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Raj K, Paul D, Rishi P, Shukla G, Dhotre D, YogeshSouche. Decoding the role of oxidative stress resistance and alternative carbon substrate assimilation in the mature biofilm growth mode of Candida glabrata. BMC Microbiol 2024; 24:128. [PMID: 38641593 PMCID: PMC11031924 DOI: 10.1186/s12866-024-03274-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Accepted: 03/22/2024] [Indexed: 04/21/2024] Open
Abstract
BACKGROUND Biofilm formation is viewed as a vital mechanism in C. glabrata pathogenesis. Although, it plays a significant role in virulence but transcriptomic architecture and metabolic pathways governing the biofilm growth mode of C. glabrata remain elusive. The present study intended to investigate the genes implicated in biofilm growth phase of C. glabrata through global transcriptomic approach. RESULTS Functional analysis of Differentially expressed genes (DEGs) using gene ontology and pathways analysis revealed that upregulated genes are involved in the glyoxylate cycle, carbon-carbon lyase activity, pre-autophagosomal structure membrane and vacuolar parts whereas, down- regulated genes appear to be associated with glycolysis, ribonucleoside biosynthetic process, ribosomal and translation process in the biofilm growth condition. The RNA-Seq expression of eight selected DEGs (CgICL1, CgMLS1, CgPEP1, and CgNTH1, CgERG9, CgERG11, CgTEF3, and CgCOF1) was performed with quantitative real-time PCR (RT-qPCR). The gene expression profile of selected DEGs with RT-qPCR displayed a similar pattern of expression as observed in RNA-Seq. Phenotype screening of mutant strains generated for genes CgPCK1 and CgPEP1, showed that Cgpck1∆ failed to grow on alternative carbon substrate (Glycerol, Ethanol, Oleic acid) and similarly, Cgpep1∆ unable to grow on YPD medium supplemented with hydrogen peroxide. Our results suggest that in the absence of glucose, C. glabrata assimilate glycerol, oleic acid and generate acetyl coenzyme-A (acetyl-CoA) which is a central and connecting metabolite between catabolic and anabolic pathways (glyoxylate and gluconeogenesis) to produce glucose and fulfil energy requirements. CONCLUSIONS The study was executed using various approaches (transcriptomics, functional genomics and gene deletion) and it revealed that metabolic plasticity of C. glabrata (NCCPF-100,037) in biofilm stage modulates its virulence and survival ability to counter the stress and may promote its transition from commensal to opportunistic pathogen. The observations deduced from the present study along with future work on characterization of the proteins involved in this intricate process may prove to be beneficial for designing novel antifungal strategies.
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Affiliation(s)
- Khem Raj
- Department of Microbiology Basic Medical Sciences Block I, South Campus, Panjab University, Sector-25, Chandigarh, 160014, India.
| | - Dhiraj Paul
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland.
| | - Praveen Rishi
- Department of Microbiology Basic Medical Sciences Block I, South Campus, Panjab University, Sector-25, Chandigarh, 160014, India
| | - Geeta Shukla
- Department of Microbiology Basic Medical Sciences Block I, South Campus, Panjab University, Sector-25, Chandigarh, 160014, India
| | - Dhiraj Dhotre
- National Centre for Microbial Resource, National Centre for Cell Sciences (NCCS), Pune, India
| | - YogeshSouche
- National Centre for Microbial Resource, National Centre for Cell Sciences (NCCS), Pune, India
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2
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Maroc L, Shaker H, Shapiro RS. Functional genetic characterization of stress tolerance and biofilm formation in Nakaseomyces ( Candida) glabrata via a novel CRISPR activation system. mSphere 2024; 9:e0076123. [PMID: 38265239 PMCID: PMC10900893 DOI: 10.1128/msphere.00761-23] [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: 12/07/2023] [Accepted: 12/13/2023] [Indexed: 01/25/2024] Open
Abstract
The overexpression of genes frequently arises in Nakaseomyces (formerly Candida) glabrata via gain-of-function mutations, gene duplication, or aneuploidies, with important consequences on pathogenesis traits and antifungal drug resistance. This highlights the need to develop specific genetic tools to mimic and study genetic amplification in this important fungal pathogen. Here, we report the development, validation, and applications of the first clustered regularly interspaced short palindromic repeats (CRISPR) activation (CRISPRa) system in N. glabrata for targeted genetic overexpression. Using this system, we demonstrate the ability of CRISPRa to drive high levels of gene expression in N. glabrata, and further assess optimal guide RNA targeting for robust overexpression. We demonstrate the applications of CRISPRa to overexpress genes involved in fungal pathogenesis and drug resistance and detect corresponding phenotypic alterations in these key traits, including the characterization of novel phenotypes. Finally, we capture strain variation using our CRISPRa system in two commonly used N. glabrata genetic backgrounds. Together, this tool will expand our capacity for functional genetic overexpression in this pathogen, with numerous possibilities for future applications.IMPORTANCENakaseomyces (formerly Candida) glabrata is an important fungal pathogen that is now the second leading cause of candidiasis infections. A common strategy that this pathogen employs to resist antifungal treatment is through the upregulation of gene expression, but we have limited tools available to study this phenomenon. Here, we develop, optimize, and apply the use of CRISPRa as a means to overexpress genes in N. glabrata. We demonstrate the utility of this system to overexpress key genes involved in antifungal susceptibility, stress tolerance, and biofilm growth. This tool will be an important contribution to our ability to study the biology of this important fungal pathogen.
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Affiliation(s)
- Laetitia Maroc
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Canada
| | - Hajer Shaker
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Canada
| | - Rebecca S Shapiro
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Canada
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3
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Pavesic MW, Gale AN, Nickels TJ, Harrington AA, Bussey M, Cunningham KW. Calcineurin-dependent contributions to fitness in the opportunistic pathogen Candida glabrata. mSphere 2024; 9:e0055423. [PMID: 38171022 PMCID: PMC10826367 DOI: 10.1128/msphere.00554-23] [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: 09/22/2023] [Accepted: 11/19/2023] [Indexed: 01/05/2024] Open
Abstract
The protein phosphatase calcineurin is vital for the virulence of the opportunistic fungal pathogen Candida glabrata. The host-induced stresses that activate calcineurin signaling are unknown, as are the targets of calcineurin relevant to virulence. To potentially shed light on these processes, millions of transposon insertion mutants throughout the genome of C. glabrata were profiled en masse for fitness defects in the presence of FK506, a specific inhibitor of calcineurin. Eighty-seven specific gene deficiencies depended on calcineurin signaling for full viability in vitro both in wild-type and pdr1∆ null strains lacking pleiotropic drug resistance. Three genes involved in cell wall biosynthesis (FKS1, DCW1, FLC1) possess co-essential paralogs whose expression depended on calcineurin and Crz1 in response to micafungin, a clinical antifungal that interferes with cell wall biogenesis. Interestingly, 80% of the FK506-sensitive mutants were deficient in different aspects of vesicular trafficking, such as endocytosis, exocytosis, sorting, and biogenesis of secretory proteins in the endoplasmic reticulum (ER). In response to the experimental antifungal manogepix that blocks GPI-anchor biosynthesis in the ER, calcineurin signaling increased and strongly prevented cell death independent of Crz1, one of its major targets. Comparisons between manogepix, micafungin, and the ER-stressing tunicamycin reveal a correlation between the degree of calcineurin signaling and the degree of cell survival. These findings suggest that calcineurin plays major roles in mitigating stresses of vesicular trafficking. Such stresses may arise during host infection and in response to antifungal therapies.IMPORTANCECalcineurin plays critical roles in the virulence of most pathogenic fungi. This study sheds light on those roles in the opportunistic pathogen Candida glabrata using a genome-wide analysis in vitro. The findings could lead to antifungal developments that also avoid immunosuppression.
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Affiliation(s)
- Matthew W. Pavesic
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Andrew N. Gale
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Timothy J. Nickels
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | | | - Maya Bussey
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Kyle W. Cunningham
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
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4
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Thompson GR, Jenks JD, Baddley JW, Lewis JS, Egger M, Schwartz IS, Boyer J, Patterson TF, Chen SCA, Pappas PG, Hoenigl M. Fungal Endocarditis: Pathophysiology, Epidemiology, Clinical Presentation, Diagnosis, and Management. Clin Microbiol Rev 2023; 36:e0001923. [PMID: 37439685 PMCID: PMC10512793 DOI: 10.1128/cmr.00019-23] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2023] Open
Abstract
Fungal endocarditis accounts for 1% to 3% of all infective endocarditis cases, is associated with high morbidity and mortality (>70%), and presents numerous challenges during clinical care. Candida spp. are the most common causes of fungal endocarditis, implicated in over 50% of cases, followed by Aspergillus and Histoplasma spp. Important risk factors for fungal endocarditis include prosthetic valves, prior heart surgery, and injection drug use. The signs and symptoms of fungal endocarditis are nonspecific, and a high degree of clinical suspicion coupled with the judicious use of diagnostic tests is required for diagnosis. In addition to microbiological diagnostics (e.g., blood culture for Candida spp. or galactomannan testing and PCR for Aspergillus spp.), echocardiography remains critical for evaluation of potential infective endocarditis, although radionuclide imaging modalities such as 18F-fluorodeoxyglucose positron emission tomography/computed tomography are increasingly being used. A multimodal treatment approach is necessary: surgery is usually required and should be accompanied by long-term systemic antifungal therapy, such as echinocandin therapy for Candida endocarditis or voriconazole therapy for Aspergillus endocarditis.
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Affiliation(s)
- George R. Thompson
- Department of Internal Medicine, Division of Infectious Diseases, University of California-Davis Medical Center, Sacramento, California, USA
- Department of Medical Microbiology and Immunology, University of California-Davis, Davis, California, USA
| | - Jeffrey D. Jenks
- Durham County Department of Public Health, Durham, North Carolina, USA
- Division of Infectious Diseases, Department of Medicine, Duke University, Durham, North Carolina, USA
| | - John W. Baddley
- Department of Medicine, Division of Infectious Diseases, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - James S. Lewis
- Department of Pharmacy, Oregon Health & Science University, Portland, Oregon, USA
| | - Matthias Egger
- Division of Infectious Diseases, ECMM Excellence Center for Medical Mycology, Department of Medicine, Medical University of Graz, Graz, Austria
| | - Ilan S. Schwartz
- Division of Infectious Diseases, Department of Medicine, Duke University, Durham, North Carolina, USA
| | - Johannes Boyer
- Division of Infectious Diseases, ECMM Excellence Center for Medical Mycology, Department of Medicine, Medical University of Graz, Graz, Austria
| | - Thomas F. Patterson
- Department of Medicine, Division of Infectious Diseases, The University of Texas Health Science Center, San Antonio, Texas, USA
| | - Sharon C.-A. Chen
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Sydney, New South Wales, Australia
- Centre for Infectious Diseases and Microbiology, Westmead Hospital, The University of Sydney, Sydney, New South Wales, Australia
| | - Peter G. Pappas
- Department of Medicine Division of Infectious Diseases, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Martin Hoenigl
- Division of Infectious Diseases, ECMM Excellence Center for Medical Mycology, Department of Medicine, Medical University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
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5
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Rai MN, Rai R, Sethiya P, Parsania C. Transcriptome analysis reveals a common adaptive transcriptional response of Candida glabrata to diverse environmental stresses. Res Microbiol 2023:104073. [PMID: 37100335 DOI: 10.1016/j.resmic.2023.104073] [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: 10/12/2022] [Revised: 04/10/2023] [Accepted: 04/17/2023] [Indexed: 04/28/2023]
Abstract
Candida glabrata, an opportunistic fungal pathogen, causes superficial and life-threatening infections in humans. In the host microenvironment, C. glabrata encounters a variety of stresses, and its ability to cope with these stresses is crucial for its pathogenesis. To gain insights into how C. glabrata adapts to adverse environmental conditions, we examined its transcriptional landscape under heat, osmotic, cell wall, oxidative, and genotoxic stresses using RNA sequencing and reveal that C. glabrata displays a diverse transcriptional response involving ∼75% of its genome for adaptation to different environmental stresses. C. glabrata mounts a central common adaptation response wherein ∼25% of all genes (n = 1370) are regulated in a similar fashion at different environmental stresses. Elevated cellular translation and diminished mitochondrial activity-associated transcriptional signature characterize the common adaptation response. Transcriptional regulatory association networks of common adaptation response genes revealed a set of 29 transcription factors acting as potential activators and repressors of associated adaptive response genes. Overall, the current work delineates the adaptive responses of C. glabrata to diverse environmental stresses and reports the existence of a common adaptive transcriptional response upon prolonged exposure to environmental stresses.
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Affiliation(s)
- Maruti Nandan Rai
- Institute for Sustainability, Energy, and Environment, University of Illinois at Urbana Champaign, IL, USA.
| | - Rikky Rai
- Citrus Research and Education Center, University of Florida, FL, USA.
| | - Pooja Sethiya
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, Westmead 2145 NSW, University of Sydney, Australia.
| | - Chirag Parsania
- Gene and Stem Cell Therapy Program Centenary Institute, Camperdown, NSW, 2050, Faculty of medicine and health, University of Sydney, Australia.
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6
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Raj K, Rishi P, Shukla G, Rudramurhty SM, Mongad DS, Kaur A. Possible Contribution of Alternative Transcript Isoforms in Mature Biofilm Growth Phase of Candida glabrata. Indian J Microbiol 2022; 62:583-601. [PMID: 36458226 PMCID: PMC9705674 DOI: 10.1007/s12088-022-01036-7] [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: 06/22/2022] [Accepted: 08/04/2022] [Indexed: 11/05/2022] Open
Abstract
Expression of genome-wide alternative transcript isoforms and differential transcript isoform usage in different biological conditions (isoform switching) are responsible for the varied proteomic functional diversity in higher eukaryotic organisms. However, these mechanisms have not been studied in Candida glabrata, which is a potent eukaryotic opportunistic pathogen. Biofilm formation is an important virulence factor of C. glabrata that withstands antifungal drug stress and overcomes the host-immune response. Here, we present the genome-wide differential transcript isoform expression (DTE) and differential transcript isoform usage (DTU) in a mature biofilm growth phase of C. glabrata (clinical isolate; NCCPF 100,037) using the RNA sequencing approach. The DTE analysis generated 7837 transcript isoforms from the C. glabrata genome (5293 genes in total), and revealed that transcript isoforms generated from 292 genes showed significant DTU in the mature biofilm cells. Gene ontology, pathway analysis and protein-protein interactions of significant transcript isoforms, further substantiated that their specific expression and differential usage is required for transitioning the planktonic cells to biofilm in C. glabrata. The present study reported the possible role of expression of alternative transcript isoforms and differential transcript isoform usage in the mature biofilms of C. glabrata. The observation derived from the study may prove to be beneficial for making future antifungal therapeutic strategies. Supplementary Information The online version contains supplementary material available at 10.1007/s12088-022-01036-7.
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Affiliation(s)
- Khem Raj
- Department of Microbiology, Basic Medical Sciences Block I, South Campus, Panjab University, Sector-25, Chandigarh, 160014 India
| | - Praveen Rishi
- Department of Microbiology, Basic Medical Sciences Block I, South Campus, Panjab University, Sector-25, Chandigarh, 160014 India
| | - Geeta Shukla
- Department of Microbiology, Basic Medical Sciences Block I, South Campus, Panjab University, Sector-25, Chandigarh, 160014 India
| | - Shivaprakash M. Rudramurhty
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | - Dattatray S. Mongad
- National Centre for Microbial Resource, National Centre for Cell Sciences (NCCS), Pune, India
| | - Amrita Kaur
- Department of Microbiology, Basic Medical Sciences Block I, South Campus, Panjab University, Sector-25, Chandigarh, 160014 India
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7
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Surachat K, Taylor TD, Wattanamatiphot W, Sukpisit S, Jeenkeawpiam K. aTAP: automated transcriptome analysis platform for processing RNA-seq data by de novo assembly. Heliyon 2022; 8:e10255. [PMID: 36033257 PMCID: PMC9404342 DOI: 10.1016/j.heliyon.2022.e10255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 04/27/2022] [Accepted: 08/05/2022] [Indexed: 11/05/2022] Open
Abstract
RNA-seq is a sequencing technique that uses next-generation sequencing (NGS) to explore and study the entire transcriptome of a biological sample. NGS-based analyses are mostly performed via command-line interfaces, which is an obstacle for molecular biologists and researchers. Therefore, the higher throughputs from NGS can only be accessed with the help of bioinformatics and computer science expertise. As the cost of sequencing is continuously falling, the use of RNA-seq seems certain to increase. To minimize the problems encountered by biologists and researchers in RNA-seq data analysis, we propose an automated platform with a web application that integrates various bioinformatics pipelines. The platform is intended to enable academic users to more easily analyze transcriptome datasets. Our automated Transcriptome Analysis Platform (aTAP) offers comprehensive bioinformatics workflows, including quality control of raw reads, trimming of low-quality reads, de novo transcriptome assembly, transcript expression quantification, differential expression analysis, and transcript annotation. aTAP has a user-friendly graphical interface, allowing researchers to interact with and visualize results in the web browser. This project offers an alternative way to analyze transcriptome data, by integrating efficient and well-known tools, that is simpler and more accessible to research communities. aTAP is freely available to academic users at https://atap.psu.ac.th/.
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Affiliation(s)
- Komwit Surachat
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand.,Translational Medicine Research Center, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand.,Molecular Evolution and Computational Biology Research Unit, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand
| | - Todd Duane Taylor
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Wanicbut Wattanamatiphot
- Division of Computational Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand
| | - Sukgamon Sukpisit
- Division of Computational Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand
| | - Kongpop Jeenkeawpiam
- Molecular Evolution and Computational Biology Research Unit, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand
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8
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Shantal CJN, Juan CC, Lizbeth BUS, Carlos HGJ, Estela GPB. Candida glabrata is a successful pathogen: an artist manipulating the immune response. Microbiol Res 2022; 260:127038. [DOI: 10.1016/j.micres.2022.127038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 04/02/2022] [Accepted: 04/07/2022] [Indexed: 02/07/2023]
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9
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Li X, He L, Krom BP, Cheng L, de Soet JJ, Deng DM. Niacin Limitation Promotes Candida glabrata Adhesion to Abiotic Surfaces. Pathogens 2022; 11:pathogens11040387. [PMID: 35456062 PMCID: PMC9028596 DOI: 10.3390/pathogens11040387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 03/18/2022] [Accepted: 03/19/2022] [Indexed: 02/01/2023] Open
Abstract
Candida glabrata is a prevalent fungal pathogen in humans, which is able to adhere to host cells and abiotic surfaces. Nicotinic acid (NA) limitation has been shown to promote the adherence of C. glabrata to human epithelial cells. Clinically, the elderly and hospitalized patients who are prone to C. glabrata–related denture stomatitis often suffer from vitamin deficiency. This study aimed to investigate C. glabrata adhesion to abiotic surfaces, including acrylic resin (a denture material) surfaces, cell surface hydrophobicity and adhesion gene expression. C. glabrata CBS138 was grown in media containing decreasing NA concentrations (40, 0.4, 0.04 and 0.004 µM). Adherence of C. glabrata to glass coverslips and acrylic resin was analyzed. C. glabrata adhesion to both surfaces generally increased with decreasing NA concentrations. The highest adhesion was found for the cells grown with 0.004 µM NA. The cell surface hydrophobicity test indicated that NA limitation enhanced hydrophobicity of C. glabrata cells. Quantitative PCR showed that of all adhesion genes tested, EPA1, EPA3 and EPA7 were significantly up-regulated in both 0.004 µM NA and 0.04 µM NA groups compared to those in the 40 µM NA group. No significant up- or down-regulation under NA limitation was observed for the other tested adhesion genes, namely AWP3, AWP4, AWP6 and EPA6. NA limitation resulted in increased expression of some adhesion genes, higher surface hydrophobicity of C. glabrata and enhanced adhesion to abiotic surfaces. NA deficiency is likely a risk factor for C. glabrata–related denture stomatitis in the elderly.
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Affiliation(s)
- Xiaolan Li
- Guanghua School of Stomatology, Guangdong Province Key Laboratory of Stomatology, Department of Operative Dentistry and Endodontics, Sun Yat-sen University, Guangzhou 510055, China
- Academic Centre for Dentistry Amsterdam (ACTA), Department of Preventive Dentistry, Universiteit van Amsterdam and Vrije Universiteit, 1081 LA Amsterdam, The Netherlands; (B.P.K.); (J.J.d.S.); (D.M.D.)
- Correspondence:
| | - Libang He
- West China School of Stomatology, State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Operative Dentistry and Endodontics, Sichuan University, Chengdu 610041, China; (L.H.); (L.C.)
| | - Bastiaan P. Krom
- Academic Centre for Dentistry Amsterdam (ACTA), Department of Preventive Dentistry, Universiteit van Amsterdam and Vrije Universiteit, 1081 LA Amsterdam, The Netherlands; (B.P.K.); (J.J.d.S.); (D.M.D.)
| | - Lei Cheng
- West China School of Stomatology, State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Operative Dentistry and Endodontics, Sichuan University, Chengdu 610041, China; (L.H.); (L.C.)
| | - Johannes J. de Soet
- Academic Centre for Dentistry Amsterdam (ACTA), Department of Preventive Dentistry, Universiteit van Amsterdam and Vrije Universiteit, 1081 LA Amsterdam, The Netherlands; (B.P.K.); (J.J.d.S.); (D.M.D.)
| | - Dong M. Deng
- Academic Centre for Dentistry Amsterdam (ACTA), Department of Preventive Dentistry, Universiteit van Amsterdam and Vrije Universiteit, 1081 LA Amsterdam, The Netherlands; (B.P.K.); (J.J.d.S.); (D.M.D.)
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10
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Nasuno R, Suzuki S, Oiki S, Hagiwara D, Takagi H. Identification and Functional Analysis of GTP Cyclohydrolase II in Candida glabrata in Response to Nitrosative Stress. Front Microbiol 2022; 13:825121. [PMID: 35308400 PMCID: PMC8924521 DOI: 10.3389/fmicb.2022.825121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 01/14/2022] [Indexed: 11/18/2022] Open
Abstract
Reactive nitrogen species (RNS) are signal molecules involved in various biological events; however, excess levels of RNS cause nitrosative stress, leading to cell death and/or cellular dysfunction. During the process of infection, pathogens are exposed to nitrosative stress induced by host-derived RNS. Therefore, the nitrosative stress resistance mechanisms of pathogenic microorganisms are important for their infection and pathogenicity, and could be promising targets for antibiotics. Previously, we demonstrated that the RIB1 gene encoding GTP cyclohydrolase II (GCH2), which catalyzes the first step of the riboflavin biosynthesis pathway, is important for nitrosative stress resistance in the yeast Saccharomyces cerevisiae. Here, we identified and characterized the RIB1 gene in the opportunistic pathogenic yeast Candida glabrata. Our genetic and biochemical analyses indicated that the open reading frame of CAGL0F04279g functions as RIB1 in C. glabrata (CgRIB1). Subsequently, we analyzed the effect of CgRIB1 on nitrosative stress resistance by a growth test in the presence of RNS. Overexpression or deletion of CgRIB1 increased or decreased the nitrosative stress resistance of C. glabrata, respectively, indicating that GCH2 confers nitrosative stress resistance on yeast cells. Moreover, we showed that the proliferation of C. glabrata in cultures of macrophage-like cells required the GCH2-dependent nitrosative stress detoxifying mechanism. Additionally, an infection assay using silkworms as model host organisms indicated that CgRIB1 is indispensable for the virulence of C. glabrata. Our findings suggest that the GCH2-dependent nitrosative stress detoxifying mechanism is a promising target for the development of novel antibiotics.
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Affiliation(s)
- Ryo Nasuno
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
| | - Soma Suzuki
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
| | - Sayoko Oiki
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Daisuke Hagiwara
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan.,Microbiology Research Center for Sustainability, University of Tsukuba, Tsukuba, Japan
| | - Hiroshi Takagi
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
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11
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Kim J, Oh SH, Rodriguez-Bobadilla R, Vuong VM, Hubka V, Zhao X, Hoyer LL. Peering Into Candida albicans Pir Protein Function and Comparative Genomics of the Pir Family. Front Cell Infect Microbiol 2022; 12:836632. [PMID: 35372132 PMCID: PMC8975586 DOI: 10.3389/fcimb.2022.836632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 02/11/2022] [Indexed: 11/24/2022] Open
Abstract
The fungal cell wall, comprised primarily of protein and polymeric carbohydrate, maintains cell structure, provides protection from the environment, and is an important antifungal drug target. Pir proteins (proteins with internal repeats) are linked to cell wall β-1,3-glucan and are best studied in Saccharomyces cerevisiae. Sequential deletion of S. cerevisiae PIR genes produces strains with increasingly notable cell wall damage. However, a true null mutant lacking all five S. cerevisiae PIR genes was never constructed. Because only two PIR genes (PIR1, PIR32) were annotated in the Candida albicans genome, the initial goal of this work was to construct a true Δpir/Δpir null strain in this species. Unexpectedly, the phenotype of the null strain was almost indistinguishable from its parent, leading to the search for other proteins with Pir function. Bioinformatic approaches revealed nine additional C. albicans proteins that share a conserved Pir functional motif (minimally DGQ). Examination of the protein sequences revealed another conserved motif (QFQFD) toward the C-terminal end of each protein. Sequence similarities and presence of the conserved motif(s) were used to identify a set of 75 proteins across 16 fungal species that are proposed here as Pir proteins. The Pir family is greatly expanded in C. albicans and C. dubliniensis compared to other species and the orthologs are known to have specialized function during chlamydospore formation. Predicted Pir structures showed a conserved core of antiparallel beta-sheets and sometimes-extensive loops that contain amino acids with the potential to form linkages to cell wall components. Pir phylogeny demonstrated emergence of specific ortholog groups among the fungal species. Variation in gene expression patterns was noted among the ortholog groups during growth in rich medium. PIR allelic variation was quite limited despite the presence of a repeated sequence in many loci. Results presented here demonstrate that the Pir family is larger than previously recognized and lead to new hypotheses to test to better understand Pir proteins and their role in the fungal cell wall.
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Affiliation(s)
- Jisoo Kim
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Soon-Hwan Oh
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | | | - Vien M. Vuong
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Vit Hubka
- Department of Botany, Faculty of Science, Charles University, Prague, Czechia
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology, Czech Academy of Sciences, Prague, Czechia
| | - Xiaomin Zhao
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Lois L. Hoyer
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- *Correspondence: Lois L. Hoyer,
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12
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The long non-coding RNA landscape of Candida yeast pathogens. Nat Commun 2021; 12:7317. [PMID: 34916523 PMCID: PMC8677757 DOI: 10.1038/s41467-021-27635-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 11/30/2021] [Indexed: 12/29/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) constitute a poorly studied class of transcripts with emerging roles in key cellular processes. Despite efforts to characterize lncRNAs across a wide range of species, these molecules remain largely unexplored in most eukaryotic microbes, including yeast pathogens of the Candida clade. Here, we analyze thousands of publicly available sequencing datasets to infer and characterize the lncRNA repertoires of five major Candida pathogens: Candida albicans, Candida tropicalis, Candida parapsilosis, Candida auris and Candida glabrata. Our results indicate that genomes of these species encode hundreds of lncRNAs that show levels of evolutionary constraint intermediate between those of intergenic genomic regions and protein-coding genes. Despite their low sequence conservation across the studied species, some lncRNAs are syntenic and are enriched in shared sequence motifs. We find co-expression of lncRNAs with certain protein-coding transcripts, hinting at potential functional associations. Finally, we identify lncRNAs that are differentially expressed during infection of human epithelial cells for four of the studied species. Our comprehensive bioinformatic analyses of Candida lncRNAs pave the way for future functional characterization of these transcripts. Long non-coding RNAs (lncRNAs) play roles in key cellular processes, but remain largely unexplored in fungal pathogens such as Candida. Here, Hovhannisyan and Gabaldón analyze thousands of sequencing datasets to infer and characterize the lncRNA repertoires of five Candida species, paving the way for their future functional characterization.
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13
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Muzafar S, Sharma RD, Chauhan N, Prasad R. Intron distribution and emerging role of alternative splicing in fungi. FEMS Microbiol Lett 2021; 368:6414529. [PMID: 34718529 DOI: 10.1093/femsle/fnab135] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 10/28/2021] [Indexed: 12/16/2022] Open
Abstract
Spliceosomal introns are noncoding sequences that are spliced from pre-mRNA. They are ubiquitous in eukaryotic genomes, although the average number of introns per gene varies considerably between different eukaryotic species. Fungi are diverse in terms of intron numbers ranging from 4% to 99% genes with introns. Alternative splicing is one of the most common modes of posttranscriptional regulation in eukaryotes, giving rise to multiple transcripts from a single pre-mRNA and is widespread in metazoans and drives extensive proteome diversity. Earlier, alternative splicing was considered to be rare in fungi, but recently, increasing numbers of studies have revealed that alternative splicing is also widespread in fungi and has been implicated in the regulation of fungal growth and development, protein localization and the improvement of survivability, likely underlying their unique capacity to adapt to changing environmental conditions. However, the role of alternative splicing in pathogenicity and development of drug resistance is only recently gaining attention. In this review, we describe the intronic landscape in fungi. We also present in detail the newly discovered functions of alternative splicing in various cellular processes and outline areas particularly in pathogenesis and clinical drug resistance for future studies that could lead to the development of much needed new therapeutics.
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Affiliation(s)
- Suraya Muzafar
- Amity Institute of Integrative Sciences and Health, Amity University Gurgaon, Gurgaon 122413, Haryana, India
| | - Ravi Datta Sharma
- Amity Institute of Integrative Sciences and Health, Amity University Gurgaon, Gurgaon 122413, Haryana, India
| | - Neeraj Chauhan
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ 07103, USA
| | - Rajendra Prasad
- Amity Institute of Integrative Sciences and Health, Amity University Gurgaon, Gurgaon 122413, Haryana, India
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14
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Hassan Y, Chew SY, Than LTL. Candida glabrata: Pathogenicity and Resistance Mechanisms for Adaptation and Survival. J Fungi (Basel) 2021; 7:jof7080667. [PMID: 34436206 PMCID: PMC8398317 DOI: 10.3390/jof7080667] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/05/2021] [Accepted: 08/05/2021] [Indexed: 02/06/2023] Open
Abstract
Candida glabrata is a yeast of increasing medical relevance, particularly in critically ill patients. It is the second most isolated Candida species associated with invasive candidiasis (IC) behind C. albicans. The attributed higher incidence is primarily due to an increase in the acquired immunodeficiency syndrome (AIDS) population, cancer, and diabetic patients. The elderly population and the frequent use of indwelling medical devices are also predisposing factors. This work aimed to review various virulence factors that facilitate the survival of pathogenic C. glabrata in IC. The available published research articles related to the pathogenicity of C. glabrata were retrieved and reviewed from four credible databases, mainly Google Scholar, ScienceDirect, PubMed, and Scopus. The articles highlighted many virulence factors associated with pathogenicity in C. glabrata, including adherence to susceptible host surfaces, evading host defences, replicative ageing, and producing hydrolytic enzymes (e.g., phospholipases, proteases, and haemolysins). The factors facilitate infection initiation. Other virulent factors include iron regulation and genetic mutations. Accordingly, biofilm production, tolerance to high-stress environments, resistance to neutrophil killings, and development of resistance to antifungal drugs, notably to fluconazole and other azole derivatives, were reported. The review provided evident pathogenic mechanisms and antifungal resistance associated with C. glabrata in ensuring its sustenance and survival.
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Affiliation(s)
- Yahaya Hassan
- Department of Medical Laboratory Science, Faculty of Allied Health Sciences, Bayero University Kano, Kano 700241, Nigeria;
- Department of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia (UPM), Serdang 43400, Selangor, Malaysia;
| | - Shu Yih Chew
- Department of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia (UPM), Serdang 43400, Selangor, Malaysia;
| | - Leslie Thian Lung Than
- Department of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia (UPM), Serdang 43400, Selangor, Malaysia;
- Institute of Bioscience, Universiti Putra Malaysia (UPM), Serdang 43400, Selangor, Malaysia
- Correspondence: ; Tel.: +60-39769-2373
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15
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Essen LO, Vogt MS, Mösch HU. Diversity of GPI-anchored fungal adhesins. Biol Chem 2021; 401:1389-1405. [PMID: 33035180 DOI: 10.1515/hsz-2020-0199] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 09/21/2020] [Indexed: 12/28/2022]
Abstract
Selective adhesion of fungal cells to one another and to foreign surfaces is fundamental for the development of multicellular growth forms and the successful colonization of substrates and host organisms. Accordingly, fungi possess diverse cell wall-associated adhesins, mostly large glycoproteins, which present N-terminal adhesion domains at the cell surface for ligand recognition and binding. In order to function as robust adhesins, these glycoproteins must be covalently linkedto the cell wall via C-terminal glycosylphosphatidylinositol (GPI) anchors by transglycosylation. In this review, we summarize the current knowledge on the structural and functional diversity of so far characterized protein families of adhesion domains and set it into a broad context by an in-depth bioinformatics analysis using sequence similarity networks. In addition, we discuss possible mechanisms for the membrane-to-cell wall transfer of fungal adhesins by membrane-anchored Dfg5 transglycosidases.
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Affiliation(s)
- Lars-Oliver Essen
- Department of Biochemistry, Faculty of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, D-35043Marburg, Germany.,Center for Synthetic Microbiology, Philipps-Universität Marburg, Karl-von-Frisch-Str. 6, D-35043Marburg, Germany
| | - Marian Samuel Vogt
- Department of Biochemistry, Faculty of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, D-35043Marburg, Germany
| | - Hans-Ulrich Mösch
- Department of Genetics, Philipps-Universität Marburg, Karl-von-Frisch-Str. 8, D-35043Marburg, Germany.,Center for Synthetic Microbiology, Philipps-Universität Marburg, Karl-von-Frisch-Str. 6, D-35043Marburg, Germany
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16
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Pais P, Oliveira J, Almeida V, Yilmaz M, Monteiro PT, Teixeira MC. Transcriptome-wide differences between Saccharomyces cerevisiae and Saccharomyces cerevisiae var. boulardii: Clues on host survival and probiotic activity based on promoter sequence variability. Genomics 2021; 113:530-539. [PMID: 33482324 DOI: 10.1016/j.ygeno.2020.11.034] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 11/23/2020] [Accepted: 11/26/2020] [Indexed: 02/06/2023]
Abstract
Although Saccharomyces cerevisiae and S. cerevisiae var. boulardii share more than 95% genome sequence homology, only S. cerevisiae var. boulardii displays probiotic activity. In this study, the transcriptomic differences exhibited by S. cerevisiae and S. cerevisiae var. boulardii in intestinal like medium were evaluated. S. cerevisiae was found to display stress response overexpression, consistent with higher ability of S. cerevisiae var. boulardii to survive within the human host, while S. cerevisiae var. boulardii exhibited transcriptional patterns associated with probiotic activity, suggesting increased acetate biosynthesis. Resorting to the creation of a S. cerevisiae var. boulardii genomic database within Yeastract+, a possible correlation between loss or gain of transcription factor binding sites in S. cerevisiae var. boulardii promoters and the transcriptomic pattern is discussed. This study suggests that S. cerevisiae var. boulardii probiotic activity, when compared to S. cerevisiae, relies, at least partially, on differential expression regulation, based on promoter variability.
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Affiliation(s)
- Pedro Pais
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal; iBB - Institute for Bioengineering and Biosciences, Biological Sciences Research Group, Instituto Superior Técnico, Lisboa, Portugal
| | | | - Vanda Almeida
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal; iBB - Institute for Bioengineering and Biosciences, Biological Sciences Research Group, Instituto Superior Técnico, Lisboa, Portugal
| | - Melike Yilmaz
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal; iBB - Institute for Bioengineering and Biosciences, Biological Sciences Research Group, Instituto Superior Técnico, Lisboa, Portugal
| | - Pedro T Monteiro
- Department of Computer Science and Engineering, Instituto Superior Técnico (IST), Universidade de Lisboa, Lisbon, Portugal; INESC-ID, Lisbon, Portugal.
| | - Miguel C Teixeira
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal; iBB - Institute for Bioengineering and Biosciences, Biological Sciences Research Group, Instituto Superior Técnico, Lisboa, Portugal.
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17
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Identification of Essential Genes and Fluconazole Susceptibility Genes in Candida glabrata by Profiling Hermes Transposon Insertions. G3-GENES GENOMES GENETICS 2020; 10:3859-3870. [PMID: 32819971 PMCID: PMC7534453 DOI: 10.1534/g3.120.401595] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Within the budding yeasts, the opportunistic pathogen Candida glabrata and other members of the Nakaseomyces clade have developed virulence traits independently from C. albicans and C. auris. To begin exploring the genetic basis of C. glabrata virulence and its innate resistance to antifungals, we launched the Hermes transposon from a plasmid and sequenced more than 500,000 different semi-random insertions throughout the genome. With machine learning, we identified 1278 protein-encoding genes (25% of total) that could not tolerate transposon insertions and are likely essential for C. glabrata fitness in vitro. Interestingly, genes involved in mRNA splicing were less likely to be essential in C. glabrata than their orthologs in S. cerevisiae, whereas the opposite is true for genes involved in kinetochore function and chromosome segregation. When a pool of insertion mutants was challenged with the first-line antifungal fluconazole, insertions in several known resistance genes (e.g., PDR1, CDR1, PDR16, PDR17, UPC2A, DAP1, STV1) and 15 additional genes (including KGD1, KGD2, YHR045W) became hypersensitive to fluconazole. Insertions in 200 other genes conferred significant resistance to fluconazole, two-thirds of which function in mitochondria and likely down-regulate Pdr1 expression or function. Knockout mutants of KGD2 and IDH2, which consume and generate alpha-ketoglutarate in mitochondria, exhibited increased and decreased resistance to fluconazole through a process that depended on Pdr1. These findings establish the utility of transposon insertion profiling in forward genetic investigations of this important pathogen of humans.
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18
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Giosa D, Felice MR, Giuffrè L, Aiese Cigliano R, Paytuví-Gallart A, Lo Passo C, Barresi C, D'Alessandro E, Huang H, Criseo G, Mora-Montes HM, de Hoog S, Romeo O. Transcriptome-wide expression profiling of Sporothrix schenckii yeast and mycelial forms and the establishment of the Sporothrix Genome DataBase. Microb Genom 2020; 6:mgen000445. [PMID: 33034552 PMCID: PMC7660252 DOI: 10.1099/mgen.0.000445] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 09/14/2020] [Indexed: 12/13/2022] Open
Abstract
Sporothrix schenckii is a dimorphic fungus existing as mould in the environment and as yeast in the host. The morphological shift between mycelial/yeast phases is crucial for its virulence, but the transcriptional networks implicated in dimorphic transition are still not fully understood. Here, we report the global transcriptomic differences occurring between mould and yeast phases of S. schenckii, including changes in gene expression profiles associated with these distinct cellular phenotypes. Moreover, we also propose a new genome annotation, which reveals a more complex transcriptional architecture than previously assumed. Using RNA-seq, we identified a total of 17 307 genes, of which 11 217 were classified as protein-encoding genes, whereas 6090 were designated as non-coding RNAs (ncRNAs). Approximately ~71 % of all annotated genes were found to overlap and the different-strand overlapping type was the most common. Gene expression analysis revealed that 8795 genes were differentially regulated among yeast and mould forms. Differential gene expression was also observed for antisense ncRNAs overlapping neighbouring protein-encoding genes. The release of transcriptome-wide data and the establishment of the Sporothrix Genome DataBase (http://sporothrixgenomedatabase.unime.it) represent an important milestone for Sporothrix research, because they provide a strong basis for future studies on the molecular pathways involved in numerous biological processes.
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Affiliation(s)
- Domenico Giosa
- Department of Clinical and Experimental Medicine, University Hospital of Messina, Messina 98125, Italy
| | - Maria Rosa Felice
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina 98166, Italy
| | - Letterio Giuffrè
- Department of Veterinary Sciences, Division of Animal Production, University of Messina, Messina 98168, Italy
| | | | | | - Carla Lo Passo
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina 98166, Italy
| | - Cinzia Barresi
- Department of Veterinary Sciences, Division of Animal Production, University of Messina, Messina 98168, Italy
| | - Enrico D'Alessandro
- Department of Veterinary Sciences, Division of Animal Production, University of Messina, Messina 98168, Italy
| | - Huaiqiu Huang
- Department of Dermatology and Venereology, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou 510630, Guangdong, PR China
- Department of Dermatology and Venereology, Baoan District People’s Hospital of Shenzhen, Shenzhen 518012, PR China
| | - Giuseppe Criseo
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina 98166, Italy
| | - Héctor M. Mora-Montes
- Departamento de Biología, División de Ciencias Naturales y Exactas, Campus Guanajuato, Universidad de Guanajuato, Guanajuato 36050, Mexico
| | - Sybren de Hoog
- Center of Expertise in Mycology, Radboud University Medical Center/Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
| | - Orazio Romeo
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina 98166, Italy
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19
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Identification of Genomewide Alternative Splicing Events in Sequential, Isogenic Clinical Isolates of Candida albicans Reveals a Novel Mechanism of Drug Resistance and Tolerance to Cellular Stresses. mSphere 2020; 5:5/4/e00608-20. [PMID: 32817456 PMCID: PMC7426172 DOI: 10.1128/msphere.00608-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The emergence of resistance in Candida albicans, an opportunistic pathogen, against the commonly used antifungals is becoming a major obstacle in its treatment. The necessity to identify new drug targets demands fundamental insights into the mechanisms used by this organism to develop drug resistance. C. albicans has introns in 4 to 6% of its genes, the functions of which remain largely unknown. Using the RNA-sequencing data from isogenic pairs of azole-sensitive and -resistant isolates of C. albicans, here, we show how C. albicans uses modulations in mRNA splicing to overcome antifungal drug stress. Alternative splicing (AS)—a process by which a single gene gives rise to different protein isoforms in eukaryotes—has been implicated in many basic cellular processes, but little is known about its role in drug resistance and fungal pathogenesis. The most common human fungal pathogen, Candida albicans, has introns in 4 to 6% of its genes, the functions of which remain largely unknown. Here, we report AS regulating drug resistance in C. albicans. Comparative RNA-sequencing of two different sets of sequential, isogenic azole-sensitive and -resistant isolates of C. albicans revealed differential expression of splice isoforms of 14 genes. One of these was the superoxide dismutase gene SOD3, which contains a single intron. The sod3Δ/Δ mutant was susceptible to the antifungals amphotericin B (AMB) and menadione (MND). While AMB susceptibility was rescued by overexpression of both the spliced and unspliced SOD3 isoforms, only the spliced isoform could overcome MND susceptibility, demonstrating the functional relevance of this splicing in developing drug resistance. Furthermore, unlike AMB, MND inhibits SOD3 splicing and acts as a splicing inhibitor. Consistent with these observations, MND exposure resulted in increased levels of unspliced SOD3 isoform that are unable to scavenge reactive oxygen species (ROS), resulting in increased drug susceptibility. Collectively, these observations suggest that AS is a novel mechanism for stress adaptation and overcoming drug susceptibility in C. albicans. IMPORTANCE The emergence of resistance in Candida albicans, an opportunistic pathogen, against the commonly used antifungals is becoming a major obstacle in its treatment. The necessity to identify new drug targets demands fundamental insights into the mechanisms used by this organism to develop drug resistance. C. albicans has introns in 4 to 6% of its genes, the functions of which remain largely unknown. Using the RNA-sequencing data from isogenic pairs of azole-sensitive and -resistant isolates of C. albicans, here, we show how C. albicans uses modulations in mRNA splicing to overcome antifungal drug stress.
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20
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Rodríguez A, Guillemyn B, Coucke P, Vaneechoutte M. Nucleic acids enrichment of fungal pathogens to study host-pathogen interactions. Sci Rep 2019; 9:18037. [PMID: 31792282 PMCID: PMC6889467 DOI: 10.1038/s41598-019-54608-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 11/15/2019] [Indexed: 12/11/2022] Open
Abstract
Fungal infections, ranging from superficial to life-threatening infections, represent a major public health problem that affects 25% of the worldwide population. In this context, the study of host-pathogen interactions within the host is crucial to advance antifungal therapy. However, since fungal cells are usually outnumbered by host cells, the fungal transcriptome frequently remains uncovered. We compared three different methods to selectively lyse human cells from in vitro mixes, composed of Candida cells and peripheral blood mononuclear cells. In order to prevent transcriptional modification, the mixes were stored in RNAlater. We evaluated the enrichment of fungal cells through cell counting using microscopy and aimed to further enrich fungal nucleic acids by centrifugation and by reducing contaminant nucleic acids from the host. We verified the enrichment of fungal DNA and RNA through qPCR and RT-qPCR respectively and confirmed that the resulting RNA has high integrity scores, suitable for downstream applications. The enrichment method provided here, i.e., lysis with Buffer RLT followed by centrifugation, may contribute to increase the proportion of nucleic acids from fungi in clinical samples, thus promoting more comprehensive analysis of fungal transcriptional profiles. Although we focused on C. albicans, the enrichment may be applicable to other fungal pathogens.
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Affiliation(s)
- Antonio Rodríguez
- Laboratory Bacteriology Research, Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Ghent, 9000, Belgium.
| | - Brecht Guillemyn
- Center for Medical Genetics Ghent, Ghent University Hospital, Department of Biomolecular Medicine, Ghent, 9000, Belgium
| | - Paul Coucke
- Center for Medical Genetics Ghent, Ghent University Hospital, Department of Biomolecular Medicine, Ghent, 9000, Belgium
| | - Mario Vaneechoutte
- Laboratory Bacteriology Research, Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Ghent, 9000, Belgium
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21
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Ma Q, Bu D, Zhang J, Wu Y, Pei D. The Transcriptome Landscape of Walnut Interspecies Hybrid ( Juglans hindsii × Juglans regia) and Regulation of Cambial Activity in Relation to Grafting. Front Genet 2019; 10:577. [PMID: 31293615 PMCID: PMC6598599 DOI: 10.3389/fgene.2019.00577] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 06/03/2019] [Indexed: 12/18/2022] Open
Abstract
Walnuts (Juglans, Juglandaceae) are known throughout the world as economically important trees that provide fat, protein, vitamins, and minerals as a food source, and produce high-quality timber. We have amended the purpose section to say "However," the omics resources are limited, which hampered the elucidation of molecular mechanisms resulting in their economically important traits (such as yield, fertility alternation, oil synthesis, and wood formation). To enrich the omics database of walnut, there is great need for analyses of its genomic and transcriptomic characteristics. In this study, we reported for the first time of the transcriptome landscape of six important organs or tissues in walnut interspecies hybrid using next-generation sequencing technology. Over 338 million clean reads were obtained. This yielded 74,072 unigenes with an average length of 782.71 bp. To develop an understanding of gene functions and regulatory pathways, 66,355 of the unigenes were identified as homologs of annotated genes and classified into three general categories with 61 functional subcategories. 2,288 out of 2,549 unmapped unigenes had at least one BLAST hit against the public databases. A total of 1,237 transcription factor-encoding genes (TFs) and 2,297 tissue-specific unigenes were identified. Interestingly, in the new shoot between an adult seedling and a grafted tree, the expression of 9,494 unigenes were significantly different, among which 4,388 were up-regulated and 5,106 were down-regulated. Of these, 195, 177, 232, 75, 114, and 68 unigenes were related to transcription factors, cell wall, defense response, transport, plant hormone biosynthesis, and other cambial activity-related functions, respectively. The obtained sequences and putative functional data constitute a resource for future functional analyses in walnut and other woody plants. These findings will be useful in further studies addressing the molecular mechanisms underlying grafting-related cambial activity.
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Affiliation(s)
- Qingguo Ma
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Dechao Bu
- Key Laboratory of Intelligent Information Processing, Advanced Computing Research Laboratory, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
| | - Junpei Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Yang Wu
- Key Laboratory of Intelligent Information Processing, Advanced Computing Research Laboratory, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
| | - Dong Pei
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
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22
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Rahi ML, Mather PB, Ezaz T, Hurwood DA. The Molecular Basis of Freshwater Adaptation in Prawns: Insights from Comparative Transcriptomics of Three Macrobrachium Species. Genome Biol Evol 2019; 11:1002-1018. [PMID: 30840062 PMCID: PMC6450038 DOI: 10.1093/gbe/evz045] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/12/2019] [Indexed: 12/17/2022] Open
Abstract
Elucidating the molecular basis of adaptation to different environmental conditions is important because adaptive ability of a species can shape its distribution, influence speciation, and also drive a variety of evolutionary processes. For crustaceans, colonization of freshwater habitats has significantly impacted diversity, but the molecular basis of this process is poorly understood. In the current study, we examined three prawn species from the genus Macrobrachium (M. australiense, M. tolmerum, and M. novaehollandiae) to better understand the molecular basis of freshwater adaptation using a comparative transcriptomics approach. Each of these species naturally inhabit environments with different salinity levels; here, we exposed them to the same experimental salinity conditions (0‰ and 15‰), to compare expression patterns of candidate genes that previously have been shown to influence phenotypic traits associated with freshwater adaptation (e.g., genes associated with osmoregulation). Differential gene expression analysis revealed 876, 861, and 925 differentially expressed transcripts under the two salinities for M. australiense, M. tolmerum, and M. novaehollandiae, respectively. Of these, 16 were found to be unannotated novel transcripts and may be taxonomically restricted or orphan genes. Functional enrichment and molecular pathway mapping revealed 13 functionally enriched categories and 11 enriched molecular pathways that were common to the three Macrobrachium species. Pattern of selection analysis revealed 26 genes with signatures of positive selection among pairwise species comparisons. Overall, our results indicate that the same key genes and similar molecular pathways are likely to be involved with freshwater adaptation widely across this decapod group; with nonoverlapping sets of genes showing differential expression (mainly osmoregulatory genes) and signatures of positive selection (genes involved with different life history traits).
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Affiliation(s)
- Md Lifat Rahi
- Science and Engineering Faculty, School of Earth Environment and Biological Sciences (EEBS), Queensland University of Technology (QUT), Brisbane, Queensland, Australia
| | - Peter B Mather
- Science and Engineering Faculty, School of Earth Environment and Biological Sciences (EEBS), Queensland University of Technology (QUT), Brisbane, Queensland, Australia
| | - Tariq Ezaz
- Wildlife Genetics Laboratory, Institute for Applied Ecology, University of Canberra, Australian Capital Territory, Australia
| | - David A Hurwood
- Science and Engineering Faculty, School of Earth Environment and Biological Sciences (EEBS), Queensland University of Technology (QUT), Brisbane, Queensland, Australia
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23
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Denecker T, Durand W, Maupetit J, Hébert C, Camadro JM, Poulain P, Lelandais G. Pixel: a content management platform for quantitative omics data. PeerJ 2019; 7:e6623. [PMID: 30944779 PMCID: PMC6441322 DOI: 10.7717/peerj.6623] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 02/14/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND In biology, high-throughput experimental technologies, also referred as "omics" technologies, are increasingly used in research laboratories. Several thousands of gene expression measurements can be obtained in a single experiment. Researchers are routinely facing the challenge to annotate, store, explore and mine all the biological information they have at their disposal. We present here the Pixel web application (Pixel Web App), an original content management platform to help people involved in a multi-omics biological project. METHODS The Pixel Web App is built with open source technologies and hosted on the collaborative development platform GitHub (https://github.com/Candihub/pixel). It is written in Python using the Django framework and stores all the data in a PostgreSQL database. It is developed in the open and licensed under the BSD 3-clause license. The Pixel Web App is also heavily tested with both unit and functional tests, a strong code coverage and continuous integration provided by CircleCI. To ease the development and the deployment of the Pixel Web App, Docker and Docker Compose are used to bundle the application as well as its dependencies. RESULTS The Pixel Web App offers researchers an intuitive way to annotate, store, explore and mine their multi-omics results. It can be installed on a personal computer or on a server to fit the needs of many users. In addition, anyone can enhance the application to better suit their needs, either by contributing directly on GitHub (encouraged) or by extending Pixel on their own. The Pixel Web App does not provide any computational programs to analyze the data. Still, it helps to rapidly explore and mine existing results and holds a strategic position in the management of research data.
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Affiliation(s)
- Thomas Denecker
- CEA, CNRS, Univ. Paris-Sud, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | | | | | | | | | - Pierre Poulain
- CNRS, Univ. Paris Diderot, Institut Jacques Monod (IJM), Paris, France
| | - Gaëlle Lelandais
- CEA, CNRS, Univ. Paris-Sud, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
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Tondini F, Lang T, Chen L, Herderich M, Jiranek V. Linking gene expression and oenological traits: Comparison between Torulaspora delbrueckii and Saccharomyces cerevisiae strains. Int J Food Microbiol 2019; 294:42-49. [PMID: 30763906 DOI: 10.1016/j.ijfoodmicro.2019.01.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 01/21/2019] [Accepted: 01/22/2019] [Indexed: 11/16/2022]
Abstract
Wine fermentations typically involve the yeast Saccharomyces cerevisiae. However, many other yeast species participate to the fermentation process, some with interesting oenological traits. In this study the species Torulaspora delbrueckii, used occasionally in mixed or sequential fermentation with S. cerevisiae to improve wine sensory profile, was investigated to understand the physiological differences between the two. Next generation sequencing was used to characterize the transcriptome of T. delbrueckii and highlight the different genomic response of these yeasts during growth under wine-like conditions. Of particular interest were the basic differences in the glucose fermentation pathway and the formation of aromatic and flavour compounds such as glycerol, esters and acetic acid. Paralog genes were missing in glycolysis and glycerol biosynthesis in T. delbrueckii. Results indicate the tendency of T. delbrueckii to produce less acetic acid relied on a higher expression of alcoholic fermentation related genes, whereas acetate esters were influenced by the absence of esterases, ATF1-2. Additionally, in the Δbap2 S. cerevisiae strain, the final concentration of short branched chain ethyl esters (SBCEEs) was related to branched chain amino acid (BCAA) uptake. In conclusion, different adaption strategies are apparent for T. delbrueckii and S. cerevisiae yeasts, an understanding of which will allow winemakers to make better use of such microbial tools to achieve a desired wine sensory outcome.
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Affiliation(s)
- Federico Tondini
- Department of Wine & Food Science, University of Adelaide, Glen Osmond, South Australia 5064, Australia; Australian Research Council Industrial Transformation Training Centre for Innovative Wine Production, Glen Osmond, South Australia 5064, Australia
| | - Tom Lang
- Department of Wine & Food Science, University of Adelaide, Glen Osmond, South Australia 5064, Australia
| | - Liang Chen
- Department of Wine & Food Science, University of Adelaide, Glen Osmond, South Australia 5064, Australia
| | - Markus Herderich
- Australian Research Council Industrial Transformation Training Centre for Innovative Wine Production, Glen Osmond, South Australia 5064, Australia; The Australian Wine Research Institute, Glen Osmond, South Australia 5064, Australia
| | - Vladimir Jiranek
- Department of Wine & Food Science, University of Adelaide, Glen Osmond, South Australia 5064, Australia; Australian Research Council Industrial Transformation Training Centre for Innovative Wine Production, Glen Osmond, South Australia 5064, Australia.
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25
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Candida glabrata: A Lot More Than Meets the Eye. Microorganisms 2019; 7:microorganisms7020039. [PMID: 30704135 PMCID: PMC6407134 DOI: 10.3390/microorganisms7020039] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 01/21/2019] [Accepted: 01/29/2019] [Indexed: 01/17/2023] Open
Abstract
Candida glabrata is an opportunistic human fungal pathogen that causes superficial mucosal and life-threatening bloodstream infections in individuals with a compromised immune system. Evolutionarily, it is closer to the non-pathogenic yeast Saccharomyces cerevisiae than to the most prevalent Candida bloodstream pathogen, C. albicans. C. glabrata is a haploid budding yeast that predominantly reproduces clonally. In this review, we summarize interactions of C. glabrata with the host immune, epithelial and endothelial cells, and the ingenious strategies it deploys to acquire iron and phosphate from the external environment. We outline various attributes including cell surface-associated adhesins and aspartyl proteases, biofilm formation and stress response mechanisms, that contribute to the virulence of C. glabrata. We further discuss how, C. glabrata, despite lacking morphological switching and secreted proteolytic activity, is able to disarm macrophage, dampen the host inflammatory immune response and replicate intracellularly.
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26
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Cook DE, Valle-Inclan JE, Pajoro A, Rovenich H, Thomma BP, Faino L. Long-Read Annotation: Automated Eukaryotic Genome Annotation Based on Long-Read cDNA Sequencing. PLANT PHYSIOLOGY 2019; 179:38-54. [PMID: 30401722 PMCID: PMC6324239 DOI: 10.1104/pp.18.00848] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 10/19/2018] [Indexed: 05/16/2023]
Abstract
Single-molecule full-length complementary DNA (cDNA) sequencing can aid genome annotation by revealing transcript structure and alternative splice forms, yet current annotation pipelines do not incorporate such information. Here we present long-read annotation (LoReAn) software, an automated annotation pipeline utilizing short- and long-read cDNA sequencing, protein evidence, and ab initio prediction to generate accurate genome annotations. Based on annotations of two fungal genomes (Verticillium dahliae and Plicaturopsis crispa) and two plant genomes (Arabidopsis [Arabidopsis thaliana] and Oryza sativa), we show that LoReAn outperforms popular annotation pipelines by integrating single-molecule cDNA-sequencing data generated from either the Pacific Biosciences or MinION sequencing platforms, correctly predicting gene structure, and capturing genes missed by other annotation pipelines.
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Affiliation(s)
- David E. Cook
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
| | - Jose Espejo Valle-Inclan
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
| | - Alice Pajoro
- Laboratory of Molecular Biology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
| | - Hanna Rovenich
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
| | - Bart P.H.J. Thomma
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
- Author for contact:
| | - Luigi Faino
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
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27
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Pais P, Galocha M, Teixeira MC. Genome-Wide Response to Drugs and Stress in the Pathogenic Yeast Candida glabrata. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2019; 58:155-193. [PMID: 30911893 DOI: 10.1007/978-3-030-13035-0_7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Candida glabrata is the second most common cause of candidemia worldwide and its prevalence has continuously increased over the last decades. C. glabrata infections are especially worrisome in immunocompromised patients, resulting in serious systemic infections, associated to high mortality rates. Intrinsic resistance to azole antifungals, widely used drugs in the clinical setting, and the ability to efficiently colonize the human host and medical devices, withstanding stress imposed by the immune system, are thought to underlie the emergence of C. glabrata. There is a clear clinical need to understand drug and stress resistance in C. glabrata. The increasing prevalence of multidrug resistant isolates needs to be addressed in order to overcome the decrease of viable therapeutic strategies and find new therapeutic targets. Likewise, the understanding of the mechanisms underlying its impressive ability thrive under oxidative, nitrosative, acidic and metabolic stresses, is crucial to design drugs that target these pathogenesis features. The study of the underlying mechanisms that translate C. glabrata plasticity and its competence to evade the immune system, as well as survive host stresses to establish infection, will benefit from extensive scrutiny. This chapter provides a review on the contribution of genome-wide studies to uncover clinically relevant drug resistance and stress response mechanisms in the human pathogenic yeast C. glabrata.
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Affiliation(s)
- Pedro Pais
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal.,Biological Sciences Research Group, Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Mónica Galocha
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal.,Biological Sciences Research Group, Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Miguel Cacho Teixeira
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal. .,Biological Sciences Research Group, Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal.
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28
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Mattenberger F, Sabater-Muñoz B, Toft C, Sablok G, Fares MA. Expression properties exhibit correlated patterns with the fate of duplicated genes, their divergence, and transcriptional plasticity in Saccharomycotina. DNA Res 2018. [PMID: 28633360 PMCID: PMC5726480 DOI: 10.1093/dnares/dsx025] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Gene duplication is an important source of novelties and genome complexity. What genes are preserved as duplicated through long evolutionary times can shape the evolution of innovations. Identifying factors that influence gene duplicability is therefore an important aim in evolutionary biology. Here, we show that in the yeast Saccharomyces cerevisiae the levels of gene expression correlate with gene duplicability, its divergence, and transcriptional plasticity. Genes that were highly expressed before duplication are more likely to be preserved as duplicates for longer evolutionary times and wider phylogenetic ranges than genes that were lowly expressed. Duplicates with higher expression levels exhibit greater divergence between their gene copies. Duplicates that exhibit higher expression divergence are those enriched for TATA-containing promoters. These duplicates also show transcriptional plasticity, which seems to be involved in the origin of adaptations to environmental stresses in yeast. While the expression properties of genes strongly affect their duplicability, divergence and transcriptional plasticity are enhanced after gene duplication. We conclude that highly expressed genes are more likely to be preserved as duplicates due to their promoter architectures, their greater tolerance to expression noise, and their ability to reduce the noise-plasticity conflict.
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Affiliation(s)
- Florian Mattenberger
- Department of Abiotic Stress, Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Valencia 46022, Spain.,Systems Biology of Molecular Interactions and Regulation Department, Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones, Científicas-Universitat de Valencia (CSIC-UV), Valencia 46980, Spain
| | - Beatriz Sabater-Muñoz
- Department of Abiotic Stress, Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Valencia 46022, Spain.,Systems Biology of Molecular Interactions and Regulation Department, Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones, Científicas-Universitat de Valencia (CSIC-UV), Valencia 46980, Spain.,Department of Genetics, Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin, Ireland
| | - Christina Toft
- Department of Genetics, University of Valencia, Burjasot, Valencia 46100, Spain.,Department of Biotechnology, Instituto de Agroquímica y Tecnología de los Alimentos, Consejo Superior de Investigaciones Científicas (CSIC), Burjasot, Valencia, Spain
| | - Gaurav Sablok
- Plant Functional Biology and Climate Change Cluster (C3), University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Mario A Fares
- Department of Abiotic Stress, Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Valencia 46022, Spain.,Systems Biology of Molecular Interactions and Regulation Department, Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones, Científicas-Universitat de Valencia (CSIC-UV), Valencia 46980, Spain.,Department of Genetics, Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin, Ireland
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Timmermans B, De Las Peñas A, Castaño I, Van Dijck P. Adhesins in Candida glabrata. J Fungi (Basel) 2018; 4:E60. [PMID: 29783771 PMCID: PMC6023314 DOI: 10.3390/jof4020060] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 05/15/2018] [Accepted: 05/17/2018] [Indexed: 12/31/2022] Open
Abstract
The human fungal pathogen Candida glabrata is causing more and more problems in hospitals, as this species shows an intrinsic antifungal drug resistance or rapidly becomes resistant when challenged with antifungals. C. glabrata only grows in the yeast form, so it is lacking a yeast-to-hyphae switch, which is one of the main virulence factors of C. albicans. An important virulence factor of C. glabrata is its capacity to strongly adhere to many different substrates. To achieve this, C. glabrata expresses a large number of adhesin-encoding genes and genome comparisons with closely related species, including the non-pathogenic S. cerevisiae, which revealed a correlation between the number of adhesin-encoding genes and pathogenicity. The adhesins are involved in the first steps during an infection; they are the first point of contact with the host. For several of these adhesins, their importance in adherence to different substrates and subsequent biofilm formation was demonstrated in vitro or in vivo. In this review, we provide an overview of the role of C. glabrata adhesins during adhesion and biofilm formation both, under in vitro and in vivo conditions.
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Affiliation(s)
- Bea Timmermans
- KU Leuven, Laboratory of Molecular Cell Biology, Kasteelpark Arenberg 31 bus 2438, 3001 Leuven, Belgium.
- VIB-KU Leuven Center for Microbiology, 3001 Leuven, Belgium.
| | - Alejandro De Las Peñas
- IPICYT, División de Biología Molecular, Camino a la Presa San José 2055, C.P., San Luis Potosí 78216 San Luis Potosí, Mexico.
| | - Irene Castaño
- IPICYT, División de Biología Molecular, Camino a la Presa San José 2055, C.P., San Luis Potosí 78216 San Luis Potosí, Mexico.
| | - Patrick Van Dijck
- KU Leuven, Laboratory of Molecular Cell Biology, Kasteelpark Arenberg 31 bus 2438, 3001 Leuven, Belgium.
- VIB-KU Leuven Center for Microbiology, 3001 Leuven, Belgium.
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30
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Construction and Use of a Recyclable Marker To Examine the Role of Major Facilitator Superfamily Protein Members in Candida glabrata Drug Resistance Phenotypes. mSphere 2018; 3:mSphere00099-18. [PMID: 29600281 PMCID: PMC5874441 DOI: 10.1128/msphere.00099-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 02/27/2018] [Indexed: 11/27/2022] Open
Abstract
Export of drugs is a problem for chemotherapy of infectious organisms. A class of membrane proteins called the major facilitator superfamily contains a large number of proteins that often elevate drug resistance when overproduced but do not impact this phenotype when the gene is removed. We wondered if this absence of a phenotype for a disruption allele might be due to the redundancy of this group of membrane proteins. We describe the production of an easy-to-use recyclable marker cassette that will allow construction of strains lacking multiple members of the MFS family of transporter proteins. Candida glabrata is the second most common species causing candidiasis. C. glabrata can also readily acquire resistance to azole drugs, complicating its treatment. Here we add to the collection of disruption markers to aid in genetic analysis of this yeast. This new construct is marked with a nourseothricin resistance cassette that produces an estrogen-activated form of Cre recombinase in a methionine-regulated manner. This allows eviction and reuse of this cassette in a facile manner. Using this new disruption marker, we have constructed a series of strains lacking different members of the major facilitator superfamily (MFS) of membrane transporter proteins. The presence of 15 MFS proteins that may contribute to drug resistance in C. glabrata placed a premium on development of a marker that could easily be reused to construct multiple gene-disrupted strains. Employing this recyclable marker, we found that loss of the MFS transporter-encoding gene FLR1 caused a dramatic increase in diamide resistance (as seen before), and deletion of two other MFS-encoding genes did not influence this phenotype. Interestingly, loss of FLR1 led to an increase in levels of oxidized glutathione, suggesting a possible molecular explanation for this enhanced oxidant sensitivity. We also found that while overproduction of the transcription factor Yap1 could suppress the fluconazole sensitivity caused by loss of the important ATP-binding cassette transporter protein Cdr1, this required the presence of FLR1. IMPORTANCE Export of drugs is a problem for chemotherapy of infectious organisms. A class of membrane proteins called the major facilitator superfamily contains a large number of proteins that often elevate drug resistance when overproduced but do not impact this phenotype when the gene is removed. We wondered if this absence of a phenotype for a disruption allele might be due to the redundancy of this group of membrane proteins. We describe the production of an easy-to-use recyclable marker cassette that will allow construction of strains lacking multiple members of the MFS family of transporter proteins.
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31
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Khakhina S, Simonicova L, Moye-Rowley WS. Positive autoregulation and repression of transactivation are key regulatory features of the Candida glabrata Pdr1 transcription factor. Mol Microbiol 2018; 107:747-764. [PMID: 29363861 DOI: 10.1111/mmi.13913] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 01/15/2018] [Accepted: 01/19/2018] [Indexed: 12/23/2022]
Abstract
Resistance to azole drugs, the major clinical antifungal compounds, is most commonly due to gain-of-function (GOF) substitution mutations in a gene called PDR1 in the fungal pathogen Candida glabrata. PDR1 encodes a zinc cluster-containing transcription factor. GOF forms of Pdr1 drive high level expression of downstream target gene expression with accompanying azole resistance. PDR1 has two homologous genes in Saccharomyces cerevisiae, called ScPDR1 and ScPDR3. This study provides evidence that the PDR1 gene in C. glabrata represents a blend of the properties found in the two S. cerevisiae genes. We demonstrated that GOF Pdr1 derivatives are overproduced at the protein level and less stable than the wild-type protein. Overproduction of wild-type Pdr1 increased target gene expression but to a lesser extent than GOF derivatives. Site-directed mutagenesis of Pdr1 binding sites in the PDR1 promoter provided clear demonstration that autoregulation of PDR1 is required for its normal function. An internal deletion mutant of Pdr1 lacking its central regulatory domain behaved as a hyperactive transcription factor that was lethal unless conditionally expressed. A full understanding of the regulation of Pdr1 will provide a new avenue of interfering with azole resistance in C. glabrata.
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Affiliation(s)
- Svetlana Khakhina
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Lucia Simonicova
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - W Scott Moye-Rowley
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
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32
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Lott SC, Wolfien M, Riege K, Bagnacani A, Wolkenhauer O, Hoffmann S, Hess WR. Customized workflow development and data modularization concepts for RNA-Sequencing and metatranscriptome experiments. J Biotechnol 2017; 261:85-96. [DOI: 10.1016/j.jbiotec.2017.06.1203] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 06/22/2017] [Accepted: 06/26/2017] [Indexed: 12/14/2022]
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33
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Hirai K, Inukai T, Nakayama H. Promising Therapies for Fungal Infection Based on the Study to Elucidate Mechanisms to Cope with Stress in Candida Species [Translated Article]. Med Mycol J 2017. [PMID: 28566663 DOI: 10.3314/mmj.17.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
In recent years, the incidence of fungal infections has been increasing, particularly among patients with immune systems compromised by human immunodeficiency virus infection, organ transplantation, and/or chemotherapy for cancer. Current therapies for treating systemic fungal infection have limited effectiveness and have created problems of adverse reactions and drug resistance. These issues therefore motivate us to develop novel antifungals. Elucidation of stress response mechanisms and virulence factors in pathogenic fungi is required in developing an effective antifungal strategy. There are actually numerous studies concerning various stress responses in several important fungal pathogens. Among these responses, we focused on stress response for iron starvation to identify potential targets for novel antifungals because iron starvation occurs in blood, where pathogenic fungi often infect. Here we show recent progress of studies on iron homeostasis in Candida species, especially focusing on Candida glabrata, and propose novel antifungal targets.
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Affiliation(s)
- Kazuyuki Hirai
- Faculty of Pharmaceutical Sciences, Suzuka University of Medical Science
| | - Tatsuya Inukai
- Department of Chemotherapy and Mycoses, National Institute of Infectious Diseases.,Diseases Division of Pathology, Immunology and Microbiology, Graduate School of Medicine, The University of Tokyo
| | - Hironobu Nakayama
- Faculty of Pharmaceutical Sciences, Suzuka University of Medical Science
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34
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Posch W, Heimdörfer D, Wilflingseder D, Lass-Flörl C. Invasive candidiasis: future directions in non-culture based diagnosis. Expert Rev Anti Infect Ther 2017; 15:829-838. [PMID: 28829207 DOI: 10.1080/14787210.2017.1370373] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
INTRODUCTION Delayed initial antifungal therapy is associated with high mortality rates caused by invasive candida infections, since accurate detection of the opportunistic pathogenic yeast and its identification display a diagnostic challenge. diagnosis of candida infections relies on time-consuming methods such as blood cultures, serologic and histopathologic examination. to allow for fast detection and characterization of invasive candidiasis, there is a need to improve diagnostic tools. trends in diagnostics switch to non-culture-based methods, which allow specified diagnosis within significantly shorter periods of time in order to provide early and appropriate antifungal treatment. Areas covered: within this review comprise novel pathogen- and host-related testing methods, e.g. multiplex-PCR analyses, T2 magnetic resonance, fungus-specific DNA microarrays, microRNA characterization or analyses of IL-17 as biomarker for early detection of invasive candidiasis. Expert commentary: Early recognition and diagnosis of fungal infections is a key issue for improved patient management. As shown in this review, a broad range of novel molecular based tests for the detection and identification of Candida species is available. However, several assays are in-house assays and lack standardization, clinical validation as well as data on sensitivity and specificity. This underscores the need for the development of faster and more accurate diagnostic tests.
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Affiliation(s)
- Wilfried Posch
- a Division of Hygiene and Medical Microbiology , Medical University of Innsbruck , Innsbruck , Austria
| | - David Heimdörfer
- a Division of Hygiene and Medical Microbiology , Medical University of Innsbruck , Innsbruck , Austria
| | - Doris Wilflingseder
- a Division of Hygiene and Medical Microbiology , Medical University of Innsbruck , Innsbruck , Austria
| | - Cornelia Lass-Flörl
- a Division of Hygiene and Medical Microbiology , Medical University of Innsbruck , Innsbruck , Austria
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35
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Vale-Silva L, Beaudoing E, Tran VDT, Sanglard D. Comparative Genomics of Two Sequential Candida glabrata Clinical Isolates. G3 (BETHESDA, MD.) 2017; 7:2413-2426. [PMID: 28663342 PMCID: PMC5555451 DOI: 10.1534/g3.117.042887] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Accepted: 06/26/2017] [Indexed: 01/14/2023]
Abstract
Candida glabrata is an important fungal pathogen which develops rapid antifungal resistance in treated patients. It is known that azole treatments lead to antifungal resistance in this fungal species and that multidrug efflux transporters are involved in this process. Specific mutations in the transcriptional regulator PDR1 result in upregulation of the transporters. In addition, we showed that the PDR1 mutations can contribute to enhance virulence in animal models. In this study, we were interested to compare genomes of two specific C. glabrata-related isolates, one of which was azole susceptible (DSY562) while the other was azole resistant (DSY565). DSY565 contained a PDR1 mutation (L280F) and was isolated after a time-lapse of 50 d of azole therapy. We expected that genome comparisons between both isolates could reveal additional mutations reflecting host adaptation or even additional resistance mechanisms. The PacBio technology used here yielded 14 major contigs (sizes 0.18-1.6 Mb) and mitochondrial genomes from both DSY562 and DSY565 isolates that were highly similar to each other. Comparisons of the clinical genomes with the published CBS138 genome indicated important genome rearrangements, but not between the clinical strains. Among the unique features, several retrotransposons were identified in the genomes of the investigated clinical isolates. DSY562 and DSY565 each contained a large set of adhesin-like genes (101 and 107, respectively), which exceed by far the number of reported adhesins (63) in the CBS138 genome. Comparison between DSY562 and DSY565 yielded 17 nonsynonymous SNPs (among which the was the expected PDR1 mutation) as well as small size indels in coding regions (11) but mainly in adhesin-like genes. The genomes contained a DNA mismatch repair allele of MSH2 known to be involved in the so-called hyper-mutator phenotype of this yeast species and the number of accumulated mutations between both clinical isolates is consistent with the presence of a MSH2 defect. In conclusion, this study is the first to compare genomes of C. glabrata sequential clinical isolates using the PacBio technology as an approach. The genomes of these isolates taken in the same patient at two different time points exhibited limited variations, even if submitted to the host pressure.
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Affiliation(s)
- Luis Vale-Silva
- Institute of Microbiology, University of Lausanne, CH-1011, Switzerland
- Lausanne University Hospital, CH-1011, Switzerland
| | - Emmanuel Beaudoing
- Center for Integrative Genomics, Lausanne Genomic Technologies Facility, CH-1015, Switzerland
| | - Van Du T Tran
- Vital-IT Group, SIB Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Dominique Sanglard
- Institute of Microbiology, University of Lausanne, CH-1011, Switzerland
- Lausanne University Hospital, CH-1011, Switzerland
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36
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Bonnet A, Grosso AR, Elkaoutari A, Coleno E, Presle A, Sridhara SC, Janbon G, Géli V, de Almeida SF, Palancade B. Introns Protect Eukaryotic Genomes from Transcription-Associated Genetic Instability. Mol Cell 2017; 67:608-621.e6. [PMID: 28757210 DOI: 10.1016/j.molcel.2017.07.002] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 05/19/2017] [Accepted: 06/30/2017] [Indexed: 12/31/2022]
Abstract
Transcription is a source of genetic instability that can notably result from the formation of genotoxic DNA:RNA hybrids, or R-loops, between the nascent mRNA and its template. Here we report an unexpected function for introns in counteracting R-loop accumulation in eukaryotic genomes. Deletion of endogenous introns increases R-loop formation, while insertion of an intron into an intronless gene suppresses R-loop accumulation and its deleterious impact on transcription and recombination in yeast. Recruitment of the spliceosome onto the mRNA, but not splicing per se, is shown to be critical to attenuate R-loop formation and transcription-associated genetic instability. Genome-wide analyses in a number of distant species differing in their intron content, including human, further revealed that intron-containing genes and the intron-richest genomes are best protected against R-loop accumulation and subsequent genetic instability. Our results thereby provide a possible rationale for the conservation of introns throughout the eukaryotic lineage.
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Affiliation(s)
- Amandine Bonnet
- Institut Jacques Monod, CNRS, UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, 75013 Paris, France
| | - Ana R Grosso
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, 1600-276 Lisboa, Portugal
| | - Abdessamad Elkaoutari
- Cancer Research Center of Marseille (CRCM), Equipe Labellisée Ligue, U1068 INSERM, UMR7258 CNRS, Institut Paoli-Calmettes, Aix Marseille University, 13284 Marseille, France
| | - Emeline Coleno
- Institut Jacques Monod, CNRS, UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, 75013 Paris, France
| | - Adrien Presle
- Institut Jacques Monod, CNRS, UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, 75013 Paris, France
| | - Sreerama C Sridhara
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, 1600-276 Lisboa, Portugal
| | - Guilhem Janbon
- Institut Pasteur, Unité Biologie des ARN des Pathogènes Fongiques, Département de Mycologie, 75015 Paris, France
| | - Vincent Géli
- Cancer Research Center of Marseille (CRCM), Equipe Labellisée Ligue, U1068 INSERM, UMR7258 CNRS, Institut Paoli-Calmettes, Aix Marseille University, 13284 Marseille, France
| | - Sérgio F de Almeida
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, 1600-276 Lisboa, Portugal
| | - Benoit Palancade
- Institut Jacques Monod, CNRS, UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, 75013 Paris, France.
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37
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Schleicher J, Conrad T, Gustafsson M, Cedersund G, Guthke R, Linde J. Facing the challenges of multiscale modelling of bacterial and fungal pathogen-host interactions. Brief Funct Genomics 2017; 16:57-69. [PMID: 26857943 PMCID: PMC5439285 DOI: 10.1093/bfgp/elv064] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Recent and rapidly evolving progress on high-throughput measurement techniques and computational performance has led to the emergence of new disciplines, such as systems medicine and translational systems biology. At the core of these disciplines lies the desire to produce multiscale models: mathematical models that integrate multiple scales of biological organization, ranging from molecular, cellular and tissue models to organ, whole-organism and population scale models. Using such models, hypotheses can systematically be tested. In this review, we present state-of-the-art multiscale modelling of bacterial and fungal infections, considering both the pathogen and host as well as their interaction. Multiscale modelling of the interactions of bacteria, especially Mycobacterium tuberculosis, with the human host is quite advanced. In contrast, models for fungal infections are still in their infancy, in particular regarding infections with the most important human pathogenic fungi, Candida albicans and Aspergillus fumigatus. We reflect on the current availability of computational approaches for multiscale modelling of host-pathogen interactions and point out current challenges. Finally, we provide an outlook for future requirements of multiscale modelling.
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Affiliation(s)
| | | | | | | | | | - Jörg Linde
- Corresponding author: Jörg Linde, Leibniz Institute for Natural Product Research and Infection Biology—Hans Knöll Institute, Jena, Germany. Tel.: +49-3641-532-1290; E-mail:
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38
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Dix A, Czakai K, Leonhardt I, Schäferhoff K, Bonin M, Guthke R, Einsele H, Kurzai O, Löffler J, Linde J. Specific and Novel microRNAs Are Regulated as Response to Fungal Infection in Human Dendritic Cells. Front Microbiol 2017; 8:270. [PMID: 28280489 PMCID: PMC5322194 DOI: 10.3389/fmicb.2017.00270] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 02/08/2017] [Indexed: 11/15/2022] Open
Abstract
Within the last two decades, the incidence of invasive fungal infections has been significantly increased. They are characterized by high mortality rates and are often caused by Candida albicans and Aspergillus fumigatus. The increasing number of infections underlines the necessity for additional anti-fungal therapies, which require extended knowledge of gene regulations during fungal infection. MicroRNAs are regulators of important cellular processes, including the immune response. By analyzing their regulation and impact on target genes, novel therapeutic and diagnostic approaches may be developed. Here, we examine the role of microRNAs in human dendritic cells during fungal infection. Dendritic cells represent the bridge between the innate and the adaptive immune systems. Therefore, analysis of gene regulation of dendritic cells is of particular significance. By applying next-generation sequencing of small RNAs, we quantify microRNA expression in monocyte-derived dendritic cells after 6 and 12 h of infection with C. albicans and A. fumigatus as well as treatment with lipopolysaccharides (LPS). We identified 26 microRNAs that are differentially regulated after infection by the fungi or LPS. Three and five of them are specific for fungal infections after 6 and 12 h, respectively. We further validated interactions of miR-132-5p and miR-212-5p with immunological relevant target genes, such as FKBP1B, KLF4, and SPN, on both RNA and protein level. Our results indicate that these microRNAs fine-tune the expression of immune-related target genes during fungal infection. Beyond that, we identified previously undiscovered microRNAs. We validated three novel microRNAs via qRT-PCR. A comparison with known microRNAs revealed possible relations with the miR-378 family and miR-1260a/b for two of them, while the third one features a unique sequence with no resemblance to known microRNAs. In summary, this study analyzes the effect of known microRNAs in dendritic cells during fungal infections and proposes novel microRNAs that could be experimentally verified.
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Affiliation(s)
- Andreas Dix
- Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute Jena, Germany
| | - Kristin Czakai
- Department of Internal Medicine II, University Hospital of Würzburg Würzburg, Germany
| | - Ines Leonhardt
- Septomics Research Centre, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Friedrich Schiller UniversityJena, Germany; IMGM Laboratories GmbHMartinsried, Germany
| | - Karin Schäferhoff
- Institute of Medical Genetics and Applied Genomics, University of Tübingen Tübingen, Germany
| | | | - Reinhard Guthke
- Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute Jena, Germany
| | - Hermann Einsele
- Department of Internal Medicine II, University Hospital of Würzburg Würzburg, Germany
| | - Oliver Kurzai
- Septomics Research Centre, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Friedrich Schiller UniversityJena, Germany; Center for Sepsis Control and Care, University HospitalJena, Germany; Institute for Microbiology, University of WuerzburgWuerzburg, Germany
| | - Jürgen Löffler
- Department of Internal Medicine II, University Hospital of Würzburg Würzburg, Germany
| | - Jörg Linde
- Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute Jena, Germany
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39
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The Phenotypic Plasticity of Duplicated Genes in Saccharomyces cerevisiae and the Origin of Adaptations. G3-GENES GENOMES GENETICS 2017; 7:63-75. [PMID: 27799339 PMCID: PMC5217124 DOI: 10.1534/g3.116.035329] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Gene and genome duplication are the major sources of biological innovations in plants and animals. Functional and transcriptional divergence between the copies after gene duplication has been considered the main driver of innovations . However, here we show that increased phenotypic plasticity after duplication plays a more major role than thought before in the origin of adaptations. We perform an exhaustive analysis of the transcriptional alterations of duplicated genes in the unicellular eukaryote Saccharomyces cerevisiae when challenged with five different environmental stresses. Analysis of the transcriptomes of yeast shows that gene duplication increases the transcriptional response to environmental changes, with duplicated genes exhibiting signatures of adaptive transcriptional patterns in response to stress. The mechanism of duplication matters, with whole-genome duplicates being more transcriptionally altered than small-scale duplicates. The predominant transcriptional pattern follows the classic theory of evolution by gene duplication; with one gene copy remaining unaltered under stress, while its sister copy presents large transcriptional plasticity and a prominent role in adaptation. Moreover, we find additional transcriptional profiles that are suggestive of neo- and subfunctionalization of duplicate gene copies. These patterns are strongly correlated with the functional dependencies and sequence divergence profiles of gene copies. We show that, unlike singletons, duplicates respond more specifically to stress, supporting the role of natural selection in the transcriptional plasticity of duplicates. Our results reveal the underlying transcriptional complexity of duplicated genes and its role in the origin of adaptations.
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40
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Chakdar H, Singha A, Satya P. New Generation Markers for Fingerprinting and Structural Analysis of Fungal Community. Fungal Biol 2017. [DOI: 10.1007/978-3-319-34106-4_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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41
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Wu Y, Li YH, Yu SB, Li WG, Liu XS, Zhao L, Lu JX. A Genome-Wide Transcriptional Analysis of Yeast-Hyphal Transition in Candida tropicalis by RNA-Seq. PLoS One 2016; 11:e0166645. [PMID: 27851809 PMCID: PMC5112795 DOI: 10.1371/journal.pone.0166645] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 11/01/2016] [Indexed: 12/28/2022] Open
Abstract
Candida tropicalis is considered as the leading pathogen in nosocomial fungemia and hepatosplenic fungal infections in patients with cancer, particularly in leukemia. The yeast-filament transition is required for virulent infection by Candida. Several studies have explored the genome-wide transcription profile of Candida, however, no report on the transcriptional profile of C. tropicalis under yeast-filament transition has been published. In this study, the transcriptomes of three C. tropicalis isolates with different adhesion and biofilm formation abilities, identified in our previous studies, were analyzed in both the yeast and filament states using RNA-Seq. Differentially expressed genes were found for each isolate during the transition. A total of 115 genes were up- or down- regulated in the two hyphal-producing isolates (ZRCT 4 and ZRCT 45). Among these differentially expressed genes, only two were down-regulated during the yeast-filament transition. Furthermore, six filament-associated genes were up-regulated in the hyphae-producing isolates. According to Candida Hypha Growth Database established in this study, 331 hyphae- related genes were discovered in C. tropicalis. ALS1 and ALS3 were down-regulated and up-regulated, respectively, during filamentous growth of C. tropicalis. These findings proved a better understanding of gene expression dynamics during the yeast-filament transition in C. tropicalis.
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Affiliation(s)
- Yuan Wu
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Chang bai Road 155, Chang ping District, Beijing, China
| | - Yin-hu Li
- Microbial Research Department, BGI-Shenzhen, Main building, Beishan Industry Zone, Yantian District, Shenzhen, China
| | - Shuan-bao Yu
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Chang bai Road 155, Chang ping District, Beijing, China
| | - Wen-ge Li
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Chang bai Road 155, Chang ping District, Beijing, China
| | - Xiao-shu Liu
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Chang bai Road 155, Chang ping District, Beijing, China
| | - Lei Zhao
- Department of Molecular Physiology and Biophysics, Holden Comprehensive Cancer Center, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, United States of America
| | - Jin-xing Lu
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Chang bai Road 155, Chang ping District, Beijing, China
- * E-mail:
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42
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Prasad TSK, Mohanty AK, Kumar M, Sreenivasamurthy SK, Dey G, Nirujogi RS, Pinto SM, Madugundu AK, Patil AH, Advani J, Manda SS, Gupta MK, Dwivedi SB, Kelkar DS, Hall B, Jiang X, Peery A, Rajagopalan P, Yelamanchi SD, Solanki HS, Raja R, Sathe GJ, Chavan S, Verma R, Patel KM, Jain AP, Syed N, Datta KK, Khan AA, Dammalli M, Jayaram S, Radhakrishnan A, Mitchell CJ, Na CH, Kumar N, Sinnis P, Sharakhov IV, Wang C, Gowda H, Tu Z, Kumar A, Pandey A. Integrating transcriptomic and proteomic data for accurate assembly and annotation of genomes. Genome Res 2016; 27:133-144. [PMID: 28003436 PMCID: PMC5204337 DOI: 10.1101/gr.201368.115] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 11/10/2016] [Indexed: 01/05/2023]
Abstract
Complementing genome sequence with deep transcriptome and proteome data could enable more accurate assembly and annotation of newly sequenced genomes. Here, we provide a proof-of-concept of an integrated approach for analysis of the genome and proteome of Anopheles stephensi, which is one of the most important vectors of the malaria parasite. To achieve broad coverage of genes, we carried out transcriptome sequencing and deep proteome profiling of multiple anatomically distinct sites. Based on transcriptomic data alone, we identified and corrected 535 events of incomplete genome assembly involving 1196 scaffolds and 868 protein-coding gene models. This proteogenomic approach enabled us to add 365 genes that were missed during genome annotation and identify 917 gene correction events through discovery of 151 novel exons, 297 protein extensions, 231 exon extensions, 192 novel protein start sites, 19 novel translational frames, 28 events of joining of exons, and 76 events of joining of adjacent genes as a single gene. Incorporation of proteomic evidence allowed us to change the designation of more than 87 predicted “noncoding RNAs” to conventional mRNAs coded by protein-coding genes. Importantly, extension of the newly corrected genome assemblies and gene models to 15 other newly assembled Anopheline genomes led to the discovery of a large number of apparent discrepancies in assembly and annotation of these genomes. Our data provide a framework for how future genome sequencing efforts should incorporate transcriptomic and proteomic analysis in combination with simultaneous manual curation to achieve near complete assembly and accurate annotation of genomes.
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Affiliation(s)
- T S Keshava Prasad
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore 575018, India.,NIMHANS-IOB Proteomics and Bioinformatics Laboratory, Neurobiology Research Centre, National Institute of Mental Health and Neuro Sciences, Bangalore, Karnataka 560029, India
| | - Ajeet Kumar Mohanty
- National Institute of Malaria Research, Field Station, Goa 403001, India.,Department of Zoology, Goa University, Taleigao Plateau, Goa 403206, India
| | - Manish Kumar
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,Manipal University, Madhav Nagar, Manipal, Karnataka 576104, India
| | - Sreelakshmi K Sreenivasamurthy
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,Manipal University, Madhav Nagar, Manipal, Karnataka 576104, India
| | - Gourav Dey
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,Manipal University, Madhav Nagar, Manipal, Karnataka 576104, India
| | - Raja Sekhar Nirujogi
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,Centre for Bioinformatics, Pondicherry University, Puducherry 605014, India
| | - Sneha M Pinto
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore 575018, India
| | - Anil K Madugundu
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,Centre for Bioinformatics, Pondicherry University, Puducherry 605014, India
| | - Arun H Patil
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,School of Biotechnology, KIIT University, Bhubaneswar, Odisha 751024, India
| | - Jayshree Advani
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,Manipal University, Madhav Nagar, Manipal, Karnataka 576104, India
| | - Srikanth S Manda
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,Centre for Bioinformatics, Pondicherry University, Puducherry 605014, India
| | - Manoj Kumar Gupta
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,Manipal University, Madhav Nagar, Manipal, Karnataka 576104, India
| | - Sutopa B Dwivedi
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India
| | - Dhanashree S Kelkar
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India
| | - Brantley Hall
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
| | - Xiaofang Jiang
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
| | - Ashley Peery
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
| | - Pavithra Rajagopalan
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,School of Biotechnology, KIIT University, Bhubaneswar, Odisha 751024, India
| | - Soujanya D Yelamanchi
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,School of Biotechnology, KIIT University, Bhubaneswar, Odisha 751024, India
| | - Hitendra S Solanki
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,School of Biotechnology, KIIT University, Bhubaneswar, Odisha 751024, India
| | - Remya Raja
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India
| | - Gajanan J Sathe
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,Manipal University, Madhav Nagar, Manipal, Karnataka 576104, India
| | - Sandip Chavan
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,Manipal University, Madhav Nagar, Manipal, Karnataka 576104, India
| | - Renu Verma
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,School of Biotechnology, KIIT University, Bhubaneswar, Odisha 751024, India
| | - Krishna M Patel
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India
| | - Ankit P Jain
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,School of Biotechnology, KIIT University, Bhubaneswar, Odisha 751024, India
| | - Nazia Syed
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,Department of Biochemistry and Molecular Biology, Pondicherry University, Puducherry 605014, India
| | - Keshava K Datta
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,School of Biotechnology, KIIT University, Bhubaneswar, Odisha 751024, India
| | - Aafaque Ahmed Khan
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,School of Biotechnology, KIIT University, Bhubaneswar, Odisha 751024, India
| | - Manjunath Dammalli
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,Department of Biotechnology, Siddaganga Institute of Technology, Tumkur, Karnataka 572103, India
| | - Savita Jayaram
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,Manipal University, Madhav Nagar, Manipal, Karnataka 576104, India
| | - Aneesha Radhakrishnan
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,Department of Biochemistry and Molecular Biology, Pondicherry University, Puducherry 605014, India
| | - Christopher J Mitchell
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Chan-Hyun Na
- Department of Neurology, Johns Hopkins University, Baltimore, Maryland 21205, USA
| | - Nirbhay Kumar
- Department of Tropical Medicine, Tulane University School of Public Health and Tropical Medicine, New Orleans, Louisiana 70112, USA
| | - Photini Sinnis
- Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, USA
| | - Igor V Sharakhov
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
| | - Charles Wang
- Center for Genomics and Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, California 92350, USA
| | - Harsha Gowda
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore 575018, India
| | - Zhijian Tu
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
| | - Ashwani Kumar
- National Institute of Malaria Research, Field Station, Goa 403001, India
| | - Akhilesh Pandey
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.,Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.,Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.,Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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43
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Genomic, Transcriptomic, and Proteomic Analysis Provide Insights Into the Cold Adaptation Mechanism of the Obligate Psychrophilic Fungus Mrakia psychrophila. G3-GENES GENOMES GENETICS 2016; 6:3603-3613. [PMID: 27633791 PMCID: PMC5100859 DOI: 10.1534/g3.116.033308] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Mrakia psychrophila is an obligate psychrophilic fungus. The cold adaptation mechanism of psychrophilic fungi remains unknown. Comparative genomics analysis indicated that M. psychrophila had a specific codon usage preference, especially for codons of Gly and Arg and its major facilitator superfamily (MFS) transporter gene family was expanded. Transcriptomic analysis revealed that genes involved in ribosome and energy metabolism were upregulated at 4°, while genes involved in unfolded protein binding, protein processing in the endoplasmic reticulum, proteasome, spliceosome, and mRNA surveillance were upregulated at 20°. In addition, genes related to unfolded protein binding were alternatively spliced. Consistent with other psychrophiles, desaturase and glycerol 3-phosphate dehydrogenase, which are involved in biosynthesis of unsaturated fatty acid and glycerol respectively, were upregulated at 4°. Cold adaptation of M. psychrophila is mediated by synthesizing unsaturated fatty acids to maintain membrane fluidity and accumulating glycerol as a cryoprotectant. The proteomic analysis indicated that the correlations between the dynamic patterns between transcript level changes and protein level changes for some pathways were positive at 4°, but negative at 20°. The death of M. psychrophila above 20° might be caused by an unfolded protein response.
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44
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Enkler L, Richer D, Marchand AL, Ferrandon D, Jossinet F. Genome engineering in the yeast pathogen Candida glabrata using the CRISPR-Cas9 system. Sci Rep 2016; 6:35766. [PMID: 27767081 PMCID: PMC5073330 DOI: 10.1038/srep35766] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 10/05/2016] [Indexed: 12/31/2022] Open
Abstract
Among Candida species, the opportunistic fungal pathogen Candida glabrata has become the second most common causative agent of candidiasis in the world and a major public health concern. Yet, few molecular tools and resources are available to explore the biology of C. glabrata and to better understand its virulence during infection. In this study, we describe a robust experimental strategy to generate loss-of-function mutants in C. glabrata. The procedure is based on the development of three main tools: (i) a recombinant strain of C. glabrata constitutively expressing the CRISPR-Cas9 system, (ii) an online program facilitating the selection of the most efficient guide RNAs for a given C. glabrata gene, and (iii) the identification of mutant strains by the Surveyor technique and sequencing. As a proof-of-concept, we have tested the virulence of some mutants in vivo in a Drosophila melanogaster infection model. Our results suggest that yps11 and a previously uncharacterized serine/threonine kinase are involved, directly or indirectly, in the ability of the pathogenic yeast to infect this model host organism.
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Affiliation(s)
- Ludovic Enkler
- Architecture et Réactivité de l'ARN, UPR9022 du CNRS, Université de Strasbourg, Institut de biologie moléculaire et cellulaire du CNRS, 15 rue René Descartes, 67084, Strasbourg, France
| | - Delphine Richer
- Architecture et Réactivité de l'ARN, UPR9022 du CNRS, Université de Strasbourg, Institut de biologie moléculaire et cellulaire du CNRS, 15 rue René Descartes, 67084, Strasbourg, France
| | - Anthony L Marchand
- Architecture et Réactivité de l'ARN, UPR9022 du CNRS, Université de Strasbourg, Institut de biologie moléculaire et cellulaire du CNRS, 15 rue René Descartes, 67084, Strasbourg, France
| | - Dominique Ferrandon
- Architecture et Réactivité de l'ARN, UPR9022 du CNRS, Université de Strasbourg, Institut de biologie moléculaire et cellulaire du CNRS, 15 rue René Descartes, 67084, Strasbourg, France
| | - Fabrice Jossinet
- Architecture et Réactivité de l'ARN, UPR9022 du CNRS, Université de Strasbourg, Institut de biologie moléculaire et cellulaire du CNRS, 15 rue René Descartes, 67084, Strasbourg, France
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45
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A Novel Hybrid Iron Regulation Network Combines Features from Pathogenic and Nonpathogenic Yeasts. mBio 2016; 7:mBio.01782-16. [PMID: 27795405 PMCID: PMC5082906 DOI: 10.1128/mbio.01782-16] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Iron is an essential micronutrient for both pathogens and their hosts, which restrict iron availability during infections in an effort to prevent microbial growth. Successful human pathogens like the yeast Candida glabrata have thus developed effective iron acquisition strategies. Their regulation has been investigated well for some pathogenic fungi and in the model organism Saccharomyces cerevisiae, which employs an evolutionarily derived system. Here, we show that C. glabrata uses a regulation network largely consisting of components of the S. cerevisiae regulon but also of elements of other pathogenic fungi. Specifically, similarly to baker's yeast, Aft1 is the main positive regulator under iron starvation conditions, while Cth2 degrades mRNAs encoding iron-requiring enzymes. However, unlike the case with S. cerevisiae, a Sef1 ortholog is required for full growth under iron limitation conditions, making C. glabrata an evolutionary intermediate to SEF1-dependent fungal pathogens. Therefore, C. glabrata has evolved an iron homeostasis system which seems to be unique within the pathogenic fungi. IMPORTANCE The fungus Candida glabrata represents an evolutionarily close relative of the well-studied and benign baker's yeast and model organism Saccharomyces cerevisiae On the other hand, C. glabrata is an important opportunistic human pathogen causing both superficial and systemic infections. The ability to acquire trace metals, in particular, iron, and to tightly regulate this process during infection is considered an important virulence attribute of a variety of pathogens. Importantly, S. cerevisiae uses a highly derivative regulatory system distinct from those of other fungi. Until now, the regulatory mechanism of iron homeostasis in C. glabrata has been mostly unknown. Our study revealed a hybrid iron regulation network that is unique to C. glabrata and is placed at an evolutionary midpoint between those of S. cerevisiae and related fungal pathogens. We thereby show that, in the host, even a successful human pathogen can rely largely on a strategy normally found in nonpathogenic fungi from a terrestrial environment.
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Skrzypek MS, Binkley J, Binkley G, Miyasato SR, Simison M, Sherlock G. The Candida Genome Database (CGD): incorporation of Assembly 22, systematic identifiers and visualization of high throughput sequencing data. Nucleic Acids Res 2016; 45:D592-D596. [PMID: 27738138 PMCID: PMC5210628 DOI: 10.1093/nar/gkw924] [Citation(s) in RCA: 254] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 10/05/2016] [Indexed: 01/29/2023] Open
Abstract
The Candida Genome Database (CGD, http://www.candidagenome.org/) is a freely available online resource that provides gene, protein and sequence information for multiple Candida species, along with web-based tools for accessing, analyzing and exploring these data. The mission of CGD is to facilitate and accelerate research into Candida pathogenesis and biology, by curating the scientific literature in real time, and connecting literature-derived annotations to the latest version of the genomic sequence and its annotations. Here, we report the incorporation into CGD of Assembly 22, the first chromosome-level, phased diploid assembly of the C. albicans genome, coupled with improvements that we have made to the assembly using additional available sequence data. We also report the creation of systematic identifiers for C. albicans genes and sequence features using a system similar to that adopted by the yeast community over two decades ago. Finally, we describe the incorporation of JBrowse into CGD, which allows online browsing of mapped high throughput sequencing data, and its implementation for several RNA-Seq data sets, as well as the whole genome sequencing data that was used in the construction of Assembly 22.
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Affiliation(s)
- Marek S Skrzypek
- Department of Genetics, Stanford University Medical School, Stanford, CA 94305-5120, USA
| | - Jonathan Binkley
- Department of Genetics, Stanford University Medical School, Stanford, CA 94305-5120, USA
| | - Gail Binkley
- Department of Genetics, Stanford University Medical School, Stanford, CA 94305-5120, USA
| | - Stuart R Miyasato
- Department of Genetics, Stanford University Medical School, Stanford, CA 94305-5120, USA
| | - Matt Simison
- Department of Genetics, Stanford University Medical School, Stanford, CA 94305-5120, USA
| | - Gavin Sherlock
- Department of Genetics, Stanford University Medical School, Stanford, CA 94305-5120, USA
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Manchanda H, Seidel N, Blaess MF, Claus RA, Linde J, Slevogt H, Sauerbrei A, Guthke R, Schmidtke M. Differential Biphasic Transcriptional Host Response Associated with Coevolution of Hemagglutinin Quasispecies of Influenza A Virus. Front Microbiol 2016; 7:1167. [PMID: 27536272 PMCID: PMC4971777 DOI: 10.3389/fmicb.2016.01167] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 07/13/2016] [Indexed: 01/20/2023] Open
Abstract
Severe influenza associated with strong symptoms and lung inflammation can be caused by intra-host evolution of quasispecies with aspartic acid or glycine in hemagglutinin position 222 (HA-222D/G; H1 numbering). To gain insights into the dynamics of host response to this coevolution and to identify key mechanisms contributing to copathogenesis, the lung transcriptional response of BALB/c mice infected with an A(H1N1)pdm09 isolate consisting HA-222D/G quasispecies was analyzed from days 1 to 12 post infection (p.i). At day 2 p.i. 968 differentially expressed genes (DEGs) were detected. The DEG number declined to 359 at day 4 and reached 1001 at day 7 p.i. prior to recovery. Interestingly, a biphasic expression profile was shown for the majority of these genes. Cytokine assays confirmed these results on protein level exemplarily for two key inflammatory cytokines, interferon gamma and interleukin 6. Using a reverse engineering strategy, a regulatory network was inferred to hypothetically explain the biphasic pattern for selected DEGs. Known regulatory interactions were extracted by Pathway Studio 9.0 and integrated during network inference. The hypothetic gene regulatory network revealed a positive feedback loop of Ifng, Stat1, and Tlr3 gene signaling that was triggered by the HA-G222 variant and correlated with a clinical symptom score indicating disease severity.
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Affiliation(s)
- Himanshu Manchanda
- Research Group Systems Biology and Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knoell InstituteJena, Germany; Department of Virology and Antiviral Therapy, Jena University HospitalJena, Germany
| | - Nora Seidel
- Department of Virology and Antiviral Therapy, Jena University Hospital Jena, Germany
| | - Markus F Blaess
- Integrated Research and Treatment Center - Center for Sepsis Control and Care, Jena University HospitalJena, Germany; Department of Anaesthesiology and Intensive Care Medicine, Research Unit Experimental Anesthesiology, Jena University HospitalJena, Germany
| | - Ralf A Claus
- Integrated Research and Treatment Center - Center for Sepsis Control and Care, Jena University HospitalJena, Germany; Department of Anaesthesiology and Intensive Care Medicine, Research Unit Experimental Anesthesiology, Jena University HospitalJena, Germany
| | - Joerg Linde
- Research Group Systems Biology and Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knoell Institute Jena, Germany
| | - Hortense Slevogt
- Centre of Innovation Competence (ZIK) Septomics, Jena University Hospital Jena, Germany
| | - Andreas Sauerbrei
- Department of Virology and Antiviral Therapy, Jena University Hospital Jena, Germany
| | - Reinhard Guthke
- Research Group Systems Biology and Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knoell Institute Jena, Germany
| | - Michaela Schmidtke
- Department of Virology and Antiviral Therapy, Jena University Hospital Jena, Germany
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Hirai K, Inukai T, Nakayama H. Promising Therapies for Fungal Infection Based on the Study to Elucidate Mechanisms to Cope with Stress in <I>Candida</I> Species. Med Mycol J 2016; 57:J163-J170. [DOI: 10.3314/mmj.16.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Kazuyuki Hirai
- Faculty of Pharmaceutical Sciences, Suzuka University of Medical Science
| | - Tatsuya Inukai
- Department of Chemotherapy and Mycoses, National Institute of Infectious Diseases
- Diseases Division of Pathology, Immunology and Microbiology, Graduate School of Medicine, The University of Tokyo
| | - Hironobu Nakayama
- Faculty of Pharmaceutical Sciences, Suzuka University of Medical Science
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Han Y, Gao S, Muegge K, Zhang W, Zhou B. Advanced Applications of RNA Sequencing and Challenges. Bioinform Biol Insights 2015; 9:29-46. [PMID: 26609224 PMCID: PMC4648566 DOI: 10.4137/bbi.s28991] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 09/30/2015] [Accepted: 10/02/2015] [Indexed: 12/18/2022] Open
Abstract
Next-generation sequencing technologies have revolutionarily advanced sequence-based research with the advantages of high-throughput, high-sensitivity, and high-speed. RNA-seq is now being used widely for uncovering multiple facets of transcriptome to facilitate the biological applications. However, the large-scale data analyses associated with RNA-seq harbors challenges. In this study, we present a detailed overview of the applications of this technology and the challenges that need to be addressed, including data preprocessing, differential gene expression analysis, alternative splicing analysis, variants detection and allele-specific expression, pathway analysis, co-expression network analysis, and applications combining various experimental procedures beyond the achievements that have been made. Specifically, we discuss essential principles of computational methods that are required to meet the key challenges of the RNA-seq data analyses, development of various bioinformatics tools, challenges associated with the RNA-seq applications, and examples that represent the advances made so far in the characterization of the transcriptome.
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Affiliation(s)
- Yixing Han
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Shouguo Gao
- Bioinformatics and Systems Biology Core, National Heart Lung Blood Institute, National Institutes of Health, Rockville Pike, Bethesda, MD, USA
| | - Kathrin Muegge
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA. ; Leidos Biomedical Research, Inc., Basic Science Program, Frederick National Laboratory, Frederick, MD, USA
| | - Wei Zhang
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Bing Zhou
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
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Roy S, Thompson D. Evolution of regulatory networks in Candida glabrata: learning to live with the human host. FEMS Yeast Res 2015; 15:fov087. [PMID: 26449820 DOI: 10.1093/femsyr/fov087] [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] [Accepted: 09/17/2015] [Indexed: 12/12/2022] Open
Abstract
The opportunistic human fungal pathogen Candida glabrata is second only to C. albicans as the cause of Candida infections and yet is more closely related to Saccharomyces cerevisiae. Recent advances in functional genomics technologies and computational approaches to decipher regulatory networks, and the comparison of these networks among these and other Ascomycete species, have revealed both unique and shared strategies in adaptation to a human commensal/opportunistic pathogen lifestyle and antifungal drug resistance in C. glabrata. Recently, several C. glabrata sister species in the Nakeseomyces clade representing both human associated (commensal) and environmental isolates have had their genomes sequenced and analyzed. This has paved the way for comparative functional genomics studies to characterize the regulatory networks in these species to identify informative patterns of conservation and divergence linked to phenotypic evolution in the Nakaseomyces lineage.
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Affiliation(s)
- Sushmita Roy
- Department of Biostatistics and Medical Informatics, University of Wisconsin Madison, Madison, WI 53715, USA Wisconsin Institute for Discovery, University of Wisconsin, Madison, WI 53715, USA
| | - Dawn Thompson
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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