Abstract
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.
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References
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
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
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
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
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
Forsburg SL (2001) The art and design of genetic screens: yeast. Nat Rev Genet 2(9):659–668. https://doi.org/10.1038/35088500
Hughes TR, de Boer CG (2013) Mapping yeast transcriptional networks. Genetics 195(1):9–36. https://doi.org/10.1534/genetics.113.153262
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
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
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
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
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
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
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
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
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
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
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Usher, J. (2022). Using Synthetic Genetic Interactions in Candida glabrata as a Novel Method to Detect Genes with Roles in Antifungal Drug Resistance. In: Calderone, R. (eds) Candida Species. Methods in Molecular Biology, vol 2542. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2549-1_7
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DOI: https://doi.org/10.1007/978-1-0716-2549-1_7
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