76 4 Rational Efforts to Streamline the Escherichia coli Genome
44 Gerdes, S.Y., Scholle, M.D., Campbell, J.W., Balazsi, G. et al. (2003) Experimental
determination and system level analysis of essential genes in Escherichia coli
MG1655. J. Bacteriol., 185 , 5673–5684.
45 Baba, T., Ara, T., Hasegawa, M., Takay, Y. et al. (2006) Construction of
Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio
collection. Mol. Syst. Biol., 2 , 0008.
46 Koonin, E.V. (2003) Comparative genomics, minimal gene-sets and the last
universal common ancestor. Nat. Rev. Microbiol., 1 , 127–136.
47 Mizoguchi, H., Sawano, Y., Kato, J., and Mori, H. (2008) Superpositioning
of deletions promotes growth of Escherichia coli with a reduced genome.
DNA Res., 15 , 277–284.
48 McCloskey, D., Palsson, B.O., and Feist, A.H. (2013) Basic and applied uses of
genome-scale metabolic network reconstructions of Escherichia coli. Mol. Syst.
Biol., 9 , 661.
49 Feist, A.M., Herrgard, M.J., Thiele, I., Reed, J.L. et al. (2009) Reconstruction
of biochemical networks in microorganisms. Nat. Rev. Microbiol., 7 , 129–143.
50 Herrgard, M.J., Covert, M.W., and Palsson, B.O. (2004) Reconstruction of
microbial transcriptional regulatory networks. Curr. Opin. Biotechnol., 15 ,
70–77.
51 Thiele, I., Jamshidi, N., Fleming, R.M., and Palsson, B.O. (2009) Genome-
scale reconstruction of Escherichia coli’s transcriptional and translational
machinery: a knowledge base, its mathematical formulation, and its functional
characterization. PLoS Comput. Biol., 5 , e1000312.
52 Kato, J. and Hashimoto, M. (2007) Construction of consecutive deletions of the
Escherichia coli chromosome. Mol. Syst. Biol., 3 , 7.
53 Casjens, S. (2003) Prophages and bacterial genomes: what have we learned so
far? Mol. Microbiol., 49 , 277–300.
54 Cardinale, C.J., Washburn, R.S., Tadigotla, V.R., Brown, L.M. et al. (2008)
Termination factor Rho and its cofactors NusA and NusG silences foreign DNA
in E-coli. Science, 320 , 935–938.
55 Czyz, A., Los, M., Wrobel, B., and Wegrzyn, G. (2001) Inhibition of spontaneous
induction of lambdoid prophages in Escherichia coli cultures: simple procedures
with possible biotechnological applications. BMC Biotech., 1 , 1.
56 Wang, X.X., Kim, Y., Ma, Q., Hong, S.H. et al. (2010) Cryptic prophages help
bacteria cope with adverse environments. Nat. Commun., 1 , 147.
57 Los, M., Czyz, A., Sell, E., Wegrzyn, A. et al. (2004) Bacteriophage
contamination: is there a simple method to reduce its deleterious effects
in laboratory cultures and biotechnological factories? J. Appl. Genet., 45 ,
111–120.
58 Siguier, P., Filee, J., and Chandler, M. (2006) Insertion sequences in prokaryotic
genomes. Curr. Opin. Microbiol., 9 , 526–531.
59 Lynch, M. (2007) The Origins of Genome Architecture, Sinauer Press, Sunderland,
MA.
60 Bhaya, D., Davison, M., and Barrangou, R. (2011) CRISPS-Cas systems in
bacteria and archaea: versatile small RNAs for adaptive defense and regulation.
Annu. Rev. Genet., 45 , 273–297.