Glycogen is the primary source of glucose during the lag phase of E. coli proliferation

Biochimica et Biophysica Acta - Proteins and Proteomics

Volumn 1824, Issue 12, 2012, Pages 1442-1448

  Yamamotoya, Tomoaki ^a,d   Dose, Hitomi ^b   Tian, Zhongyuan ^a   Fauré, Adrien ^a   Toya, Yoshihiro ^c,e   Honma, Masayuki ^c   Igarashi, Kaori ^c   Nakahigashi, Kenji ^c   Soga, Tomoyoshi ^c   Mori, Hirotada ^b   Matsuno, Hiroshi ^a  

^a YAMAGUCHI UNIVERSITY   (Japan)

^b NARA INSTITUTE OF SCIENCE AND TECHNOLOGY   (Japan)

^c KEIO UNIVERSITY   (Japan)

^d Hitachi Solutions   (Japan)

^e OSAKA UNIVERSITY   (Japan)

Author keywords

Cell growth; Computational simulation; E. coli metabolism; Glycogen

Indexed keywords

GLUCOSE; GLUCOSE 6 PHOSPHATE; GLYCOGEN;

BACTERIAL CELL; BACTERIAL GROWTH; BACTERIUM CULTURE; CARBON SOURCE; CELL GROWTH; CELL METABOLISM; CELL PROLIFERATION; CONFERENCE PAPER; ENERGY RESOURCE; ESCHERICHIA COLI; GLUCOSE TRANSPORT; MASS SPECTROMETRY; MATHEMATICAL COMPUTING; METABOLITE; METABOLOMICS; NONHUMAN; PRIORITY JOURNAL; SIMULATION;

COMPUTATIONAL BIOLOGY; ESCHERICHIA COLI; GLUCOSE; GLUCOSE-6-PHOSPHATE; GLYCOGEN; MICROBIAL VIABILITY;

ESCHERICHIA COLI;

EID: 84867682550     PISSN: 15709639     EISSN: 18781454     Source Type: Journal    
DOI: 10.1016/j.bbapap.2012.06.010     Document Type: Conference Paper

References (48)

1. M. Heinemann, and U. Sauer Systems biology of microbial metabolism Curr. Opin. Microbiol. 13 2010 337 343
2. C. Chassagnole, N. Noisommit-Rizzi, J.W. Schmid, K. Mauch, and M. Reuss Dynamic modeling of the central carbon metabolism of Escherichia coli Biotechnol. Bioeng. 79 2002 53 73 (Pubitemid 34746765)
3. F.J. Bruggeman, F.C. Boogerd, and H.V. Westerhoff The multifarious short-term regulation of ammonium assimilation of Escherichia coli: dissection using an in silico replica FEBS J. 272 2005 1965 1985 (Pubitemid 40547252)
4. J. Yuan, C.D. Doucette, W.U. Fowler, X.-J. Feng, M. Piazza, H.A. Rabitz, N.S. Wingreen, and J.D. Rabinowitz Metabolomics-driven quantitative analysis of ammonia assimilation in E coli Mol. Syst. Biol. 5 2009
5. O. Kotte, J.B. Zaugg, and M. Heinemann Bacterial adaptation through distributed sensing of metabolic fluxes Mol. Syst. Biol. 6 2010
6. A. Kremling, K. Bettenbrock, and E. Gilles Analysis of global control of Escherichia coli carbohydrate uptake BMC Syst. Biol. 1 2007 42
7. A. Kremling, K. Bettenbrock, and E.D. Gilles A feed-forward loop guarantees robust behavior in Escherichia coli carbohydrate uptake Bioinformatics 24 2008 704 710 (Pubitemid 351321215)
8. G. Gosset Improvement of Escherichia coli production strains by modification of the phosphoenolpyruvate: sugar phosphotransferase system Microb. Cell Fact. 4 2005 14
9. D.L. Nelson, and M.M. Cox Lehninger Principles of Biochemistry Fifth edition 2007 W.H. Freeman
10. M. Arad, B.J. Maron, J.M. Gorham, W.H. Johnson, J.P. Saul, A.R. Perez-Atayde, P. Spirito, G.B. Wright, R.J. Kanter, C.E. Seidman, and J.G. Seidman Glycogen storage diseases presenting as hypertrophic cardiomyopathy N. Engl. J. Med. 352 2005 362 372
11. M.J. Danon, S.J. Oh, S. DiMauro, J.R. Manaligod, A. Eastwood, S. Naidu, and L.H. Schliselfeld Lysosomal glycogen storage disease with normal acid maltase Neurology 31 1981 51 57 (Pubitemid 11217453)
12. P.S. Harper Landmarks in Medical Genetics: Classic Papers With Commentaries 2004 Oxford University Press
13. J. Hay, M.J. Levin, J.M. Sondheimer, and R.R. Deterding Glycogen Storage Diseases 2007 McGraw-Hill
14. J.E. Riggs, S.S. Schochet, L. Gutmann, S. Shanske, W.A. Neal, and S. DiMauro Lysosomal glycogen storage disease without acid maltase deficiency Neurology 33 1983 873 877 (Pubitemid 13066685)
15. T.E. Starzl, A.J. Demetris, M. Trucco, C. Ricordi, S. Ildstad, P.I. Terasaki, N. Murase, R.S. Kendall, M. Kocova, W.A. Rudert, A. Zeevi, and D. Van Thiel Chimerism after liver transplantation for type IV glycogen storage disease and type 1 Gaucher's disease N. Engl. J. Med. 328 1993 745 749 (Pubitemid 23082036)
16. F. Van Hoof, L. Hue, T. de Barsy, P. Jacquemin, P. Devos, and H.G. Hers Glycogen storage diseases Biochimie 54 1972 745 751
17. M. Montero, G. Almagro, G. Eydallin, A.M. Viale, F.J. Muñoz, A. Bahaji, J. Li, M. Rahimpour, E. Baroja-Fernández, and J. Pozueta-Romero Escherichia coli glycogen genes are organized in a single glgBXCAP transcriptional unit possessing an alternative suboperonic promoter within glgC that directs glgAP expression Biochem. J. 433 2011 107 117
18. M. Montero, G. Eydallin, A.M. Viale, G. Almagro, F.J. Muñoz, M. Rahimpour, M.T. Sesma, E. Baroja-Fernández, and J. Pozueta-Romero Escherichia coli glycogen metabolism is controlled by the PhoP-PhoQ regulatory system at submillimolar environmental Mg 2+ concentrations, and is highly interconnected with a wide variety of cellular processes Biochem. J. 424 2009 129 141
19. C.R. Meyer, M. Borra, R. Igarashi, Y.-S. Lin, and M. Springsteel Characterization of ADP-glucose pyrophosphorylase from Rhodobacter sphaeroides 241: evidence for the involvement of arginine in allosteric regulation Arch. Biochem. Biophys. 372 1999 179 188
20. W.A. Wilson, P.J. Roach, M. Montero, E. Baroja-Fernández, F.J. Muñoz, G. Eydallin, A.M. Viale, and J. Pozueta-Romero Regulation of glycogen metabolism in yeast and bacteria FEMS Microbiol. Rev. 34 2010 952 985
21. G. Eydallin, A.M. Viale, M.T. Morán-Zorzano, F.J. Muñoz, M. Montero, E. Baroja-Fernández, and J. Pozueta-Romero Genome-wide screening of genes affecting glycogen metabolism in Escherichia coli K-12 FEBS Lett. 581 2007 2947 2953 (Pubitemid 46899034)
22. G. Eydallin, M. Montero, G. Almagro, M.T. Sesma, A.M. Viale, F.J. Muñoz, M. Rahimpour, E. Baroja-Fernández, and J. Pozueta-Romero Genome-wide screening of genes whose enhanced expression affects glycogen accumulation in Escherichia coli DNA Res. 17 2010 61 71
23. T. Romeo, and J. Preiss Genetic regulation of glycogen biosynthesis in Escherichia coli: in vitro effects of cyclic AMP and guanosine 5′-diphosphate 3′-diphosphate and analysis of in vivo transcripts J. Bacteriol. 171 1989 2773 2782
24. T. Romeo, J. Black, and J. Preiss Genetic regulation of glycogen biosynthesis in Escherichia coli: in vivo effects of the catabolite repression and stringent response systems inglg gene expression Curr. Microbiol. 21 1990 131 137
25. T. Romeo, A. Kumar, and J. Preiss Analysis of the Escherichia coli glycogen gene cluster suggests that catabolic enzymes are encoded among the biosynthetic genes Gene 70 1988 363 376
26. G. Stephanopoulos, A.A. Aristidou, and J. Nielsen Metabolic Engineering: Principles and Methodologies 1998 Academic Press
27. H. Harry Flux analysis and control of the central metabolic pathways in Escherichia coli FEMS Microbiol. Rev. 19 1996 85 116
28. Q. Hua, C. Yang, T. Baba, H. Mori, and K. Shimizu Responses of the central metabolism in Escherichia coli to phosphoglucose isomerase and glucose-6-phosphate dehydrogenase knockouts J. Bacteriol. 185 2003 7053 7067 (Pubitemid 37509820)
29. D.J. Korz, U. Rinas, K. Hellmuth, E.A. Sanders, and W.-D. Deckwer Simple fed-batch technique for high cell density cultivation of Escherichia coli J. Biotechnol. 39 1995 59 65
30. D.M. LeMaster, and D.M. Kushlan Dynamical mapping of E. coli thioredoxin via 13C NMR relaxation analysis J. Am. Chem. Soc. 118 2011 9255 9264
31. Y. Toya, N. Ishii, K. Nakahigashi, T. Hirasawa, T. Soga, M. Tomita, and K. Shimizu 13C-metabolic flux analysis for batch culture of Escherichia coli and its pyk and pgi gene knockout mutants based on mass isotopomer distribution of intracellular metabolites Biotechnol. Prog. 26 2010 975 992
32. K. Tuty, M. Ahmad, M.F. Johnjoe, and S. Kazuyuki Modeling and simulation of the main metabolism in Escherichia coli and its several single-gene knockout mutants with experimental verification Microb. Cell Fact. 9 2010 88
33. W. Wiechert, M. Möllney, S. Petersen, and A.A. de Graaf A universal framework for 13C metabolic flux analysis Metab. Eng. 3 2001 265 283 (Pubitemid 32748170)
34. W. Wolfgang 13C metabolic flux analysis Metab. Eng. 3 2001 195 206
35. B. Xu, M. Jahic, and S. Enfors Modeling of overflow metabolism in batch and fed-batch cultures of Escherichia coli Biotechnol. Prog. 15 1999 81 90 (Pubitemid 29087591)
36. M.F. Traxler, D.-E. Chang, and T. Conway Guanosine 3′,5′- bispyrophosphate coordinates global gene expression during glucose-lactose diauxie in Escherichia coli PNAS 103 2006 2374 2379 (Pubitemid 43271677)
37. M.F. Traxler, S.M. Summers, H. Nguyen, V.M. Zacharia, G.A. Hightower, J.T. Smith, and T. Conway The global, ppGpp-mediated stringent response to amino acid starvation in Escherichia coli Mol. Microbiol. 68 2008 1128 1148 (Pubitemid 351670199)
38. M.F. Traxler, V.M. Zacharia, S. Marquardt, S.M. Summers, H. Nguyen, S.E. Stark, and T. Conway Discretely calibrated regulatory loops controlled by ppGpp partition gene induction across the feast to famine gradient in Escherichia coli Mol. Microbiol. 79 2011 830 845
39. J. Preiss, E. Greenberg, and A. Sabraw Biosynthesis of bacterial glycogen kinetic studies of a glucose-1-phosphate adenylyltransferase (EC 27727) from a glycogen-deficient mutant of Escherichia coli B J. Biol. Chem. 250 1975 7631 7638
40. N. Sigal, J. Cattaneo, and I.H. Segel Glycogen accumulation by wild-type and uridine diphosphate glucose pyrophosphorylase-negative strains of Escherichia coli Arch. Biochem. Biophys. 108 1964 440 451
41. B.L. Wanner Gene expression in bacteria using TnphoA and TnphoA′ elements to make and switch phoA gene, lacZ (op), and lacZ (pr) fusions Mol. Microbiol. Tech. 3 1994 291
42. T. Soga, Y. Ohashi, Y. Ueno, H. Naraoka, M. Tomita, and T. Nishioka Quantitative metabolome analysis using capillary electrophoresis mass spectrometry J. Proteome Res. 2 2003 488 494 (Pubitemid 37376843)
43. A.K. Laird Dynamics of tumour growth Br. J. Cancer 18 1964 490 502
44. A. D'Onofrio A general framework for modeling tumor-immune system competition and immunotherapy: mathematical analysis and biomedical inferences Phys. D 208 2005 220 235 (Pubitemid 41085168)
45. H. Matsuno, Y. Tanaka, H. Aoshima, A. Doi, M. Matsui, and S. Miyano Biopathways representation and simulation on hybrid functional Petri net In Silico Biol. 3 2003 389 404 (Pubitemid 37493057)
46. J.V. Lawrence, and S. Maier Correction for the inherent error in optical density readings Appl. Environ. Microbiol. 33 1977 482 484 (Pubitemid 8099803)
47. M.A. Bonafonte, C. Solano, B. Sesma, M. Alvarez, L. Montuenga, D. García-Ros, and C. Gamazo The relationship between glycogen synthesis, biofilm formation and virulence in Salmonella enteritidis FEMS Microbiol. Lett. 191 2000 31 36
48. L. Bourassa, and A. Camilli Glycogen contributes to the environmental persistence and transmission of Vibrio cholerae Mol. Microbiol. 72 2009 124 138