Large‐scale essential gene identification in <i>Candida albicans</i> and applications to antifungal drug discovery

Roemer, Terry; Jiang, Bo; Davison, John; Ketela, Troy; Veillette, Karynn; Breton, Anouk; Tandia, Fatou; Linteau, Annie; Sillaots, Susan; Marta, Catarina; Martel, Nick; Véronneau, Steeve; Lemieux, Sébastien; Kauffman, Sarah; Becker, Jeff; Storms, Reginald; Boone, Charles; Bussey, Howard

doi:10.1046/j.1365-2958.2003.03697.x

Cited by 482 publications

(470 citation statements)

References 45 publications

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“…For example, in Pal et al's study (10), the complete genome closest to S. cerevisiae was C. albicans. However, recent high-throughput gene deletion studies of this species (16) have revealed that many genes that are essential in S. cerevisiae have nonessential orthologs in C. albicans (and vice versa), suggesting that estimates of dispensability from S. cerevisiae are only rough correlates of the actual level of dispensability over the sampled evolutionary period. Among prokaryotes, closer evolutionary comparisons are possible, but growth rates of deletion mutants have not been systematically measured, so studies must use exclusively binary fitness data.…”

mentioning

confidence: 99%

Functional genomic analysis of the rates of protein evolution

Wall

Hirsh²,

Fraser³

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

259

256

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The evolutionary rates of proteins vary over several orders of magnitude. Recent work suggests that analysis of large data sets of evolutionary rates in conjunction with the results from high-throughput functional genomic experiments can identify the factors that cause proteins to evolve at such dramatically different rates. To this end, we estimated the evolutionary rates of >3,000 proteins in four species of the yeast genus Saccharomyces and investigated their relationship with levels of expression and protein dispensability. Each protein's dispensability was estimated by the growth rate of mutants deficient for the protein. Our analyses of these improved evolutionary and functional genomic data sets yield three main results. First, dispensability and expression have independent, significant effects on the rate of protein evolution. Second, measurements of expression levels in the laboratory can be used to filter data sets of dispensability estimates, removing variates that are unlikely to reflect real biological effects. Third, structural equation models show that although we may reasonably infer that dispensability and expression have significant effects on protein evolutionary rate, we cannot yet accurately estimate the relative strengths of these effects

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mentioning

confidence: 99%

Functional genomic analysis of the rates of protein evolution

Wall

Hirsh²,

Fraser³

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

259

256

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“…The HOG1 and MCK1 genes were deleted in the myo5⌬ and/or CAI4 backgrounds by use of PCR-amplified disruption cassettes. For disruption of HOG1, PCR was performed using oligonucleotides UO186 (5ЈATTTTAAACAAGTTATAGAAAGAAAATTTTTACAAAGATA AAGCATATAAGAAAATGTCTGCAGATGGAGAATTTACAAGAACCG TAAAACGACGGCCAG3Ј) and UO187 (5ЈCTTTTAAATTTATTTCTATAA TTGCTAGCTTGTATTTTTGAAGATTAAGCTCCGTTGGCGGAATCCAA GTTGTTTTGCTCCGGAAACAGCTATGACCATG3Ј) to amplify a 2.0-kb fragment from pBS-URA3, a kind gift from Catherine Bachewich, and oligonucleotides UO210 (5ЈTTCAAGTCGTCTTTGAAAACATACACCGTGGAATA ATAACAACAACATTTTAAACAAGTTATAGAAAGAAAATTTTTACAA AGATAAAGCATATAAGAAACCCGGGATCGATAGAGCT3Ј) and UO211 (5ЈATGCTCCCATTCCCACGGGATTTAGCTCAGTGTATCTATTGGTGA TTTCAAAAACAGTCCCAAATATCTGGGTTCTTGTAAATTCTCCATCT GCAGACATATCCGGTAATTTAGTGTG3Ј) to amplify a 2.4-kb fragment from pSAT-tet (47). PCR products were purified using a QIAquick PCR kit.…”

Section: Methodsmentioning

confidence: 99%

“…For disruption of MKC1, PCR was performed using oligonucleotides UO214 (5ЈAACCTGAAACCCAAAAAAAAAAATTTTTTTTTGCTCACTACTAGT TGTCCTTTTTAAACTTTCTCTTGAACAGCAGTTTTATAAAGAACCAA TTTCCATAGGAAACAGCTATGACCATG3Ј) and UO187 (5ЈAAAAGGAG GTACTAAAGGTCAATATATATAATAACCACCACTAATGGATAGACT AATTCGAGAGTAACATACCCCGGGATAACGTGGTTGTGTGTTTCAA GTAAAACGACGGCCAGT3Ј) to amplify a 2.0-kb fragment from pBS-URA3 and oligonucleotides UO225 (5ЈAACTGAAACCCAAAAAAAAAAATTTTTT TTTGCTCACTACTAGTTGTCCTTTTTAAACTTTCTCTTGAACAGCAGT TTTATAAAGAACCAATTTCCATACCCGGGATCGATAGAGC3Ј) and UO226 (5ЈACTCCTTGACTATTTTGAATCGACTATCAATGATAAATTCC TGGTTGTAGACCTTATTTACGGATCTGCCATAATATATGGGTGCTTC TTGTTGATCCATATCCGGTAATTTAGTGTGTG3Ј) to amplify a 2.4-kb fragment from pSAT-tet (47). PCR products were purified using a QIAquick PCR kit.…”

Section: Methodsmentioning

confidence: 99%

Transcript Profiles of Candida albicans Cortical Actin Patch Mutants Reflect Their Cellular Defects: Contribution of the Hog1p and Mkc1p Signaling Pathways

et al. 2006

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In Candida albicans, Myo5p and Sla2p are required for the polarized localization and function of cortical actin patches, for hyphal formation, and for endocytosis. Deletion of either the MYO5 or the SLA2 gene generated a common transcriptional response that involved changes in the transcript levels of cell wall proteinand membrane protein-encoding genes. However, these profiles were distinct from those observed for a mutant with specific deletions of the actin-organizing domains of Myo5p or for wild-type cells treated with cytochalasin A, both of which also generate defects in the organization of cortical actin patches. The profiles observed for the myo5⌬ and sla2⌬ mutants had similarities to those of wild-type cells subjected to an osmotic shock, and the defects in cortical patch function found with myo5⌬ and sla2⌬ mutants, but not cortical actin patch distribution per se, affected sensitivity to various stresses, including heat and osmotic shocks and cell wall damage. Secondary effects coupled with defective endocytosis, such as lack of polarized lipid rafts and associated protein Rvs167-GFP (where GFP is green fluorescent protein) and lack of polarized wall remodeling protein GFP-Gsc1, were also observed for the myo5⌬ and sla2⌬ mutants. The mitogen-activated protein kinases Hog1p and Mkc1p, which mediate signaling in response to osmotic stress and cell wall damage, do not play a major role in regulating the transcript level changes in the myo5⌬ and sla2⌬ mutants. Hog1p was not hyperphosphorylated in the myo5⌬ and sla2⌬ mutants, and the transcript levels of only a subset of genes affected in the myo5⌬ mutant were dependent upon the presence of Hog1p and Mkc1p. However, it appears that Hog1p and Mkc1p play important roles in the myo5⌬ mutant cells because double deletion of myosin I and either Hog1p or Mkc1p resulted in very-slow-growing cells.

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“…Subsequently, a heterozygous mutant library of 3633 unique strains was constructed that allowed easier identification of the disrupted locus and facilitated pooling experiments by bar coding each heterozygous mutant [142]. A further development was a library in which one allele was deleted and the second was placed under the control of a tetracycline-repressible promoter [143]. This library, known as the gene replacement and controlled expression (GRACE) collection, includes 2356 genes and has proven useful in assessing conditional lethality [143], functional conservation between S. cerevisiae and C. albicans genes [142], chemical genetic approaches for novel therapeutics [144] and gene function [145].…”

Section: Construction Of Systematic Strain Collectionsmentioning

confidence: 99%

“…A further development was a library in which one allele was deleted and the second was placed under the control of a tetracycline-repressible promoter [143]. This library, known as the gene replacement and controlled expression (GRACE) collection, includes 2356 genes and has proven useful in assessing conditional lethality [143], functional conservation between S. cerevisiae and C. albicans genes [142], chemical genetic approaches for novel therapeutics [144] and gene function [145]. However, leaky gene expression at some loci can complicate analysis [143] and argues for the use of complementary approaches to define function.…”

Section: Construction Of Systematic Strain Collectionsmentioning

confidence: 99%

Budding off: bringing functional genomics toCandida albicans

Anderson¹,

Bennett²

2015

Briefings in Functional Genomics

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Candida species are the most prevalent human fungal pathogens, with Candida albicans being the most clinically relevant species. Candida albicans resides as a commensal of the human gastrointestinal tract but is a frequent cause of opportunistic mucosal and systemic infections. Investigation of C. albicans virulence has traditionally relied on candidate gene approaches, but recent advances in functional genomics have now facilitated global, unbiased studies of gene function. Such studies include comparative genomics (both between and within Candida species), analysis of total RNA expression, and regulation and delineation of protein-DNA interactions. Additionally, large collections of mutant strains have begun to aid systematic screening of clinically relevant phenotypes. Here, we will highlight the development of functional genomics in C. albicans and discuss the use of these approaches to addressing both commensalism and pathogenesis in this species.

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Large‐scale essential gene identification in Candida albicans and applications to antifungal drug discovery

Cited by 482 publications

References 45 publications

Functional genomic analysis of the rates of protein evolution

Functional genomic analysis of the rates of protein evolution

Transcript Profiles of Candida albicans Cortical Actin Patch Mutants Reflect Their Cellular Defects: Contribution of the Hog1p and Mkc1p Signaling Pathways

Budding off: bringing functional genomics toCandida albicans

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