Mapping bacterial functional networks and pathways in Escherichia coli using synthetic genetic arrays

Journal of Visualized Experiments

Volumn , Issue 69, 2012, Pages

  Gagarinova, Alla ^a   Babu, Mohan ^b,c   Greenblatt, Jack ^a,b   Emili, Andrew ^a,b  

^a UNIVERSITY OF TORONTO   (Canada)

^b UNIVERSITY OF TORONTO   (Canada)

^c UNIVERSITY OF REGINA   (Canada)

Author keywords

Aggravating; Alleviating; Biochemistry; Conjugation; Double mutant; Escherichia coli; Genetic interaction; Genetics; Gram negative bacteria; Homologous recombination; Issue 69; Medicine; Microbiology; Molecular Biology; Network; Suppression; Synthetic lethality or sickness

Indexed keywords

EID: 84869467898     PISSN: 1940087X     EISSN: None     Source Type: Journal    
DOI: 10.3791/4056     Document Type: Article

References (34)

1. Bandyopadhyay, S., Kelley, R., Krogan, N.J., & Ideker, T. Functional maps of protein complexes from quantitative genetic interaction data. PLoS Comput. Biol. 4, e1000065 (2008).
2. Costanzo, M., Baryshnikova, A., Myers, C.L., Andrews, B., & Boone, C. Charting the genetic interaction map of a cell. Curr. Opin. Biotechnol. 22, 66-74 (2011).
3. Costanzo, M., et al. The genetic landscape of a cell. Science. 327, 425-31 (2010).
4. Fiedler, D., et al. Functional organization of the S. cerevisiae phosphorylation network. Cell. 136, 952-63 (2009).
5. Roguev, A., et al. Conservation and rewiring of functional modules revealed by an epistasis map in fission yeast. Science. 322, 405-10 (2008).
6. Schuldiner, M., et al. Exploration of the function and organization of the yeast early secretory pathway through an epistatic miniarray profile. Cell. 123, 507-19 (2005).
7. Wilmes, G.M., et al. A genetic interaction map of RNA-processing factors reveals links between Sem1/Dss1-containing complexes and mRNA export and splicing. Mol. Cell. 32, 735-46 (2008).
8. Babu, M., et al. Systems-level approaches for identifying and analyzing genetic interaction networks in Escherichia coli and extensions to other prokaryotes. Mol. Biosyst. 12, 1439-1455 (2009).
9. Butland, G., et al. eSGA: E. coli synthetic genetic array analysis. Nat. Methods. 5, 789-95 (2008).
10. Typas, A., et al. Regulation of peptidoglycan synthesis by outer-membrane proteins. Cell. 143, 1097-109 (2010).
11. Baba, T., et al. Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol. Syst. Biol. 2, 2006.0008 (2006).
12. Babu, M., et al. Genetic interaction maps in Escherichia coli reveal functional crosstalk among cell envelope biogenesis pathways. PLoS Genet. 7, e1002377 (2011).
13. Nichols, R.J., et al. Phenotypic landscape of a bacterial cell. Cell. 144, 143-56 (2011).
14. Babu, M., Gagarinova, A., Greenblatt, J., & Emili, A. Array-based synthetic genetic screens to map bacterial pathways and functional networks in Escherichia coli. Methods Mol Biol. 765, 125-53 (2011).
15. Datsenko, K.A. & Wanner, B.L. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Natl. Acad. Sci. U.S.A. 97, 6640-5 (2000).
16. Yu, D., et al. An efficient recombination system for chromosome engineering in Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 97, 5978-83 (2000).
17. Typas, A., et al. High-throughput, quantitative analyses of genetic interactions in E. coli. Nat. Methods. 5, 781-787 (2008).
18. Zeghouf, M., et al. Sequential Peptide Affinity (SPA) system for the identification of mammalian and bacterial protein complexes. J. Proteome Res. 3, 463-8 (2004).
19. Davierwala, A.P., et al. In: Nat. Genet. 1147-52 (2005).
20. Breslow, D.K., et al. A comprehensive strategy enabling high-resolution functional analysis of the yeast genome. Nat. Methods. 5, 711-718 (2008).
21. Babu, M., et al. Sequential peptide affinity purification system for the systematic isolation and identification of protein complexes from Escherichia coli. Methods Mol. Biol. 564, 373-400 (2009).
22. Butland, G., et al. Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature. 433, 531-7 (2005).
23. Hu, P., Janga, S.C., Babu, M., Diaz-Mejia, J.J., & Butland, G. Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 7, e1000096 (2009).
24. Anderson, R.P. & Roth, J.R. Tandem genetic duplications in phage and bacteria. Annu. Rev. Microbiol. 31, 473-505 (1977).
25. Boone, C., Bussey, H., & Andrews, B. J. Exploring genetic interactions and networks with yeast. Nat. Rev. Genet. 8, 437-49 (2007).
26. Collins, S.R., et al. Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map. Nature. 446, 806-10 (2007).
27. Le Meur, N. & Gentleman, R. Modeling synthetic lethality. Genome Biol. 9, R135 (2008).
28. Tong, A.H., et al. Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science. 294, 2364-8 (2001).
29. Tong, A.H., et al. Global mapping of the yeast genetic interaction network. Science. 303, 808-13 (2004).
30. Wong, S.L., et al. Combining biological networks to predict genetic interactions. Proc. Natl. Acad. Sci. U.S.A. 101, 15682-7 (2004).
31. van Opijnen, T., Bodi, K.L., & Camilli, A. Tn-seq: high-throughput parallel sequencing for fitness and genetic interaction studies in microorganisms. Nat. Methods. 6, 767-72 (2009).
32. Gagarinova, A. & Emili, A. Genome-scale genetic manipulation methods for exploring bacterial molecular biology. Mol. Biosyst. 8, 1626-38 (2012).
33. Dewey, C.N. Positional orthology: putting genomic evolutionary relationships into context. Brief Bioinform. 12, 401-12 (2011).
34. St Onge, R.P., et al. Systematic pathway analysis using high-resolution fitness profiling of combinatorial gene deletions. Nat. Genet. 39, 199-206 (2007).