Transcription of foreign DNA in Escherichia coli

Genome Research

Volumn 18, Issue 11, 2008, Pages 1798-1805

  Warren, René L ^a   Freeman, John D ^a   Levesque, Roger C ^b   Smailus, Duane E ^a   Flibotte, Stephane ^a   Holt, Robert A ^a  

^a BRITISH COLUMBIA CANCER AGENCY   (Canada)

^b UNIVERSITÉ LAVAL   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA;

ARTICLE; BACTERIAL GENE; ENERGY METABOLISM; ESCHERICHIA COLI; GENE CLUSTER; GENE EXPRESSION; GENE TRANSFER; GENETIC TRANSCRIPTION; HAEMOPHILUS INFLUENZAE; MOLECULAR CLONING; NONHUMAN; OPERON; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN BINDING; PROTEIN MOTIF; PSEUDOMONAS AERUGINOSA; REAL TIME POLYMERASE CHAIN REACTION; UPREGULATION;

CHROMOSOMES, ARTIFICIAL, BACTERIAL; DNA, BACTERIAL; DNA, RECOMBINANT; DNA-DIRECTED RNA POLYMERASES; ESCHERICHIA COLI; GENE EXPRESSION PROFILING; GENE TRANSFER, HORIZONTAL; GENES, BACTERIAL; GENETIC ENGINEERING; HAEMOPHILUS INFLUENZAE; HUMANS; MULTIGENE FAMILY; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROMOTER REGIONS, GENETIC; PSEUDOMONAS AERUGINOSA; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SIGMA FACTOR; SPECIES SPECIFICITY; TRANSCRIPTION, GENETIC;

BACTERIA (MICROORGANISMS); ENTEROBACTERIA PHAGE MU; ESCHERICHIA COLI;

EID: 55549144015     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.080358.108     Document Type: Article

References (28)

1. Bailey, T.L. and Elkan, C. 1994. Fitting a mixture model by expectation maximization to discover motifs in biopolymersin. In Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36. AAAI Press, Menlo Park, CA.
2. Bentley, R. and Meganathan, R. 1982. Biosynthesis of vitamin K (menaquinone) in bacteria. Bacteriol. Rev. 46: 241-280.
3. Chen, I., Christie, P.J., and Dubnau, D. 2005. The ins and outs of DNA transfer in bacteria. Science 310: 1456-1460.
4. Darwin, A.J. 2005. The phage-shock-protein response. Mol. Microbiol. 57: 621-628.
5. The ENCODE Project Consortium. 2007. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447: 799-816.
6. Gibson, D.G., Benders, G.A., Andrews-Pfannkoch, C., Denisova, E.A., Baden-Tillson, H., Zaveri, J., Stockwell, T.B., Brownley, A., Thomas, D.W., Algire, M.A., et al. 2008. Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome. Science 319: 1215-1220.
7. Gross, C., Lonetto, M., and Losick, R. 1992. Sigma factors. In Transcriptional regulation (eds. S.L. McKnight and K.R. Yamamoto), pp. 129-176. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
8. Haddock, B.A. and Jones, C.W. 1977. Bacterial respiration. Bacteriol. Rev. 41: 74-99.
9. Hershberg, R., Bejerano, G., Santos-Zavaleta, A., and Margalit, H. 2001. PromEC: An updated database of Escherichia coli mRNA promoters with experimentally identified transcriptional start sites. Nucleic Acids Res. 29: 277.
10. Holt, R.A., Warren, R.L., Flibotte, S., Missirlis, P.I., and Smailus, D.E. 2007. Rebuilding microbial genomes. Bioessays 29: 580-590.
11. Itaya, M., Tsuge, K., Koizumi, M., and Fujita, K. 2005. Combining two genomes in one cell: Stable cloning of the Synechocystis PCC6803 genome in the Bacillus subtilis 168 genome. Proc. Natl. Acad. Sci. 102: 15971-15976.
12. Itaya, M., Fujita, K., Kuroki, A., and Tsuge, K. 2008. Bottom-up genome assembly using the Bacillus subtilis genome vector. Nat. Methods 5: 41-43.
13. Karlin, S. and Mrazek, J. 2000. Predicted highly expressed genes of diverse prokaryotic genomes. J. Bacteriol. 182: 5238-5250.
14. Kodumal, S.J., Patel, K.G., Reid, R., Menzella, H.G., Welch, M., and Santi, D.V. 2004. Total synthesis of long DNA sequences: Synthesis of a contiguous 32-kb polyketide synthase gene cluster. Proc. Natl. Acad. Sci. 101: 15573-15578.
15. Lartigue, C., Glass, J.I., Alperovich, N., Pieper, R., Parmar, P.P., Hutchison 3rd, C.A., Smith, H.O., and Venter, J.C. 2007. Genome transplantation in bacteria: Changing one species to another. Science 317: 632-638.
16. Maydan, J.S., Flibotte, S., Edgley, M.L., Lau, J., Selzer, R.R., Richmond, T.A., Pofahl, N.J., Thomas, J.H., and Moerman, D.G. 2007. Efficient high-resolution deletion discovery in Caenorhabditis elegans by array comparative genomic hybridization. Genome Res. 17: 337-347.
17. McCarter, L.L. 2006. Regulation of flagella. Curr. Opin. Microbiol. 9: 180-186.
18. Model, P., Jovanovic, G., and Dworkin, J. 1997. The Escherichia coli phage-shock-protein (psp) operon. Mol. Microbiol. 24: 255-261.
19. Morgan, G.J., Hatfull, G.F., Casjens, S., and Hendrix, R.W. 2002. Bacteriophage Mu genome sequence: Analysis and comparison with Mu-like prophages in Haemophilus, Neisseria and Deinococcus. J. Mol. Biol. 317: 337-359.
20. Ochman, H., Lawrence, J.G., and Groisman, E.A. 2000. Lateral gene transfer and the nature of bacterial innovation. Nature 405: 299-304.
21. Ro, D.K., Paradise, E.M., Ouellet, M., Fisher, K.J., Newman, K.L., Ndungu, J.M., Ho, K.A., Eachus, R.A., Ham, T.S., Kirby, J., et al. 2006. Production of the antimalarial drug precursor artemisinic acid in engineered yeast. Nature 440: 940-943.
22. Salgado, H., Santos-Zavaleta, A., Gama-Castro, S., Millán- Zárate, D., Díaz-Peredo, E., Sánchez-Solano, F., Pérez-Rueda, E., Bonavides-Martínez, C., and Collado-Vides, J. 2001. RegulonDB (version 3.2): Transcriptional regulation and operon organization in Escherichia coli K-12. Nucleic Acids Res. 29: 72-74.
23. Schneider, T.D. and Stephens, R.M. 1990. Sequence logos: A new way to display consensus sequences. Nucleic Acids Res. 18: 6097-6100.
24. 70 promoters. Nucleic Acids Res. 35: 771-788.
25. Sorek, R., Zhu, Y., Creevey, C.J., Francino, M.P., Bork, P., and Rubin, E.M. 2007. Genome-wide experimental determination of barriers to horizontal gene transfer. Science 318: 1449-1452.
26. Sorek, R., Kunin, V., and Hugenholtz, P. 2008. CRISPR - A widespread system that provides acquired resistance against phages in bacteria and archaea. Nat. Rev. Microbiol. 6: 181-186.
27. Soutourina, O.A. and Bertin, P.N. 2003. Regulation cascade of flagellar expression in Gram-negative bacteria. FEMS Microbiol. Rev. 27: 505-523.
28. Zeeberg, B.R., Qin, H., Narasimhan, S., Sunshine, M., Cao, H., Kane, D.W., Reimers, M., Stephens, R.M., Bryant, D., Burt, S.K., et al. 2005. High-Throughput GoMiner, an "industrial-strength" integrative gene ontology tool for interpretation of multiple-microarray experiments, with application to studies of Common Variable Immune Deficiency (CVID). BMC Bioinformatics 6: 168. doi: 10.1186/1471-2105-6-168.