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PLOS ONE  2013 

Inactivation of Metabolic Genes Causes Short- and Long-Range dys-Regulation in Escherichia coli Metabolic Network

DOI: 10.1371/journal.pone.0078360

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Abstract:

The metabolic network in E. coli can be severely affected by the inactivation of metabolic genes that are required to catabolize a nutrient (D-galactose). We hypothesized that the resulting accumulation of small molecules can yield local as well as systemic effects on the metabolic network. Analysis of metabolomics data in wild-type and D-galactose non-utilizing mutants, galT, galU and galE, reveal the large metabolic differences between the wild-type and the mutants when the strains were grown in D-galactose. Network mapping suggested that the enzymatic defects affected the metabolic modules located both at short- and long-ranges from the D-galactose metabolic module. These modules suggested alterations in glutathione, energy, nucleotide and lipid metabolism and disturbed carbon to nitrogen ratio in mutant strains. The altered modules are required for normal cell growth for the wild-type strain, explaining why the cell growth is inhibited in the mutants in the presence of D-galactose. Identification of these distance-based dys-regulations would enhance the systems level understanding of metabolic networks of microorganisms having importance in biomedical and biotechnological research.

References

[1]  Orth JD, Conrad TM, Na J, Lerman JA, Nam H et al. (2011) A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011. Mol Syst Biol 7: 535. PubMed: 21988831.
[2]  Spirin V, Gelfand MS, Mironov AA, Mirny LA (2006) A metabolic network in the evolutionary context: multiscale structure and modularity. Proc Natl Acad Sci U S A 103: 8774-8779. doi:10.1073/pnas.0510258103. PubMed: 16731630.
[3]  Buescher JM, Liebermeister W, Jules M, Uhr M, Muntel J et al. (2012) Global network reorganization during dynamic adaptations of Bacillus subtilis metabolism. Science 335: 1099-1103. doi:10.1126/science.1206871. PubMed: 22383848.
[4]  Karr JR, Sanghvi JC, Macklin DN, Gutschow MV, Jacobs JM et al. (2012) A whole-cell computational model predicts phenotype from genotype. Cell 150: 389-401. doi:10.1016/j.cell.2012.05.044. PubMed: 22817898.
[5]  Covert MW, Xiao N, Chen TJ, Karr JR (2008) Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli. Bioinformatics 24: 2044-2050. doi:10.1093/bioinformatics/btn352. PubMed: 18621757.
[6]  Seshasayee AS, Fraser GM, Babu MM, Luscombe NM (2009) Principles of transcriptional regulation and evolution of the metabolic system in E. coli. Genome Res 19: 79-91. PubMed: 18836036.
[7]  Covert MW, Palsson BO (2002) Transcriptional regulation in constraints-based metabolic models of Escherichia coli. J Biol Chem 277: 28058-28064. doi:10.1074/jbc.M201691200. PubMed: 12006566.
[8]  Kreimer A, Borenstein E, Gophna U, Ruppin E (2008) The evolution of modularity in bacterial metabolic networks. Proc Natl Acad Sci U S A 105: 6976-6981. doi:10.1073/pnas.0712149105. PubMed: 18460604.
[9]  Feist AM, Palsson BO (2008) The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli. Nat Biotechnol 26: 659-667. doi:10.1038/nbt1401. PubMed: 18536691.
[10]  Orth JD, Thiele I, Palsson BO (2010) What is flux balance analysis? Nat Biotechnol 28: 245-248. doi:10.1038/nbt.1614. PubMed: 20212490.
[11]  Lee SJ, Trostel A, Le P, Harinarayanan R, Fitzgerald PC et al. (2009) Cellular stress created by intermediary metabolite imbalances. Proc Natl Acad Sci U S A 106: 19515-19520. doi:10.1073/pnas.0910586106. PubMed: 19887636.
[12]  Jeong H, Tombor B, Albert R, Oltvai ZN, Barabási AL (2000) The large-scale organization of metabolic networks. Nature 407: 651-654. doi:10.1038/35036627. PubMed: 11034217.
[13]  Arita M (2004) The metabolic world of Escherichia coli is not small. Proc Natl Acad Sci U S A 101: 1543-1547. doi:10.1073/pnas.0306458101. PubMed: 14757824.
[14]  Barupal DK, Haldiya PK, Wohlgemuth G, Kind T, Kothari SL et al. (2012) MetaMapp: mapping and visualizing metabolomic data by integrating information from biochemical pathways and chemical and mass spectral similarity. BMC Bioinformatics 13: 99. doi:10.1186/1471-2105-13-99. PubMed: 22591066.
[15]  Ringnér M (2008) What is principal component analysis? Nat Biotechnol 26: 303-304. doi:10.1038/nbt0308-303. PubMed: 18327243.
[16]  Carmel-Harel O, Storz G (2000) Roles of the glutathione- and thioredoxin-dependent reduction systems in the Escherichia coli and saccharomyces cerevisiae responses to oxidative stress. Annu Rev Microbiol 54: 439-461. doi:10.1146/annurev.micro.54.1.439. PubMed: 11018134.
[17]  Turnbough CL Jr., Switzer RL (2008) Regulation of pyrimidine biosynthetic gene expression in bacteria: repression without repressors. Microbiol Mol Biol Rev 72: 266-300, table of contents.
[18]  Jozefczuk S, Klie S, Catchpole G, Szymanski J, Cuadros-Inostroza A et al. (2010) Metabolomic and transcriptomic stress response of Escherichia coli. Mol Syst Biol 6: 364. PubMed: 20461071.
[19]  MacRae James I, Sheiner L, Nahid A, Tonkin C, Striepen B et al. (2012) Mitochondrial Metabolism of Glucose and Glutamine Is Required for Intracellular Growth of Toxoplasma gondii. Cell Host Microbe 12: 682-692. doi:10.1016/j.chom.2012.09.013. PubMed: 23159057.
[20]  Fuqua C, Greenberg EP (2002) Listening in on bacteria: acyl-homoserine lactone signalling. Nat Rev Mol Cell Biol 3: 685-695. doi:10.1038/nrm907. PubMed: 12209128.
[21]  Brouquisse R, James F, Pradet A, Raymond P (1992) Asparagine metabolism and nitrogen distribution during protein degradation in sugar-starved maize root tips. Planta 188: 384-395. PubMed: 24178329.
[22]  Decker K, Peist R, Reidl J, Kossmann M, Brand B et al. (1993) Maltose and maltotriose can be formed endogenously in Escherichia coli from glucose and glucose-1-phosphate independently of enzymes of the maltose system. J Bacteriol 175: 5655-5665. PubMed: 8366051.
[23]  Fischer E, Sauer U (2003) Metabolic flux profiling of Escherichia coli mutants in central carbon metabolism using GC-MS. Eur J Biochem 270: 880-891. doi:10.1046/j.1432-1033.2003.03448.x. PubMed: 12603321.
[24]  B?hringer J, Fischer D, Mosler G, Hengge-Aronis R (1995) UDP-glucose is a potential intracellular signal molecule in the control of expression of sigma S and sigma S-dependent genes in Escherichia coli. J Bacteriol 177: 413-422. PubMed: 7814331.
[25]  Rosenberg H, Hardy CM (1984) Conversion of D-mannitol to D-ribose: a newly discovered pathway in Escherichia coli. J Bacteriol 158: 69-72. PubMed: 6201477.
[26]  Adhya SL, Shapiro JA (1969) The galactose operon of E. coli K-12. I. Structural and pleiotropic mutations of the operon. Genetics 62: 231-247. PubMed: 4905871.
[27]  Fiehn O, Barupal DK, Kind T (2011) Extending biochemical databases by metabolomic surveys. J Biol Chem 286: 23637-23643. doi:10.1074/jbc.R110.173617. PubMed: 21566124.
[28]  Plaimas K, Eils R, Konig R (2010) Identifying essential genes in bacterial metabolic networks with machine learning methods. BMC. Syst Biol 4: 56.
[29]  Keren I, Shah D, Spoering A, Kaldalu N, Lewis K (2004) Specialized persister cells and the mechanism of multidrug tolerance in Escherichia coli. J Bacteriol 186: 8172-8180. doi:10.1128/JB.186.24.8172-8180.2004. PubMed: 15576765.
[30]  Devkota S, Wang Y, Musch MW, Leone V, Fehlner-Peach H et al. (2012) Dietary-fat-induced taurocholic acid promotes pathobiont expansion and colitis in Il10-/- mice. Nature 487: 104-108. PubMed: 22722865.
[31]  Martin VJ, Pitera DJ, Withers ST, Newman JD, Keasling JD (2003) Engineering a mevalonate pathway in Escherichia coli for production of terpenoids. Nat Biotechnol 21: 796-802. doi:10.1038/nbt833. PubMed: 12778056.
[32]  Huo YX, Cho KM, Rivera JG, Monte E, Shen CR et al. (2011) Conversion of proteins into biofuels by engineering nitrogen flux. Nat Biotechnol 29: 346-351. doi:10.1038/nbt.1789. PubMed: 21378968.
[33]  Rahman SA, Schomburg D (2006) Observing local and global properties of metabolic pathways: 'load points' and 'chock points' in the metabolic networks. Bioinformatics 22: 1767-1774. doi:10.1093/bioinformatics/btl181. PubMed: 16682421.
[34]  Yeh I, Hanekamp T, Tsoka S, Karp PD, Altman RB (2004) Computational analysis of Plasmodium falciparum metabolism: organizing genomic information to facilitate drug discovery. Genome Res 14: 917-924. doi:10.1101/gr.2050304. PubMed: 15078855.
[35]  Murphy DJ, Brown JR (2007) Idnetification of gene targets against dormant phase Mycobacterium tuberculosis infections. BMC Infect Dis 7: 84. doi:10.1186/1471-2334-7-84. PubMed: 17655757.
[36]  Lee DH, Palsson BO (2010) Adaptive evolution of Escherichia coli K-12 MG1655 during growth on a Nonnative carbon source, L-1,2-propanediol. Appl Environ Microbiol 76: 4158-4168. doi:10.1128/AEM.00373-10. PubMed: 20435762.
[37]  Charusanti P, Conrad TM, Knight EM, Venkataraman K, Fong NL et al. (2010) Genetic basis of growth adaptation of Escherichia coli after deletion of pgi, a major metabolic gene. PLOS Genet 6: e1001186.

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