15/2011] [Indexed: 11/20/2022] Open
Abstract
"Candidatus Liberibacter asiaticus" is a psyllid-transmitted, phloem-limited alphaproteobacterium and the most prevalent species of "Ca. Liberibacter" associated with a devastating worldwide citrus disease known as huanglongbing (HLB). Two related and hypervariable genes (hyv(I) and hyv(II)) were identified in the prophage regions of the Psy62 "Ca. Liberibacter asiaticus" genome. Sequence analyses of the hyv(I) and hyv(II) genes in 35 "Ca. Liberibacter asiaticus" DNA isolates collected globally revealed that the hyv(I) gene contains up to 12 nearly identical tandem repeats (NITRs, 132 bp) and 4 partial repeats, while hyv(II) contains up to 2 NITRs and 4 partial repeats and shares homology with hyv(I). Frequent deletions or insertions of these repeats within the hyv(I) and hyv(II) genes were observed, none of which disrupted the open reading frames. Sequence conservation within the individual repeats but an extensive variation in repeat numbers, rearrangement, and the sequences flanking the repeat region indicate the diversity and plasticity of "Ca. Liberibacter asiaticus" bacterial populations in the world. These differences were found not only in samples of distinct geographical origins but also in samples from a single origin and even from a single "Ca. Liberibacter asiaticus"-infected sample. This is the first evidence of different "Ca. Liberibacter asiaticus" populations coexisting in a single HLB-affected sample. The Florida "Ca. Liberibacter asiaticus" isolates contain both hyv(I) and hyv(II), while all other global "Ca. Liberibacter asiaticus" isolates contain either one or the other. Interclade assignments of the putative Hyv(I) and Hyv(II) proteins from Florida isolates with other global isolates in phylogenetic trees imply multiple "Ca. Liberibacter asiaticus" populations in the world and a multisource introduction of the "Ca. Liberibacter asiaticus" bacterium into Florida.
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Affiliation(s)
- Lijuan Zhou
- University of Florida, IFAS-IRREC, Ft. Pierce, Florida 34945
| | | | | | - Wenbin Li
- USDA-APHIS-PPQ-CPHST-NPGBL, Beltsville, Maryland 20705
| | - Guocheng Fan
- Citrus Huanglongbing Research Center, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350002, China
| | - Bo Liu
- Citrus Huanglongbing Research Center, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350002, China
| | - Hong Lin
- San Joaquin Valley Agricultural Sciences Center, USDA-ARS, Parlier, California 93658
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Molecular mechanism of Aspergillus fumigatus adherence to host constituents. Curr Opin Microbiol 2011; 14:375-9. [PMID: 21784698 DOI: 10.1016/j.mib.2011.07.006] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2011] [Revised: 06/14/2011] [Accepted: 07/01/2011] [Indexed: 11/23/2022]
Abstract
Inhaled conidia of Aspergillus fumigatus rapidly adhere to pulmonary epithelial cells and other host constituents. Identifying molecular mechanisms underlying A. fumigatus adherence has therefore been the focus of a number of studies aimed at identifying novel therapeutic targets. Early studies of A. fumigatus adherence to host constituents focused on fungal proteins, including RodA and AspF2. None of these proteins however has been found to play a role in virulence in experimental animal models. Recent advances have suggested an important role for fungal carbohydrate components of the cell wall and extracellular matrix in adherence, including sialic acid and mannose residues, and the newly described polysaccharide galactosaminogalactan. Despite these advances, the host cell receptors that are bound by these ligands remain unknown.
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Abstract
Multiple reasons may justify a need for strain typing purposes, but the most common reason is to delineate the epidemiological relationships between isolates. The availability of whole genome sequences has greatly influenced our ability to develop highly targeted and efficient strain typing methods fur these purposes. Some strain typing methods may serve dual goals: not only can they be used to discriminate between multiple isolates of a certain species, they can also aid in the recognition, identification, description and validation process of a fungal species.
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Affiliation(s)
- C H W Klaassen
- Department of Medical Microbiology and Infectious Diseases, Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
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Brückner S, Mösch HU. Choosing the right lifestyle: adhesion and development in Saccharomyces cerevisiae. FEMS Microbiol Rev 2011; 36:25-58. [PMID: 21521246 DOI: 10.1111/j.1574-6976.2011.00275.x] [Citation(s) in RCA: 127] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The budding yeast Saccharomyces cerevisiae is a eukaryotic microorganism that is able to choose between different unicellular and multicellular lifestyles. The potential of individual yeast cells to switch between different growth modes is advantageous for optimal dissemination, protection and substrate colonization at the population level. A crucial step in lifestyle adaptation is the control of self- and foreign adhesion. For this purpose, S. cerevisiae contains a set of cell wall-associated proteins, which confer adhesion to diverse biotic and abiotic surfaces. Here, we provide an overview of different aspects of S. cerevisiae adhesion, including a detailed description of known lifestyles, recent insights into adhesin structure and function and an outline of the complex regulatory network for adhesin gene regulation. Our review shows that S. cerevisiae is a model system suitable for studying not only the mechanisms and regulation of cell adhesion, but also the role of this process in microbial development, ecology and evolution.
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Affiliation(s)
- Stefan Brückner
- Department of Genetics, Philipps-Universität Marburg, Marburg, Germany
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Goto Y, Duthie MS, Kawazu SI, Inoue N, Carter D. Biased cellular locations of tandem repeat antigens in African trypanosomes. Biochem Biophys Res Commun 2011; 405:434-8. [PMID: 21241659 PMCID: PMC3042534 DOI: 10.1016/j.bbrc.2011.01.048] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2011] [Accepted: 01/12/2011] [Indexed: 02/04/2023]
Abstract
Trypanosoma brucei subspecies cause African trypanosomiasis in humans and animals. These parasites possess genes encoding proteins with large tandem repeat (TR) domains as do the other trypanosomatid parasites. We have previously demonstrated that TR protein of Leishmania infantum and Trypanosoma cruzi are often targets of B-cell responses. However, African trypanosomes are susceptible to antibody-mediated immunity, and it may be detrimental for the parasites to have such B-cell antigens on the cell surface. Here we show TR proteins of T. brucei subspecies are also antigenic: recombinant TR proteins of these parasites detect antibodies in sera from mice infected with the parasites by ELISA. Analysis of amino acid sequences revealed that, different from TR proteins of Leishmania species or T. cruzi, the presence of predicted signal peptides, trans-membrane domains and GPI anchor signals in T. brucei TR proteins are significantly lower than those of the whole proteome. Many of the T. brucei TR proteins are specific in the species or conserved only in the closely related species, as is the same case for Leishmania major and T. cruzi. These results suggest that, despite their sharing some common characteristics, such abundance in large TR domains and immunological dominance, TR genes have evolved independently among the trypanosomatid parasites.
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Affiliation(s)
- Yasuyuki Goto
- Laboratory of Molecular Immunology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Japan.
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Tscherner M, Schwarzmüller T, Kuchler K. Pathogenesis and Antifungal Drug Resistance of the Human Fungal Pathogen Candida glabrata. Pharmaceuticals (Basel) 2011. [PMCID: PMC4052548 DOI: 10.3390/ph4010169] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Candida glabrata is a major opportunistic human fungal pathogen causing superficial as well as systemic infections in immunocompromised individuals and several other patient cohorts. C. glabrata represents the second most prevalent cause of candidemia and a better understanding of its virulence and drug resistance mechanisms is thus of high medical relevance. In contrast to the diploid dimorphic pathogen C. albicans, whose ability to undergo filamentation is considered a major virulence trait, C. glabrata has a haploid genome and lacks the ability to switch to filamentous growth. A major impediment for the clinical therapy of C. glabrata infections is its high intrinsic resistance to several antifungal drugs, especially azoles. Further, the development of antifungal resistance, particularly during prolonged and prophylactic therapies is diminishing efficacies of therapeutic interventions. In addition, C. glabrata harbors a large repertoire of adhesins involved in the adherence to host epithelia. Interestingly, genome plasticity, phenotypic switching or the remarkable ability to persist and survive inside host immune cells further contribute to the pathogenicity of C. glabrata. In this comprehensive review, we want to emphasize and discuss the mechanisms underlying virulence and drug resistance of C. glabrata, and discuss its ability to escape from the host immune surveillance or persist inside host cells.
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Affiliation(s)
| | | | - Karl Kuchler
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +43-1-4277-61807; Fax: +43-1-4277-9618
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Adhesive activity of the haemophilus cryptic genospecies cha autotransporter is modulated by variation in tandem Peptide repeats. J Bacteriol 2010; 193:329-39. [PMID: 21037000 DOI: 10.1128/jb.00933-10] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Haemophilus cryptic genospecies is an important cause of maternal genital tract and neonatal systemic infections and initiates infection by colonizing the genital or respiratory epithelium. In recent work, we identified a unique Haemophilus cryptic genospecies protein called Cha, which mediates efficient adherence to genital and respiratory epithelia. The Cha adhesin belongs to the trimeric autotransporter family and contains an N-terminal signal peptide, an internal passenger domain that harbors adhesive activity, and a C-terminal membrane anchor domain. The passenger domain in Cha contains clusters of YadA-like head domains and neck motifs as well as a series of tandem 28-amino-acid peptide repeats. In the current study, we report that variation in peptide repeat number gradually modulates Cha adhesive activity, associated with a direct effect on the length of Cha fibers on the bacterial cell surface. The N-terminal 404 residues of the Cha passenger domain mediate binding to host cells and also facilitate bacterial aggregation through intermolecular Cha-Cha binding. As the tandem peptide repeats expand, the Cha fiber becomes longer and Cha adherence activity decreases. The expansion and contraction of peptide repeats represent a novel mechanism for modulating adhesive capacity, potentially balancing the need of the organism to colonize the genital and respiratory tracts with the ability to attach to alternative substrates, disperse within the host, or evade the host immune system.
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Tan JC, Tan A, Checkley L, Honsa CM, Ferdig MT. Variable numbers of tandem repeats in Plasmodium falciparum genes. J Mol Evol 2010; 71:268-78. [PMID: 20730584 DOI: 10.1007/s00239-010-9381-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2009] [Accepted: 08/09/2010] [Indexed: 11/29/2022]
Abstract
Genome variation studies in Plasmodium falciparum have focused on SNPs and, more recently, large-scale copy number polymorphisms and ectopic rearrangements. Here, we examine another source of variation: variable number tandem repeats (VNTRs). Interspersed low complexity features, including the well-studied P. falciparum microsatellite sequences, are commonly classified as VNTRs; however, this study is focused on longer coding VNTR polymorphisms, a small class of copy number variations. Selection against frameshift mutation is a main constraint on tandem repeats (TRs) in coding regions, while limited propagation of TRs longer than 975 nt total length is a minor restriction in coding regions. Comparative analysis of three P. falciparum genomes reveals that more than 9% of all P. falciparum ORFs harbor VNTRs, much more than has been reported for any other species. Moreover, genotyping of VNTR loci in a drug-selected line, progeny of a genetic cross, and 334 field isolates demonstrates broad variability in these sequences. Functional enrichment analysis of ORFs harboring VNTRs identifies stress and DNA damage responses along with chromatin modification activities, suggesting an influence on genome mutability and functional variation. Analysis of the repeat units and their flanking regions in both P. falciparum and Plasmodium reichenowi sequences implicates a replication slippage mechanism in the generation of TRs from an initially unrepeated sequence. VNTRs can contribute to rapid adaptation by localized sequence duplication. They also can confound SNP-typing microarrays or mapping short-sequence reads and therefore must be accounted for in such analyses.
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Affiliation(s)
- John C Tan
- The Eck Institute for Global Health, University of Notre Dame, 100 Galvin Life Sciences, Notre Dame, IN, 46556, USA.
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