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Kramara J, Kim MJ, Ollinger TL, Ristow LC, Wakade RS, Zarnowski R, Wellington M, Andes DR, Mitchell AG, Krysan DJ. Systematic analysis of the Candida albicans kinome reveals environmentally contingent protein kinase-mediated regulation of filamentation and biofilm formation in vitro and in vivo. mBio 2024; 15:e0124924. [PMID: 38949302 PMCID: PMC11323567 DOI: 10.1128/mbio.01249-24] [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: 04/25/2024] [Accepted: 05/20/2024] [Indexed: 07/02/2024] Open
Abstract
Protein kinases are critical regulatory proteins in both prokaryotes and eukaryotes. Accordingly, protein kinases represent a common drug target for a wide range of human diseases. Therefore, understanding protein kinase function in human pathogens such as the fungus Candida albicans is likely to extend our knowledge of its pathobiology and identify new potential therapies. To facilitate the study of C. albicans protein kinases, we constructed a library of 99 non-essential protein kinase homozygous deletion mutants marked with barcodes in the widely used SN genetic background. Here, we describe the construction of this library and the characterization of the competitive fitness of the protein kinase mutants under 11 different growth and stress conditions. We also screened the library for protein kinase mutants with altered filamentation and biofilm formation, two critical virulence traits of C. albicans. An extensive network of protein kinases governs these virulence traits in a manner highly dependent on the specific environmental conditions. Studies on specific protein kinases revealed that (i) the cell wall integrity MAPK pathway plays a condition-dependent role in filament initiation and elongation; (ii) the hyper-osmolar glycerol MAPK pathway is required for both filamentation and biofilm formation, particularly in the setting of in vivo catheter infection; and (iii) Sok1 is dispensable for filamentation in hypoxic environments at the basal level of a biofilm but is required for filamentation in normoxia. In addition to providing a new genetic resource for the community, these observations emphasize the environmentally contingent function of C. albicans protein kinases.IMPORTANCECandida albicans is one of the most common causes of fungal disease in humans for which new therapies are needed. Protein kinases are key regulatory proteins and are increasingly targeted by drugs for the treatment of a wide range of diseases. Understanding protein kinase function in C. albicans pathogenesis may facilitate the development of new antifungal drugs. Here, we describe a new library of 99 protein kinase deletion mutants to facilitate the study of protein kinases. Furthermore, we show that the function of protein kinases in two virulence-related processes, filamentation and biofilm formation, is dependent on the specific environmental conditions.
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Affiliation(s)
- Juraj Kramara
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Min-Ju Kim
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - Tomye L. Ollinger
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Laura C. Ristow
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Rohan S. Wakade
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Robert Zarnowski
- Department of Medicine, Section of Infectious Disease, University of Wisconsin, Madison, Wisconsin, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, Wisconsin, USA
| | - Melanie Wellington
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - David R. Andes
- Department of Medicine, Section of Infectious Disease, University of Wisconsin, Madison, Wisconsin, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, Wisconsin, USA
| | - Aaron G. Mitchell
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - Damian J. Krysan
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
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Abstract
Candida albicans is an important etiological agent of superficial and life-threatening infections in individuals with compromised immune systems. To date, we know of several overlapping genetic networks that govern virulence attributes in this fungal pathogen. Classical use of deletion mutants has led to the discovery of numerous virulence factors over the years, and genome-wide functional analysis has propelled gene discovery at an even faster pace. Indeed, a number of recent studies using large-scale genetic screens followed by genome-wide functional analysis has allowed for the unbiased discovery of many new genes involved in C. albicans biology. Here we share our perspectives on the role of these studies in analyzing fundamental aspects of C. albicans virulence properties.
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Affiliation(s)
- Thabiso E Motaung
- a Agricultural Research Council - Small Grain Institute , Bethlehem , South Africa
| | - Ruan Ells
- b University of the Free Sate , Bloemfontein , South Africa
| | | | | | - Toi J Tsilo
- a Agricultural Research Council - Small Grain Institute , Bethlehem , South Africa.,c Department of Life and Consumer Sciences , University of South Africa , Pretoria , South Africa
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A model system for mitochondrial biogenesis reveals evolutionary rewiring of protein import and membrane assembly pathways. Proc Natl Acad Sci U S A 2012; 109:E3358-66. [PMID: 23151513 DOI: 10.1073/pnas.1206345109] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The controlled biogenesis of mitochondria is a key cellular system coordinated with the cell division cycle, and major efforts in systems biology currently are directed toward understanding of the control points at which this coordination is achieved. Here we present insights into the function, evolution, and regulation of mitochondrial biogenesis through the study of the protein import machinery in the human fungal pathogen, Candida albicans. Features that distinguish C. albicans from baker's yeast (Saccharomyces cerevisiae) include the stringency of metabolic control at the level of oxygen consumption, the potential for ATP exchange through the porin in the outer membrane, and components and domains in the sorting and assembling machinery complex, a molecular machine that drives the assembly of proteins in the outer mitochondrial membrane. Analysis of targeting sequences and assays of mitochondrial protein import show that components of the electron transport chain are imported by distinct pathways in C. albicans and S. cerevisiae, representing an evolutionary rewiring of mitochondrial import pathways. We suggest that studies using this pathogen as a model system for mitochondrial biogenesis will greatly enhance our knowledge of how mitochondria are made and controlled through the course of the cell-division cycle.
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Kabir MA, Hussain MA, Ahmad Z. Candida albicans: A Model Organism for Studying Fungal Pathogens. ISRN MICROBIOLOGY 2012; 2012:538694. [PMID: 23762753 PMCID: PMC3671685 DOI: 10.5402/2012/538694] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2012] [Accepted: 08/30/2012] [Indexed: 01/12/2023]
Abstract
Candida albicans is an opportunistic human fungal pathogen that causes candidiasis. As healthcare has been improved worldwide, the number of immunocompromised patients has been increased to a greater extent and they are highly susceptible to various pathogenic microbes and C. albicans has been prominent among the fungal pathogens. The complete genome sequence of this pathogen is now available and has been extremely useful for the identification of repertoire of genes present in this pathogen. The major challenge is now to assign the functions to these genes of which 13% are specific to C. albicans. Due to its close relationship with yeast Saccharomyces cerevisiae, an edge over other fungal pathogens because most of the technologies can be directly transferred to C. albicans from S. cerevisiae and it is amenable to mutation, gene disruption, and transformation. The last two decades have witnessed enormous amount of research activities on this pathogen that leads to the understanding of host-parasite interaction, infections, and disease propagation. Clearly, C. albicans has emerged as a model organism for studying fungal pathogens along with other two fungi Aspergillus fumigatus and Cryptococcus neoformans. Understanding its complete life style of C. albicans will undoubtedly be useful for developing potential antifungal drugs and tackling Candida infections. This will also shed light on the functioning of other fungal pathogens.
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Affiliation(s)
- M Anaul Kabir
- Molecular Genetics Laboratory, School of Biotechnology, National Institute of Technology Calicut, Calicut 673601, Kerala, India
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5
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Bharucha N, Chabrier-Roselló Y, Xu T, Johnson C, Sobczynski S, Song Q, Dobry CJ, Eckwahl MJ, Anderson CP, Benjamin AJ, Kumar A, Krysan DJ. A large-scale complex haploinsufficiency-based genetic interaction screen in Candida albicans: analysis of the RAM network during morphogenesis. PLoS Genet 2011; 7:e1002058. [PMID: 22103005 PMCID: PMC3084211 DOI: 10.1371/journal.pgen.1002058] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The morphogenetic transition between yeast and filamentous forms of the human
fungal pathogen Candida albicans is regulated by a variety of
signaling pathways. How these pathways interact to orchestrate morphogenesis,
however, has not been as well characterized. To address this question and to
identify genes that interact with the Regulation of Ace2 and Morphogenesis (RAM)
pathway during filamentation, we report the first large-scale genetic
interaction screen in C. albicans. Our strategy for this screen
was based on the concept of complex haploinsufficiency (CHI). A heterozygous
mutant of CBK1
(cbk1Δ/CBK1), a key RAM pathway
protein kinase, was subjected to transposon-mediated, insertional mutagenesis.
The resulting double heterozygous mutants (6,528 independent strains) were
screened for decreased filamentation on Spider Medium (SM). From the 441 mutants
showing altered filamentation, 139 transposon insertion sites were sequenced,
yielding 41 unique CBK1-interacting genes. This gene set was
enriched in transcriptional targets of Ace2 and, strikingly, the cAMP-dependent
protein kinase A (PKA) pathway, suggesting an interaction between these two
pathways. Further analysis indicates that the RAM and PKA pathways co-regulate a
common set of genes during morphogenesis and that hyper-activation of the PKA
pathway may compensate for loss of RAM pathway function. Our data also indicate
that the PKA–regulated transcription factor Efg1 primarily localizes to
yeast phase cells while the RAM–pathway regulated transcription factor
Ace2 localizes to daughter nuclei of filamentous cells, suggesting that Efg1 and
Ace2 regulate a common set of genes at separate stages of morphogenesis. Taken
together, our observations indicate that CHI–based screening is a useful
approach to genetic interaction analysis in C. albicans and
support a model in which these two pathways regulate a common set of genes at
different stages of filamentation. Candida albicans is the most common cause of fungal infections
in humans. As a diploid yeast without a classical sexual cycle, many genetic
approaches developed for large-scale genetic interaction studies in the model
yeast Saccharomyces cerevisiae cannot be applied to C.
albicans. Genetic interaction studies have proven to be powerful
genetic tools for the analysis of complex biological processes. Here, we
demonstrate that libraries of C. albicans strains containing
heterozygous mutations in two different genes can be generated and used to study
genetic interactions in C. albicans on a large scale. Double
heterozygous mutants that show more severe phenotypes than strains with single
heterozygous mutations are indicative of genetic interactions through a
phenomenon referred to as complex haploinsufficiency (CHI). We applied this
approach to the study of the RAM (Regulation of Ace2 and Morphogenesis)
signaling network during the morphogenetic transition of C.
albicans from yeast to filamentous growth. Among the genes that
interacted with CBK1, the key signaling kinase of the RAM
pathway, were transcriptional targets of the RAM pathway and the protein kinase
A pathway. Further analysis supports a model in which these two pathways
co-regulate a common set of genes at different stages of filamentation.
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Affiliation(s)
- Nike Bharucha
- Department of Molecular, Cellular, and
Developmental Biology, University of Michigan, Ann Arbor, Michigan, United
States of America
| | - Yeissa Chabrier-Roselló
- Department of Pediatrics, University of
Rochester School of Medicine and Dentistry, Rochester, New York, United States
of America
| | - Tao Xu
- Department of Molecular, Cellular, and
Developmental Biology, University of Michigan, Ann Arbor, Michigan, United
States of America
| | - Cole Johnson
- Department of Molecular, Cellular, and
Developmental Biology, University of Michigan, Ann Arbor, Michigan, United
States of America
| | - Sarah Sobczynski
- Department of Microbiology/Immunology,
University of Rochester School of Medicine and Dentistry, Rochester, New York,
United States of America
| | - Qingxuan Song
- Department of Molecular, Cellular, and
Developmental Biology, University of Michigan, Ann Arbor, Michigan, United
States of America
| | - Craig J. Dobry
- Department of Molecular, Cellular, and
Developmental Biology, University of Michigan, Ann Arbor, Michigan, United
States of America
| | - Matthew J. Eckwahl
- Department of Molecular, Cellular, and
Developmental Biology, University of Michigan, Ann Arbor, Michigan, United
States of America
| | - Christopher P. Anderson
- Department of Molecular, Cellular, and
Developmental Biology, University of Michigan, Ann Arbor, Michigan, United
States of America
| | - Andrew J. Benjamin
- Department of Molecular, Cellular, and
Developmental Biology, University of Michigan, Ann Arbor, Michigan, United
States of America
| | - Anuj Kumar
- Department of Molecular, Cellular, and
Developmental Biology, University of Michigan, Ann Arbor, Michigan, United
States of America
- * E-mail: (DJK); (AK)
| | - Damian J. Krysan
- Department of Pediatrics, University of
Rochester School of Medicine and Dentistry, Rochester, New York, United States
of America
- Department of Microbiology/Immunology,
University of Rochester School of Medicine and Dentistry, Rochester, New York,
United States of America
- * E-mail: (DJK); (AK)
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Antifungal resistance and new strategies to control fungal infections. Int J Microbiol 2011; 2012:713687. [PMID: 22187560 PMCID: PMC3236459 DOI: 10.1155/2012/713687] [Citation(s) in RCA: 262] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Accepted: 09/06/2011] [Indexed: 11/28/2022] Open
Abstract
Despite improvement of antifungal therapies over the last 30 years, the phenomenon of antifungal resistance is still of major concern in clinical practice. In the last 10 years the molecular mechanisms underlying this phenomenon were extensively unraveled. In this paper, after a brief overview of currently available antifungals, molecular mechanisms of antifungal resistance will be detailed. It appears that major mechanisms of resistance are essential due to the deregulation of antifungal resistance effector genes. This deregulation is a consequence of point mutations occurring in transcriptional regulators of these effector genes. Resistance can also follow the emergence of point mutations directly in the genes coding antifungal targets. In addition we further describe new strategies currently undertaken to discover alternative therapy targets and antifungals. Identification of new antifungals is essentially achieved by the screening of natural or synthetic chemical compound collections. Discovery of new putative antifungal targets is performed through genome-wide approaches for a better understanding of the human pathogenic fungi biology.
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The quorum-sensing molecules farnesol/homoserine lactone and dodecanol operate via distinct modes of action in Candida albicans. EUKARYOTIC CELL 2011; 10:1034-42. [PMID: 21666074 DOI: 10.1128/ec.05060-11] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Living as a commensal, Candida albicans must adapt and respond to environmental cues generated by the mammalian host and by microbes comprising the natural flora. These signals have opposing effects on C. albicans, with host cues promoting the yeast-to-hyphal transition and bacteria-derived quorum-sensing molecules inhibiting hyphal development. Hyphal development is regulated through modulation of the cyclic AMP (cAMP)/protein kinase A (PKA) signaling pathway, and it has been postulated that quorum-sensing molecules can affect filamentation by inhibiting the cAMP pathway. Here, we show that both farnesol and 3-oxo-C(12)-homoserine lactone, a quorum-sensing molecule secreted by Pseudomonas aeruginosa, block hyphal development by affecting cAMP signaling; they both directly inhibited the activity of the Candida adenylyl cyclase, Cyr1p. In contrast, the 12-carbon alcohol dodecanol appeared to modulate hyphal development and the cAMP signaling pathway without directly affecting the activity of Cyr1p. Instead, we show that dodecanol exerted its effects through a mechanism involving the C. albicans hyphal repressor, Sfl1p. Deletion of SFL1 did not affect the response to farnesol but did interfere with the response to dodecanol. Therefore, quorum sensing in C. albicans is mediated via multiple mechanisms of action. Interestingly, our experiments raise the possibility that the Burkholderia cenocepacia diffusible signal factor, BDSF, also mediates its effects via Sfl1p, suggesting that dodecanol's mode of action, but not farnesol or 3-oxo-C(12)-homoserine lactone, may be used by other quorum-sensing molecules.
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Yuan X, Mitchell BM, Hua X, Davis DA, Wilhelmus KR. The RIM101 signal transduction pathway regulates Candida albicans virulence during experimental keratomycosis. Invest Ophthalmol Vis Sci 2010; 51:4668-76. [PMID: 20375342 DOI: 10.1167/iovs.09-4726] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
PURPOSE To examine the role of the fungal RIM101 signal transduction pathway in the pathogenesis of Candida albicans keratitis. METHODS C. albicans wild-type strain SC5314, prototrophic mutant control DAY185, and homozygous fungal mutants for the rim8, rim13, rim20, rim101, and phr1 genes were evaluated in vitro using proliferation and filamentation assays. Scarified corneas of BALB/c and C57BL/6J mice were topically inoculated and observed daily for keratitis severity. Corneal adaptation and pathogenicity were assessed ex vivo by maintaining infected porcine corneas for 3 days in an explantation culture system for histologic evaluation of hyphal penetration. RESULTS All C. albicans strains had similar growth kinetics, and SC5314 and DAY185 demonstrated pH-induced filamentation. Fungal mutants had reduced hyphal formation at alkaline and neutral pH, but normal acidic assays ascertained that mutant strains did not have a generalized filamentation defect. SC5314 and DAY185 caused moderate to severe keratitis in mice, whereas fungal strains lacking constituents of the RIM101 pathway had significantly (P<0.05) attenuated severity in vivo. Three days after inoculation of porcine corneas, SC5314 and DAY185 produced hyphae that penetrated 28% and 25%, respectively, of the corneal thickness, and all five mutant strains showed significantly (P<0.05) less stromal penetration. CONCLUSIONS The RIM101 signal transduction pathway plays an important role in the development of C. albicans keratitis. The fungal pathway intermediates Rim8p, Rim13p, Rim20p, and Rim101p and the downstream cell-wall protein Phr1p are pivotal in the process of corneal invasion by C. albicans.
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Affiliation(s)
- Xiaoyong Yuan
- Sid W. Richardson Ocular Microbiology Laboratory, Cullen Eye Institute, Department of Ophthalmology, Baylor College of Medicine, Houston, Texas 77030, USA
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Kabir MA, Hussain MA. Human fungal pathogen Candida albicans in the postgenomic era: an overview. Expert Rev Anti Infect Ther 2009; 7:121-34. [PMID: 19622061 DOI: 10.1586/14787210.7.1.121] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Candida albicans is an opportunistic human fungal pathogen and is responsible for candidiasis. Owing to the improvement in healthcare, the number of immunocompromised patients in hospitals has increased worldwide and these individuals are susceptible to infections caused by many pathogenic microbes, among which C. albicans is one of the major players. Currently, the complete genome sequence of this pathogen is available and the size of this was estimated to be of 16 Mb. Annotation of C. albicans genome revealed that there are 6114 open reading frames (ORFs), of which 774 are specific to C. albicans. This poses a challenge as well as an opportunity to the Candida community to understand the functions of the unknown genes, especially those specific to C. albicans. Efforts have been made by the Candida community to systematically delete the ORFs and assign the functions. This will, in turn, help in understanding the biology of C. albicans and its interactions with animals as well as humans, and better drugs can be developed to treat Candida infections. In this article, we review updates on the Candida biology in the context of the availability of the genome sequence, its functional analysis and anti-Candida therapy. Finally, in the light of present trends in Candida research and current challenges, various opportunities are identified and suggestions are made.
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Affiliation(s)
- M Anaul Kabir
- Department of Biotechnology, PA College of Engineering, Kairangala, Mangalore-574153, Karnataka, India.
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Sanglard D, Coste A, Ferrari S. Antifungal drug resistance mechanisms in fungal pathogens from the perspective of transcriptional gene regulation. FEMS Yeast Res 2009; 9:1029-50. [PMID: 19799636 DOI: 10.1111/j.1567-1364.2009.00578.x] [Citation(s) in RCA: 179] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Fungi are primitive eukaryotes and have adapted to a variety of niches during evolution. Some fungal species may interact with other life forms (plants, insects, mammals), but are considered as pathogens when they cause mild to severe diseases. Chemical control strategies have emerged with the development of several drugs with antifungal activity against pathogenic fungi. Antifungal agents have demonstrated their efficacy by improving patient health in medicine. However, fungi have counteracted antifungal agents in several cases by developing resistance mechanisms. These mechanisms rely on drug resistance genes including multidrug transporters and drug targets. Their regulation is crucial for the development of antifungal drug resistance and therefore transcriptional factors critical for their regulation are being characterized. Recent genome-wide studies have revealed complex regulatory circuits involving these genetic and transcriptional regulators. Here, we review the current understanding of the transcriptional regulation of drug resistance genes from several fungal pathogens including Candida and Aspergillus species.
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Affiliation(s)
- Dominique Sanglard
- Institute of Microbiology, University of Lausanne and University Hospital Center, 1011 Lausanne, Switzerland.
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11
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Abstract
The detection of protein-protein interactions through two-hybrid assays has revolutionized our understanding of biology. The remarkable impact of two-hybrid assay platforms derives from their speed, simplicity, and broad applicability. Yet for many organisms, the need to express test proteins in Saccharomyces cerevisiae or Escherichia coli presents a substantial barrier because variations in codon specificity or bias may result in aberrant protein expression. In particular, nonstandard genetic codes are characteristic of several eukaryotic pathogens, for which there are currently no genetically based systems for detection of protein-protein interactions. We have developed a protein-protein interaction assay that is carried out in native host cells by using GFP as the only foreign protein moiety, thus circumventing these problems. We show that interaction can be detected between two protein pairs in both the model yeast S. cerevisiae and the fungal pathogen Candida albicans. We use computational analysis of microscopic images to provide a quantitative and automated assessment of confidence.
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Two-component signal transduction proteins as potential drug targets in medically important fungi. Infect Immun 2008; 76:4795-803. [PMID: 18765727 DOI: 10.1128/iai.00834-08] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Dias MVS, Basso LR, Coelho PSR. New transposons to generate GFP protein fusions in Candida albicans. Gene 2008; 417:13-8. [DOI: 10.1016/j.gene.2008.03.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2007] [Revised: 03/11/2008] [Accepted: 03/11/2008] [Indexed: 11/17/2022]
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van het Hoog M, Rast TJ, Martchenko M, Grindle S, Dignard D, Hogues H, Cuomo C, Berriman M, Scherer S, Magee BB, Whiteway M, Chibana H, Nantel A, Magee PT. Assembly of the Candida albicans genome into sixteen supercontigs aligned on the eight chromosomes. Genome Biol 2007; 8:R52. [PMID: 17419877 PMCID: PMC1896002 DOI: 10.1186/gb-2007-8-4-r52] [Citation(s) in RCA: 120] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2006] [Revised: 02/28/2007] [Accepted: 04/09/2007] [Indexed: 11/10/2022] Open
Abstract
For Assembly 20 of the Candida albicans genome, the sequence of each of the eight chromosomes was determined, revealing new insights into gene family creation and dispersion, subtelomere organization, and chromosome evolution. Background The 10.9× genomic sequence of Candida albicans, the most important human fungal pathogen, was published in 2004. Assembly 19 consisted of 412 supercontigs, of which 266 were a haploid set, since this fungus is diploid and contains an extensive degree of heterozygosity but lacks a complete sexual cycle. However, sequences of specific chromosomes were not determined. Results Supercontigs from Assembly 19 (183, representing 98.4% of the sequence) were assigned to individual chromosomes purified by pulse-field gel electrophoresis and hybridized to DNA microarrays. Nine Assembly 19 supercontigs were found to contain markers from two different chromosomes. Assembly 21 contains the sequence of each of the eight chromosomes and was determined using a synteny analysis with preliminary versions of the Candida dubliniensis genome assembly, bioinformatics, a sequence tagged site (STS) map of overlapping fosmid clones, and an optical map. The orientation and order of the contigs on each chromosome, repeat regions too large to be covered by a sequence run, such as the ribosomal DNA cluster and the major repeat sequence, and telomere placement were determined using the STS map. Sequence gaps were closed by PCR and sequencing of the products. The overall assembly was compared to an optical map; this identified some misassembled contigs and gave a size estimate for each chromosome. Conclusion Assembly 21 reveals an ancient chromosome fusion, a number of small internal duplications followed by inversions, and a subtelomeric arrangement, including a new gene family, the TLO genes. Correlations of position with relatedness of gene families imply a novel method of dispersion. The sequence of the individual chromosomes of C. albicans raises interesting biological questions about gene family creation and dispersion, subtelomere organization, and chromosome evolution.
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Affiliation(s)
- Marco van het Hoog
- Biotechnology Research Institute, National Research Council of Canada, Montreal, Quebec, H4P 2R2, Canada
| | | | - Mikhail Martchenko
- Biotechnology Research Institute, National Research Council of Canada, Montreal, Quebec, H4P 2R2, Canada
| | | | - Daniel Dignard
- Biotechnology Research Institute, National Research Council of Canada, Montreal, Quebec, H4P 2R2, Canada
| | - Hervé Hogues
- Biotechnology Research Institute, National Research Council of Canada, Montreal, Quebec, H4P 2R2, Canada
| | | | | | | | - BB Magee
- University of Minnesota, Minneapolis, MN, 55455, USA
| | - Malcolm Whiteway
- Biotechnology Research Institute, National Research Council of Canada, Montreal, Quebec, H4P 2R2, Canada
| | - Hiroji Chibana
- Research Center for Pathogenic Fungi and Microbial Toxicoses, Chiba University, Chiba, 260-8673, Japan
| | - André Nantel
- Biotechnology Research Institute, National Research Council of Canada, Montreal, Quebec, H4P 2R2, Canada
| | - PT Magee
- University of Minnesota, Minneapolis, MN, 55455, USA
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15
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Biswas S, Van Dijck P, Datta A. Environmental sensing and signal transduction pathways regulating morphopathogenic determinants of Candida albicans. Microbiol Mol Biol Rev 2007; 71:348-76. [PMID: 17554048 PMCID: PMC1899878 DOI: 10.1128/mmbr.00009-06] [Citation(s) in RCA: 396] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Candida albicans is an opportunistic fungal pathogen that is found in the normal gastrointestinal flora of most healthy humans. However, under certain environmental conditions, it can become a life-threatening pathogen. The shift from commensal organism to pathogen is often correlated with the capacity to undergo morphogenesis. Indeed, under certain conditions, including growth at ambient temperature, the presence of serum or N-acetylglucosamine, neutral pH, and nutrient starvation, C. albicans can undergo reversible transitions from the yeast form to the mycelial form. This morphological plasticity reflects the interplay of various signal transduction pathways, either stimulating or repressing hyphal formation. In this review, we provide an overview of the different sensing and signaling pathways involved in the morphogenesis and pathogenesis of C. albicans. Where appropriate, we compare the analogous pathways/genes in Saccharomyces cerevisiae in an attempt to highlight the evolution of the different components of the two organisms. The downstream components of these pathways, some of which may be interesting antifungal targets, are also discussed.
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Affiliation(s)
- Subhrajit Biswas
- National Centre for Plant Genome Research, New Delhi 110 067, India
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16
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Moyrand F, Fontaine T, Janbon G. Systematic capsule gene disruption reveals the central role of galactose metabolism on Cryptococcus neoformans virulence. Mol Microbiol 2007; 64:771-81. [PMID: 17462022 DOI: 10.1111/j.1365-2958.2007.05695.x] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The polysaccharidic capsule is the main virulence factor of Cryptococcus neoformans. It primarily comprised of two polysaccharides: glucuronoxylomannan (GXM, 88% of the capsule mass) and galactoxylomannan (GalXM, 7% of the capsule mass). We constructed a large collection of mutant strains in which genes potentially involved in capsule biosynthesis were deleted. We used a new post-genomic approach to study the virulence of the strains. Primers specific for unique tags associated with the disruption cassette were used in a real-time PCR virulence assay to measure the fungal burden of each strain in different organs of mice in multi-infection experiments. With this very sensitive assay, we identified a putative UDP-glucose epimerase (Uge1p) and a putative UDP-galactose transporter (Ugt1p) essential for C. neoformans virulence. The uge1Delta and ugt1Delta strains are temperature sensitive and do not produce GalXM but synthesize a larger capsule. These mutant strains (GalXM negative, GXM positive) are not able to colonize the brain even at the first day of infection whereas GXM-negative strains (GalXM positive) can still colonize the brain, although less efficiently than the wild-type strain.
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Matsumoto S, Hatano K, Maki K. [New advances in antifungal agents]. Nihon Yakurigaku Zasshi 2007; 130:45-51. [PMID: 17634680 DOI: 10.1254/fpj.130.45] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
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18
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Abstract
Fungal infections represent a serious health problem in industrialized countries. In particular, multimorbid patients are highly susceptible to life-threatening infections by opportunistic fungi, most often Candida or Aspergillus species. In Europe, fungal infections account for 17% of intensive care unit infections. In addition, common non-life-threatening superficial infections impose significant restrictions on patients, resulting in a reduced quality of life. One of the first steps of pathogens during infection of the host is to attach to the surface of host tissues. This step in host–pathogen interaction is crucial for colonization by the pathogen and for the persistance of the pathogen in the host. Commensal organisms, such as Candida albicans, are able to persistently colonize the host without causing symptoms. However, the balance between commensalism and pathogenicity is delicate. How these two states are modulated during C. albicans colonization is a major area of research in medical mycology, with the aim of utilizing the knowledge gained for the benefit of the patient.
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Affiliation(s)
- Steffen Rupp
- Fraunhofer Institute for Interfacial Engineering & Biotechnology, Department of Molecular Biotechnology, Stuttgart, Germany.
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Chauhan N, Latge JP, Calderone R. Signalling and oxidant adaptation in Candida albicans and Aspergillus fumigatus. Nat Rev Microbiol 2006; 4:435-44. [PMID: 16710324 DOI: 10.1038/nrmicro1426] [Citation(s) in RCA: 140] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Candida species and Aspergillus fumigatus were once thought to be relatively benign organisms. However, it is now known that this is not the case - Candida species rank among the top four causes of nosocomial infectious diseases in humans and A. fumigatus is the most deadly mould, often having a 90% mortality rate in immunocompromised transplant recipients. Adaptation to stress, including oxidative stress, is a necessary requisite for survival of these organisms during infection. Here, we describe the latest information on the signalling pathways and target proteins that contribute to oxidant adaptation in C. albicans and A. fumigatus, which has been obtained primarily through the analysis of mutants or inference from genome annotation.
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Affiliation(s)
- Neeraj Chauhan
- Georgetown University Medical Center, Department of Microbiology & Immunology, Washington, DC 20057, USA
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Lebel K, MacPherson S, Turcotte B. New tools for phenotypic analysis in Candida albicans: the WAR1 gene confers resistance to sorbate. Yeast 2006; 23:249-59. [PMID: 16544288 DOI: 10.1002/yea.1346] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Availability of the complete sequence of the Candida albicans genome allows for global gene analysis. We designed a gene deletion method to facilitate such studies. First, we constructed C. albicans strains that are both Deltaura3 and Deltatrp1. Second, we designed a system that relies on in vitro recombination, using the Gateway((R)) technology, for efficient generation of deletion cassettes. They are generated in two steps: (a) upstream and downstream DNA fragments of the chromosomal region to be deleted are amplified by PCR and introduced into two separate entry vectors; (b) the second step involves a quadruple recombination event including the two entry vectors, a plasmid bearing a marker of interest and a destination vector, in order to generate a plasmid containing the deletion cassette. The deletion plasmid contains very rare restriction sites for convenient excision of the knockout cassette. Selection in C. albicans can be performed with one of the following markers: the C. albicans URA3 gene, a modified S. cerevisiae TRP1 gene or the mycophenolic acid resistance (MPA(R)) gene. Upon integration into the genome, these markers can be removed by the use of 5-fluoroorotic acid (URA3), 5-fluoroanthranilic acid (TRP1) or the FLP recombinase (MPA(R)). Using this approach, we show that removal of the C. albicans orf19.1035 gene results in sensitivity to the weak acid sorbate, while its overexpression increases resistance to this compound. We named it WAR1, in analogy to its S. cerevisiae orthologue.
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Affiliation(s)
- Karine Lebel
- Department of Medicine, Royal Victoria Hospital, McGill University, 687 Pine Avenue West, Montréal, Québec, Canada H3A 1A1
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21
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Nantel A. The long hard road to a completed Candida albicans genome. Fungal Genet Biol 2006; 43:311-5. [PMID: 16517185 DOI: 10.1016/j.fgb.2006.01.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2005] [Revised: 01/11/2006] [Accepted: 01/13/2006] [Indexed: 11/21/2022]
Abstract
After almost a decade of work, the sequencing, assembly, and annotation of the genome of the fungal pathogen Candida albicans is finally close at hand. This review covers the early history of the C. albicans genome project, from the release of early assemblies that provided the impetus for an explosion in functional genomics research, to a community-based annotation and a preview of the work that was necessary for the production of a final genome assembly.
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Affiliation(s)
- André Nantel
- Biotechnology Research Institute, National Research Council, 6100 Royalmount, Montreal, PQ, Canada H4P 2R2.
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22
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Herbeck JT, Wall DP. Converging on a general model of protein evolution. Trends Biotechnol 2006; 23:485-7. [PMID: 16054255 DOI: 10.1016/j.tibtech.2005.07.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2005] [Revised: 06/08/2005] [Accepted: 07/18/2005] [Indexed: 10/25/2022]
Abstract
The availability of high-throughput genomic databases that establish protein dispensability, expression and interaction networks enables rigorous tests of competing models of protein evolution. Recent research utilizing these new data sets shows that protein evolution is more complex than was previously thought. Several variables, including protein dispensability, expression, functional density, and genetic modularity, appear to have independent effects on the evolutionary rate of proteins, suggesting that proteomes have evolved via an assembly of selectional regimes. These results indicate that a general model of protein evolution will emerge as more functional genomic data from a diversity of organisms accumulate.
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Affiliation(s)
- Joshua T Herbeck
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98103, USA.
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Richard ML, Nobile CJ, Bruno VM, Mitchell AP. Candida albicans biofilm-defective mutants. EUKARYOTIC CELL 2005; 4:1493-502. [PMID: 16087754 PMCID: PMC1214533 DOI: 10.1128/ec.4.8.1493-1502.2005] [Citation(s) in RCA: 119] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Biofilm formation plays a key role in the life cycles and subsistence of many microorganisms. For the human fungal pathogen Candida albicans, biofilm development is arguably a virulence trait, because medical implants that serve as biofilm substrates are significant risk factors for infection. The development of C. albicans biofilms in vitro proceeds through an early phase, in which yeast cells populate a substrate, an intermediate phase, in which pseudohyphal and hyphal cell types are produced, and a maturation phase, in which continued cell growth is accompanied by accumulation of an extracellular matrix. Here we report the results of a screen for C. albicans biofilm-defective mutants, in which homozygous insertions in NUP85, MDS3, KEM1, and SUV3 were found to block biofilm development. Confocal microscopic examination suggests that nup85, suv3, and mds3 mutations cause early-phase arrest, whereas the kem1 mutation causes intermediate-phase arrest. All of the mutants are defective in hypha production in several media. Analysis of mixed-biofilm development indicates that all of the mutants are defective in the production of hyphae in the context of a biofilm. Because all of the mutants are defective in the retention of cells in the biofilm, we infer that hyphae provide an adherent scaffold that stabilizes the biofilm structure.
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Affiliation(s)
- Mathias L Richard
- Department of Microbiology, Columbia University, New York, NY 10032, USA
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Nobile CJ, Mitchell AP. Regulation of cell-surface genes and biofilm formation by the C. albicans transcription factor Bcr1p. Curr Biol 2005; 15:1150-5. [PMID: 15964282 DOI: 10.1016/j.cub.2005.05.047] [Citation(s) in RCA: 362] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2005] [Revised: 05/10/2005] [Accepted: 05/12/2005] [Indexed: 11/26/2022]
Abstract
The impact of many microorganisms on their environment depends upon their ability to form surface bound communities called biofilms [1]. Biofilm formation on implanted medical devices has severe consequences for human health by providing both a portal of entry and a sanctuary for invasive bacterial and fungal pathogens [1 and 2]. Biofilm regulators and adherence molecules are extensively defined for many bacterial pathogens [3, 4, and 5], but not for fungal pathogens such as Candida albicans. Elongated filaments called hyphae are a prominent feature of C. albicans biofilms, and known genes that promote biofilm formation are required for hyphal development [2, 6, 7 and 8]. From a new library of transcription-factor mutants, we identify Bcr1p, a zinc finger protein required for formation of biofilms but not hyphae. Expression analysis shows that Bcr1p activates cell-surface protein and adhesin genes, including several induced during hyphal development. BCR1 expression depends upon the hyphal regulator Tec1p. Thus, BCR1 is a downstream component of the hyphal regulatory network that couples expression of cell-surface genes to hyphal differentiation. Our results indicate that hyphal cells are specialized to present adherence molecules that support biofilm integrity.
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Affiliation(s)
- Clarissa J Nobile
- Department of Microbiology, Columbia University, New York, NY 10032, USA
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