1
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Varelias A, Bunting MD, Ormerod KL, Koyama M, Olver SD, Straube J, Kuns RD, Robb RJ, Henden AS, Cooper L, Lachner N, Gartlan KH, Lantz O, Kjer-Nielsen L, Mak JY, Fairlie DP, Clouston AD, McCluskey J, Rossjohn J, Lane SW, Hugenholtz P, Hill GR. Recipient mucosal-associated invariant T cells control GVHD within the colon. J Clin Invest 2018; 128:1919-1936. [PMID: 29629900 DOI: 10.1172/jci91646] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 02/16/2018] [Indexed: 12/11/2022] Open
Abstract
Mucosal-associated invariant T (MAIT) cells are a unique innate-like T cell subset that responds to a wide array of bacteria and yeast through recognition of riboflavin metabolites presented by the MHC class I-like molecule MR1. Here, we demonstrate using MR1 tetramers that recipient MAIT cells are present in small but definable numbers in graft-versus-host disease (GVHD) target organs and protect from acute GVHD in the colon following bone marrow transplantation (BMT). Consistent with their preferential juxtaposition to microbial signals in the colon, recipient MAIT cells generate large amounts of IL-17A, promote gastrointestinal tract integrity, and limit the donor alloantigen presentation that in turn drives donor Th1 and Th17 expansion specifically in the colon after BMT. Allogeneic BMT recipients deficient in IL-17A also develop accelerated GVHD, suggesting MAIT cells likely regulate GVHD, at least in part, by the generation of this cytokine. Indeed, analysis of stool microbiota and colon tissue from IL-17A-/- and MR1-/- mice identified analogous shifts in microbiome operational taxonomic units (OTU) and mediators of barrier integrity that appear to represent pathways controlled by similar, IL-17A-dependent mechanisms. Thus, MAIT cells act to control barrier function to attenuate pathogenic T cell responses in the colon and, given their very high frequency in humans, likely represent an important population in clinical BMT.
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Affiliation(s)
- Antiopi Varelias
- Bone Marrow Transplantation Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia.,Faculty of Medicine, and
| | - Mark D Bunting
- Bone Marrow Transplantation Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Kate L Ormerod
- Australian Centre for Ecogenomics, The University of Queensland, Brisbane, Australia
| | - Motoko Koyama
- Bone Marrow Transplantation Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Stuart D Olver
- Bone Marrow Transplantation Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Jasmin Straube
- Gordon and Jessie Gilmour Leukaemia Research Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Rachel D Kuns
- Bone Marrow Transplantation Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Renee J Robb
- Bone Marrow Transplantation Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Andrea S Henden
- Bone Marrow Transplantation Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia.,The Royal Brisbane and Women's Hospital, Brisbane, Australia
| | - Leanne Cooper
- Gordon and Jessie Gilmour Leukaemia Research Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Nancy Lachner
- Australian Centre for Ecogenomics, The University of Queensland, Brisbane, Australia
| | - Kate H Gartlan
- Bone Marrow Transplantation Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia.,Faculty of Medicine, and
| | - Olivier Lantz
- INSERM U932 and Department de Biologie des Tumeurs, Institute Curie and Centre d'Investigation Clinique, CICBT507 IGR/Curie, Paris, France
| | - Lars Kjer-Nielsen
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Australia
| | - Jeffrey Yw Mak
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - David P Fairlie
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | | | - James McCluskey
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program and The Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute Monash University, Clayton, Australia.,Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Australia
| | - Steven W Lane
- Faculty of Medicine, and.,Gordon and Jessie Gilmour Leukaemia Research Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia.,The Royal Brisbane and Women's Hospital, Brisbane, Australia
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, The University of Queensland, Brisbane, Australia
| | - Geoffrey R Hill
- Bone Marrow Transplantation Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia.,Faculty of Medicine, and.,The Royal Brisbane and Women's Hospital, Brisbane, Australia
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2
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Arras SDM, Ormerod KL, Erpf PE, Espinosa MI, Carpenter AC, Blundell RD, Stowasser SR, Schulz BL, Tanurdzic M, Fraser JA. Convergent microevolution of Cryptococcus neoformans hypervirulence in the laboratory and the clinic. Sci Rep 2017; 7:17918. [PMID: 29263343 PMCID: PMC5738413 DOI: 10.1038/s41598-017-18106-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 12/05/2017] [Indexed: 12/30/2022] Open
Abstract
Reference strains are a key component of laboratory research, providing a common background allowing for comparisons across a community of researchers. However, laboratory passage of these strains has been shown to lead to reduced fitness and the attenuation of virulence in some species. In this study we show the opposite in the fungal pathogen Cryptococcus neoformans, with analysis of a collection of type strain H99 subcultures revealing that the most commonly used laboratory subcultures belong to a mutant lineage of the type strain that is hypervirulent. The pleiotropic mutant phenotypes in this H99L (for “Laboratory”) lineage are the result of a deletion in the gene encoding the SAGA Associated Factor Sgf29, a mutation that is also present in the widely-used H99L-derived KN99a/α congenic pair. At a molecular level, loss of this gene results in a reduction in histone H3K9 acetylation. Remarkably, analysis of clinical isolates identified loss of function SGF29 mutations in C. neoformans strains infecting two of fourteen patients, demonstrating not only the first example of hypervirulence in clinical C. neoformans samples, but also parallels between in vitro and in vivo microevolution for hypervirulence in this important pathogen.
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Affiliation(s)
- Samantha D M Arras
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia.,School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Kate L Ormerod
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia.,School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Paige E Erpf
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia.,School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Monica I Espinosa
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia.,School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Alex C Carpenter
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia.,School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Ross D Blundell
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia.,School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Samantha R Stowasser
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia.,School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Benjamin L Schulz
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia.,School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Milos Tanurdzic
- School of Biological Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - James A Fraser
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia. .,School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia.
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3
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Upadhya R, Lam WC, Maybruck BT, Donlin MJ, Chang AL, Kayode S, Ormerod KL, Fraser JA, Doering TL, Lodge JK. A fluorogenic C. neoformans reporter strain with a robust expression of m-cherry expressed from a safe haven site in the genome. Fungal Genet Biol 2017; 108:13-25. [PMID: 28870457 PMCID: PMC5681388 DOI: 10.1016/j.fgb.2017.08.008] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 08/30/2017] [Accepted: 08/31/2017] [Indexed: 12/25/2022]
Abstract
C. neoformans is an encapsulated fungal pathogen with defined asexual and sexual life cycles. Due to the availability of genetic and molecular tools for its manipulation, it has become a model organism for studies of fungal pathogens, even though it lacks a reliable system for maintaining DNA fragments as extrachromosomal plasmids. To compensate for this deficiency, we identified a genomic gene-free intergenic region where heterologous DNA could be inserted by homologous recombination without adverse effects on the phenotype of the recipient strain. Since such a site in the C. neoformans genome at a different location has been named previously as "safe haven", we named this locus second safe haven site (SH2). Insertion of DNA into this site in the genome of the KN99 congenic strain pair caused minimal change in the growth of the engineered strain under a variety of in vitro and in vivo conditions. We exploited this 'safe' locus to create a genetically stable highly fluorescent strain expressing mCherry protein (KN99mCH); this strain closely resembled its wild-type parent (KN99α) in growth under a variety of in vitro stress conditions and in the expression of virulence traits. The efficiency of phagocytosis and the proliferation of KN99mCH inside human monocyte-derived macrophages were comparable to those of KN99α, and the engineered strain showed the expected organ dissemination after inoculation, although there was a slight reduction in virulence. The mCherry fluorescence allowed us to measure specific association of cryptococci with leukocytes in the lungs and mediastinal lymph nodes of infected animals and, for the first-time, to assess their live/dead status in vivo. These results highlight the utility of KN99mCH for elucidation of host-pathogen interactions in vivo. Finally, we generated drug-resistant KN99 strains of both mating types that are marked at the SH2 locus with a specific drug resistant gene cassette; these strains will facilitate the generation of mutant strains by mating.
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Affiliation(s)
- Rajendra Upadhya
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Woei C Lam
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Brian T Maybruck
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Maureen J Donlin
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, USA
| | - Andrew L Chang
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Sarah Kayode
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Kate L Ormerod
- Australian Infectious Diseases Research Centre and School of Chemistry& Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - James A Fraser
- Australian Infectious Diseases Research Centre and School of Chemistry& Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Tamara L Doering
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Jennifer K Lodge
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA.
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4
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Varelias A, Ormerod KL, Bunting MD, Koyama M, Gartlan KH, Kuns RD, Lachner N, Locke KR, Lim CY, Henden AS, Zhang P, Clouston AD, Hasnain SZ, McGuckin MA, Blazar BR, MacDonald KPA, Hugenholtz P, Hill GR. Acute graft-versus-host disease is regulated by an IL-17-sensitive microbiome. The Journal of Immunology 2017. [DOI: 10.4049/jimmunol.198.supp.82.8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
Donor T cell-derived IL-17A can mediate late immunopathology in graft-versus-host disease (GVHD), however protective roles remain unclear. Using multiple cytokine and cytokine receptor subunit knockout mice we demonstrate that stem cell transplant (SCT) recipients lacking the ability to generate or signal IL-17 develop intestinal hyper-acute GVHD. This protective effect is restricted to the molecular interaction of IL-17A and/or IL-17F with the IL-17RA/C receptor. The protection from GVHD afforded by IL-17A required secretion from, and signaling in, both hematopoietic and non-hematopoietic host tissue. Given the intestinal-specificity of the disease in these animals, we hypothesized a microbiome contribution. Cohousing of WT with IL-17RA and IL-17RC deficient mice, dramatically enhanced the susceptibility of WT mice to acute GVHD. Furthermore, the gut microbiome of WT mice shifted towards that of the IL-17RA/C mice during cohousing prior to transplant, confirming that IL-17-sensitive gut microbiota controls susceptibility to acute GVHD. Finally, induced IL-17A deletion peri-transplant also enhanced acute GVHD, consistent with an additional protective role for this cytokine independent of effects on dysbiosis. Importantly, this implies that blocking IL-17 in a clinical trial could have adverse effects via dysbiosis, particularly in the early post-transplant setting and raises caution about their potential effects if used long term.
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Affiliation(s)
| | - Kate L Ormerod
- 2Australian Centre for Ecogenomics, The University of Queensland, Australia
| | | | | | | | | | - Nancy Lachner
- 2Australian Centre for Ecogenomics, The University of Queensland, Australia
| | | | - Chun Y Lim
- 1QIMR Berghofer Med. Res. Inst., Australia
| | | | - Ping Zhang
- 1QIMR Berghofer Med. Res. Inst., Australia
| | | | - Sumaira Z Hasnain
- 4Mater Research Institute, The University of Queensland, Translational Research Institute, Australia
| | - Michael A McGuckin
- 4Mater Research Institute, The University of Queensland, Translational Research Institute, Australia
| | | | | | - Philip Hugenholtz
- 2Australian Centre for Ecogenomics, The University of Queensland, Australia
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5
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Ormerod KL, Wood DLA, Lachner N, Gellatly SL, Daly JN, Parsons JD, Dal'Molin CGO, Palfreyman RW, Nielsen LK, Cooper MA, Morrison M, Hansbro PM, Hugenholtz P. Genomic characterization of the uncultured Bacteroidales family S24-7 inhabiting the guts of homeothermic animals. Microbiome 2016; 4:36. [PMID: 27388460 PMCID: PMC4936053 DOI: 10.1186/s40168-016-0181-2] [Citation(s) in RCA: 414] [Impact Index Per Article: 51.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 06/23/2016] [Indexed: 05/05/2023]
Abstract
BACKGROUND Our view of host-associated microbiota remains incomplete due to the presence of as yet uncultured constituents. The Bacteroidales family S24-7 is a prominent example of one of these groups. Marker gene surveys indicate that members of this family are highly localized to the gastrointestinal tracts of homeothermic animals and are increasingly being recognized as a numerically predominant member of the gut microbiota; however, little is known about the nature of their interactions with the host. RESULTS Here, we provide the first whole genome exploration of this family, for which we propose the name "Candidatus Homeothermaceae," using 30 population genomes extracted from fecal samples of four different animal hosts: human, mouse, koala, and guinea pig. We infer the core metabolism of "Ca. Homeothermaceae" to be that of fermentative or nanaerobic bacteria, resembling that of related Bacteroidales families. In addition, we describe three trophic guilds within the family, plant glycan (hemicellulose and pectin), host glycan, and α-glucan, each broadly defined by increased abundance of enzymes involved in the degradation of particular carbohydrates. CONCLUSIONS "Ca. Homeothermaceae" representatives constitute a substantial component of the murine gut microbiota, as well as being present within the human gut, and this study provides important first insights into the nature of their residency. The presence of trophic guilds within the family indicates the potential for niche partitioning and specific roles for each guild in gut health and dysbiosis.
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Affiliation(s)
- Kate L Ormerod
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - David L A Wood
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Nancy Lachner
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Shaan L Gellatly
- Priority Research Centre for Healthy Lungs, The University of Newcastle and Hunter Medical Research Institute, Newcastle, Australia
| | - Joshua N Daly
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Jeremy D Parsons
- QFAB Bioinformatics, The University of Queensland, Brisbane, Australia
| | - Cristiana G O Dal'Molin
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Australia
| | - Robin W Palfreyman
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Australia
| | - Lars K Nielsen
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Australia
| | - Matthew A Cooper
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Mark Morrison
- Microbial Biology and Metagenomics, The University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Australia
| | - Philip M Hansbro
- Priority Research Centre for Healthy Lungs, The University of Newcastle and Hunter Medical Research Institute, Newcastle, Australia
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia.
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6
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Ormerod KL, George NM, Fraser JA, Wainwright C, Hugenholtz P. Comparative genomics of non-pseudomonal bacterial species colonising paediatric cystic fibrosis patients. PeerJ 2015; 3:e1223. [PMID: 26401445 PMCID: PMC4579023 DOI: 10.7717/peerj.1223] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 08/10/2015] [Indexed: 12/16/2022] Open
Abstract
The genetic disorder cystic fibrosis is a life-limiting condition affecting ∼70,000 people worldwide. Targeted, early, treatment of the dominant infecting species, Pseudomonas aeruginosa, has improved patient outcomes; however, there is concern that other species are now stepping in to take its place. In addition, the necessarily long-term antibiotic therapy received by these patients may be providing a suitable environment for the emergence of antibiotic resistance. To investigate these issues, we employed whole-genome sequencing of 28 non-Pseudomonas bacterial strains isolated from three paediatric patients. We did not find any trend of increasing antibiotic resistance (either by mutation or lateral gene transfer) in these isolates in comparison with other examples of the same species. In addition, each isolate contained a virulence gene repertoire that was similar to other examples of the relevant species. These results support the impaired clearance of the CF lung not demanding extensive virulence for survival in this habitat. By analysing serial isolates of the same species we uncovered several examples of strain persistence. The same strain of Staphylococcus aureus persisted for nearly a year, despite administration of antibiotics to which it was shown to be sensitive. This is consistent with previous studies showing antibiotic therapy to be inadequate in cystic fibrosis patients, which may also explain the lack of increasing antibiotic resistance over time. Serial isolates of two naturally multi-drug resistant organisms, Achromobacter xylosoxidans and Stenotrophomonas maltophilia, revealed that while all S. maltophilia strains were unique, A. xylosoxidans persisted for nearly five years, making this a species of particular concern. The data generated by this study will assist in developing an understanding of the non-Pseudomonas species associated with cystic fibrosis.
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Affiliation(s)
- Kate L. Ormerod
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Narelle M. George
- Health Support Queensland, Department of Health, Queensland Government, Herston, Queensland, Australia
| | - James A. Fraser
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Claire Wainwright
- School of Medicine, University of Queensland, Brisbane, Queensland, Australia
- Department of Respiratory and Sleep Medicine, Lady Cilento Children’s Hospital, South Brisbane, Queensland, Australia
- Queensland Children’s Medical Research Insitute, Herston, Queensland, Australia
| | - Philip Hugenholtz
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
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7
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Janbon G, Ormerod KL, Paulet D, Byrnes EJ, Yadav V, Chatterjee G, Mullapudi N, Hon CC, Billmyre RB, Brunel F, Bahn YS, Chen W, Chen Y, Chow EWL, Coppée JY, Floyd-Averette A, Gaillardin C, Gerik KJ, Goldberg J, Gonzalez-Hilarion S, Gujja S, Hamlin JL, Hsueh YP, Ianiri G, Jones S, Kodira CD, Kozubowski L, Lam W, Marra M, Mesner LD, Mieczkowski PA, Moyrand F, Nielsen K, Proux C, Rossignol T, Schein JE, Sun S, Wollschlaeger C, Wood IA, Zeng Q, Neuvéglise C, Newlon CS, Perfect JR, Lodge JK, Idnurm A, Stajich JE, Kronstad JW, Sanyal K, Heitman J, Fraser JA, Cuomo CA, Dietrich FS. Analysis of the genome and transcriptome of Cryptococcus neoformans var. grubii reveals complex RNA expression and microevolution leading to virulence attenuation. PLoS Genet 2014; 10:e1004261. [PMID: 24743168 PMCID: PMC3990503 DOI: 10.1371/journal.pgen.1004261] [Citation(s) in RCA: 268] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 02/07/2014] [Indexed: 02/07/2023] Open
Abstract
Cryptococcus neoformans is a pathogenic basidiomycetous yeast responsible for more than 600,000 deaths each year. It occurs as two serotypes (A and D) representing two varieties (i.e. grubii and neoformans, respectively). Here, we sequenced the genome and performed an RNA-Seq-based analysis of the C. neoformans var. grubii transcriptome structure. We determined the chromosomal locations, analyzed the sequence/structural features of the centromeres, and identified origins of replication. The genome was annotated based on automated and manual curation. More than 40,000 introns populating more than 99% of the expressed genes were identified. Although most of these introns are located in the coding DNA sequences (CDS), over 2,000 introns in the untranslated regions (UTRs) were also identified. Poly(A)-containing reads were employed to locate the polyadenylation sites of more than 80% of the genes. Examination of the sequences around these sites revealed a new poly(A)-site-associated motif (AUGHAH). In addition, 1,197 miscRNAs were identified. These miscRNAs can be spliced and/or polyadenylated, but do not appear to have obvious coding capacities. Finally, this genome sequence enabled a comparative analysis of strain H99 variants obtained after laboratory passage. The spectrum of mutations identified provides insights into the genetics underlying the micro-evolution of a laboratory strain, and identifies mutations involved in stress responses, mating efficiency, and virulence. Cryptococcus neoformans var. grubii is a major human pathogen responsible for deadly meningoencephalitis in immunocompromised patients. Here, we report the sequencing and annotation of its genome. Evidence for extensive intron splicing, antisense transcription, non-coding RNAs, and alternative polyadenylation indicates the potential for highly intricate regulation of gene expression in this opportunistic pathogen. In addition, detailed molecular, genetic, and genomic studies were performed to characterize structural features of the genome, including centromeres and origins of replication. Finally, the phenotypic and genome re-sequencing analysis of a collection of isolates of the reference H99 strain resulting from laboratory passage revealed that microevolutionary processes during in vitro culturing of pathogenic fungi can impact virulence.
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Affiliation(s)
- Guilhem Janbon
- Institut Pasteur, Unité Biologie et Pathogénicité Fongiques, Département Génomes et Génétique, Paris, France
- INRA, USC2019, Paris, France
- * E-mail: (GJ); (JH); (CAC); (FSD)
| | - Kate L. Ormerod
- University of Queensland, School of Chemistry and Molecular Biosciences, Brisbane, Queensland, Australia
| | - Damien Paulet
- Institut Pasteur, Plate-forme Transcriptome et Epigénome, Département Génomes et Génétique, Paris, France
| | - Edmond J. Byrnes
- Duke University Medical Center, Department of Molecular Genetics and Microbiology, Durham, North Carolina, United States of America
| | - Vikas Yadav
- Jawaharlal Nehru Centre for Advanced Scientific Research, Molecular Biology and Genetics Unit, Bangalore, India
| | - Gautam Chatterjee
- Jawaharlal Nehru Centre for Advanced Scientific Research, Molecular Biology and Genetics Unit, Bangalore, India
| | | | - Chung-Chau Hon
- Institut Pasteur, Unité Biologie Cellulaire du Parasitisme, Département Biologie Cellulaire et Infection, Paris, France
| | - R. Blake Billmyre
- Duke University Medical Center, Department of Molecular Genetics and Microbiology, Durham, North Carolina, United States of America
| | | | - Yong-Sun Bahn
- Yonsei University, Center for Fungal Pathogenesis, Department of Biotechnology, Seoul, Republic of Korea
| | - Weidong Chen
- Rutgers New Jersey Medical School, Department of Microbiology and Molecular Genetics, Newark, New Jersey, United States of America
| | - Yuan Chen
- Duke University Medical Center, Department of Molecular Genetics and Microbiology, Durham, North Carolina, United States of America
| | - Eve W. L. Chow
- University of Queensland, School of Chemistry and Molecular Biosciences, Brisbane, Queensland, Australia
| | - Jean-Yves Coppée
- Institut Pasteur, Plate-forme Transcriptome et Epigénome, Département Génomes et Génétique, Paris, France
| | - Anna Floyd-Averette
- Duke University Medical Center, Department of Molecular Genetics and Microbiology, Durham, North Carolina, United States of America
| | | | - Kimberly J. Gerik
- Washington University School of Medicine, Department of Molecular Microbiology, St. Louis, Missouri, United States of America
| | - Jonathan Goldberg
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Sara Gonzalez-Hilarion
- Institut Pasteur, Unité Biologie et Pathogénicité Fongiques, Département Génomes et Génétique, Paris, France
- INRA, USC2019, Paris, France
| | - Sharvari Gujja
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Joyce L. Hamlin
- University of Virginia, Department of Biochemistry and Molecular Genetics, Charlottesville, Virginia, United States of America
| | - Yen-Ping Hsueh
- Duke University Medical Center, Department of Molecular Genetics and Microbiology, Durham, North Carolina, United States of America
- California Institute of Technology, Division of Biology, Pasadena, California, United States of America
| | - Giuseppe Ianiri
- University of Missouri-Kansas City, School of Biological Sciences, Division of Cell Biology and Biophysics, Kansas City, Missouri, United States of America
| | - Steven Jones
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Chinnappa D. Kodira
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Lukasz Kozubowski
- Clemson University, Department of Genetics and Biochemistry, Clemson, South Carolina, United States of America
| | - Woei Lam
- Washington University School of Medicine, Department of Molecular Microbiology, St. Louis, Missouri, United States of America
| | - Marco Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Larry D. Mesner
- University of Virginia, Department of Biochemistry and Molecular Genetics, Charlottesville, Virginia, United States of America
| | - Piotr A. Mieczkowski
- University of North Carolina, Department of Genetics, Chapel Hill, North Carolina, United States of America
| | - Frédérique Moyrand
- Institut Pasteur, Unité Biologie et Pathogénicité Fongiques, Département Génomes et Génétique, Paris, France
- INRA, USC2019, Paris, France
| | - Kirsten Nielsen
- Duke University Medical Center, Department of Molecular Genetics and Microbiology, Durham, North Carolina, United States of America
- University of Minnesota, Microbiology Department, Minneapolis, Minnesota, United States of America
| | - Caroline Proux
- Institut Pasteur, Plate-forme Transcriptome et Epigénome, Département Génomes et Génétique, Paris, France
| | | | - Jacqueline E. Schein
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Sheng Sun
- Duke University Medical Center, Department of Molecular Genetics and Microbiology, Durham, North Carolina, United States of America
| | - Carolin Wollschlaeger
- Institut Pasteur, Unité Biologie et Pathogénicité Fongiques, Département Génomes et Génétique, Paris, France
- INRA, USC2019, Paris, France
| | - Ian A. Wood
- University of Queensland, School of Mathematics and Physics, Brisbane, Queensland, Australia
| | - Qiandong Zeng
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | | | - Carol S. Newlon
- Rutgers New Jersey Medical School, Department of Microbiology and Molecular Genetics, Newark, New Jersey, United States of America
| | - John R. Perfect
- Duke University Medical Center, Duke Department of Medicine and Molecular Genetics and Microbiology, Durham, North Carolina, United States of America
| | - Jennifer K. Lodge
- Washington University School of Medicine, Department of Molecular Microbiology, St. Louis, Missouri, United States of America
| | - Alexander Idnurm
- University of Missouri-Kansas City, School of Biological Sciences, Division of Cell Biology and Biophysics, Kansas City, Missouri, United States of America
| | - Jason E. Stajich
- Duke University Medical Center, Department of Molecular Genetics and Microbiology, Durham, North Carolina, United States of America
- University of California, Department of Plant Pathology & Microbiology, Riverside, California, United States of America
| | - James W. Kronstad
- Michael Smith Laboratories, Department of Microbiology and Immunology, Vancouver, British Columbia, Canada
| | - Kaustuv Sanyal
- Jawaharlal Nehru Centre for Advanced Scientific Research, Molecular Biology and Genetics Unit, Bangalore, India
| | - Joseph Heitman
- Duke University Medical Center, Department of Molecular Genetics and Microbiology, Durham, North Carolina, United States of America
- * E-mail: (GJ); (JH); (CAC); (FSD)
| | - James A. Fraser
- University of Queensland, School of Chemistry and Molecular Biosciences, Brisbane, Queensland, Australia
| | - Christina A. Cuomo
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- * E-mail: (GJ); (JH); (CAC); (FSD)
| | - Fred S. Dietrich
- Duke University Medical Center, Department of Molecular Genetics and Microbiology, Durham, North Carolina, United States of America
- * E-mail: (GJ); (JH); (CAC); (FSD)
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Affiliation(s)
- Kate L. Ormerod
- Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - James A. Fraser
- Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
- * E-mail:
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Lee IR, Lim JWC, Ormerod KL, Morrow CA, Fraser JA. Characterization of an Nmr homolog that modulates GATA factor-mediated nitrogen metabolite repression in Cryptococcus neoformans. PLoS One 2012; 7:e32585. [PMID: 22470421 PMCID: PMC3314646 DOI: 10.1371/journal.pone.0032585] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Accepted: 02/01/2012] [Indexed: 11/18/2022] Open
Abstract
Nitrogen source utilization plays a critical role in fungal development, secondary metabolite production and pathogenesis. In both the Ascomycota and Basidiomycota, GATA transcription factors globally activate the expression of catabolic enzyme-encoding genes required to degrade complex nitrogenous compounds. However, in the presence of preferred nitrogen sources such as ammonium, GATA factor activity is inhibited in some species through interaction with co-repressor Nmr proteins. This regulatory phenomenon, nitrogen metabolite repression, enables preferential utilization of readily assimilated nitrogen sources. In the basidiomycete pathogen Cryptococcus neoformans, the GATA factor Gat1/Are1 has been co-opted into regulating multiple key virulence traits in addition to nitrogen catabolism. Here, we further characterize Gat1/Are1 function and investigate the regulatory role of the predicted Nmr homolog Tar1. While GAT1/ARE1 expression is induced during nitrogen limitation, TAR1 transcription is unaffected by nitrogen availability. Deletion of TAR1 leads to inappropriate derepression of non-preferred nitrogen catabolic pathways in the simultaneous presence of favoured sources. In addition to exhibiting its evolutionary conserved role of inhibiting GATA factor activity under repressing conditions, Tar1 also positively regulates GAT1/ARE1 transcription under non-repressing conditions. The molecular mechanism by which Tar1 modulates nitrogen metabolite repression, however, remains open to speculation. Interaction between Tar1 and Gat1/Are1 was undetectable in a yeast two-hybrid assay, consistent with Tar1 and Gat1/Are1 each lacking the conserved C-terminus regions present in ascomycete Nmr proteins and GATA factors that are known to interact with each other. Importantly, both Tar1 and Gat1/Are1 are suppressors of C. neoformans virulence, reiterating and highlighting the paradigm of nitrogen regulation of pathogenesis.
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Affiliation(s)
- I. Russel Lee
- Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Jonathan W. C. Lim
- Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Kate L. Ormerod
- Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Carl A. Morrow
- Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - James A. Fraser
- Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
- * E-mail:
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