1
|
Wang JM, Woodruff AL, Dunn MJ, Fillinger RJ, Bennett RJ, Anderson MZ. Intraspecies Transcriptional Profiling Reveals Key Regulators of Candida albicans Pathogenic Traits. mBio 2021; 12:e00586-21. [PMID: 33879584 PMCID: PMC8092256 DOI: 10.1128/mbio.00586-21] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 03/17/2021] [Indexed: 12/27/2022] Open
Abstract
The human commensal and opportunistic fungal pathogen Candida albicans displays extensive genetic and phenotypic variation across clinical isolates. Here, we performed RNA sequencing on 21 well-characterized isolates to examine how genetic variation contributes to gene expression differences and to link these differences to phenotypic traits. C. albicans adapts primarily through clonal evolution, and yet hierarchical clustering of gene expression profiles in this set of isolates did not reproduce their phylogenetic relationship. Strikingly, strain-specific gene expression was prevalent in some strain backgrounds. Association of gene expression with phenotypic data by differential analysis, linear correlation, and assembly of gene networks connected both previously characterized and novel genes with 23 C. albicans traits. Construction of de novo gene modules produced a gene atlas incorporating 67% of C. albicans genes and revealed correlations between expression modules and important phenotypes such as systemic virulence. Furthermore, targeted investigation of two modules that have novel roles in growth and filamentation supported our bioinformatic predictions. Together, these studies reveal widespread transcriptional variation across C. albicans isolates and identify genetic and epigenetic links to phenotypic variation based on coexpression network analysis.IMPORTANCE Infectious fungal species are often treated uniformly despite clear evidence of genotypic and phenotypic heterogeneity being widespread across strains. Identifying the genetic basis for this phenotypic diversity is extremely challenging because of the tens or hundreds of thousands of variants that may distinguish two strains. Here, we use transcriptional profiling to determine differences in gene expression that can be linked to phenotypic variation among a set of 21 Candida albicans isolates. Analysis of this transcriptional data set uncovered clear trends in gene expression characteristics for this species and new genes and pathways that were associated with variation in pathogenic processes. Direct investigation confirmed functional predictions for a number of new regulators associated with growth and filamentation, demonstrating the utility of these approaches in linking genes to important phenotypes.
Collapse
Affiliation(s)
- Joshua M Wang
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Andrew L Woodruff
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Matthew J Dunn
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Robert J Fillinger
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Richard J Bennett
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Matthew Z Anderson
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, Ohio, USA
| |
Collapse
|
2
|
Dunn MJ, Fillinger RJ, Anderson LM, Anderson MZ. Automated quantification of Candida albicans biofilm-related phenotypes reveals additive contributions to biofilm production. NPJ Biofilms Microbiomes 2020; 6:36. [PMID: 33037223 PMCID: PMC7547077 DOI: 10.1038/s41522-020-00149-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 09/11/2020] [Indexed: 12/15/2022] Open
Abstract
Biofilms are organized communities of microbial cells that promote persistence among bacterial and fungal species. Biofilm formation by host-associated Candida species of fungi occurs on both tissue surfaces and implanted devices, contributing to host colonization and disease. In C. albicans, biofilms are built sequentially by adherence of yeast to a surface, invasion into the substrate, the formation of aerial hyphal projections, and the secretion of extracellular matrix. Measurement of these biofilm-related phenotypes remains highly qualitative and often subjective. Here, we designed an informatics pipeline for quantifying filamentation, adhesion, and invasion of Candida species on solid agar media and utilized this approach to determine the importance of these component phenotypes to C. albicans biofilm production. Characterization of 23 C. albicans clinical isolates across three media and two temperatures revealed a wide range of phenotypic responses among isolates in any single condition. Media profoundly altered all biofilm-related phenotypes among these isolates, whereas temperature minimally impacted these traits. Importantly, the extent of biofilm formation correlated significantly with the additive score for its component phenotypes under some conditions, experimentally linking the strength of each component to biofilm mass. In addition, the response of the genome reference strain, SC5314, across these conditions was an extreme outlier compared to all other strains, suggesting it may not be representative of the species. Taken together, development of a high-throughput, unbiased approach to quantifying Candida biofilm-related phenotypes linked variability in these phenotypes to biofilm production and can facilitate genetic dissection of these critical processes to pathogenesis in the host.
Collapse
Affiliation(s)
- Matthew J Dunn
- Department of Microbiology, The Ohio State University, Columbus, OH, 43210, USA
| | - Robert J Fillinger
- Biomedical Sciences Graduate Program, The Ohio State University, Columbus, OH, 43210, USA
| | - Leah M Anderson
- Department of Microbiology, The Ohio State University, Columbus, OH, 43210, USA
| | - Matthew Z Anderson
- Department of Microbiology, The Ohio State University, Columbus, OH, 43210, USA.
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, 43210, USA.
| |
Collapse
|
3
|
Chemudupati M, Kenney AD, Smith AC, Fillinger RJ, Zhang L, Zani A, Liu SL, Anderson MZ, Sharma A, Yount JS. Butyrate Reprograms Expression of Specific Interferon-Stimulated Genes. J Virol 2020; 94:e00326-20. [PMID: 32461320 PMCID: PMC7394905 DOI: 10.1128/jvi.00326-20] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [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: 02/25/2020] [Accepted: 05/22/2020] [Indexed: 12/31/2022] Open
Abstract
Butyrate is an abundant metabolite produced by gut microbiota. While butyrate is a known histone deacetylase inhibitor that activates expression of many genes involved in immune system pathways, its effects on virus infections and on the antiviral type I interferon (IFN) response have not been adequately investigated. We found that butyrate increases cellular infection with viruses relevant to human and animal health, including influenza virus, reovirus, HIV-1, human metapneumovirus, and vesicular stomatitis virus. Mechanistically, butyrate suppresses levels of specific antiviral IFN-stimulated gene (ISG) products, such as RIG-I and IFITM3, in human and mouse cells without inhibiting IFN-induced phosphorylation or nuclear translocation of the STAT1 and STAT2 transcription factors. Accordingly, we discovered that although butyrate globally increases baseline expression of more than 800 cellular genes, it strongly represses IFN-induced expression of 60% of ISGs and upregulates 3% of ISGs. Our findings reveal that there are differences in the IFN responsiveness of major subsets of ISGs depending on the presence of butyrate in the cell environment, and overall, they identify a new mechanism by which butyrate influences virus infection of cells.IMPORTANCE Butyrate is a lipid produced by intestinal bacteria. Here, we newly show that butyrate reprograms the innate antiviral immune response mediated by type I interferons (IFNs). Many of the antiviral genes induced by type I IFNs are repressed in the presence of butyrate, resulting in increased virus infection and replication. Our research demonstrates that metabolites produced by the gut microbiome, such as butyrate, can have complex effects on cellular physiology, including dampening of an inflammatory innate immune pathway resulting in a proviral cellular environment. Our work further suggests that butyrate could be broadly used as a tool to increase growth of virus stocks for research and for the generation of vaccines.
Collapse
Affiliation(s)
- Mahesh Chemudupati
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, Ohio, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
| | - Adam D Kenney
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, Ohio, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
| | - Anna C Smith
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, Ohio, USA
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
| | - Robert J Fillinger
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, Ohio, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Lizhi Zhang
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, Ohio, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
| | - Ashley Zani
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, Ohio, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
| | - Shan-Lu Liu
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, Ohio, USA
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Matthew Z Anderson
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, Ohio, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Amit Sharma
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, Ohio, USA
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
| | - Jacob S Yount
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, Ohio, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| |
Collapse
|
4
|
Fillinger RJ, Anderson MZ. Seasons of change: Mechanisms of genome evolution in human fungal pathogens. Infect Genet Evol 2019; 70:165-174. [PMID: 30826447 DOI: 10.1016/j.meegid.2019.02.031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 02/23/2019] [Accepted: 02/26/2019] [Indexed: 06/09/2023]
Abstract
Fungi are a diverse kingdom of organisms capable of thriving in various niches across the world including those in close association with multicellular eukaryotes. Fungal pathogens that contribute to human disease reside both within the host as commensal organisms of the microbiota and the environment. Their niche of origin dictates how infection initiates but also places specific selective pressures on the fungal pathogen that contributes to its genome organization and genetic repertoire. Recent efforts to catalogue genomic variation among major human fungal pathogens have unveiled evolutionary themes that shape the fungal genome. Mechanisms ranging from large scale changes such as aneuploidy and ploidy cycling as well as more targeted mutations like base substitutions and gene copy number variations contribute to the evolution of these species, which are often under multiple competing selective pressures with their host, environment, and other microbes. Here, we provide an overview of the major selective pressures and mechanisms acting to evolve the genome of clinically important fungal pathogens of humans.
Collapse
Affiliation(s)
- Robert J Fillinger
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210, USA
| | - Matthew Z Anderson
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210, USA; Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.
| |
Collapse
|