Genome-scale identification of conditionally essential genes in E. coli by DNA microarrays

Biochemical and Biophysical Research Communications

Volumn 322, Issue 1, 2004, Pages 347-354

  Tong, Xin ^a   Campbell, John W ^b   Balázsi, Gábor ^a   Kay, Krin A ^a   Wanner, Barry L ^c   Gerdes, Svetlana Y ^b   Oltvai, Zoltán N ^a  

^a NORTHWESTERN UNIVERSITY   (United States)

^b Integrated Genomics Inc   (United States)

^c PURDUE UNIVERSITY   (United States)

Author keywords

Aerobic and anaerobic conditions; DNA microarray; E. coli; Essential gene; Transposon mutagenesis

Indexed keywords

DNA; GENE PRODUCT;

ACCELERATION; ARTICLE; BACTERIAL GROWTH; CONTROLLED STUDY; DNA MICROARRAY; ESCHERICHIA COLI; GENE IDENTIFICATION; GENE MAPPING; GENOME; MUTAGENESIS; NONHUMAN; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; RELIABILITY; STANDARD;

AEROBIOSIS; ANAEROBIOSIS; CELL DIVISION; DNA FOOTPRINTING; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, BACTERIAL; GENOME, BACTERIAL; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OXYGEN; PROTEIN FOOTPRINTING; PROTEOME;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; INSERTION SEQUENCES; TRANSPOSONS;

EID: 4143148491     PISSN: 0006291X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bbrc.2004.07.110     Document Type: Article

References (29)

1. C.A. Hutchison, S.N. Peterson, S.R. Gill, R.T. Cline, O. White, C.M. Fraser, H.O. Smith, and J.C. Venter Global transposon mutagenesis and a minimal Mycoplasma genome Science 286 1999 2165 2169
2. G. Giaever, A.M. Chu, L. Ni, C. Connelly, L. Riles, S. Veronneau, S. Dow, A. Lucau-Danila, K. Anderson, and B. Andre Functional profiling of the Saccharomyces cerevisiae Nature 418 2002 387 391
3. E.A. Winzeler, D.D. Shoemaker, A. Astromoff, H. Liang, K. Anderson, B. Andre, R. Bangham, R. Benito, J.D. Boeke, and H. Bussey Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis Science 285 1999 901 906
4. S.K. Kim, J. Lund, M. Kiraly, K. Duke, M. Jiang, J.M. Stuart, A. Eizinger, B.N. Wylie, and G.S. Davidson A gene expression map for Caenorhabditis elegans Science 293 2001 2087 2092
5. R.S. Kamath, A.G. Fraser, Y. Dong, G. Poulin, R. Durbin, M. Gotta, A. Kanapin, N. Le Bot, S. Moreno, and M. Sohrmann Systematic functional analysis of the Caenorhabditis elegans genome using RNAi Nature 421 2003 231 237
6. R.S. Hare, S.S. Walker, T.E. Dorman, J.R. Greene, L.M. Guzman, T.J. Kenney, M.C. Sulavik, K. Baradaran, C. Houseweart, and H. Yu Genetic footprinting in bacteria J. Bacteriol. 183 2001 1694 1706
7. B.J. Akerley, E.J. Rubin, V.L. Novick, K. Amaya, N. Judson, and J.J. Mekalanos A genome-scale analysis for identification of genes required for growth or survival of Haemophilus influenzae Proc. Natl. Acad. Sci. USA 99 2002 966 971
8. V. Smith, D. Botstein, and P.O. Brown Genetic footprinting: a genomic strategy for determining a gene's function given its sequence Proc. Natl. Acad. Sci. USA 92 1995 6479 6483
9. P. Ross-Macdonald, P.S. Coelho, T. Roemer, S. Agarwal, A. Kumar, R. Jansen, K.H. Cheung, A. Sheehan, D. Symoniatis, and L. Umansky Large-scale analysis of the yeast genome by transposon tagging and gene disruption Nature 402 1999 413 418
10. M. Schena, D. Shalon, R.W. Davis, and P.O. Brown Quantitative monitoring of gene expression patterns with a complementary DNA microarray Science 270 1995 467 470
11. J.R. Pollack, C.M. Perou, A.A. Alizadeh, M.B. Eisen, A. Pergamenschikov, C.F. Williams, S.S. Jeffrey, D. Botstein, and P.O. Brown Genome-wide analysis of DNA copy-number changes using cDNA microarrays Nat. Genet. 23 1999 41 46
12. B. Ren, F. Robert, J.J. Wyrick, O. Aparicio, E.G. Jennings, I. Simon, J. Zeitlinger, J. Schreiber, N. Hannett, and E. Kanin Genome-wide location and function of DNA binding proteins Science 290 2000 2306 2309
13. V. Badarinarayana, P.W. Estep III, J. Shendure, J. Edwards, S. Tavazoie, F. Lam, and G.M. Church Selection analyses of insertional mutants using subgenic-resolution arrays Nat. Biotechnol. 19 2001 1060 1065
14. C.M. Sassetti, D.H. Boyd, and E.J. Rubin Comprehensive identification of conditionally essential genes in mycobacteria Proc. Natl. Acad. Sci. USA 98 2001 12712 12717
15. C.M. Sassetti, D.H. Boyd, and E.J. Rubin Genes required for mycobacterial growth defined by high density mutagenesis Mol. Microbiol. 48 2003 77 84
16. K.F. Jensen The Escherichia coli K-12 wild types W3110 and MG1655 have an rph frameshift mutation that leads to pyrimidine starvation due to low pyrE expression levels J. Bacteriol. 175 1993 3401 3407
17. S.Y. Gerdes, M.D. Scholle, M. D'Souza, A. Bernal, M.V. Baev, M. Farrell, O.V. Kurnasov, M.D. Daugherty, F. Mseeh, and B.M. Polanuyer From genetic footprinting to antimicrobial drug targets: examples in cofactor biosynthetic pathways J. Bacteriol. 184 2002 4555 4572
18. I.Y. Goryshin, J. Jendrisak, L.M. Hoffman, R. Meis, and W.S. Reznikoff Insertional transposon mutagenesis by electroporation of released Tn5 transposition complexes Nat. Biotechnol. 18 2000 97 100
19. X. Garriga, R. Eliasson, E. Torrents, A. Jordan, J. Barbe, I. Gibert, and P. Reichard nrdD and nrdG genes are essential for strict anaerobic growth of Escherichia coli Biochem. Biophys. Res. Commun. 229 1996 189 192
20. S.F. Altschul, W. Gish, W. Miller, E.W. Myers, and D.J. Lipman Basic local alignment search tool J. Mol. Biol. 215 1990 403 410
21. R. Overbeek, N. Larsen, T. Walunas, M. D'Souza, G. Pusch, E. Selkov Jr., K. Liolios, V. Joukov, D. Kaznadzey, and I. Anderson The ERGO genome analysis and discovery system Nucleic Acids Res. 31 2003 164 171
22. A.B. Khodursky, B.J. Peter, D. Botstein, P.O. Brown, and C. Yanofsky DNA microarray analysis of gene expression in response to physiological and genetic changes that affect tryptophan metabolism in Escherichia coli Proc. Natl. Acad. Sci. USA 97 2000 12170 12175
23. Y.H. Yang, S. Dudoit, P. Luu, D.M. Lin, V. Peng, J. Ngai, and T.P. Speed Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation Nucleic Acids Res. 30 2002 e15
24. G. Balazsi, K.A. Kay, A.L. Barabasi, and Z.N. Oltvai Spurious spatial periodicity of co-expression in microarray data due to printing design Nucleic Acids Res. 31 2003 4425 4433
25. J. Quackenbush Microarray data normalization and transformation Nat. Genet. 32 Suppl 2002 496 501
26. S.Y. Gerdes, M.D. Scholle, J.W. Campbell, G. Balazsi, E. Ravasz, M.D. Daugherty, A.L. Somera, N.C. Kyrpides, I. Anderson, and M.S. Gelfand Experimental determination and system level analysis of essential genes in Escherichia coli MG1655 J. Bacteriol. 185 2003 5673 5684
27. M. Riley Genes and proteins of Escherichia coli K-12 Nucleic Acids Res. 26 1998 54
28. S.C. Andrews, B.C. Berks, J. McClay, A. Ambler, M.A. Quail, P. Golby, and J.R. Guest A 12-cistron Escherichia coli operon (hyf) encoding a putative proton-translocating formate hydrogenlyase system Microbiology 143 1997 3633 3647
29. D. Sambasivarao, and J.H. Weiner Dimethyl sulfoxide reductase of Escherichia coli: an investigation of function and assembly by use of in vivo complementation J. Bacteriol. 173 1991 5935 5943