The plasticity of global proteome and genome expression analyzed in closely related W3110 and MG1655 strains of a well-studied model organism, Escherichia coli-K12
Introduction
Currently, more than 300 completely sequenced genomes are publicly available and more than four times that number are in the process of being sequenced (Bernal et al., 2001, Liolios et al., 2006). The genomes of closely related species are of particular interest since they lead to the elucidation of genome diversity, evolution and pathogenicity. In the case of the proteobacterium Escherichia coli, five genomes have been determined and thirteen projects are in progress (Bernal et al., 2001, Liolios et al., 2006). Among the completed E. coli genomes, two are from non-pathogenic strains, MG1655 and W3110, which are our loci of interest in this study.
Many subtly different strains are in daily use in numerous laboratories for validating new analytical techniques, provoking critical and unanswered questions such as: do sub-strains with almost identical genome structures exhibit similar behaviour in cellular metabolism? Although E. coli is such a well-studied model organism, and many of the strains in use around the world differ from the strain of origin only in known genetic characteristics, many more differences remain to be explored. A justifiable question is: why do closely related sub-strains of E. coli grow with different efficiencies on the same media, when the characterized genetic differences between them do not affect the growth pattern? Furthermore, there is a surprising lack of information on how global aspects of cell metabolism, protein synthesis and gene expression differ among closely related sub-strains of the same species, which may reveal the complexities of cellular metabolism. To address this lack of information we analyzed the growth, the proteomes and the transcriptome pools of the frequently used laboratory E. coli sub-strains W3110 and MG1655, which originated from W1485, a derivative of E. coli K12 (Fig. 1) (Barbara, 1996). The whole genome sequences of both sub-strains are publicly available (Blattner et al., 1997; Genobase http://ecoli.naist.jp/). Their growth patterns and genome structures are almost identical (Fig. 2). Most of the major differences in genome structures between these two sub-strains result from recombination events mediated by insertion sequences. However, the rate of nucleotide changes between them is estimated to be relatively low (Hayashi et al., 2006, Itoh et al., 1999). Hence, the major question arises: is this high degree of similarity at the nucleotide level reflected in the metabolic phenotype? A further query focused on unravelling the changes resulting from the aforementioned insertion sequences, and subsequently on obtaining a clear view of the regulation of metabolic processes in these closely related laboratory sub-strains. In order to reveal the patterns of protein and gene expression at different levels of growth in the same medium under the same conditions, we analyzed these expression patterns during the exponential and early stationary phases of growth.
A detailed study of the relevant proteomics and genomics showed that the patterns of global protein and gene expression differed considerably between the sub-strains despite their close relationship and absence of significant genomic differences, and despite the provision of strict and controlled growth conditions. Previous studies have demonstrated that the expression levels of many genes show abundant natural variation in species from yeast to humans (Brem et al., 2002, Cheung et al., 2003, Enard et al., 2002, Oleksiak et al., 2002, Schadt et al., 2003, Steinmetz et al., 2002). There is emerging evidence to suggest that mRNA expression patterns are necessary, but not by themselves sufficient, for describing the state of a biological system (Gygi et al., 1999, Ideker et al., 2001). Hence, we included global proteomics analyses. In this study, the genes and proteins showing differential regulation belonged to the functional categories of sigma subunit of RNA polymerase (RpoS)-regulated genes, osmotic stress-related genes, enterobactin-related genes, and genes related to the energy metabolism of E. coli: the glycolysis pathway, the tricarboxylic acid cycle and the glyoxylate bypass.
Section snippets
Strain and medium
E. coli K12 strain W3110 was obtained from DSMZ (The German National Resource Centre for Biological Material); MG1655, obtained from the laboratory of A. Nishimura, had a culture background originating from the laboratory of M. Singer having no physiological defects, such as deletion around the fumarate-nitrate respiration (fnr) regulatory gene (Soupene et al., 2003). Both sub-strains were grown on M9 minimal medium with 0.4% glucose as carbon source in a 7 l bioreactor (MBR Bioreactors).
Expression of RpoS-dependent genes
A set of 76 genes known to be regulated by the sigma factor RpoS (Altuvia et al., 1994, Arnqvist et al., 1994, Castanie-Cornet et al., 1999, Conter et al., 1997, Gordia and Gutierrez, 1996, Hengge-Aronis et al., 1991, Ibanez-Ruiz et al., 2000, Lacour and Landini, 2004, Patten et al., 2004, Rahman et al., 2006, Schellhorn et al., 1998, Strom and Kaasen, 1993, Weber et al., 2005, Yang et al., 1993) were considerably down-regulated in W3110 in comparison to MG1655 during exponential growth phase (
Acknowledgements
We would like to thank Thomas Schäffer and Eberhard Wünsch for their technical assistance. The work was supported by a scholarship from the NRW International Graduate School in Bioinformatics and Genome Research.
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Present address: Institute of Molecular Microbiology and Biotechnology, Westfalian Wilhelms University Muenster, Corrensstr. 3, D-48149 Muenster, Germany.