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Growth of Escherichia coli MG1655 on LB medium: monitoring utilization of amino acids, peptides, and nucleotides with transcriptional microarrays

  • Genomics and Proteomics
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Abstract

Analysis of gene expression data related to assimilation and biosynthesis of nitrogen-containing compounds amino acids, peptides, and nucleotides was used to monitor availability of these nutrients to Escherichia coli MG1655 growing on Luria–Bertani medium. The data indicate that free amino acids and nucleotides only transiently support the nitrogen requirement for growth and are no longer available by 3.5 h of fermentation. The resulting shortage of available nitrogen sources induces the Ntr response, which involves induction of the glnALG, glnK-amtB, dppABCDF, and oppABCDF operons as well as the genes coding for outer membrane proteins, porins OmpA and OmpC, and proteases OmpP and OmpT. The increased uptake of peptides facilitated by the products of dppABCDF, oppABCDF, ompA, ompC, ompP, and ompT alleviates nitrogen limitation of the growth.

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References

  • Abouhamad WN, Manson MD (1994) The dipeptide permease of Escherichia coli closely resembles other bacterial transport systems and shows growth-phase-dependent expression. Mol Microbiol 14:1077–1092

    Article  CAS  Google Scholar 

  • Baev MV, Baev D, Jancso Radek A, Campbell JW (2006) Growth of Escherichia coli MG1655 on LB medium: monitoring utilization of sugars, alcohols and organic acids with transcriptional microarrays. Appl Microbiol Biotechnol (in press). DOI 10.1007/s00253-006-0317-6

  • Castano I, Bastarrachea F (1984) glnF–lacZ fusions in Escherichia coli: studies on glnF expression and its chromosomal orientation. Mol Gen Genet 195:228–233

    Article  CAS  Google Scholar 

  • Cox WG, Singer VL (2004) Fluorescent DNA hybridization probe preparation using amine modification and reactive dye coupling. Biotechniques 36:114–122

    Article  CAS  Google Scholar 

  • Diehl F, Grahemann S, Beier M, Hoheisel JD (2001) Manufacturing DNA microarrays at high spot homogeneity and reduced background signal. Nucleic Acids Res 29:e38

    Article  CAS  Google Scholar 

  • Gottesman S (1996) Proteases and their targets in Escherichia coli. Annu Rev Genet 30:465–506

    Article  CAS  Google Scholar 

  • Han L, Doverskog M, Enfors SO, Haggstrom L (2002) Effect of glycine on the cell yield and growth rate of Escherichia coli: evidence for cell-density-dependent glycine degradation as determined by 13C NMR spectroscopy. J Biotechnol 92:237–249

    Article  CAS  Google Scholar 

  • He B, Zalkin H (1994) Regulation of Escherichia coli purA by purine repressor, one component of a dual control mechanism. J Bacteriol 76:1009–1013

    Article  Google Scholar 

  • Hedge P, Qi R, Abernathy K, Gay G, Dharap S, Gaspard R, Hughes GE, Snesrud E, Lee N, Quackenbush J (2000) A concise guide to cDNA microarray analysis. Biotechniques 29:548–562

    Article  Google Scholar 

  • Jishage M, Iwata A, Ueda S, Ishihama A (1996) Regulation of RNA polymerase sigma subunit synthesis in Escherichia coli: intracellular levels of four species of sigma subunit under various growth conditions. J Bacteriol 178:5447–5451

    Article  CAS  Google Scholar 

  • Kaufmann A, Stierhof Y-D, Henning U (1994) New outer-membrane associated protease of Escherichia coli K-12. J Bacteriol 176:359–367

    Article  CAS  Google Scholar 

  • Kerr MK (2003) Experimental design to make the most of microarray studies. In: Brownstein MJ, Khodursky AB (eds) Functional genomics: methods and protocols, vol 224. Humana, Totawa, pp 137–147

    Chapter  Google Scholar 

  • Khodursky AB, Bernstein JA, Peter BJ, Rhodius V, Wendisch F, Zimmer DP (2003) Escherichia coli spotted double-strand DNA microarrays: RNA extraction, labeling, hybridization, quality control and data management. In: Brownstein MJ, Khodursky AB (eds) Functional genomics: methods and protocols, vol 224. Humana, Totawa, pp 61–78

    Chapter  Google Scholar 

  • Lendenmann U, Snozzi M, Egli T (2000) Growth kinetics of Escherichia coli with galactose and several other sugars in carbon-limited chemostat culture. Can J Microbiol 46:72–80

    Article  CAS  Google Scholar 

  • McFall E, Newman EB (1996) Amino acids as carbon sources. In: Neidhardt FC, Curtis R III, Ingraham JL, Lin ECC, Low KB, Magasanik B, Reznikoff WS, Riley M, Schaschter M, Umbarger HE (eds) Escherichia coli and Salmonella: cellular and molecular biology, 2nd edn. ASM, Washington, DC, pp 358–379

    Google Scholar 

  • Mehra RK, Drabble WT (1981) Dual control of the gua operon of Escherichia coli K12 by adenine and guanine nucleotides. J Gen Microbiol 123:27–37

    CAS  PubMed  Google Scholar 

  • Miller JH (1972) Experiments in molecular genetics. Cold Spring Harbor Laboratory, Cold Spring Harbor

    Google Scholar 

  • Neuhard J, Kelln RA (1996) Biosynthesis and conversion of pyrimidines. In: Neidhardt FC, Curtis R III, Ingraham JL, Lin ECC, Low KB, Magasanik B, Reznikoff WS, Riley M, Schaschter M, Umbarger HE (eds) Escherichia coli and Salmonella: cellular and molecular biology, 2nd edn. ASM, Washington, DC, pp 580–599

    Google Scholar 

  • Newman EB, Walker C (1982) l-Serine degradation in Escherichia coli K-12: a combination of l-serine, glycine and leucine used as a source of carbon. J Bacteriol 151:777–782

    Article  CAS  Google Scholar 

  • Oliver DB (1996) Periplasm. In: Neidhardt FC, Curtis R III, Ingraham JL, Lin ECC, Low KB, Magasanik B, Reznikoff WS, Riley M, Schaschter M, Umbarger HE (eds) Escherichia coli and Salmonella: cellular and molecular biology, 2nd edn. ASM, Washington, DC, pp 88–103

    Google Scholar 

  • Olson ER, Dunyak DS, Jurrs LM, Poorman RA (1991) Identification and characterization of ddpA, an Escherichia coli gene encoding a periplasmic dipeptide transport protein. J Bacteriol 173:234–244

    Article  CAS  Google Scholar 

  • Payne JW, Smith MW (1994) Peptide transport by micro-organisms. Adv Microb Physiol 36:1–80

    Article  CAS  Google Scholar 

  • Prüβ BM, Nelms JM, Park C, Wolfe A (1994) Mutations in NADH:ubiquinone oxidoreductase of Escherichia coli affect growth on mixed amino acids. J Bacteriol 176:2143–2150

    Article  Google Scholar 

  • Reitzer L (2003) Nitrogen assimilation and global regulation in Escherichia coli. Annu Rev Microbiol 57:155–176

    Article  CAS  Google Scholar 

  • Reitzer L, Schneider BL (2001) Metabolic contest and possible physiological themes of σ54-dependent genes in Escherichia coli. Microbiol Mol Biol Rev 65:422–444

    Article  CAS  Google Scholar 

  • Urbanowski ML, Stauffer LT, Stauffer GV (2000) The gcvB gene encodes a small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli. Mol Microbiol 37:856–868

    Article  CAS  Google Scholar 

  • Zalkin H, Nygaard P (1996) Biosynthesis of purine nucleotides. In: Neidhardt FC, Curtis R III, Ingraham JL, Lin ECC, Low KB, Magasanik B, Reznikoff WS, Riley M, Schaschter M, Umbarger HE (eds) Escherichia coli and Salmonella: cellular and molecular biology, 2nd edn. ASM, Washington, DC, pp 561–579

    Google Scholar 

  • Zimmer DP, Soupene E, Lee HL, Wendisch VF, Khodursky AB, Peter BJ, Bender RA, Kustu S (2000) Nitrogen regulatory protein C-controlled genes of Escherichia coli: scavenging as a defense against nitrogen limitation. Proc Natl Acad Sci U S A 97:14674–14679

    Article  CAS  Google Scholar 

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Author notes

  1. Dmitry Baev

    Present address: IBM Toronto Software Lab, 8200 Warden Ave., Markham, ON, L6G 1C7, Canada

  2. Agnes Jansco Radek

    Present address: Epicentre Technologies, 726 Post Road, Madison, WI, 53713, USA

  3. John W. Campbell

    Present address: Scarab Genomics LLC, 1202 Ann St., Madison, WI, 53713, USA

Authors and Affiliations

  1. Integrated Genomics Inc.,, 2201 W. Campbell Park Drive, Chicago, IL, 60612, USA

    Mark V. Baev, Agnes Jansco Radek & John W. Campbell

  2. Department of Computer Science, University of Toronto, Ontario, Canada

    Dmitry Baev

Authors
  1. Mark V. Baev
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  2. Dmitry Baev
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  4. John W. Campbell
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Correspondence to Mark V. Baev.

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Baev, M.V., Baev, D., Jansco Radek, A. et al. Growth of Escherichia coli MG1655 on LB medium: monitoring utilization of amino acids, peptides, and nucleotides with transcriptional microarrays. Appl Microbiol Biotechnol 71, 317–322 (2006). https://doi.org/10.1007/s00253-005-0310-5

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  • DOI: https://doi.org/10.1007/s00253-005-0310-5

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