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Physiological Studies of Escherichia coli Strain MG1655: Growth Defects and Apparent Cross-Regulation of Gene Expression

Eric Soupene,¹ Wally C. van Heeswijk,^1, Jacqueline Plumbridge,² Valley Stewart,³ Daniel Bertenthal,^1, Haidy Lee,^1, Gyaneshwar Prasad,¹ Oleg Paliy,¹ Parinya Charernnoppakul,¹ and Sydney Kustu^1*

Department of Plant and Microbial Biology, University of California, Berkeley, California 94720-3102,¹ Institut de Biologie Physico-chimique, UPR9073, CNRS, 75005 Paris, France,² Section of Microbiology, University of California, Davis, California 95616-8665³

Received 28 April 2003/ Accepted 2 July 2003

Escherichia coli strain MG1655 was chosen for sequencing because the few mutations it carries (ilvG rfb-50 rph-1) were considered innocuous. However, it has a number of growth defects. Internal pyrimidine starvation due to polarity of the rph-1 allele on pyrE was problematic in continuous culture. Moreover, the isolate of MG1655 obtained from the E. coli Genetic Stock Center also carries a large deletion around the fnr (fumarate-nitrate respiration) regulatory gene. Although studies on DNA microarrays revealed apparent cross-regulation of gene expression between galactose and lactose metabolism in the Stock Center isolate of MG1655, this was due to the occurrence of mutations that increased lacY expression and suppressed slow growth on galactose. The explanation for apparent cross-regulation between galactose and N-acetylglucosamine metabolism was similar. By contrast, cross-regulation between lactose and maltose metabolism appeared to be due to generation of internal maltosaccharides in lactose-grown cells and may be physiologically significant. Lactose is of restricted distribution: it is normally found together with maltosaccharides, which are starch degradation products, in the mammalian intestine. Strains designated MG1655 and obtained from other sources differed from the Stock Center isolate and each other in several respects. We confirmed that use of other E. coli strains with MG1655-based DNA microarrays works well, and hence these arrays can be used to study any strain of interest. The responses to nitrogen limitation of two urinary tract isolates and an intestinal commensal strain isolated recently from humans were remarkably similar to those of MG1655.

Present address: Laboratory for Microbiology, Swammerdam Institute for Life Sciences, University of Amsterdam, 1018 WV Amsterdam, The Netherlands.

Present address: Health Services Research Enhancement Award Program, San Francisco Veterans Affairs Medical Center, San Francisco, CA 94121.

Present address: UC Irvine College of Medicine, Irvine, CA 92697-4089.

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