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Hovhannisyan H, Rodríguez A, Saus E, Vaneechoutte M, Gabaldón T. Multiplexed target enrichment of coding and non-coding transcriptomes enables studying Candida spp. infections from human derived samples. Front Cell Infect Microbiol 2023; 13:1093178. [PMID: 36761895 PMCID: PMC9902369 DOI: 10.3389/fcimb.2023.1093178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 01/03/2023] [Indexed: 01/26/2023] Open
Abstract
The study of transcriptomic interactions between host and pathogens in in vivo conditions is challenged by the low relative amounts of the pathogen RNA. Yeast opportunistic pathogens of the genus Candida can cause life-threatening systemic infections in immunocompromised patients, and are of growing medical concern. Four phylogenetically diverse species account for over 90% of Candida infections, and their specific interactions with various human tissues are still poorly understood. To enable in vivo transcriptomic analysis in these species, we designed and validated pan-Candida target capture probes to enrich protein-coding and non-coding transcriptomes. The probe-based enrichment approach outperformed enrichment based on differential lysis of host cells, and showed similar enrichment performance as an existing capture design, yet achieving better fidelity of expression levels, enabling species multiplexing and capturing of lncRNAs. In addition, we show that our probe-based enrichment strategy allows robust genotype-based identification of the infecting strain present in the sample.
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Affiliation(s)
- Hrant Hovhannisyan
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona, Spain,Mechanisms of Disease Department, Institute for Research in Biomedicine (IRB), Barcelona, Spain
| | - Antonio Rodríguez
- Laboratory Bacteriology Research, Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Ester Saus
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona, Spain,Mechanisms of Disease Department, Institute for Research in Biomedicine (IRB), Barcelona, Spain
| | - Mario Vaneechoutte
- Laboratory Bacteriology Research, Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Toni Gabaldón
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona, Spain,Mechanisms of Disease Department, Institute for Research in Biomedicine (IRB), Barcelona, Spain,Department of Biomedicine and Life Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain,Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, Barcelona, Spain,*Correspondence: Toni Gabaldón,
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2
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Korn VL, Pennerman KK, Padhi S, Bennett JW. Trans-2-hexenal downregulates several pathogenicity genes of Pseudogymnoascus destructans, the causative agent of white-nose syndrome in bats. J Ind Microbiol Biotechnol 2021; 48:kuab060. [PMID: 34415032 PMCID: PMC8788850 DOI: 10.1093/jimb/kuab060] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 08/13/2021] [Indexed: 11/29/2022]
Abstract
White-nose syndrome is an emergent wildlife disease that has killed millions of North American bats. It is caused by Pseudogymnoascus destructans, a cold-loving, invasive fungal pathogen that grows on bat tissues and disrupts normal hibernation patterns. Previous work identified trans-2-hexenal as a fungistatic volatile compound that potentially could be used as a fumigant against P. destructans in bat hibernacula. To determine the physiological responses of the fungus to trans-2-hexenal exposure, we characterized the P. destructans transcriptome in the presence and absence of trans-2-hexenal. Specifically, we analyzed the effects of sublethal concentrations (5 μmol/L, 10 μmol/L, and 20 μmol/L) of gas-phase trans-2-hexenal of the fungus grown in liquid culture. Among the three treatments, a total of 407 unique differentially expressed genes (DEGs) were identified, of which 74 were commonly affected across all three treatments, with 44 upregulated and 30 downregulated. Downregulated DEGs included several probable virulence genes including those coding for a high-affinity iron permease, a superoxide dismutase, and two protein-degrading enzymes. There was an accompanying upregulation of an ion homeostasis gene, as well as several genes involved in transcription, translation, and other essential cellular processes. These data provide insights into the mechanisms of action of trans-2-hexenal as an anti-fungal fumigant that is active at cold temperatures and will guide future studies on the molecular mechanisms by which six carbon volatiles inhibit growth of P. destructans and other pathogenic fungi.
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Affiliation(s)
| | - Kayla K Pennerman
- Joint Institute for Food Safety and Applied Nutrition, University of Maryland, College Park, MD 20742, USA
| | - Sally Padhi
- Department of Plant Biology, Rutgers University, The State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Joan W Bennett
- Department of Plant Biology, Rutgers University, The State University of New Jersey, New Brunswick, NJ 08901, USA
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Nadarajah K, Abdul Rahman NSN. Plant-Microbe Interaction: Aboveground to Belowground, from the Good to the Bad. Int J Mol Sci 2021; 22:ijms221910388. [PMID: 34638728 PMCID: PMC8508622 DOI: 10.3390/ijms221910388] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/14/2021] [Accepted: 09/17/2021] [Indexed: 02/06/2023] Open
Abstract
Soil health and fertility issues are constantly addressed in the agricultural industry. Through the continuous and prolonged use of chemical heavy agricultural systems, most agricultural lands have been impacted, resulting in plateaued or reduced productivity. As such, to invigorate the agricultural industry, we would have to resort to alternative practices that will restore soil health and fertility. Therefore, in recent decades, studies have been directed towards taking a Magellan voyage of the soil rhizosphere region, to identify the diversity, density, and microbial population structure of the soil, and predict possible ways to restore soil health. Microbes that inhabit this region possess niche functions, such as the stimulation or promotion of plant growth, disease suppression, management of toxicity, and the cycling and utilization of nutrients. Therefore, studies should be conducted to identify microbes or groups of organisms that have assigned niche functions. Based on the above, this article reviews the aboveground and below-ground microbiomes, their roles in plant immunity, physiological functions, and challenges and tools available in studying these organisms. The information collected over the years may contribute toward future applications, and in designing sustainable agriculture.
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Chung M, Bruno VM, Rasko DA, Cuomo CA, Muñoz JF, Livny J, Shetty AC, Mahurkar A, Dunning Hotopp JC. Best practices on the differential expression analysis of multi-species RNA-seq. Genome Biol 2021; 22:121. [PMID: 33926528 PMCID: PMC8082843 DOI: 10.1186/s13059-021-02337-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 04/01/2021] [Indexed: 02/07/2023] Open
Abstract
Advances in transcriptome sequencing allow for simultaneous interrogation of differentially expressed genes from multiple species originating from a single RNA sample, termed dual or multi-species transcriptomics. Compared to single-species differential expression analysis, the design of multi-species differential expression experiments must account for the relative abundances of each organism of interest within the sample, often requiring enrichment methods and yielding differences in total read counts across samples. The analysis of multi-species transcriptomics datasets requires modifications to the alignment, quantification, and downstream analysis steps compared to the single-species analysis pipelines. We describe best practices for multi-species transcriptomics and differential gene expression.
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Affiliation(s)
- Matthew Chung
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.,Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Vincent M Bruno
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.,Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - David A Rasko
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.,Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Christina A Cuomo
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA, 02142, USA
| | - José F Muñoz
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA, 02142, USA
| | - Jonathan Livny
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA, 02142, USA
| | - Amol C Shetty
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Anup Mahurkar
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Julie C Dunning Hotopp
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA. .,Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA. .,Greenebaum Cancer Center, University of Maryland, Baltimore, MD, 21201, USA.
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5
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Davy CM, Donaldson ME, Bandouchova H, Breit AM, Dorville NA, Dzal YA, Kovacova V, Kunkel EL, Martínková N, Norquay KJ, Paterson JE, Zukal J, Pikula J, Willis CK, Kyle CJ. Transcriptional host-pathogen responses of Pseudogymnoascus destructans and three species of bats with white-nose syndrome. Virulence 2020; 11:781-794. [PMID: 32552222 PMCID: PMC7549942 DOI: 10.1080/21505594.2020.1768018] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 03/07/2020] [Accepted: 03/31/2020] [Indexed: 12/13/2022] Open
Abstract
Understanding how context (e.g., host species, environmental conditions) drives disease susceptibility is an essential goal of disease ecology. We hypothesized that in bat white-nose syndrome (WNS), species-specific host-pathogen interactions may partly explain varying disease outcomes among host species. We characterized bat and pathogen transcriptomes in paired samples of lesion-positive and lesion-negative wing tissue from bats infected with Pseudogymnoascus destructans in three parallel experiments. The first two experiments analyzed samples collected from the susceptible Nearctic Myotis lucifugus and the less-susceptible Nearctic Eptesicus fuscus, following experimental infection and hibernation in captivity under controlled conditions. The third experiment applied the same analyses to paired samples from infected, free-ranging Myotis myotis, a less susceptible, Palearctic species, following natural infection and hibernation (n = 8 sample pairs/species). Gene expression by P. destructans was similar among the three host species despite varying environmental conditions among the three experiments and was similar within each host species between saprophytic contexts (superficial growth on wings) and pathogenic contexts (growth in lesions on the same wings). In contrast, we observed qualitative variation in host response: M. lucifugus and M. myotis exhibited systemic responses to infection, while E. fuscus up-regulated a remarkably localized response. Our results suggest potential phylogenetic determinants of response to WNS and can inform further studies of context-dependent host-pathogen interactions.
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Affiliation(s)
- Christina M. Davy
- Environmental and Life Sciences Program, Trent University, Peterborough, Canada
- Wildlife Research and Monitoring Section, Ontario Ministry of Natural Resources and Forestry, Peterborough, Canada
| | | | - Hana Bandouchova
- Department of Ecology and Diseases of Game, Fish and Bees, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic
| | - Ana M. Breit
- Department of Biology and Centre for Forest Interdisciplinary Research (C-FIR), University of Winnipeg, Winnipeg, Canada
| | - Nicole A.S. Dorville
- Department of Biology and Centre for Forest Interdisciplinary Research (C-FIR), University of Winnipeg, Winnipeg, Canada
| | - Yvonne A. Dzal
- Department of Biology and Centre for Forest Interdisciplinary Research (C-FIR), University of Winnipeg, Winnipeg, Canada
| | - Veronika Kovacova
- Department of Ecology and Diseases of Game, Fish and Bees, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic
| | - Emma L. Kunkel
- Department of Biology and Centre for Forest Interdisciplinary Research (C-FIR), University of Winnipeg, Winnipeg, Canada
| | - Natália Martínková
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Kaleigh J.O. Norquay
- Department of Biology and Centre for Forest Interdisciplinary Research (C-FIR), University of Winnipeg, Winnipeg, Canada
| | - James E. Paterson
- Environmental and Life Sciences Program, Trent University, Peterborough, Canada
| | - Jan Zukal
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Jiri Pikula
- Department of Ecology and Diseases of Game, Fish and Bees, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic
| | - Craig K.R. Willis
- Department of Biology and Centre for Forest Interdisciplinary Research (C-FIR), University of Winnipeg, Winnipeg, Canada
| | - Christopher J. Kyle
- Environmental and Life Sciences Program, Trent University, Peterborough, Canada
- Natural Resources DNA Profiling and Forensics Centre, Trent University, Peterborough, Canada
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A Comprehensive Gene Expression Profile of Pectin Degradation Enzymes Reveals the Molecular Events during Cell Wall Degradation and Pathogenesis of Rice Sheath Blight Pathogen Rhizoctonia solani AG1-IA. J Fungi (Basel) 2020; 6:jof6020071. [PMID: 32466257 PMCID: PMC7345747 DOI: 10.3390/jof6020071] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/16/2020] [Accepted: 05/17/2020] [Indexed: 11/16/2022] Open
Abstract
Sheath blight disease of rice caused by Rhizoctonia solani Kühn (teleomorph: Thanatephorus cucumeris) remains a global challenge due to the absence of reliable resistance genes and poor understanding of pathogen biology. Pectin, one of the most vital constituents of the plant cell wall, is targeted by pectin methylesterases, polygalacturonases, and few other enzymes of fungal pathogens. In this study, we catalogued the expressed genes of the fungal genome from RNAseq of R. solani infected four rice genotypes. Analysis of RNAseq revealed 3325 pathogen genes commonly expressed in all rice genotypes, in which 49, 490, and 83 genes were specific to BPT5204, Tetep, and Pankaj genotypes, respectively. To identify the early and late responding genes of R. solani during plant cell wall degradation, a real-time PCR analysis of 30 pectinolytic enzymes was done at six different time points after inoculation. The majority of these genes showed maximum induction at the 72 h time point, suggesting that it is the most crucial stage of infection. Pankaj showed lesser induction of these genes as compared to other genotypes. Leaf-blade tissue and 45 days old-growth stage are more favorable for the expression of pectin degradation genes of R. solani. Additionally, the expression analysis of these genes from four different strains of R. solani suggested differential regulation of genes but no distinct expression pattern between highly virulent and mild strains. The implications of the differential regulation of these genes in disease development have been discussed. This study provides the first such comprehensive analysis of R. solani genes encoding pectin degrading enzymes, which would help to decipher the pathogen biology and sheath blight disease development.
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7
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Gabaldón T. Recent trends in molecular diagnostics of yeast infections: from PCR to NGS. FEMS Microbiol Rev 2019; 43:517-547. [PMID: 31158289 PMCID: PMC8038933 DOI: 10.1093/femsre/fuz015] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 05/31/2019] [Indexed: 12/29/2022] Open
Abstract
The incidence of opportunistic yeast infections in humans has been increasing over recent years. These infections are difficult to treat and diagnose, in part due to the large number and broad diversity of species that can underlie the infection. In addition, resistance to one or several antifungal drugs in infecting strains is increasingly being reported, severely limiting therapeutic options and showcasing the need for rapid detection of the infecting agent and its drug susceptibility profile. Current methods for species and resistance identification lack satisfactory sensitivity and specificity, and often require prior culturing of the infecting agent, which delays diagnosis. Recently developed high-throughput technologies such as next generation sequencing or proteomics are opening completely new avenues for more sensitive, accurate and fast diagnosis of yeast pathogens. These approaches are the focus of intensive research, but translation into the clinics requires overcoming important challenges. In this review, we provide an overview of existing and recently emerged approaches that can be used in the identification of yeast pathogens and their drug resistance profiles. Throughout the text we highlight the advantages and disadvantages of each methodology and discuss the most promising developments in their path from bench to bedside.
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Affiliation(s)
- Toni Gabaldón
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- ICREA, Pg Lluís Companys 23, 08010 Barcelona, Spain
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8
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Donaldson ME, Davy CM, Vanderwolf KJ, Willis CKR, Saville BJ, Kyle CJ. Growth medium and incubation temperature alter the Pseudogymnoascus destructans transcriptome: implications in identifying virulence factors. Mycologia 2018; 110:300-315. [PMID: 29737946 DOI: 10.1080/00275514.2018.1438223] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Pseudogymnoascus destructans is the causal agent of bat white-nose syndrome (WNS), which is devastating some North American bat populations. Previous transcriptome studies provided insight regarding the molecular mechanisms involved in WNS; however, it is unclear how different environmental parameters could influence pathogenicity. This information could be useful in developing management strategies to mitigate the negative impacts of P. destructans on bats. We cultured three P. destructans isolates from Atlantic Canada on two growth media (potato dextrose agar and Sabouraud dextrose agar) that differ in their nitrogen source, and at two separate incubation temperatures (4 C and 15 C) that approximate the temperature range of bat hibernacula during the winter and a temperature within its optimal mycelial growth range. We conducted RNA sequencing to determine transcript levels in each sample and performed differential gene expression (DGE) analyses to test the influence of growth medium and incubation temperature on gene expression. We also compared our in vitro results with previous RNA-sequencing data sets generated from P. destructans growing on the wings of a susceptible host, Myotis lucifugus. Our findings point to a critical role for substrate and incubation temperature in influencing the P. destructans transcriptome. DGE analyses suggested that growth medium plays a larger role than temperature in determining P. destructans gene expression and that although the psychrophilic fungus responds to different nitrogen sources, it may have evolved for continued growth at a broad range of low temperatures. Further, our data suggest that down-regulation of the RNA-interference pathway and increased fatty acid metabolism are involved in the P. destructans-bat interaction. Finally, we speculate that to reduce the activation of host defense responses, P. destructans minimizes changes in the expression of genes encoding secreted proteins during bat colonization.
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Affiliation(s)
- Michael E Donaldson
- a Environmental and Life Sciences Graduate Program , Trent University , 2140 East Bank Drive, Peterborough , Ontario , K9L 1Z8, Canada
| | - Christina M Davy
- a Environmental and Life Sciences Graduate Program , Trent University , 2140 East Bank Drive, Peterborough , Ontario , K9L 1Z8, Canada.,b Wildlife Research and Monitoring Section , Ontario Ministry of Natural Resources and Forestry , 2140 East Bank Drive, Peterborough , Ontario , K9L 1Z8, Canada
| | - Karen J Vanderwolf
- c New Brunswick Museum , 277 Douglas Avenue, Saint John , New Brunswick , E2K 1E5, Canada.,d Department of Pathobiological Sciences , University of Wisconsin-Madison , 2015 Linden Drive, Madison , Wisconsin 53706
| | - Craig K R Willis
- e Department of Biology , University of Winnipeg , 515 Portage Avenue, Winnipeg , Manitoba , R3B 2E9, Canada
| | - Barry J Saville
- a Environmental and Life Sciences Graduate Program , Trent University , 2140 East Bank Drive, Peterborough , Ontario , K9L 1Z8, Canada.,f Forensic Science Department , Trent University , 2140 East Bank Drive, Peterborough , Ontario, K9L 1Z8 , Canada
| | - Christopher J Kyle
- a Environmental and Life Sciences Graduate Program , Trent University , 2140 East Bank Drive, Peterborough , Ontario , K9L 1Z8, Canada.,f Forensic Science Department , Trent University , 2140 East Bank Drive, Peterborough , Ontario, K9L 1Z8 , Canada
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9
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Davy CM, Donaldson ME, Willis CKR, Saville BJ, McGuire LP, Mayberry H, Wilcox A, Wibbelt G, Misra V, Bollinger T, Kyle CJ. The other white-nose syndrome transcriptome: Tolerant and susceptible hosts respond differently to the pathogen Pseudogymnoascus destructans. Ecol Evol 2017; 7:7161-7170. [PMID: 28944007 PMCID: PMC5606880 DOI: 10.1002/ece3.3234] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 06/11/2017] [Accepted: 06/12/2017] [Indexed: 12/30/2022] Open
Abstract
Mitigation of emerging infectious diseases that threaten global biodiversity requires an understanding of critical host and pathogen responses to infection. For multihost pathogens where pathogen virulence or host susceptibility is variable, host–pathogen interactions in tolerant species may identify potential avenues for adaptive evolution in recently exposed, susceptible hosts. For example, the fungus Pseudogymnoascus destructans causes white‐nose syndrome (WNS) in hibernating bats and is responsible for catastrophic declines in some species in North America, where it was recently introduced. Bats in Europe and Asia, where the pathogen is endemic, are only mildly affected. Different environmental conditions among Nearctic and Palearctic hibernacula have been proposed as an explanation for variable disease outcomes, but this hypothesis has not been experimentally tested. We report the first controlled, experimental investigation of response to P. destructans in a tolerant, European species of bat (the greater mouse‐eared bat, Myotis myotis). We compared body condition, disease outcomes and gene expression in control (sham‐exposed) and exposed M. myotis that hibernated under controlled environmental conditions following treatment. Tolerant M. myotis experienced extremely limited fungal growth and did not exhibit symptoms of WNS. However, we detected no differential expression of genes associated with immune response in exposed bats, indicating that immune response does not drive tolerance of P. destructans in late hibernation. Variable responses to P. destructans among bat species cannot be attributed solely to environmental or ecological factors. Instead, our results implicate coevolution with the pathogen, and highlight the dynamic nature of the “white‐nose syndrome transcriptome.” Interspecific variation in response to exposure by the host (and possibly pathogen) emphasizes the importance of context in studies of the bat‐WNS system, and robust characterization of genetic responses to exposure in various hosts and the pathogen should precede any attempts to use particular bat species as generalizable “model hosts.”
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Affiliation(s)
- Christina M Davy
- Environmental and Life Sciences Graduate Program Trent University Peterborough ON Canada.,Department of Biology University of Winnipeg Winnipeg MB Canada.,Present address: Ontario Ministry of Natural Resources and Forestry, Wildlife Research and Monitoring Section Trent University Peterborough ON Canada
| | - Michael E Donaldson
- Environmental and Life Sciences Graduate Program Trent University Peterborough ON Canada
| | | | - Barry J Saville
- Forensic Science Department Trent University Peterborough ON Canada
| | - Liam P McGuire
- Department of Biology University of Winnipeg Winnipeg MB Canada.,Department of Biological Sciences Texas Tech University Lubbock TX USA
| | | | - Alana Wilcox
- Department of Biology University of Winnipeg Winnipeg MB Canada
| | - Gudrun Wibbelt
- Leibniz Institute of Zoo and Wildlife Research Berlin Germany
| | - Vikram Misra
- Department of Microbiology Western College of Veterinary Medicine University of Saskatchewan Saskatoon SK Canada
| | - Trent Bollinger
- Department of Veterinary Pathology Western College of Veterinary Medicine University of Saskatchewan Saskatoon SK Canada
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10
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Reeder SM, Palmer JM, Prokkola JM, Lilley TM, Reeder DM, Field KA. Pseudogymnoascus destructans transcriptome changes during white-nose syndrome infections. Virulence 2017; 8:1695-1707. [PMID: 28614673 PMCID: PMC5810475 DOI: 10.1080/21505594.2017.1342910] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
White nose syndrome (WNS) is caused by the psychrophilic fungus Pseudogymnoascus destructans that can grow in the environment saprotrophically or parasitically by infecting hibernating bats. Infections are pathological in many species of North American bats, disrupting hibernation and causing mortality. To determine what fungal pathways are involved in infection of living tissue, we examined fungal gene expression using RNA-Seq. We compared P. destructans gene expression when grown in culture to that during infection of a North American bat species, Myotis lucifugus, that shows high WNS mortality. Cultured P. destructans was grown at 10 to 14 C and P. destructans growing in vivo was presumably exposed to temperatures ranging from 4 to 8 C during torpor and up to 37 C during periodic arousals. We found that when P. destructans is causing WNS, the most significant differentially expressed genes were involved in heat shock responses, cell wall remodeling, and micronutrient acquisition. These results indicate that this fungal pathogen responds to host-pathogen interactions by regulating gene expression in ways that may contribute to evasion of host responses. Alterations in fungal cell wall structures could allow P. destructans to avoid detection by host pattern recognition receptors and antibody responses. This study has also identified several fungal pathways upregulated during WNS infection that may be candidates for mitigating infection pathology. By identifying host-specific pathogen responses, these observations have important implications for host-pathogen evolutionary relationships in WNS and other fungal diseases.
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Affiliation(s)
- Sophia M Reeder
- a Department of Biology , Bucknell University , Lewisburg , PA , USA
| | - Jonathan M Palmer
- b Center for Forest Mycology Research , Northern Research Station, US Forest Service , Madison , WI , USA
| | - Jenni M Prokkola
- a Department of Biology , Bucknell University , Lewisburg , PA , USA
| | - Thomas M Lilley
- a Department of Biology , Bucknell University , Lewisburg , PA , USA
| | - DeeAnn M Reeder
- a Department of Biology , Bucknell University , Lewisburg , PA , USA
| | - Kenneth A Field
- a Department of Biology , Bucknell University , Lewisburg , PA , USA
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11
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Evangelisti E, Gogleva A, Hainaux T, Doumane M, Tulin F, Quan C, Yunusov T, Floch K, Schornack S. Time-resolved dual transcriptomics reveal early induced Nicotiana benthamiana root genes and conserved infection-promoting Phytophthora palmivora effectors. BMC Biol 2017; 15:39. [PMID: 28494759 PMCID: PMC5427549 DOI: 10.1186/s12915-017-0379-1] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 04/24/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Plant-pathogenic oomycetes are responsible for economically important losses in crops worldwide. Phytophthora palmivora, a tropical relative of the potato late blight pathogen, causes rotting diseases in many tropical crops including papaya, cocoa, oil palm, black pepper, rubber, coconut, durian, mango, cassava and citrus. Transcriptomics have helped to identify repertoires of host-translocated microbial effector proteins which counteract defenses and reprogram the host in support of infection. As such, these studies have helped in understanding how pathogens cause diseases. Despite the importance of P. palmivora diseases, genetic resources to allow for disease resistance breeding and identification of microbial effectors are scarce. RESULTS We employed the model plant Nicotiana benthamiana to study the P. palmivora root infections at the cellular and molecular levels. Time-resolved dual transcriptomics revealed different pathogen and host transcriptome dynamics. De novo assembly of P. palmivora transcriptome and semi-automated prediction and annotation of the secretome enabled robust identification of conserved infection-promoting effectors. We show that one of them, REX3, suppresses plant secretion processes. In a survey for early transcriptionally activated plant genes we identified a N. benthamiana gene specifically induced at infected root tips that encodes a peptide with danger-associated molecular features. CONCLUSIONS These results constitute a major advance in our understanding of P. palmivora diseases and establish extensive resources for P. palmivora pathogenomics, effector-aided resistance breeding and the generation of induced resistance to Phytophthora root infections. Furthermore, our approach to find infection-relevant secreted genes is transferable to other pathogen-host interactions and not restricted to plants.
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Affiliation(s)
| | - Anna Gogleva
- Sainsbury Laboratory Cambridge University (SLCU), Cambridge, UK
| | - Thomas Hainaux
- Sainsbury Laboratory Cambridge University (SLCU), Cambridge, UK
- Present address: Université Libre de Bruxelles, Bruxelles, Belgium
| | - Mehdi Doumane
- Sainsbury Laboratory Cambridge University (SLCU), Cambridge, UK
- Present address: École Normale Supérieure de Lyon, Lyon, France
| | - Frej Tulin
- Sainsbury Laboratory Cambridge University (SLCU), Cambridge, UK
| | - Clément Quan
- Sainsbury Laboratory Cambridge University (SLCU), Cambridge, UK
| | - Temur Yunusov
- Sainsbury Laboratory Cambridge University (SLCU), Cambridge, UK
| | - Kévin Floch
- Sainsbury Laboratory Cambridge University (SLCU), Cambridge, UK
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Poyntner C, Blasi B, Arcalis E, Mirastschijski U, Sterflinger K, Tafer H. The Transcriptome of Exophiala dermatitidis during Ex-vivo Skin Model Infection. Front Cell Infect Microbiol 2016; 6:136. [PMID: 27822460 PMCID: PMC5075926 DOI: 10.3389/fcimb.2016.00136] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 10/06/2016] [Indexed: 12/12/2022] Open
Abstract
The black yeast Exophiala dermatitidis is a widespread polyextremophile and human pathogen, that is found in extreme natural habitats and man-made environments such as dishwashers. It can cause various diseases ranging from phaeohyphomycosis and systemic infections, with fatality rates reaching 40%. While the number of cases in immunocompromised patients are increasing, knowledge of the infections, virulence factors and host response is still scarce. In this study, for the first time, an artificial infection of an ex-vivo skin model with Exophiala dermatitidis was monitored microscopically and transcriptomically. Results show that Exophiala dermatitidis is able to actively grow and penetrate the skin. The analysis of the genomic and RNA-sequencing data delivers a rich and complex transcriptome where circular RNAs, fusion transcripts, long non-coding RNAs and antisense transcripts are found. Changes in transcription strongly affect pathways related to nutrients acquisition, energy metabolism, cell wall, morphological switch, and known virulence factors. The L-Tyrosine melanin pathway is specifically upregulated during infection. Moreover the production of secondary metabolites, especially alkaloids, is increased. Our study is the first that gives an insight into the complexity of the transcriptome of Exophiala dermatitidis during artificial skin infections and reveals new virulence factors.
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Affiliation(s)
- Caroline Poyntner
- Department of Biotechnology, VIBT EQ Extremophile Center, University of Natural Resources and Life Sciences Vienna, Austria
| | - Barbara Blasi
- Department of Biotechnology, VIBT EQ Extremophile Center, University of Natural Resources and Life Sciences Vienna, Austria
| | - Elsa Arcalis
- Department for Applied Genetics and Cell Biology, Molecular Plant Physiology and Crop Biotechnology, University of Natural Resources and Life Sciences Vienna, Austria
| | - Ursula Mirastschijski
- Klinikum Bremen-Mitte, Department of Plastic, Reconstructive and Aesthetic Surgery, Faculty of Biology and Chemistry, Center for Biomolecular Interactions Bremen, University Bremen Bremen, Germany
| | - Katja Sterflinger
- Department of Biotechnology, VIBT EQ Extremophile Center, University of Natural Resources and Life Sciences Vienna, Austria
| | - Hakim Tafer
- Department of Biotechnology, VIBT EQ Extremophile Center, University of Natural Resources and Life Sciences Vienna, Austria
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Imam J, Singh PK, Shukla P. Plant Microbe Interactions in Post Genomic Era: Perspectives and Applications. Front Microbiol 2016; 7:1488. [PMID: 27725809 PMCID: PMC5035750 DOI: 10.3389/fmicb.2016.01488] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 09/07/2016] [Indexed: 01/17/2023] Open
Abstract
Deciphering plant-microbe interactions is a promising aspect to understand the benefits and the pathogenic effect of microbes and crop improvement. The advancement in sequencing technologies and various 'omics' tool has impressively accelerated the research in biological sciences in this area. The recent and ongoing developments provide a unique approach to describing these intricate interactions and test hypotheses. In the present review, we discuss the role of plant-pathogen interaction in crop improvement. The plant innate immunity has always been an important aspect of research and leads to some interesting information like the adaptation of unique immune mechanisms of plants against pathogens. The development of new techniques in the post - genomic era has greatly enhanced our understanding of the regulation of plant defense mechanisms against pathogens. The present review also provides an overview of beneficial plant-microbe interactions with special reference to Agrobacterium tumefaciens-plant interactions where plant derived signal molecules and plant immune responses are important in pathogenicity and transformation efficiency. The construction of various Genome-scale metabolic models of microorganisms and plants presented a better understanding of all metabolic interactions activated during the interactions. This review also lists the emerging repertoire of phytopathogens and its impact on plant disease resistance. Outline of different aspects of plant-pathogen interactions is presented in this review to bridge the gap between plant microbial ecology and their immune responses.
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Affiliation(s)
| | | | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand UniversityRohtak, India
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How Our Other Genome Controls Our Epi-Genome. Trends Microbiol 2016; 24:777-787. [PMID: 27289569 DOI: 10.1016/j.tim.2016.05.005] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 05/03/2016] [Accepted: 05/18/2016] [Indexed: 12/12/2022]
Abstract
Eukaryotes and prokaryotes produce extracellular nanovescicles that contain RNAs and other molecules that they exploit to communicate. Recently, inter-kingdom crosstalk was demonstrated between humans and bacteria through fecal microRNAs. We suggest here how bacteria interact with humans via RNAs within membrane vesicles to alter our epigenome, thus filling the gap and closing the circle. At the same time, there are indications that there could be a wider inter-kingdom communication network that might encompass all known kingdoms. Now that the connection with our other genome has been established, we also should begin to explore the 'social' network that we have around us.
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