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Fletcher J, O’Connor-Moneley J, Frawley D, Flanagan PR, Alaalm L, Menendez-Manjon P, Estevez SV, Hendricks S, Woodruff AL, Buscaino A, Anderson MZ, Sullivan DJ, Moran GP. Deletion of the Candida albicans TLO gene family using CRISPR-Cas9 mutagenesis allows characterisation of functional differences in α-, β- and γ- TLO gene function. PLoS Genet 2023; 19:e1011082. [PMID: 38048294 PMCID: PMC10721199 DOI: 10.1371/journal.pgen.1011082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 12/14/2023] [Accepted: 11/22/2023] [Indexed: 12/06/2023] Open
Abstract
The Candida albicans genome contains between ten and fifteen distinct TLO genes that all encode a Med2 subunit of Mediator. In order to investigate the biological role of Med2/Tlo in C. albicans we deleted all fourteen TLO genes using CRISPR-Cas9 mutagenesis. ChIP-seq analysis showed that RNAP II localized to 55% fewer genes in the tloΔ mutant strain compared to the parent, while RNA-seq analysis showed that the tloΔ mutant exhibited differential expression of genes required for carbohydrate metabolism, stress responses, white-opaque switching and filamentous growth. Consequently, the tloΔ mutant grows poorly in glucose- and galactose-containing media, is unable to grow as true hyphae, is more sensitive to oxidative stress and is less virulent in the wax worm infection model. Reintegration of genes representative of the α-, β- and γ-TLO clades resulted in the complementation of the mutant phenotypes, but to different degrees. TLOα1 could restore phenotypes and gene expression patterns similar to wild-type and was the strongest activator of glycolytic and Tye7-regulated gene expression. In contrast, the two γ-TLO genes examined (i.e., TLOγ5 and TLOγ11) had a far lower impact on complementing phenotypic and transcriptomic changes. Uniquely, expression of TLOβ2 in the tloΔ mutant stimulated filamentous growth in YEPD medium and this phenotype was enhanced when Tloβ2 expression was increased to levels far in excess of Med3. In contrast, expression of reintegrated TLO genes in a tloΔ/med3Δ double mutant background failed to restore any of the phenotypes tested, suggesting that complementation of these Tlo-regulated processes requires a functional Mediator tail module. Together, these data confirm the importance of Med2/Tlo in a wide range of C. albicans cellular activities and demonstrate functional diversity within the gene family which may contribute to the success of this yeast as a coloniser and pathogen of humans.
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Affiliation(s)
- Jessica Fletcher
- Division of Oral Biosciences, Dublin Dental University Hospital, & University of Dublin, Trinity College Dublin, Dublin, Ireland
| | - James O’Connor-Moneley
- Division of Oral Biosciences, Dublin Dental University Hospital, & University of Dublin, Trinity College Dublin, Dublin, Ireland
| | - Dean Frawley
- Division of Oral Biosciences, Dublin Dental University Hospital, & University of Dublin, Trinity College Dublin, Dublin, Ireland
| | - Peter R. Flanagan
- Division of Oral Biosciences, Dublin Dental University Hospital, & University of Dublin, Trinity College Dublin, Dublin, Ireland
| | - Leenah Alaalm
- Division of Oral Biosciences, Dublin Dental University Hospital, & University of Dublin, Trinity College Dublin, Dublin, Ireland
| | | | | | - Shane Hendricks
- Department of Microbiology, The Ohio State University, Columbus, Ohio, United States of America
| | - Andrew L. Woodruff
- Department of Microbiology, The Ohio State University, Columbus, Ohio, United States of America
| | - Alessia Buscaino
- School of Biosciences, University of Kent, Canterbury, United Kingdom
| | - Matthew Z. Anderson
- Department of Microbiology, The Ohio State University, Columbus, Ohio, United States of America
| | - Derek J. Sullivan
- Division of Oral Biosciences, Dublin Dental University Hospital, & University of Dublin, Trinity College Dublin, Dublin, Ireland
| | - Gary P. Moran
- Division of Oral Biosciences, Dublin Dental University Hospital, & University of Dublin, Trinity College Dublin, Dublin, Ireland
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Wang Y, He S, Fang X. Emerging roles of phase separation in plant transcription and chromatin organization. CURRENT OPINION IN PLANT BIOLOGY 2023; 75:102387. [PMID: 37311366 DOI: 10.1016/j.pbi.2023.102387] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/07/2023] [Accepted: 05/10/2023] [Indexed: 06/15/2023]
Abstract
Transcription is a core step in gene expression. Regulation of transcription is achieved at the level of transcription machinery, local chromatin environment as well as higher-order chromatin organization. Our understanding of transcriptional regulation was advanced by recent introduction of transcription and chromatin-associated condensates, which typically arise via phase separation of proteins and nucleic acids. While studies from mammalian cells are unveiling the mechanisms of phase separation in transcription regulation, those in plants further broaden and deepen our understanding of this process. In this review, we discuss recent progress in plants how phase separation operates in RNA-mediated chromatin silencing, transcription activity, and chromatin compartmentalization.
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Affiliation(s)
- Yunhe Wang
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Shengbo He
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China.
| | - Xiaofeng Fang
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
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O'Connor-Moneley J, Alaalm L, Moran GP, Sullivan DJ. The role of the Mediator complex in fungal pathogenesis and response to antifungal agents. Essays Biochem 2023; 67:843-851. [PMID: 37013399 PMCID: PMC10500203 DOI: 10.1042/ebc20220238] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 03/15/2023] [Accepted: 03/17/2023] [Indexed: 04/05/2023]
Abstract
Mediator is a complex of polypeptides that plays a central role in the recruitment of RNA polymerase II to promoters and subsequent transcriptional activation in eukaryotic organisms. Studies have now shown that Mediator has a role in regulating expression of genes implicated in virulence and antifungal drug resistance in pathogenic fungi. The roles of specific Mediator subunits have been investigated in several species of pathogenic fungi, particularly in the most pathogenic yeast Candida albicans. Uniquely, pathogenic yeast also present several interesting examples of divergence in Mediator structure and function, most notably in C. glabrata, which possesses two orthologues of Med15, and in C. albicans, which has a massively expanded family of Med2 orthologues known as the TLO gene family. This review highlights specific examples of recent progress in characterizing the role of Mediator in pathogenic fungi.
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Affiliation(s)
- James O'Connor-Moneley
- Microbiology Research Unit, Division of Oral Biosciences, Dublin Dental University Hospital, University of Dublin, Trinity College Dublin, Dublin, Ireland
| | - Leenah Alaalm
- Microbiology Research Unit, Division of Oral Biosciences, Dublin Dental University Hospital, University of Dublin, Trinity College Dublin, Dublin, Ireland
| | - Gary P Moran
- Microbiology Research Unit, Division of Oral Biosciences, Dublin Dental University Hospital, University of Dublin, Trinity College Dublin, Dublin, Ireland
| | - Derek J Sullivan
- Microbiology Research Unit, Division of Oral Biosciences, Dublin Dental University Hospital, University of Dublin, Trinity College Dublin, Dublin, Ireland
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Mao Y, Solis NV, Filler SG, Mitchell AP. Functional Dichotomy for a Hyphal Repressor in Candida albicans. mBio 2023; 14:e0013423. [PMID: 36883818 PMCID: PMC10127614 DOI: 10.1128/mbio.00134-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 02/20/2023] [Indexed: 03/09/2023] Open
Abstract
Nrg1 is a repressor of hypha formation and hypha-associated gene expression in the fungal pathogen Candida albicans. It has been well studied in the genetic background of the type strain SC5314. Here, we tested Nrg1 function in four other diverse clinical isolates through an analysis of nrg1Δ/Δ mutants, with SC5314 included as a control. In three strains, nrg1Δ/Δ mutants unexpectedly produced aberrant hyphae under inducing conditions, as assayed by microscopic observation and endothelial cell damage. The nrg1Δ/Δ mutant of strain P57055 had the most severe defect. We examined gene expression features under hypha-inducing conditions by RNA-sequencing (RNA-Seq) for the SC5314 and P57055 backgrounds. The SC5314 nrg1Δ/Δ mutant expressed six hypha-associated genes at reduced levels compared with wild-type SC5314. The P57055 nrg1Δ/Δ mutant expressed 17 hypha-associated genes at reduced levels compared with wild-type P57055, including IRF1, RAS2, and ECE1. These findings indicate that Nrg1 has a positive role in hypha-associated gene expression and that this role is magnified in strain P57055. Remarkably, the same hypha-associated genes affected by the nrg1Δ/Δ mutation in strain P57055 were also naturally expressed at lower levels in wild-type P57055 than those in wild-type SC5314. Our results suggest that strain P57055 is defective in a pathway that acts in parallel with Nrg1 to upregulate the expression of several hypha-associated genes. IMPORTANCE Hypha formation is a central virulence trait of the fungal pathogen Candida albicans. Control of hypha formation has been studied in detail in the type strain but not in other diverse C. albicans clinical isolates. Here, we show that the hyphal repressor Nrg1 has an unexpected positive role in hypha formation and hypha-associated gene expression, as revealed by the sensitized P57055 strain background. Our findings indicate that reliance on a single type strain limits understanding of gene function and illustrate that strain diversity is a valuable resource for C. albicans molecular genetic analysis.
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Affiliation(s)
- Yinhe Mao
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - Norma V. Solis
- Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California, USA
| | - Scott G. Filler
- Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California, USA
- David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Aaron P. Mitchell
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
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Amran AI, Lim SJ, Muhd Noor ND, Salleh AB, Oslan SN. Enolase in Meyerozyma guilliermondii strain SO: Sequential and structural insights of MgEno4581 as a putative virulence factor and host-fungal interactions through comprehensive in silico approaches. Microb Pathog 2023; 176:106025. [PMID: 36754101 DOI: 10.1016/j.micpath.2023.106025] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/31/2022] [Accepted: 02/04/2023] [Indexed: 02/08/2023]
Abstract
Meyerozyma guilliermondii is a rare opportunistic fungal pathogen that causes deadly invasive candidiasis in human. M. guilliermondii strain SO is a local yeast isolate that possesses huge industrial interests but also pathogenic towards zebrafish embryos. Enolases that bind to human extracellular matrix (ECM) proteins are among the fungal virulence factors. To understand its pathogenicity mechanism down to molecular level, especially in the rare M. guilliermondii, this study aimed to identify and characterize the potentially virulence-associated enolase in M. guilliermondii strain SO using bioinformatics approaches. Profile Hidden-Markov model was implemented to identify enolase-related sequences in the fungal proteome. Sequence analysis deciphered only one (MgEno4581) out of nine sequences exhibited potent virulence traits observed similarly in the pathogenic Candida albicans. MgEno4581 structure that was predicted via SWISS-MODEL using C. albicans enolase (CaEno1; PDB ID: 7vrd) as the homology modeling template portrayed a highly identical motif with CaEno1 that facilitates ECM proteins binding. Amino acid substitutions (D234K, K235A, Y238H, K239D, G243K, V248C and Y254F) in ECM-binding motif of Saccharomyces cerevisiae enolase (ScEno) compared to MgEno4581 and CaEno1 caused changes in motif's surface charges. Protein-protein docking indicated F253 in ScEno only interacted hydrophobically with human plasminogen (HPG). Hydrogen linkages were observed for both MgEno4581 and CaEno1, suggesting a stronger interaction with HPG in the hydrophilic host microenvironments. Thus, our in silico characterizations on MgEno4581 provided new perspectives on its potential roles in candidiasis (fungal-host interactions) caused by M. guilliermondii, especially M. guilliermondii strain SO on zebrafish embryos that mimic the immunocompromised individuals as previously evident.
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Affiliation(s)
- Alia Iwani Amran
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
| | - Si Jie Lim
- Enzyme Technology and X-ray Crystallography Laboratory, VacBio 5, Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Enzyme and Microbial Technology (EMTech) Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
| | - Noor Dina Muhd Noor
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Enzyme and Microbial Technology (EMTech) Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
| | - Abu Bakar Salleh
- Enzyme and Microbial Technology (EMTech) Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
| | - Siti Nurbaya Oslan
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Enzyme Technology and X-ray Crystallography Laboratory, VacBio 5, Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Enzyme and Microbial Technology (EMTech) Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
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Patiño LH, Muñoz M, Ramírez AL, Vélez N, Escandón P, Parra-Giraldo CM, Ramírez JD. A Landscape of the Genomic Structure of Cryptococcus neoformans in Colombian Isolates. J Fungi (Basel) 2023; 9:jof9020135. [PMID: 36836249 PMCID: PMC9959405 DOI: 10.3390/jof9020135] [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: 12/14/2022] [Revised: 01/13/2023] [Accepted: 01/15/2023] [Indexed: 01/20/2023] Open
Abstract
Cryptococcus neoformans species complexes are recognized as environmental fungi responsible for lethal meningoencephalitis in immunocompromised individuals. Despite the vast knowledge about the epidemiology and genetic diversity of this fungus in different regions of the world, more studies are necessary to comprehend the genomic profiles across South America, including Colombia, considered to be the second country with the highest number of Cryptococcosis. Here, we sequenced and analyzed the genomic architecture of 29 Colombian C. neoformans isolates and evaluated the phylogenetic relationship of these strains with publicly available C. neoformans genomes. The phylogenomic analysis showed that 97% of the isolates belonged to the VNI molecular type and the presence of sub-lineages and sub-clades. We evidenced a karyotype without changes, a low number of genes with copy number variations, and a moderate number of single-nucleotide polymorphisms (SNPs). Additionally, a difference in the number of SNPs between the sub-lineages/sub-clades was observed; some were involved in crucial fungi biological processes. Our study demonstrated the intraspecific divergence of C. neoformans in Colombia. These findings provide evidence that Colombian C. neoformans isolates do not probably require significant structural changes as adaptation mechanisms to the host. To the best of our knowledge, this is the first study to report the whole genome sequence of Colombian C. neoformans isolates.
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Affiliation(s)
- Luz Helena Patiño
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 111321, Colombia
| | - Marina Muñoz
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 111321, Colombia
| | - Angie Lorena Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 111321, Colombia
| | - Nórida Vélez
- Unidad de Proteómica y Micosis Humanas, Grupo de Investigación en Enfermedades Infecciosas, Departamento de Microbiología, Pontificia Universidad Javeriana, Bogotá 111321, Colombia
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad Complutense de Madrid, 28001 Madrid, Spain
| | - Patricia Escandón
- Grupo de Microbiología, Instituto Nacional de Salud, Bogotá 111321, Colombia
| | - Claudia-Marcela Parra-Giraldo
- Unidad de Proteómica y Micosis Humanas, Grupo de Investigación en Enfermedades Infecciosas, Departamento de Microbiología, Pontificia Universidad Javeriana, Bogotá 111321, Colombia
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad Complutense de Madrid, 28001 Madrid, Spain
| | - Juan David Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 111321, Colombia
- Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Correspondence: or ; Tel.: +1-(332)-2344161
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Wang Q, Liu L, Zhang S, Wu H, Huang J. A chromosome-level genome assembly and intestinal transcriptome of Trypoxylus dichotomus (Coleoptera: Scarabaeidae) to understand its lignocellulose digestion ability. Gigascience 2022; 11:giac059. [PMID: 35764601 PMCID: PMC9239855 DOI: 10.1093/gigascience/giac059] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 03/30/2022] [Accepted: 05/27/2022] [Indexed: 12/15/2022] Open
Abstract
Lignocellulose, as the key structural component of plant biomass, is a recalcitrant structure, difficult to degrade. The traditional management of plant waste, including landfill and incineration, usually causes serious environmental pollution and health problems. Interestingly, the xylophagous beetle, Trypoxylus dichotomus, can decompose lignocellulosic biomass. However, the genomics around the digestion mechanism of this beetle remain to be elucidated. Here, we assembled the genome of T. dichotomus, showing that the draft genome size of T. dichotomus is 636.27 Mb, with 95.37% scaffolds anchored onto 10 chromosomes. Phylogenetic results indicated that a divergent evolution between the ancestors of T. dichotomus and the closely related scarabaeid species Onthophagus taurus occurred in the early Cretaceous (120 million years ago). Through gene family evolution analysis, we found 67 rapidly evolving gene families, within which there were 2 digestive gene families (encoding Trypsin and Enoyl-(Acyl carrier protein) reductase) that have experienced significant expansion, indicating that they may contribute to the high degradation efficiency of lignocellulose in T. dichotomus. Additionally, events of chromosome breakage and rearrangement were observed by synteny analysis during the evolution of T. dichotomus due to chromosomes 6 and 8 of T. dichotomus being intersected with chromosomes 2 and 10 of Tribolium castaneum, respectively. Furthermore, the comparative transcriptome analyses of larval guts showed that the digestion-related genes were more commonly expressed in the midgut or mushroom residue group than the hindgut or sawdust group. This study reports the well-assembled and annotated genome of T. dichotomus, providing genomic and transcriptomic bases for further understanding the functional and evolutionary mechanisms of lignocellulose digestion in T. dichotomus.
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Affiliation(s)
- Qingyun Wang
- National Joint Local Engineering Laboratory for High-Efficient Preparation of Biopesticide, Zhejiang A&F University, 666 Wusu Street, Lin'an, Hangzhou, Zhejiang 311300, China
| | - Liwei Liu
- National Joint Local Engineering Laboratory for High-Efficient Preparation of Biopesticide, Zhejiang A&F University, 666 Wusu Street, Lin'an, Hangzhou, Zhejiang 311300, China
- Zhejiang Museum of Natural History, No. 6 West Lake Cultural Square, Hangzhou, Zhejiang 310014, China
| | - Sujiong Zhang
- Dapanshan Insect Institute of Zhejiang, Pan'an, Zhejiang 322300, China
| | - Hong Wu
- National Joint Local Engineering Laboratory for High-Efficient Preparation of Biopesticide, Zhejiang A&F University, 666 Wusu Street, Lin'an, Hangzhou, Zhejiang 311300, China
| | - Junhao Huang
- National Joint Local Engineering Laboratory for High-Efficient Preparation of Biopesticide, Zhejiang A&F University, 666 Wusu Street, Lin'an, Hangzhou, Zhejiang 311300, China
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Genome plasticity in Candida albicans: A cutting-edge strategy for evolution, adaptation, and survival. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 99:105256. [PMID: 35231665 DOI: 10.1016/j.meegid.2022.105256] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 09/12/2021] [Accepted: 02/22/2022] [Indexed: 12/15/2022]
Abstract
Candida albicans is the most implicated fungal species that grows as a commensal or opportunistic pathogen in the human host. It is associated with many life-threatening infections, especially in immunocompromised persons. The genome of Candida albicans is very flexible and can withstand a wide assortment of variations in a continuously changing environment. Thus, genome plasticity is central to its adaptation and has long been of considerable interest. C. albicans has a diploid heterozygous genome that is highly dynamic and can display variation from small to large scale chromosomal rearrangement and aneuploidy, which have implications in drug resistance, virulence, and pathogenicity. This review presents an up-to-date overview of recent genomic studies involving C. albicans. It discusses the accumulating evidence that shows how mitotic recombination events, ploidy dynamics, aneuploidy, and loss of heterozygosity (LOH) influence evolution, adaptation, and survival in C. albicans. Understanding the factors that affect the genome is crucial for a proper understanding of species and rapid development and adjustment of therapeutic strategies to mitigate their spread.
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Liu D, Qin Z, Wei M, Kong D, Zheng Q, Bai S, Lin S, Zhang Z, Ma Y. Genome-Wide Analyses of Heat Shock Protein Superfamily Provide New Insights on Adaptation to Sulfide-Rich Environments in Urechis unicinctus (Annelida, Echiura). Int J Mol Sci 2022; 23:ijms23052715. [PMID: 35269857 PMCID: PMC8910992 DOI: 10.3390/ijms23052715] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/25/2022] [Accepted: 02/25/2022] [Indexed: 12/14/2022] Open
Abstract
The intertidal zone is a transitional area of the land-sea continuum, in which physical and chemical properties vary during the tidal cycle and highly toxic sulfides are rich in sediments due to the dynamic regimes. As a typical species thriving in this habitat, Urechis unicinctus presents strong sulfide tolerance and is expected to be a model species for sulfide stress research. Heat shock proteins (HSPs) consist of a large group of highly conserved molecular chaperones, which play important roles in stress responses. In this study, we systematically analyzed the composition and expression of HSPs in U. unicinctus. A total of eighty-six HSP genes from seven families were identified, in which two families, including sHSP and HSP70, showed moderate expansion, and this variation may be related to the benthic habitat of the intertidal zone. Furthermore, expression analysis revealed that almost all the HSP genes in U. unicinctus were significantly induced under sulfide stress, suggesting that they may be involved in sulfide stress response. Weighted gene co-expression network analysis (WGCNA) showed that 12 HSPs, including 5 sHSP and 4 HSP70 family genes, were highly correlated with the sulfide stress response which was distributed in steelblue and green modules. Our data indicate that HSPs, especially sHSP and HSP70 families, may play significant roles in response to sulfide stress in U. unicinctus. This systematic analysis provides valuable information for further understanding of the function of the HSP gene family for sulfide adaptation in U. unicinctus and contributes a better understanding of the species adaptation strategies of marine benthos in the intertidal zone.
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Affiliation(s)
- Danwen Liu
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (D.L.); (Z.Q.); (M.W.); (D.K.); (Q.Z.); (S.B.); (S.L.)
| | - Zhenkui Qin
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (D.L.); (Z.Q.); (M.W.); (D.K.); (Q.Z.); (S.B.); (S.L.)
| | - Maokai Wei
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (D.L.); (Z.Q.); (M.W.); (D.K.); (Q.Z.); (S.B.); (S.L.)
| | - Dexu Kong
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (D.L.); (Z.Q.); (M.W.); (D.K.); (Q.Z.); (S.B.); (S.L.)
| | - Qiaojun Zheng
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (D.L.); (Z.Q.); (M.W.); (D.K.); (Q.Z.); (S.B.); (S.L.)
| | - Shumiao Bai
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (D.L.); (Z.Q.); (M.W.); (D.K.); (Q.Z.); (S.B.); (S.L.)
| | - Siyu Lin
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (D.L.); (Z.Q.); (M.W.); (D.K.); (Q.Z.); (S.B.); (S.L.)
| | - Zhifeng Zhang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (D.L.); (Z.Q.); (M.W.); (D.K.); (Q.Z.); (S.B.); (S.L.)
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya 572000, China
- Correspondence: (Z.Z.); (Y.M.); Tel.: +86-532-82032780 (Y.M.); +86-532-82031647 (Z.Z.)
| | - Yubin Ma
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (D.L.); (Z.Q.); (M.W.); (D.K.); (Q.Z.); (S.B.); (S.L.)
- Correspondence: (Z.Z.); (Y.M.); Tel.: +86-532-82032780 (Y.M.); +86-532-82031647 (Z.Z.)
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Chung D, Kwon YM, Yang Y. Telomere-to-telomere genome assembly of asparaginase-producing Trichoderma simmonsii. BMC Genomics 2021; 22:830. [PMID: 34789157 PMCID: PMC8600724 DOI: 10.1186/s12864-021-08162-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 11/02/2021] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Trichoderma is a genus of fungi in the family Hypocreaceae and includes species known to produce enzymes with commercial use. They are largely found in soil and terrestrial plants. Recently, Trichoderma simmonsii isolated from decaying bark and decorticated wood was newly identified in the Harzianum clade of Trichoderma. Due to a wide range of applications in agriculture and other industries, genomes of at least 12 Trichoderma spp. have been studied. Moreover, antifungal and enzymatic activities have been extensively characterized in Trichoderma spp. However, the genomic information and bioactivities of T. simmonsii from a particular marine-derived isolate remain largely unknown. While we screened for asparaginase-producing fungi, we observed that T. simmonsii GH-Sj1 strain isolated from edible kelp produced asparaginase. In this study, we report a draft genome of T. simmonsii GH-Sj1 using Illumina and Oxford Nanopore technologies. Furthermore, to facilitate biotechnological applications of this species, RNA-sequencing was performed to elucidate the transcriptional profile of T. simmonsii GH-Sj1 in response to asparaginase-rich conditions. RESULTS We generated ~ 14 Gb of sequencing data assembled in a ~ 40 Mb genome. The T. simmonsii GH-Sj1 genome consisted of seven telomere-to-telomere scaffolds with no sequencing gaps, where the N50 length was 6.4 Mb. The total number of protein-coding genes was 13,120, constituting ~ 99% of the genome. The genome harbored 176 tRNAs, which encode a full set of 20 amino acids. In addition, it had an rRNA repeat region consisting of seven repeats of the 18S-ITS1-5.8S-ITS2-26S cluster. The T. simmonsii genome also harbored 7 putative asparaginase-encoding genes with potential medical applications. Using RNA-sequencing analysis, we found that 3 genes among the 7 putative genes were significantly upregulated under asparaginase-rich conditions. CONCLUSIONS The genome and transcriptome of T. simmonsii GH-Sj1 established in the current work represent valuable resources for future comparative studies on fungal genomes and asparaginase production.
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Affiliation(s)
- Dawoon Chung
- National Marine Biodiversity Institute of Korea, Chungchungnam-do, South Korea
| | - Yong Min Kwon
- National Marine Biodiversity Institute of Korea, Chungchungnam-do, South Korea
| | - Youngik Yang
- National Marine Biodiversity Institute of Korea, Chungchungnam-do, South Korea.
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11
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Abstract
Candida albicans is a major human fungal pathogen that encounters varied host environments during infection. In response to environmental cues, C. albicans switches between ovoid yeast and elongated hyphal growth forms, and this morphological plasticity contributes to virulence. Environmental changes that alter the cell's metabolic state could be sensed by sirtuins, which are NAD+-dependent deacetylases. Here, we studied the roles of three sirtuin deacetylases-Sir2, Hst1, and Hst2-in the hyphal growth of C. albicans We made single, double, and triple sirtuin knockout strains and tested their ability to switch from yeast to hyphae. We found that true hypha formation was significantly reduced by the deletion of SIR2 but not HST1 or HST2 Moreover, the expression of hypha-specific genes HWP1, ALS3, and ECE1 decreased in the sir2Δ/Δ mutant compared to the wild type. This regulation of hypha formation was likely dependent on the deacetylase activity of Sir2, as a similar defect in hypha formation was observed when an asparagine known to be required for deacetylation was mutated. Finally, we found that Sir2 and Hst1 were localized to the nucleus, with Sir2 specifically focused in the nucleolus. This nuclear localization suggests a role for Sir2 and Hst1 in regulating gene expression. In contrast, Hst2 was localized to the cytoplasm. In conclusion, our results suggest that Sir2 plays a critical and nonredundant role in hyphal growth of C. albicans IMPORTANCE Candida albicans is one of the most common causes of hospital-acquired systemic fungal infections in the United States. It can switch between ovoid yeast and elongated hyphal growth forms in response to environmental cues. This morphological transition is essential for its survival in the host. Thus, identifying regulators involved in this process can lead to new therapies. In this study, we examined the contribution of three regulators called sirtuins (Sir2, Hst1, and Hst2) to the yeast-to-hypha transition of C. albicans We found that loss of Sir2 but not Hst1 or Hst2 hampered hypha formation. Moreover, the defect was caused by the loss of the catalytic activity of Sir2. Our study may lay the groundwork for discovering novel targets for antifungal therapies.
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12
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Mamouei Z, Singh S, Lemire B, Gu Y, Alqarihi A, Nabeela S, Li D, Ibrahim A, Uppuluri P. An evolutionarily diverged mitochondrial protein controls biofilm growth and virulence in Candida albicans. PLoS Biol 2021; 19:e3000957. [PMID: 33720927 PMCID: PMC8007014 DOI: 10.1371/journal.pbio.3000957] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 03/29/2021] [Accepted: 01/29/2021] [Indexed: 11/19/2022] Open
Abstract
A forward genetic screening approach identified orf19.2500 as a gene controlling Candida albicans biofilm dispersal and biofilm detachment. Three-dimensional (3D) protein modeling and bioinformatics revealed that orf19.2500 is a conserved mitochondrial protein, structurally similar to, but functionally diverged from, the squalene/phytoene synthases family. The C. albicans orf19.2500 is distinguished by 3 evolutionarily acquired stretches of amino acid inserts, absent from all other eukaryotes except a small number of ascomycete fungi. Biochemical assays showed that orf19.2500 is required for the assembly and activity of the NADH ubiquinone oxidoreductase Complex I (CI) of the respiratory electron transport chain (ETC) and was thereby named NDU1. NDU1 is essential for respiration and growth on alternative carbon sources, important for immune evasion, required for virulence in a mouse model of hematogenously disseminated candidiasis, and for potentiating resistance to antifungal drugs. Our study is the first report on a protein that sets the Candida-like fungi phylogenetically apart from all other eukaryotes, based solely on evolutionary "gain" of new amino acid inserts that are also the functional hub of the protein.
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Affiliation(s)
- Zeinab Mamouei
- David Geffen School of Medicine, University of California (UCLA), Los Angeles, California, United States of America
| | - Shakti Singh
- Division of Infectious Disease, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California, United States of America
| | - Bernard Lemire
- Department of Biochemistry, University of Alberta, Alberta, Canada
| | - Yiyou Gu
- Division of Infectious Disease, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California, United States of America
| | - Abdullah Alqarihi
- Division of Infectious Disease, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California, United States of America
| | - Sunna Nabeela
- Division of Infectious Disease, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California, United States of America
| | - Dongmei Li
- Department of Microbiology and Immunology, Georgetown University Medical Center, Washington, DC, United States of America
| | - Ashraf Ibrahim
- David Geffen School of Medicine, University of California (UCLA), Los Angeles, California, United States of America
- Division of Infectious Disease, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California, United States of America
| | - Priya Uppuluri
- David Geffen School of Medicine, University of California (UCLA), Los Angeles, California, United States of America
- Division of Infectious Disease, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California, United States of America
- * E-mail:
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13
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Mengarelli DA, Zanor MI. Genome-wide characterization and analysis of the CCT motif family genes in soybean (Glycine max). PLANTA 2021; 253:15. [PMID: 33392793 DOI: 10.1007/s00425-020-03537-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 12/11/2020] [Indexed: 05/27/2023]
Abstract
MAIN CONCLUSION Soybean possesses 19 CMF genes which mainly arose from duplication events. Their features and motifs are highly conserved but transcriptional data indicated functional diversity in metabolism and stress responses. CCT [for CONSTANS, CONSTANS-like (CO-like), and timing of CAB expression1 (TOC1)] domain-containing genes play important roles in regulating flowering, plant growth, and grain yield and are also involved in stress responses. The CMF (CCT motif family) genes, included in the CCT family, contain a single CCT domain as the only identifiable domain in their predicted protein sequence and are interesting targets for breeding programs. In this study, we identified 19 putative GmCMF genes, based on the latest soybean (Glycine max) genome annotation. The predicted GmCMF proteins were characterized based on conserved structural features, and a phylogenetic tree was constructed including all CMF proteins from rice and Arabidopsis as representative examples of the monocotyledonous (monocot) and dicotyledonous (dicot) plants, respectively. High similarities in the conserved motifs of the protein sequences and the gene structures were found. In addition, by analyzing the CMF gene family in soybean, we identified seven pairs of genes that originated from segmental chromosomal duplication events attributable to the most recent whole-genome duplication (WGD) event in the Glycine lineage. Expression analysis of GmCMF genes in various tissues and after specific treatments demonstrated tissue and stress-response specific differential expression. Gene expression analysis was complemented by the identification of putative cis-elements present in the promoter regions of the genes through a bioinformatics approach, using the existing soybean reference genome sequence and gene models. Co-functional networks inferred from distinct types of genomics data-including microarrays and RNA-seq samples from soybean-revealed that GmCMF genes might play crucial roles in metabolism and transport processes. The results of this study, the first systematic analysis of the soybean CCT gene family, can serve as a strong foundation for further elucidation of their physiological functions and biological roles.
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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] [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.
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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.
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15
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Huang Y, Huang X, Zhou X, Wang J, Zhang R, Ma F, Wang K, Zhang Z, Dai X, Cao X, Zhang C, Han K, Ren Q. Immune activation by a multigene family of lectins with variable tandem repeats in oriental river prawn ( Macrobrachium nipponense). Open Biol 2020; 10:200141. [PMID: 32931720 PMCID: PMC7536079 DOI: 10.1098/rsob.200141] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Genomic regions with repeated sequences are unstable and prone to rapid DNA diversification. However, the role of tandem repeats within the coding region is not fully characterized. Here, we have identified a new hypervariable C-type lectin gene family with different numbers of tandem repeats (Rlecs; R means repeat) in oriental river prawn (Macrobrachium nipponense). Two types of repeat units (33 or 30 bp) are identified in the second exon, and the number of repeat units vary from 1 to 9. Rlecs can be classified into 15 types through phylogenetic analysis. The amino acid sequences in the same type of Rlec are highly conservative outside the repeat regions. The main differences among the Rlec types are evident in exon 5. A variable number of tandem repeats in Rlecs may be produced by slip mispairing during gene replication. Alternative splicing contributes to the multiplicity of forms in this lectin gene family, and different types of Rlecs vary in terms of tissue distribution, expression quantity and response to bacterial challenge. These variations suggest that Rlecs have functional diversity. The results of experiments on sugar binding, microbial inhibition and clearance, regulation of antimicrobial peptide gene expression and prophenoloxidase activation indicate that the function of Rlecs with the motif of YRSKDD in innate immunity is enhanced when the number of tandem repeats increases. Our results suggest that Rlecs undergo gene expansion through gene duplication and alternative splicing, which ultimately leads to functional diversity.
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Affiliation(s)
- Ying Huang
- College of Marine Science and Engineering, Nanjing Normal University, 1 Wenyuan Road, Nanjing, Jiangsu 210023, People's Republic of China.,College of Oceanography, Hohai University, 1 Xikang Road, Nanjing, Jiangsu 210098, People's Republic of China
| | - Xin Huang
- College of Marine Science and Engineering, Nanjing Normal University, 1 Wenyuan Road, Nanjing, Jiangsu 210023, People's Republic of China
| | - Xuming Zhou
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Jialin Wang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, People's Republic of China
| | - Ruidong Zhang
- College of Marine Science and Engineering, Nanjing Normal University, 1 Wenyuan Road, Nanjing, Jiangsu 210023, People's Republic of China
| | - Futong Ma
- College of Marine Science and Engineering, Nanjing Normal University, 1 Wenyuan Road, Nanjing, Jiangsu 210023, People's Republic of China
| | - Kaiqiang Wang
- College of Marine Science and Engineering, Nanjing Normal University, 1 Wenyuan Road, Nanjing, Jiangsu 210023, People's Republic of China
| | - Zhuoxing Zhang
- College of Marine Science and Engineering, Nanjing Normal University, 1 Wenyuan Road, Nanjing, Jiangsu 210023, People's Republic of China
| | - Xiaoling Dai
- College of Marine Science and Engineering, Nanjing Normal University, 1 Wenyuan Road, Nanjing, Jiangsu 210023, People's Republic of China
| | - Xueying Cao
- College of Marine Science and Engineering, Nanjing Normal University, 1 Wenyuan Road, Nanjing, Jiangsu 210023, People's Republic of China
| | - Chao Zhang
- College of Marine Science and Engineering, Nanjing Normal University, 1 Wenyuan Road, Nanjing, Jiangsu 210023, People's Republic of China
| | - Keke Han
- College of Marine Science and Engineering, Nanjing Normal University, 1 Wenyuan Road, Nanjing, Jiangsu 210023, People's Republic of China
| | - Qian Ren
- College of Marine Science and Engineering, Nanjing Normal University, 1 Wenyuan Road, Nanjing, Jiangsu 210023, People's Republic of China.,Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, Jiangsu 222005, People's Republic of China
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16
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Mba IE, Nweze EI. Mechanism of Candida pathogenesis: revisiting the vital drivers. Eur J Clin Microbiol Infect Dis 2020; 39:1797-1819. [PMID: 32372128 DOI: 10.1007/s10096-020-03912-w] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 04/17/2020] [Indexed: 12/14/2022]
Abstract
Candida is the most implicated fungal pathogen in the clinical setting. Several factors play important roles in the pathogenesis of Candida spp. Multiple transcriptional circuits, morphological and phenotypic switching, biofilm formation, tissue damaging extracellular hydrolytic enzymes, metabolic flexibility, genome plasticity, adaptation to environmental pH fluctuation, robust nutrient acquisition system, adherence and invasions (mediated by adhesins and invasins), heat shock proteins (HSPs), cytolytic proteins, escape from phagocytosis, evasion from host immune system, synergistic coaggregation with resident microbiota, resistance to antifungal agents, and the ability to efficiently respond to multiple stresses are some of the major pathogenic determinants of Candida species. The existence of multiple connections, in addition to the interactions and associations among all of these factors, are distinctive features that play important roles in the establishment of Candida infections. This review describes all the underlying factors and mechanisms involved in Candida pathogenesis by evaluating pathogenic determinants of Candida species. It reinforces the already available pool of data on the pathogenesis of Candida species by providing a clear and simplified understanding of the most important factors implicated in the pathogenesis of Candida species. The Candida pathogenesis network, an illustration linking all the major determinants of Candida pathogenesis, is also presented. Taken together, they will further improve our current understanding of how these factors modulate virulence and consequent infection(s). Development of new antifungal drugs and better therapeutic approaches to candidiasis can be achieved in the near future with continuing progress in the understanding of the mechanisms of Candida pathogenesis.
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17
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Henninger E, Teixeira MT. Telomere-driven mutational processes in yeast. Curr Opin Genet Dev 2020; 60:99-106. [DOI: 10.1016/j.gde.2020.02.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 02/13/2020] [Accepted: 02/14/2020] [Indexed: 12/18/2022]
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18
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Dunn MJ, Anderson MZ. To Repeat or Not to Repeat: Repetitive Sequences Regulate Genome Stability in Candida albicans. Genes (Basel) 2019; 10:genes10110866. [PMID: 31671659 PMCID: PMC6896093 DOI: 10.3390/genes10110866] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 10/15/2019] [Accepted: 10/23/2019] [Indexed: 12/18/2022] Open
Abstract
Genome instability often leads to cell death but can also give rise to innovative genotypic and phenotypic variation through mutation and structural rearrangements. Repetitive sequences and chromatin architecture in particular are critical modulators of recombination and mutability. In Candida albicans, four major classes of repeats exist in the genome: telomeres, subtelomeres, the major repeat sequence (MRS), and the ribosomal DNA (rDNA) locus. Characterization of these loci has revealed how their structure contributes to recombination and either promotes or restricts sequence evolution. The mechanisms of recombination that give rise to genome instability are known for some of these regions, whereas others are generally unexplored. More recent work has revealed additional repetitive elements, including expanded gene families and centromeric repeats that facilitate recombination and genetic innovation. Together, the repeats facilitate C. albicans evolution through construction of novel genotypes that underlie C. albicans adaptive potential and promote persistence across its human host.
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Affiliation(s)
- Matthew J. Dunn
- 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
- Correspondence: ; Tel.: +614-247-0058
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19
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Todd RT, Wikoff TD, Forche A, Selmecki A. Genome plasticity in Candida albicans is driven by long repeat sequences. eLife 2019; 8:45954. [PMID: 31172944 PMCID: PMC6591007 DOI: 10.7554/elife.45954] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Accepted: 06/07/2019] [Indexed: 11/13/2022] Open
Abstract
Genome rearrangements resulting in copy number variation (CNV) and loss of heterozygosity (LOH) are frequently observed during the somatic evolution of cancer and promote rapid adaptation of fungi to novel environments. In the human fungal pathogen Candida albicans, CNV and LOH confer increased virulence and antifungal drug resistance, yet the mechanisms driving these rearrangements are not completely understood. Here, we unveil an extensive array of long repeat sequences (65-6499 bp) that are associated with CNV, LOH, and chromosomal inversions. Many of these long repeat sequences are uncharacterized and encompass one or more coding sequences that are actively transcribed. Repeats associated with genome rearrangements are predominantly inverted and separated by up to ~1.6 Mb, an extraordinary distance for homology-based DNA repair/recombination in yeast. These repeat sequences are a significant source of genome plasticity across diverse strain backgrounds including clinical, environmental, and experimentally evolved isolates, and represent previously uncharacterized variation in the reference genome.
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Affiliation(s)
- Robert T Todd
- Creighton University Medical School, Omaha, United States
| | - Tyler D Wikoff
- Creighton University Medical School, Omaha, United States
| | | | - Anna Selmecki
- Creighton University Medical School, Omaha, United States
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20
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Fillinger RJ, Anderson MZ. Seasons of change: Mechanisms of genome evolution in human fungal pathogens. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 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] [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.
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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.
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21
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Liu B, Hu J, Zhang J. Evolutionary Divergence of Duplicated Hsf Genes in Populus. Cells 2019; 8:cells8050438. [PMID: 31083365 PMCID: PMC6563006 DOI: 10.3390/cells8050438] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 05/04/2019] [Accepted: 05/07/2019] [Indexed: 01/07/2023] Open
Abstract
Heat shock transcription factors (Hsfs), which function as the activator of heat shock proteins (Hsps), play multiple roles in response to environmental stress and the development of plants. The Hsf family had experienced gene expansion via whole-genome duplication from a single cell algae to higher plants. However, how the Hsf gene family went through evolutionary divergence after genome duplication is unknown. As a model wood species, Populus trichocarpa is widely distributed in North America with various ecological and climatic environments. In this study, we used P. trichocarpa as materials and identified the expression divergence of the PtHsf gene family in developmental processes, such as dormant bud formation and opening, catkins development, and in response to environments. Through the co-expression network, we further discovered the divergent co-expressed genes that related to the functional divergence of PtHsfs. Then, we studied the alternative splicing events, single nucleotide polymorphism distribution and tertiary structures of members of the PtHsf gene family. In addition to expression divergence, we uncovered the evolutionary divergence in the protein level which may be important to new function formations and for survival in changing environments. This study comprehensively analyzed the evolutionary divergence of a member of the PtHsf gene family after genome duplication, paving the way for further gene function analysis and genetic engineering.
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Affiliation(s)
- Bobin Liu
- College of Forestry, Fujian Colleges and Universities Engineering Research Institute of Conservation & Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Jianjun Hu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China.
| | - Jin Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China.
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
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22
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Legrand M, Jaitly P, Feri A, d'Enfert C, Sanyal K. Candida albicans: An Emerging Yeast Model to Study Eukaryotic Genome Plasticity. Trends Genet 2019; 35:292-307. [PMID: 30826131 DOI: 10.1016/j.tig.2019.01.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 01/25/2019] [Accepted: 01/25/2019] [Indexed: 01/07/2023]
Abstract
Saccharomyces cerevisiae and Schizosaccharomyces pombe have served as uncontested unicellular model organisms, as major discoveries made in the field of genome biology using yeast genetics have proved to be relevant from yeast to humans. The yeast Candida albicans has attracted much attention because of its ability to switch between a harmless commensal and a dreaded human pathogen. C. albicans bears unique features regarding its life cycle, genome structure, and dynamics, and their links to cell biology and adaptation to environmental challenges. Examples include a unique reproduction cycle with haploid, diploid, and tetraploid forms; a distinctive organisation of chromosome hallmarks; a highly dynamic genome, with extensive karyotypic variations, including aneuploidies, isochromosome formation, and loss-of-heterozygosity; and distinctive links between the response to DNA alterations and cell morphology. These features have made C. albicans emerge as a new and attractive unicellular model to study genome biology and dynamics in eukaryotes.
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Affiliation(s)
- Mélanie Legrand
- Fungal Biology and Pathogenicity Unit, Department of Mycology, Institut Pasteur, INRA, Paris, France
| | - Priya Jaitly
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | - Adeline Feri
- Fungal Biology and Pathogenicity Unit, Department of Mycology, Institut Pasteur, INRA, Paris, France; Université Paris Diderot, Sorbonne Paris Cité, Cellule Pasteur, Paris, France; Current address: Pathoquest, BioPark, 11 rue Watt, 75013 Paris, France
| | - Christophe d'Enfert
- Fungal Biology and Pathogenicity Unit, Department of Mycology, Institut Pasteur, INRA, Paris, France.
| | - Kaustuv Sanyal
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India.
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23
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Role of Mediator in virulence and antifungal drug resistance in pathogenic fungi. Curr Genet 2019; 65:621-630. [DOI: 10.1007/s00294-019-00932-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 01/04/2019] [Accepted: 01/05/2019] [Indexed: 10/27/2022]
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Flanagan PR, Fletcher J, Boyle H, Sulea R, Moran GP, Sullivan DJ. Expansion of the TLO gene family enhances the virulence of Candida species. PLoS One 2018; 13:e0200852. [PMID: 30028853 PMCID: PMC6054389 DOI: 10.1371/journal.pone.0200852] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 06/11/2018] [Indexed: 12/12/2022] Open
Abstract
The TLO genes are a family of subtelomeric ORFs in the fungal pathogens Candida albicans and C. dubliniensis encoding a subunit of the Mediator complex homologous to Med2. The more virulent pathogen C. albicans has 15 copies of the gene whereas the less pathogenic species C. dubliniensis has only two. To investigate if expansion of the TLO repertoire in C. dubliniensis has an effect on phenotype and virulence we expressed three representative C. albicans TLO genes (TLOβ2, TLOγ11 and TLOα12) in a wild type C. dubliniensis background, under the control of either their native or the ACT1 promoter. Expression of TLOβ2 resulted in a hyperfilamentous phenotype, while overexpression of TLOγ11 and TLOα12 resulted in enhanced resistance to oxidative stress. Expression of all three TLO genes from the ACT1 promoter resulted in increased virulence in the Galleria infection model. In order to further investigate if individual TLO genes exhibit differences in function we expressed six representative C. albicans TLO genes in a C. dubliniensis Δtlo1/Δtlo2 double mutant. Differences were observed in the ability of the expressed CaTLOs to complement the various phenotypes of the mutant. All TLO genes with the exception of TLOγ7 could restore filamentation, however only TLOα9, γ11 and α12 could restore chlamydospore formation. Differences in the ability of CaTLO genes to restore growth in the presence of H2O2, calcofluor white, Congo red and at 42°C were observed. Only TLOα3 restored wild-type levels of virulence in the Galleria infection model. These data show that expansion of the TLO gene family in C. dubliniensis results in gain of function and that there is functional diversity amongst members of the gene family. We propose that this expansion of the TLO family contributes to the success of C. albicans as a commensal and opportunistic pathogen.
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Affiliation(s)
- Peter R. Flanagan
- Microbiology Research Unit, Division of Oral Biosciences, Dublin Dental University Hospital, Dublin, Ireland
- University of Dublin, Trinity College Dublin, Dublin, Ireland
| | - Jessica Fletcher
- Microbiology Research Unit, Division of Oral Biosciences, Dublin Dental University Hospital, Dublin, Ireland
- University of Dublin, Trinity College Dublin, Dublin, Ireland
| | - Hannah Boyle
- Microbiology Research Unit, Division of Oral Biosciences, Dublin Dental University Hospital, Dublin, Ireland
- University of Dublin, Trinity College Dublin, Dublin, Ireland
| | - Razvan Sulea
- Microbiology Research Unit, Division of Oral Biosciences, Dublin Dental University Hospital, Dublin, Ireland
- University of Dublin, Trinity College Dublin, Dublin, Ireland
| | - Gary P. Moran
- Microbiology Research Unit, Division of Oral Biosciences, Dublin Dental University Hospital, Dublin, Ireland
- University of Dublin, Trinity College Dublin, Dublin, Ireland
- * E-mail: (DJS); (GPM)
| | - Derek J. Sullivan
- Microbiology Research Unit, Division of Oral Biosciences, Dublin Dental University Hospital, Dublin, Ireland
- * E-mail: (DJS); (GPM)
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