Using Synthetic Genetic Interactions in Candida glabrata as a Novel Method to Detect Genes with Roles in Antifungal Drug Resistance.
Genetic interaction
Network maps
Synthetic lethality
Journal
Methods in molecular biology (Clifton, N.J.)
ISSN: 1940-6029
Titre abrégé: Methods Mol Biol
Pays: United States
ID NLM: 9214969
Informations de publication
Date de publication:
2022
2022
Historique:
entrez:
25
8
2022
pubmed:
26
8
2022
medline:
30
8
2022
Statut:
ppublish
Résumé
Synthetic genetic interaction analysis is a powerful genetic strategy that analyzes the fitness and phenotypes of single- and double-gene mutant cells in order to dissect the interactions between genes, categorize into biological pathways, and characterize genes of unknown function. It has been extensively employed in model organisms for fundamental, systems-level assessment of the interactions between genes. However, more recently, genetic interaction mapping has been applied to fungal pathogens and has been instrumental for the study of clinically important infectious organisms. This protocol herein explains in the detail the methodology and analysis that can be employed to develop interaction maps in microbial pathogens. Such techniques can aid in bridging our understanding of complex genetic networks, with applications to diverse microbial pathogens to further our understanding of virulence, the use of antimicrobial therapies, and host-pathogen interactions.
Identifiants
pubmed: 36008659
doi: 10.1007/978-1-0716-2549-1_7
doi:
Substances chimiques
Antifungal Agents
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
103-114Informations de copyright
© 2022. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.
Références
Sopko R, Huang D, Preston N, Chua G, Papp B, Kafadar K et al (2006) Mapping pathways and phenotypes by systematic gene overexpression. Mol Cell 21(3):319–330. https://doi.org/10.1016/j.molcel.2005.12.011
doi: 10.1016/j.molcel.2005.12.011
pubmed: 16455487
Winzeler EA, Shoemaker DD, Astromoff A, Liang H, Anderson K, Andre B et al (1999) Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285(5429):901–906
doi: 10.1126/science.285.5429.901
Tong AH, Evangelista M, Parsons AB, Xu H, Bader GD et al (2001) Systematic genetics analysis with ordered arrays of yeast deletion mutants. Science 294:2364–2368
doi: 10.1126/science.1065810
Costanzo M, Baryshnikova A, Bellay J, Kim Y, Spear ED, Sevier CS et al (2010) The genetic landscape of a cell. Science 327(January):425–431
doi: 10.1126/science.1180823
Sharifpoor S, Van Dyk D, Costanzo M, Baryshnikova A, Friesen H, Douglas AC et al (2012) Functional wiring of the yeast kinome revealed by global analysis of genetic network motifs. Genome Res 22(4):791–801. https://doi.org/10.1101/gr.129213.111
doi: 10.1101/gr.129213.111
pubmed: 22282571
pmcid: 3317160
Forsburg SL (2001) The art and design of genetic screens: yeast. Nat Rev Genet 2(9):659–668. https://doi.org/10.1038/35088500
doi: 10.1038/35088500
pubmed: 11533715
Hughes TR, de Boer CG (2013) Mapping yeast transcriptional networks. Genetics 195(1):9–36. https://doi.org/10.1534/genetics.113.153262
doi: 10.1534/genetics.113.153262
pubmed: 24018767
pmcid: 3761317
Shou C, Bhardwaj N, Lam HYK, Yan K-K, Kim PM, Snyder M, Gerstein MB (2011) Measuring the evolutionary rewiring of biological networks. PLoS Comput Biol 7(1):e1001050. https://doi.org/10.1371/journal.pcbi.1001050
doi: 10.1371/journal.pcbi.1001050
pubmed: 21253555
pmcid: 3017101
Uetz P, Giot L, Cagney G, Mans TA, Judson RS, Knight JR et al (2000) A comprehensive analysis of protein ± protein interactions in Saccharomyces cerevisiae. Nature 403(February):623–627
doi: 10.1038/35001009
Zinovyev A, Kuperstein I, Barillot E, Heyer W-D (2013) Synthetic lethality between gene defects affecting a single non-essential molecular pathway with reversible steps. PLoS Comput Biol 9(4):e1003016. https://doi.org/10.1371/journal.pcbi.1003016
doi: 10.1371/journal.pcbi.1003016
pubmed: 23592964
pmcid: 3617211
Brown GD, Denning DW, Gow NAR, Levitz SM, Netea MG, White TC (2012) Hidden killers: human fungal infections. Sci Transl Med 4(165):1–10
doi: 10.1126/scitranslmed.3004404
Hajjeh RA, Sofair AN, Harrison LH, Lyon GM, Arthington-skaggs BA, Mirza SA et al (2004) Incidence of bloodstream infections due to Candida species and in vitro susceptibilities of isolates collected from 1998 to 2000 in a population-based active surveillance program. J Clin Microbiol 42(4):1519–1527. https://doi.org/10.1128/JCM.42.4.1519
doi: 10.1128/JCM.42.4.1519
pubmed: 15070998
pmcid: 387610
Butler G, Rasmussen MD, Lin MF, Santos MAS, Sakthikumar S, Munro CA et al (2009) Evolution of pathogenicity and sexual reproduction in eight Candida genomes. Nature 459(7247):657–662. https://doi.org/10.1038/nature08064
doi: 10.1038/nature08064
pubmed: 19465905
pmcid: 2834264
Kaloriti D, Tillmann A, Cook E, Jacobsen M, You T, Lenardon M et al (2012) Combinatorial stresses kill pathogenic Candida species. Med Mycol 50(7):699–709. https://doi.org/10.3109/13693786.2012.672770
doi: 10.3109/13693786.2012.672770
pubmed: 22463109
Wong S, Fares MA, Zimmermann W, Butler G, Wolfe KH (2003) Evidence from comparative genomics for a complete sexual cycle in the “asexual” pathogenic yeast Candida glabrata. Genome Biol 4(2):R10
doi: 10.1186/gb-2003-4-2-r10
Baryshnikova A, Costanzo M, Yungil K, Ding H, Koh J, Toufighi K, Youn JY, Ou J, San Luis BJ, Bandyopadhyah S, Hibbs M, Hess D, Gingras A, Bader GD, Troyanskaya OG, Brown GW, Andrews B, Boones C, Myers CL (2010) Quantitative analysis of fitness and genetic interactions in yeast on a genome scale. Nat Methods 7(12):1017–1024
doi: 10.1038/nmeth.1534
Usher J, Thomas G, Haynes K (2015) Utilising established SDL-screening methods as a tool for the functional genomic characterisation of model and non-model organisms. FEMS Yeast Res 15(8):fov091
doi: 10.1093/femsyr/fov091