Analysis of the escherichia coli response to glycerol pulse in continuous, high-cell density culture using a multivariate approach

Biotechnology and Bioengineering

Volumn 102, Issue 3, 2009, Pages 910-922

  Guebel, Daniel V ^a   Cánovas, Manuel ^b   Torres, Néstor V ^c  

^a Biotechnology Counseling Services   (Argentina)

^b UNIVERSITY OF MURCIA   (Spain)

^c UNIVERSIDAD DE LA LAGUNA   (Spain)

Author keywords

Acetate; Carnitine; Crotonobetaine; Escherichia coli; Fumarate; Gene regulatory network; Glycerol transport; Multivariate analysis; Orthogonal signal correction (OSC); Partial least squares regression (PLS); Polyamines; Principal component analysis (PCA)

Indexed keywords

ACETATE; CARNITINE; CROTONOBETAINE; FUMARATE; GENE REGULATORY NETWORK; GLYCEROL TRANSPORT; MULTIVARIATE ANALYSIS; ORTHOGONAL SIGNAL CORRECTION (OSC); PARTIAL LEAST-SQUARES REGRESSION (PLS); POLYAMINES; PRINCIPAL COMPONENT ANALYSIS (PCA);

AMINES; BIOCHEMICAL ENGINEERING; BIOCHEMISTRY; CELL CULTURE; CLUSTER ANALYSIS; COMPUTATIONAL FLUID DYNAMICS; CONTINUOUS CELL CULTURE; DECISION MAKING; ENZYMES; ESCHERICHIA COLI; ETHANOL; GLYCEROL; MULTIVARIANT ANALYSIS; NEURAL NETWORKS; REGRESSION ANALYSIS; WINDOWS;

PRINCIPAL COMPONENT ANALYSIS;

ACETIC ACID; ACETYL COENZYME A SYNTHETASE; ADENOSINE TRIPHOSPHATE; ALCOHOL; BETAINE DERIVATIVE; CARNITINE; CROTONOBETAINE; FORMIC ACID; FUMARIC ACID; GLYCEROL; HYDROLYASE; ISOCITRATE DEHYDROGENASE; ISOCITRATE LYASE; LACTIC ACID; NICOTINAMIDE ADENINE DINUCLEOTIDE; PHOSPHATE ACETYLTRANSFERASE; POLYAMINE; REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE; UNCLASSIFIED DRUG;

ARTICLE; BACTERIAL STRAIN; BIOSYNTHESIS; CELL CULTURE; CELL DENSITY; DOWN REGULATION; ESCHERICHIA COLI; KINETICS; METABOLITE; MULTIVARIATE ANALYSIS; NONHUMAN; STRESS; TIME; TRANSPORT KINETICS;

ALGORITHMS; CLUSTER ANALYSIS; ESCHERICHIA COLI; GENE REGULATORY NETWORKS; GLYCEROL; KINETICS; LEAST-SQUARES ANALYSIS; MULTIVARIATE ANALYSIS; PRINCIPAL COMPONENT ANALYSIS; STRESS, PHYSIOLOGICAL;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI;

EID: 60349106410     PISSN: 00063592     EISSN: 10970290     Source Type: Journal    
DOI: 10.1002/bit.22120     Document Type: Article

References (58)

1. Abdi H. 2003. Partial least squares (PLS) regression. In: Lews-Beck M, Bryman A, Futing T, editors. Encyclopedia of social sciences research methods. Thousand Oaks (CA): Sage. pp. 792-795.
2. Brereton R. 2003. Data analysis for the laboratory to chemistry plant. Chichester, UK: Wiley. p 183-229.
3. Canovas M, Maiquez JR, Obón JM, Iborra JL. 2002. Modeling of the biotransformation of crotonobetaine into L(-)-carnitine by Escherichia coli strains. Biotechnol Bioeng 77:327-336.
4. Cánovas M, Sevilla A, Bernal V, Iborra JL. 2006. Role of the energetic pools in the production of L-carnitine by Escherichia coli. Metabol Eng 8:603-618.
5. Cánovas M, Bernal V, Sevilla A, Iborra JL. 2007. Salt stress effects on the central and carnitine metabolisms of Escherichia coli. Biotechnol Bioeng 96:722-737.
6. Chan C, Hwang DH, Stephanopoulos GN, Yarmush ML, Stephanopoulos G. 2003. Application of multivariate analysis to optimize function of cultured hepatocytes. Biotechnol Prog 19:580-598.
7. Chesbro W. 1988. The domains of slow bacterial growth. Can J Microbiol 34:427-435.
8. de la Vega AL, Delcour AH. 1996. Polyamines decrease Escherichia coli outer membrane permeability. J Bacteriol 178:3715-3721.
9. D'haeselee P. 2005. How does gene expression clustering work? Nat Biot 23:1499-1501.
10. Eriksson L, Antti H, Gottfries J, Holmes E, Johansson E, Lindgren F, Long I, Lundstedt T, Trygg J, Wold S. 2004. Using chemometrics for navigating in the large data sets of genomics, proteomics, and metabolomics. Anal Bioanal Chem 380:419-429.
11. Geladi P, Kowalski B. 1986. Partial least squares: A tutorial. Anal Chim Acta 185:1-17.
12. Goh EB, Bledsoe PJ, Chen LL, Gyaneshwar P, Stewart V, Igo MM. 2005. Hierarchical control of anaerobic gene expression in Escherichia coli K-12: The nitrate-responsive NarX-NarL regulatory system represses
13. synthesis of the fumarate-responsive DcuS-DcuR regulatory system. J Bacteriol 187:4890-4899.
14. Golovastov VV, Mikhaleva NI, Kadyrova LY, Nesmeyanova MA. 2000. The major phospholipid of Escherichia coli, phosphatidylethanolamine, is required for efficient production and secretion of alkaline phosphatase. Biochem (Moscow) 65:1097-1104.
15. Guebel DV. 2004. Canonical sensitivities: A useful tool to deal with large perturbations in metabolic network modeling. In Silico Biol 4(2):163-182. Available in http://www.bioinfo.de/isb/2004040015/.
16. Guebel DV, Torres NV, Cánovas M. 2006. Modeling analysis of the L(-)- carnitine production process by Esherichia coli. Process Biochem 41: 281-288.
17. Hengge-Aronis R. 2002. Signal transduction and regulatory mechanisms involvedincontrolofthesigma(S) (RpoS) subunit of RNA polymerase. Microbiol Mol Biol Rev 66:373-395.
18. Höskuldsson A. 2004. PLS regression and the covariance. Homepage of Chemometrics. Editorial July. Available in: http://acc.umu.se/~tnktg/ Chemometrics/Editorial.
19. Hwang DH, Stephanopoulos G, Chan C. 2004. Inverse modeling using multi-block PLS to determine the environmental conditions that provide optimal cellular function. Bioinformatics 20:487-499.
20. Igarashi K, Kashiwagi K. 2006. Polyamine Modulon in Escherichia coli: Genes involved in the stimulation of cell growth by polyamines. J Biochem (Tokyo) 139:11-16.
21. Ihseen J, Eggli T. 2004. Specific growth rate and not cell density controls the general stress response in E. coli. Microbiology 150:1637-1648.
22. Iyer R, Wu Z, Woster PM, Delcour AH. 2000. Molecular basis for the polyamine-ompF porin interactions: Inhibitor and mutant studies. J Mol Biol 297:933-945.
23. Johnson RA, Wichner DW. 1998a. Applied multivariate statistical analysis. 4th edition. Englewood Cliffs, NJ: Prentice Hall. pp. 458-512.
24. Johnson RA, Wichner DW. 1998b. Applied multivariate statistical analysis. 4th edition. Englewood Cliffs, NJ: Prentice Hall. pp. 726-798.
25. Jørgensen B, Goegebeur Y. 2007. Partial least squares regression (Model PLS2). In: Multivariate data analysis and chemometrics. Department of Statistics, Syddansk University, Denmark: Available at: http://statmaster.sdu. dk/courses/STO2/module08/module.pdf.
26. Karp PD, Keseler IM, Shearer A, Latendresse M, Krummenacker M, Paley SM, Paulsen I, Collado-Vides J, Gama-Castro S, Peralta-Gil M, Santos-Zavaleta A, Peñaloza-Spínola MI, Bonavides-Martinez C, Ingraham J. 2007. Multidimensional annotation of the Escherichia coli K-12 genome. Nucleic Acids Res 35:7577-7590.
27. Kumari S, Beatty CM, Browning DF, Busby SJ, Simel EJ, Hovel-Miner G, Wolfe AJ. 2000a. Regulation of acetyl coenzyme A synthetase in Escherichia coli. J Bacteriol 182:4173-4179.
28. Kumari S, Simel EJ, Wolfe AJ. 2000b. Sigma(70) is the principal sigma factor responsible for transcription of acs, which encodes acetyl coenzyme A synthetase in Escherichia coli. J Bacteriol 182:551-554.
29. Lagosky PA, Chang FN. 1980. Influence of amino acid starvation on guanosine 5'-diphosphate 3'-diphosphate basal-level synthesis in Escherichia coli. J Bacteriol 144:499-508.
30. Lange R, Hengge-Aronis R. 1994. The cellular concentration of the sigma S subunit of RNA polymerase in Escherichia coli is controlled at the levels of transcription, translation, and protein stability. Genes Dev 8:1600-1612.
31. Larson TJ, Ehrmann M, Boos W. 1983. Periplasmic glycerophosphodiester phosphodiesterase of Escherichia coli, a new enzyme of the glp regulon. J Biol Chem 258:5428-5432.
32. Li Z, Chan C. 2004. Integrating gene expression and metabolic profiles. J Biol Chem 279:27124-27137.
33. Lu D, Grayson P, Schulten K. 2003. Glycerol conductance and physical asymmetry of the Escherichia coli glycerol facilitator GlpF. Biophys J 85:2977-2987.
34. Ma HW, Buer J, Zeng AP. 2004. Hierarchical structure and modules in the Escherichia coli transcriptional regulatory network revealed by a new top-down approach. BMC Bioinformatics 5:199.
35. Mikhaleva N. 2001. Depletion of phosphatidylethanolamine affects secretion of Escherichia coli alkaline phosphatase and its transcriptional expression. FEBS Lett 493:85-90.
36. Persson A, Molin G, Weibull C. 1990. Physiological and morphological changes induced by nutrient limitation of Pseudomonas fluorescens 378 in continuous culture. Appl Envir Microbiol 56:686-692.
37. Phue JN, Shiloach JJ. 2004. Transcription levels of key metabolic genes are the cause for different glucose utilization pathways in E. coli B (BL21) and E. coli K (JM109). J Biotechnol 109:21-30.
38. Postma PW, Lengeler JW, Jacobson GR. 1996. Phosphoenolpyruvate: Carbohydrate phosphotransferase systems. In: Neidhardt FC, Curtiss R III, Ingraham JL, Lin ECC, Low KB, Magasanik B, Reznikoff WS, Riley M, Schaechter M, Umbarger HE, editors. Escherichia coli and Salmonella: Cellular and molecular biology. 2nd edition. Washington, DC: ASM Press. p. 1149-1174.
39. Prost JF, Nègre D, Oudot C, Murakami K, Ishihama A, Cozzone AJ, Cortay JC. 1999. Cra-dependent transcriptional activation of the icd gene of Escherichia coli. J Bacteriol 181:893-898.
40. Robertson DG, Reily MD, Baker JD. 2007. Metabolomics in pharmaceutical discovery and development. J Proteome Res 6:526-539.
41. Schlosser PM, Holcomb T, Bailey JE. 1993. Determining metabolic sensitivity coefficients directly from experimental data. Biotechnol Bioeng 41:1027-1038.
42. Sevilla A, Schmid JW, Mauch K, Iborra JL, Reuss M, Cánovas M. 2005. Model of central and trimethylammonium metabolism for optimizing L-carnitine production by E. coli. Metab Eng 7:401 -425.
43. Terui Y, Higashi K, Taniguchi S, Shigemasa A, Nishimura K, Yamamoto K, Kashiwagi K, Ishihama A, Igarashi K. 2007. Enhancement of the synthesis of RpoN, Cra, and H-NS by polyamines at the level of translation in Escherichia coli cultured with glucose and glutamate. J Bacteriol 189:2359-2368.
44. Teschendorff AE, Jounée M, Absil PA, Sepulchre R, Caldas C. 2007. Elucidating the altered transcriptional programs in breast cancer using independent component analysis. PLoS Comput Biol 3(8): e161.
45. Tkachenko AG, Fedotova MV. 2007. Dependence of protective functions of Escherichia coli polyamines on strength of stress caused by superoxide radicals. Biochem (Moscow) 72:109-116.
46. Tkachenko AG, Pozhidaeva ON, Shumkov MS. 2006. Role of polyamines in formation of multiple antibiotic resistance of Escherichia coli under stress conditions. Biochem (Moscow) 71:1042-1049.
47. Torroglosa T. 2004. Biotransformation de compuestos de trimetilamonio con cepas de E. coli para la producción de L(-)carnitina. PhD thesis. University of Murcia. Spain.
48. Trygg J. 2002. Have you ever wondered why PLS sometimes needs more than one component for a single-y vector? Homepage of Chemo-metrics, Editorial February. Available at: http://www.chemometrics.se/editorial/feb2002.html.
49. Trygg J, Wold S. 2002. Orthogonal projections to latent structures O-PLS. J Chemom 16:119-128.
50. van der Werf MJ, Jellema RH, Hankemeier T. 2005. Microbial metabolomics: Replacing trial-and-error by the unbiased selection and ranking of targets. J Ind Microbiol Biotechnol 32:234-252.
51. van Verseveld HW, Chesbro WR, Braster M, Stouthamer AH. 1984. Eubacteria have 3 growth modes keyed to nutrient flow. Consequences for the concept of maintenance and maximal growth yield. Arch Microbiol 137:176-184.
52. Vemuri GN, Altman E, Sangurdekar DP, Khodursky AB, Eiteman MA. 2006. Overflow metabolism in Escherichia coli during steady-state growth: Transcriptional regulation and effect of the redox ratio. Appl Environ Microbiol 72:3653-3661.
53. Voegle RT, Sweet GD, Boos W. 1993. Glycerol kinase of Escherichia coli is activated by interaction with the glycerol facilitator. J Bacteriol 175: 1087-1094.
54. Wall ME, Rechtsteiner A, Rocha LM. 2003. Singular value decomposition and principal component analysis: IN A Practical Approach to Micro-array Data Analysis. D.P. Berrar, W. Dubitzky, M. Granzow, eds. pp. 91-109, Kluwer: Norwell, MA LANL LA-UR-02-4001. Available in http://public.lanl.gov/mewall/ kluwer2002.html.
55. Weber H, Polen T, Heuveling J, Wendisch VF, Hengge R. 2005. Genome-wide analysis of the general stress response network in Escherichia coli: sigmaS-dependent genes, promoters, and sigma factor selectivity. J Bacteriol 187:1591-1603.
56. Yoon SH, Han MJ, Lee HS, Lee BH, Jo J. 2003. Combined transcriptome and proteome analysis of Eschirichia coli during high cell density culture. Biotechnol Bioeng 81:753-767.
57. 28 subunit. J Biol Chem 274:16289-16295.
58. Yoshida M, Kashiwagi K, Shigemasa A, Taniguchi S, Yamamoto K, Makinoshima H, Ishihama A, Igarashi K. 2004. A unifying model for the role of polyamines in bacterial cell growth, the polyamine modulon. J Biol Chem 279:46008-46013.