scholarly journals Identification and Functional Characterization of Rca1, a Transcription Factor Involved in both Antifungal Susceptibility and Host Response in Candida albicans

2012 ◽  
Vol 11 (7) ◽  
pp. 916-931 ◽  
Author(s):  
Patrick Vandeputte ◽  
Sylvain Pradervand ◽  
Françoise Ischer ◽  
Alix T. Coste ◽  
Sélène Ferrari ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Candida Albicans ◽  
Signaling Pathway ◽  
Large Scale ◽  
Antifungal Susceptibility ◽  
Functional Characterization ◽  
Therapeutic Strategies ◽  
Content Type ◽  
High Level

ABSTRACTThe identification of novel transcription factors associated with antifungal response may allow the discovery of fungus-specific targets for new therapeutic strategies. A collection of 241Candida albicanstranscriptional regulator mutants was screened for altered susceptibility to fluconazole, caspofungin, amphotericin B, and 5-fluorocytosine. Thirteen of these mutants not yet identified in terms of their role in antifungal response were further investigated, and the function of one of them, a mutant of orf19.6102 (RCA1), was characterized by transcriptome analysis. Strand-specific RNA sequencing and phenotypic tests assigned Rca1 as the regulator of hyphal formation through the cyclic AMP/protein kinase A (cAMP/PKA) signaling pathway and the transcription factor Efg1, but also probably through its interaction with a transcriptional repressor, most likely Tup1. The mechanisms responsible for the high level of resistance to caspofungin and fluconazole observed resulting fromRCA1deletion were investigated. From our observations, we propose that caspofungin resistance was the consequence of the deregulation of cell wall gene expression and that fluconazole resistance was linked to the modulation of the cAMP/PKA signaling pathway activity. In conclusion, our large-scale screening of aC. albicanstranscription factor mutant collection allowed the identification of new effectors of the response to antifungals. The functional characterization of Rca1 assigned this transcription factor and its downstream targets as promising candidates for the development of new therapeutic strategies, as Rca1 influences host sensing, hyphal development, and antifungal response.

scholarly journals Candida albicans Czf1 and Efg1 Coordinate the Response to Farnesol during Quorum Sensing, White-Opaque Thermal Dimorphism, and Cell Death

2013 ◽  
Vol 12 (9) ◽  
pp. 1281-1292 ◽  
Author(s):  
Melanie L. Langford ◽  
Jessica C. Hargarten ◽  
Krista D. Patefield ◽  
Elizabeth Marta ◽  
Jill R. Blankenship ◽  
...  
Keyword(s):  
Cell Death ◽  
Transcription Factor ◽  
Candida Albicans ◽  
Quorum Sensing ◽  
Cyclic Amp ◽  
Signaling Pathway ◽  
Clear Understanding ◽  
Morphological Response ◽  
Content Type ◽  
Cyclic Amp Signaling

ABSTRACTQuorum sensing by farnesol inCandida albicansinhibits filamentation and may be directly related to its ability to cause both mucosal and systemic diseases. The Ras1-cyclic AMP signaling pathway is a target for farnesol inhibition. However, a clear understanding of the downstream effectors of the morphological farnesol response has yet to be unraveled. To address this issue, we screened a library for mutants that fail to respond to farnesol. Six mutants were identified, and theczf1Δ/czf1Δ mutant was selected for further characterization. Czf1 is a transcription factor that regulates filamentation in embedded agar and also white-to-opaque switching. We found that Czf1 is required for filament inhibition by farnesol under at least three distinct environmental conditions: on agar surfaces, in liquid medium, and when embedded in a semisolid agar matrix. Since Efg1 is a transcription factor of the Ras1-cyclic AMP signaling pathway that interacts with and regulates Czf1, anefg1Δ/efg1Δczf1Δ/czf1Δ mutant was tested for filament inhibition by farnesol. It exhibited an opaque-cell-like temperature-dependent morphology, and it was killed by low farnesol levels that are sublethal to wild-type cells and bothefg1Δ/efg1Δ andczf1Δ/czf1Δ single mutants. These results highlight a new role for Czf1 as a downstream effector of the morphological response to farnesol, and along with Efg1, Czf1 is involved in the control of farnesol-mediated cell death inC. albicans.

scholarly journals Functional Characterization of the DNA Gyrases in Fluoroquinolone-Resistant Mutants of Francisella novicida

2017 ◽  
Vol 61 (4) ◽  
Author(s):  
Yvan Caspar ◽  
Claire Siebert ◽  
Vivien Sutera ◽  
Corinne Villers ◽  
Alexandra Aubry ◽  
...  
Keyword(s):  
Dna Cleavage ◽  
Molecular Mechanisms ◽  
Hot Spot ◽  
Functional Characterization ◽  
Health Concern ◽  
Content Type ◽  
Francisella Novicida ◽  
High Level

ABSTRACT Fluoroquinolone (FQ) resistance is a major health concern in the treatment of tularemia. Because DNA gyrase has been described as the main target of these compounds, our aim was to clarify the contributions of both GyrA and GyrB mutations found in Francisella novicida clones highly resistant to FQs. Wild-type and mutated GyrA and GyrB subunits were overexpressed so that the in vitro FQ sensitivity of functional reconstituted complexes could be evaluated. The data obtained were compared to the MICs of FQs against bacterial clones harboring the same mutations and were further validated through complementation experiments and structural modeling. Whole-genome sequencing of highly FQ-resistant lineages was also done. Supercoiling and DNA cleavage assays demonstrated that GyrA D87 is a hot spot FQ resistance target in F. novicida and pointed out the role of the GyrA P43H substitution in resistance acquisition. An unusual feature of FQ resistance acquisition in F. novicida is that the first-step mutation occurs in GyrB, with direct or indirect consequences for FQ sensitivity. Insertion of P466 into GyrB leads to a 50% inhibitory concentration (IC50) comparable to that observed for a mutant gyrase carrying the GyrA D87Y substitution, while the D487E-ΔK488 mutation, while not active on its own, contributes to the high level of resistance that occurs following acquisition of the GyrA D87G substitution in double GyrA/GyrB mutants. The involvement of other putative targets is discussed, including that of a ParE mutation that was found to arise in the very late stage of antibiotic exposure. This study provides the first characterization of the molecular mechanisms responsible for FQ resistance in Francisella.

scholarly journals DeORFanizing Candida albicans Genes using Co-Expression

2020 ◽  
Author(s):  
Teresa R. O’Meara ◽  
Matthew J. O’Meara
Keyword(s):  
Cell Cycle ◽  
Candida Albicans ◽  
Gene Function ◽  
Fungal Pathogen ◽  
Large Scale ◽  
Functional Characterization ◽  
Open Reading Frames ◽  
Model Organisms ◽  
Reading Frames

AbstractFunctional characterization of open reading frames in non-model organisms, such as the common opportunistic fungal pathogen Candida albicans, can be labor intensive. To meet this challenge, we built a comprehensive and unbiased co-expression network for C. albicans, which we call CalCEN, from data collected from 853 RNA sequencing runs from 18 large scale studies deposited in the NCBI Sequence Read Archive. Retrospectively, CalCEN is highly predictive of known gene function annotations and can be synergistically combined with sequence similarity and interaction networks in Saccharomyces cerevisiae through orthology for additional accuracy in gene function prediction. To prospectively demonstrate the utility of the co-expression network in C. albicans, we predicted the function of under-annotated open reading frames (ORF)s and identified CCJ1 as a novel cell cycle regulator in C. albicans. This study provides a tool for future systems biology analyses of gene function in C. albicans. We provide a computational pipeline for building and analyzing the co-expression network and CalCEN itself at (http://github.com/momeara/CalCEN).ImportanceCandida albicans is a common and deadly fungal pathogen of humans, yet the genome of this organism contains many genes of unknown function. By determining gene function, we can help identify essential genes, new virulence factors, or new regulators of drug resistance, and thereby give new targets for antifungal development. Here, we use information from large scale RNAseq studies and generate a C. albicans co-expression network (CalCEN) that is robust and able to predict gene function. We demonstrate the utility of this network in both retrospective and prospective testing, and use CalCEN to predict a role for C4_06590W/CCJ1 in cell cycle. This tool will allow for a better characterization of under-annotated genes in pathogenic yeasts.

scholarly journals DeORFanizing Candida albicans Genes using Coexpression

mSphere ◽  
2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Teresa R. O’Meara ◽  
Matthew J. O’Meara
Keyword(s):  
Cell Cycle ◽  
Candida Albicans ◽  
Gene Function ◽  
Fungal Pathogen ◽  
Large Scale ◽  
Open Reading Frames ◽  
Coexpression Network ◽  
Content Type ◽  
Reading Frames

ABSTRACT Functional characterization of open reading frames in nonmodel organisms, such as the common opportunistic fungal pathogen Candida albicans, can be labor-intensive. To meet this challenge, we built a comprehensive and unbiased coexpression network for C. albicans, which we call CalCEN, from data collected from 853 RNA sequencing runs from 18 large-scale studies deposited in the NCBI Sequence Read Archive. Retrospectively, CalCEN is highly predictive of known gene function annotations and can be synergistically combined with sequence similarity and interaction networks in Saccharomyces cerevisiae through orthology for additional accuracy in gene function prediction. To prospectively demonstrate the utility of the coexpression network in C. albicans, we predicted the function of underannotated open reading frames (ORFs) and identified CCJ1 as a novel cell cycle regulator in C. albicans. This study provides a tool for future systems biology analyses of gene function in C. albicans. We provide a computational pipeline for building and analyzing the coexpression network and CalCEN itself at http://github.com/momeara/CalCEN. IMPORTANCE Candida albicans is a common and deadly fungal pathogen of humans, yet the genome of this organism contains many genes of unknown function. By determining gene function, we can help identify essential genes, new virulence factors, or new regulators of drug resistance, and thereby give new targets for antifungal development. Here, we use information from large-scale RNA sequencing (RNAseq) studies and generate a C. albicans coexpression network (CalCEN) that is robust and able to predict gene function. We demonstrate the utility of this network in both retrospective and prospective testing and use CalCEN to predict a role for C4_06590W/CCJ1 in cell cycle. This tool will allow for a better characterization of underannotated genes in pathogenic yeasts.

scholarly journals Functional characterization of a new grapevine MYB transcription factor and regulation of proanthocyanidin biosynthesis in grapes

2014 ◽  
Vol 65 (15) ◽  
pp. 4433-4449 ◽  
Author(s):  
Kazuya Koyama ◽  
Mineyo Numata ◽  
Ikuko Nakajima ◽  
Nami Goto-Yamamoto ◽  
Hideo Matsumura ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Functional Characterization ◽  
Myb Transcription Factor

scholarly journals Whole-Genome Phylogenomic Heterogeneity of Neisseria gonorrhoeae Isolates with Decreased Cephalosporin Susceptibility Collected in Canada between 1989 and 2013

2014 ◽  
Vol 53 (1) ◽  
pp. 191-200 ◽  
Author(s):  
Walter Demczuk ◽  
Tarah Lynch ◽  
Irene Martin ◽  
Gary Van Domselaar ◽  
Morag Graham ◽  
...  
Keyword(s):  
Neisseria Gonorrhoeae ◽  
Large Scale ◽  
Epidemiological Studies ◽  
23S Rrna ◽  
Genome Comparison ◽  
Whole Genome ◽  
Content Type ◽  
Genomic Epidemiology ◽  
High Level ◽  
Sequence Types

A large-scale, whole-genome comparison of CanadianNeisseria gonorrhoeaeisolates with high-level cephalosporin MICs was used to demonstrate a genomic epidemiology approach to investigate strain relatedness and dynamics. Although current typing methods have been very successful in tracing short-chain transmission of gonorrheal disease, investigating the temporal evolutionary relationships and geographical dissemination of highly clonal lineages requires enhanced resolution only available through whole-genome sequencing (WGS). Phylogenomic cluster analysis grouped 169 Canadian strains into 12 distinct clades. While someN. gonorrhoeaemultiantigen sequence types (NG-MAST) agreed with specific phylogenomic clades or subclades, other sequence types (ST) and closely related groups of ST were widely distributed among clades. Decreased susceptibility to extended-spectrum cephalosporins (ESC-DS) emerged among a group of diverse strains in Canada during the 1990s with a variety of nonmosaicpenAalleles, followed in 2000/2001 with thepenAmosaic X allele and then in 2007 with ST1407 strains with thepenAmosaic XXXIV allele. Five genetically distinct ESC-DS lineages were associated withpenAmosaic X, XXXV, and XXXIV alleles and nonmosaic XII and XIII alleles. ESC-DS with coresistance to azithromycin was observed in 5 strains with 23S rRNA C2599T or A2143G mutations. As the costs associated with WGS decline and analysis tools are streamlined, WGS can provide a more thorough understanding of strain dynamics, facilitate epidemiological studies to better resolve social networks, and improve surveillance to optimize treatment for gonorrheal infections.

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