Development of a system for discovery of genetic interactions for essential genes in Escherichia coli K-12

Genes and Genetic Systems

Volumn 88, Issue 4, 2013, Pages 233-240

  Yong, Han Tek ^a   Yamamoto, Natsuko ^a,c   Takeuchi, Rikiya ^a   Hsieh, Yi Ju ^b,d   Conrad, Tom M ^a   Datsenko, Kirill A ^b   Nakayashiki, Toru ^a   Wanner, Barry L ^b   Mori, Hirotada ^a  

^a NARA INSTITUTE OF SCIENCE AND TECHNOLOGY   (Japan)

^b PURDUE UNIVERSITY   (United States)

^c OSAKA UNIVERSITY   (Japan)

^d STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Complementing F plasmid; Epistasis; Fitness; Gene function

Indexed keywords

ARTICLE; BACTERIAL GENE; BACTERIUM CONJUGATION; BACTERIUM MUTANT; CITRIC ACID CYCLE; DNA REPLICATION; EPISTASIS; ESCHERICHIA COLI K 12; ESSENTIAL GENE; FLOW CYTOMETRY; GENE EXPRESSION; GENE FUNCTION; GENE INTERACTION; GENE MUTATION; GENOME ANALYSIS; HOMOLOGOUS RECOMBINATION; NONHUMAN; OXIDATIVE PHOSPHORYLATION; PLASMID; RNA DEGRADATION;

CONJUGATION, GENETIC; EPISTASIS, GENETIC; ESCHERICHIA COLI K12; ESCHERICHIA COLI PROTEINS; F FACTOR; GENE EXPRESSION REGULATION, BACTERIAL; GENE KNOCKOUT TECHNIQUES; GENE REGULATORY NETWORKS; GENES, BACTERIAL; GENES, ESSENTIAL; GENOME, BACTERIAL; MUTATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REPRODUCIBILITY OF RESULTS;

EID: 84893049358     PISSN: 13417568     EISSN: 18805779     Source Type: Journal    
DOI: 10.1266/ggs.88.233     Document Type: Article

References (30)

1. Baba, T., Ara, T., Hasegawa, M., Takai, Y., Okumura, Y., Baba, M., Datsenko, K. A., Tomita, M., Wanner, B. L., and Mori, H. (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol. Syst. Biol. 2, 2006.
2. Babu, M., Diaz-Mejia, J. J., Vlasblom, J., Gagarinova, A., Phanse, S., Graham, C., Yousif, F., Ding, H., Xiong, X., Nazarians-Armavil, A., et al. (2011) Genetic interaction maps in Escherichia coli reveal functional crosstalk among cell envelope biogenesis pathways. PLoS Genet. 7, e1002377.
3. Bakal, C., Linding, R., Llense, F., Heffern, E., Martin-Blanco, E., Pawson, T., and Perrimon, N. (2008) Phosphorylation networks regulating JNK activity in diverse genetic backgrounds. Science 322, 453-456.
4. Baryshnikova, A., Costanzo, M., Kim, Y., Ding, H., Koh, J., Toufighi, K., Youn, J. Y., Ou, J., San Luis, B. J., Bandyopadhyay, S., et al. (2010) Quantitative analysis of fitness and genetic interactions in yeast on a genome scale. Nat. Methods 7, 1017-1024.
5. Butland, G., Babu, M., Diaz-Mejia, J. J., Bohdana, F., Phanse, S., Gold, B., Yang, W., Li, J., Gagarinova, A. G., Pogoutse, O., et al. (2008) eSGA: E. coli synthetic genetic array analysis. Nat. Methods 5, 789-795.
6. Byrne, A. B., Weirauch, M. T., Wong, V., Koeva, M., Dixon, S. J., Stuart, J. M., and Roy, P. J. (2007) A global analysis of genetic interactions in Caenorhabditis elegans. J. Biol. 6, 8. PM:17897480.
7. Costanzo, M., Baryshnikova, A., Bellay, J., Kim, Y., Spear, E. D., Sevier, C. S., Ding, H., Koh, J. L., Toufighi, K., Mostafavi, S., et al. (2010) The genetic landscape of a cell. Science 327, 425-431.
8. Datsenko, K. A., and Wanner, B. L. (2000) One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Natl. Acad. Sci. USA 97, 6640-6645.
9. Davierwala, A. P., Haynes, J., Li, Z., Brost, R. L., Robinson, M. D., Yu, L., Mnaimneh, S., Ding, H., Zhu, H., Chen, Y., et al. (2005) The synthetic genetic interaction spectrum of essential genes. Nat. Genet. 37, 1147-1152.
10. Dekel, E., and Alon, U. (2005) Optimality and evolutionary tuning of the expression level of a protein. Nature 436, 588-592.
11. Dixon, S. J., Costanzo, M., Baryshnikova, A., Andrews, B., and Boone, C. (2009) Systematic mapping of genetic interaction networks. Annu. Rev. Genet. 43, 601-625.
12. Haldimann, A., and Wanner, B. L. (2001) Conditional-replication, integration, excision, and retrieval plasmid-host systems for gene structure-function studies of bacteria. J. Bacteriol. 183, 6384-6393.
13. Huang, D. W., Sherman, B. T., and Lempicki, R. A. (2009a) Systematic and integrative analysis of large gene lists using DAVID Bioinformatics Resources. Nature Protoc. 4, 44-57.
14. Huang, D. W., Sherman, B. T., and Lempicki, R. A. (2009b) Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res. 37, 1-13.
15. Jeong, H., Mason, S. P., Barabasi, A. L., and Oltvai, Z. N. (2001) Lethality and centrality in protein networks. Nature 411, 41-42.
16. Kawasaki, Y., Wada, C., and Yura, T. (1990) Roles of Escherichia coli heat shock proteins DnaK, DnaJ and GrpE in mini-F plasmid replication. Mol. Gen. Genet. 220, 277-282.
17. Kitagawa, M., Ara, T., Arifuzzaman, M., Ioka-Nakamichi, T., Inamoto, E., Toyonaga, H., and Mori, H. (2005) Complete set of ORF clones of Escherichia coli ASKA library (a complete set of E. coli K-12 ORF archive): unique resources for biological research. DNA Res. 12, 291-299.
18. Mani, R., St. Onge, R. P., Hartman, J. L., Giaever, G., and Roth, F. P. (2008) Defining genetic interaction. Proc. Natl. Acad. Sci. USA 105, 3461-3466.
19. Michaut, M., and Bader, G. D. (2012) Multiple genetic interaction experiments provide complementary information useful for gene function prediction. PLoS Comput. Biol. 8, e1002559.
20. Mori, H., Kondo, A., Ohshima, A., Ogura, T., and Hiraga, S. (1986) Structure and function of the F plasmid genes essential for partitioning. J. Mol. Biol. 192, 1-15.
21. Nakayashiki, T., Wanner, B. L., and Mori, H. (2013) Genome-wide screening with hydroxyurea reveals a link between nonessential ribosomal proteins and reactive oxygen species production. J. Bacteriol. 195, 1226-1235.
22. Ogura, T., and Hiraga, S. (1983) Partition mechanism of F plasmid: two plasmid gene-encoded products and a cis-acting region are involved in partition. Cell 32, 351-360.
23. Pan, X., Yuan, D. S., Ooi, S. L., Wang, X., Sookhai-Mahadeo, S., Meluh, P., and Boeke, J. D. (2007) dSLAM analysis of genome-wide genetic interactions in Saccharomyces cerevisiae. Methods 41, 206-221.
24. Roguev, A., Bandyopadhyay, S., Zofall, M., Zhang, K., Fischer, T., Collins, S. R., Qu, H., Shales, M., Park, H.-O., Hayles, J., et al. (2008) Conservation and rewiring of functional modules revealed by an epistasis map in fission yeast. Science 322, 405-410.
25. Schuldiner, M., Collins, S. R., Thompson, N. J., Denic, V., Bhamidipati, A., Punna, T., Ihmels, J., Andrews, B., Boone, C., Greenblatt, J. F., Weissman, J. S., and Krogan, N. J. (2005) Exploration of the function and organization of the yeast early secretory pathway through an epistatic miniarray profile. Cell 123, 507-519.
26. Tong, A. H., Evangelista, M., Parsons, A. B., Xu, H., Bader, G. D., Page, N., Robinson, M., Raghibizadeh, S., Hogue, C. W., Bussey, H., Andrews, B., Tyers, M., and Boone, C. (2001) Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science 294, 2364-2368.
27. Tong, A. H., Lesage, G., Bader, G. D., Ding, H., Xu, H., Xin, X., Young, J., Berriz, G. F., Brost, R. L., Chang, M., et al. (2004) Global mapping of the yeast genetic interaction network. Science 303, 808-813.
28. Typas, A., Nichols, R. J., Siegele, D. A., Shales, M., Collins, S. R., Lim, B., Braberg, H., Yamamoto, N., Takeuchi, R., Wanner, B. L., et al. (2008) High-throughput, quantitative analyses of genetic interactions in E. coli. Nat. Methods 5, 781-787.
29. Uga, H., Matsunaga, F., and Wada, C. (1999) Regulation of DNA replication by iterons: an interaction between the ori2 and incC regions mediated by RepE-bound iterons inhibits DNA replication of mini-F plasmid in Escherichia coli. EMBO J. 18, 3856-3867.
30. Yamamoto, N., Nakahigashi, K., Nakamichi, T., Yoshino, M., Takai, Y., Touda, Y., Furubayashi, A., Kinjyo, S., Dose, H., Hasegawa, M., et al. (2009) Update on the Keio collection of Escherichia coli single-gene deletion mutants. Mol. Syst. Biol. 5, 335.