| [1] | Balasubramanian D, Schneper L, Kumari H, Mathee K (2012) A dynamic and intricate regulatory network determines Pseudomonas aeruginosa virulence. Nucleic Acids Res 41: 1–20. doi: 10.1093/nar/gks1039
|
| [2] | Bereket W, Hemalatha K, Getenet B, Wondwossen T, Solomon A, et al. (2012) Update on bacterial nosocomial infections. Eur Rev Med Pharmacol Sci 16: 1039–1044.
|
| [3] | Kucheria R (2005) Urinary tract infections: new insights into a common problem. Postgrad Med J 81: 83–86. doi: 10.1136/pgmj.2004.023036
|
| [4] | Chang SL, Shortliffe LD (2006) Pediatric urinary tract infections. Pediatr Clin N Am 53: 379–400. doi: 10.1016/j.pcl.2006.02.011
|
| [5] | Mittal R, Aggarwal S, Sharma S, Chhibber S, Harjai K (2009) Urinary tract infections caused by Pseudomonas aeruginosa: A minireview. Journal Infect Public Health 2: 101–111. doi: 10.1016/j.jiph.2009.08.003
|
| [6] | Damron FH, Goldberg JB (2012) Proteolytic regulation of alginate overproduction in Pseudomonas aeruginosa. Mol Microbiol 84: 595–607. doi: 10.1111/j.1365-2958.2012.08049.x
|
| [7] | Hogardt M, Heesemann J (2013) Microevolution of Pseudomonas aeruginosa to a chronic pathogen of the cystic fibrosis lung. Curr Top Microbiol 358: 91–118. doi: 10.1007/82_2011_199
|
| [8] | Tamma PD, Cosgrove SE, Maragakis LL (2012) Combination therapy for treatment of infections with gram-negative bacteria. Clin Microbiol Rev 25: 450–470. doi: 10.1128/cmr.05041-11
|
| [9] | Breidenstein EB, La Fuente-Nú？ez Cde, Hancock RE (2011) Pseudomonas aeruginosa: all roads lead to resistance. Trends Microbiol 19: 419–426. doi: 10.1016/j.tim.2011.04.005
|
| [10] | Folkesson A, Jelsbak L, Yang L, Johansen HK, Ciofu O, et al. (2012) Adaptation of Pseudomonas aeruginosa to the cystic fibrosis airway: an evolutionary perspective. Nat Rev Micro 10: 841–851. doi: 10.1038/nrmicro2907
|
| [11] | Hoboth C, Hoffmann R, Eichner A, Henke C, Schmoldt S, et al. (2009) Dynamics of adaptive microevolution of hypermutable Pseudomonas aeruginosa during chronic pulmonary infection in patients with cystic fibrosis. J Infect Dis 200: 118–130. doi: 10.1086/599360
|
| [12] | Munger J, Bennett BD, Parikh A, Feng X, McArdle J, et al. (2008) Systems-level metabolic flux profiling identifies fatty acid synthesis as a target for antiviral therapy. Nat Biotechnol 26: 1179–1186. doi: 10.1038/nbt.1500
|
| [13] | Kelleher JK (2001) Flux estimation using isotopic tracers: Common ground for metabolic physiology and metabolic engineering. Metab Eng 3: 100–110. doi: 10.1006/mben.2001.0185
|
| [14] | Kohlstedt M, Becker J, Wittmann C (2010) Metabolic fluxes and beyond—systems biology understanding and engineering of microbial metabolism. Appl Microbiol Biotechnol 88: 1065–1075. doi: 10.1007/s00253-010-2854-2
|
| [15] | Wittmann C (2007) Fluxome analysis using GC-MS. Microb Cell Fact 6: 6.
|
| [16] | Tielen P, Narten M, Rosin N, Biegler I, Haddad I, et al. (2011) Genotypic and phenotypic characterization of Pseudomonas aeruginosa isolates from urinary tract infections. Int J Med Microbiol 301: 282–292. doi: 10.1016/j.ijmm.2010.10.005
|
| [17] | Stover CK, Pham XQ, Erwin AL, Mizoguchi SD, Warrener P, et al. (2000) Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen. Nature 406: 959–964.
|
| [18] | Dohnt K, Sauer M, Müller M, Atallah K, Weidemann M, et al. (2011) An in vitro urinary tract catheter system to investigate biofilm development in catheter-associated urinary tract infections. J Microbiol Meth 87: 302–308. doi: 10.1016/j.mimet.2011.09.002
|
| [19] | Schneider K, Schütz V, John GT, Heinzle E (2010) Optical device for parallel online measurement of dissolved oxygen and pH in shake flask cultures. Bioprocess Biosyst Eng 33: 541–547. doi: 10.1007/s00449-009-0367-0
|
| [20] | Kind S, Becker J, Wittmann C (2013) Increased lysine production by flux coupling of the tricarboxylic acid cycle and the lysine biosynthetic pathway—Metabolic engineering of the availability of succinyl-CoA in Corynebacterium glutamicum. Metab Eng 15: 184–195. doi: 10.1016/j.ymben.2012.07.005
|
| [21] | Fürch T, Preusse M, Tomasch J, Zech H, Wagner-D？bler I, et al. (2009) Metabolic fluxes in the central carbon metabolism of Dinoroseobacter shibae and Phaeobacter gallaeciensis, two members of the marine Roseobacter clade. BMC Microbiol 9: 209. doi: 10.1186/1471-2180-9-209
|
| [22] | Kretzschmar U, Khodaverdi V, Jeoung J, G？risch H (2008) Function and transcriptional regulation of the isocitrate lyase in Pseudomonas aeruginosa. Arch Microbiol 190: 151–158. doi: 10.1007/s00203-008-0381-7
|
| [23] | Wittmann C, Hans M, Heinzle E (2002) In vivo analysis of intracellular amino acid labelings by GC/MS. Anal Biochem 307: 379–382. doi: 10.1016/s0003-2697(02)00030-1
|
| [24] | Oberhardt MA, Pucha？ka J, Martins dos Santos VAP, Papin JA, Bourne PE (2011) Reconciliation of genome-scale metabolic reconstructions for comparative systems analysis. PLoS Comput Biol 7: e1001116. doi: 10.1371/journal.pcbi.1001116
|
| [25] | Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M (2011) KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res 40: D109–D114. doi: 10.1093/nar/gkr988
|
| [26] | Winsor GL, Lam DKW, Fleming L, Lo R, Whiteside MD, et al. (2010) Pseudomonas genome database: improved comparative analysis and population genomics capability for Pseudomonas genomes. Nucleic Acids Res 39: D596–D600. doi: 10.1093/nar/gkq869
|
| [27] | Blank LM, Ionidis G, Ebert BE, Bühler B, Schmid A (2008) Metabolic response of Pseudomonas putida during redox biocatalysis in the presence of a second octanol phase. FEBS J 275: 5173–5190. doi: 10.1111/j.1742-4658.2008.06648.x
|
| [28] | Neidhardt FC, Ingraham JL, Sch？chter M (1990) Physiology of the bacterial cell: a molecular approach. Sunderland, MA: Sinauer.
|
| [29] | Mann EE, Wozniak DJ (2012) Pseudomonas biofilm matrix composition and niche biology. FEMS Microbiol Rev 36: 893–916. doi: 10.1111/j.1574-6976.2011.00322.x
|
| [30] | Filisetti-Cozzi TM, Carpita NC (1991) Measurement of uronic acids without interference from neutral sugars. Anal Biochem 197: 157–162. doi: 10.1016/0003-2697(91)90372-z
|
| [31] | Quek L, Wittmann C, Nielsen LK, Kr？mer JO (2009) OpenFLUX: efficient modelling software for 13C-based metabolic flux analysis. Microb Cell Fact 8: 25. doi: 10.1186/1475-2859-8-25
|
| [32] | van Winden WA, Wittmann C, Heinzle E, Heijnen JJ (2002) Correcting mass isotopomer distributions for naturally occurring isotopes. Biotechnol Bioeng 80: 477–479. doi: 10.1002/bit.10393
|
| [33] | Wittmann C, Heinzle E (2002) Genealogy profiling through strain improvement by using metabolic network analysis: metabolic flux genealogy of several generations of lysine-producing corynebacteria. Appl Environ Microb 68: 5843–5859. doi: 10.1128/aem.68.12.5843-5859.2002
|
| [34] | Poblete-Castro I, Binger D, Rodrigues A, Becker J, Martins Dos Santos VA, et al. (2013) In-silico-driven metabolic engineering of Pseudomonas putida for enhanced production of poly-hydroxyalkanoates. Metab Eng 15: 113–123. doi: 10.1016/j.ymben.2012.10.004
|
| [35] | Melzer G, Esfandabadi M, Franco-Lara E, Wittmann C (2009) Flux design: In silico design of cell factories based on correlation of pathway fluxes to desired properties. BMC Syst Biol 3: 120. doi: 10.1186/1752-0509-3-120
|
| [36] | Pearson K (1901) On lines and planes of closest fit to systems of points in space. Philos Mag 2: 559–572. doi: 10.1080/14786440109462720
|
| [37] | Dash M, Liu H, Scheuermann P, Tan KL (2003) Fast hierarchical clustering and its validation. Data Knowl Eng 44: 109–138. doi: 10.1016/s0169-023x(02)00138-6
|
| [38] | Zamboni N, Sauer U (2004) Model-independent fluxome profiling from 2H and 13C experiments for metabolic variant discrimination. Genome Biol 5: R99.
|
| [39] | Eschbach E, Schreiber K, Trunk K, Buer J, Jahn D, et al. (2006) Long-term anaerobic survival of the opportunistic pathogen Pseudomonas aeruginosa via pyruvate fermentation. J Bacteriol 186: 4596–4604.64. doi: 10.1128/jb.186.14.4596-4604.2004
|
| [40] | Flamholz A, Noor E, Bar-Even A, Liebermeister W, Milo R (2013) Glycolytic strategy as a tradeoff between energy yield and protein cost. P Natl A Sci 110: 10039–10044. doi: 10.1073/pnas.1215283110
|
| [41] | Romano A, Conway T (1996) Evolution of carbohydrate metabolic pathways. Res Microb 147: 448–455. doi: 10.1016/0923-2508(96)83998-2
|
| [42] | Chavarría M, Nikel PI, Pérez-Pantoja D, Lorenzo Vde (2013) The Entner-Doudoroff pathway empowers Pseudomonas putida KT2440 with a high tolerance to oxidative stress. Environ Microbiol 15: 1772–1785. doi: 10.1111/1462-2920.12069
|
| [43] | Storz G, Tartaglia LA, Farr SB, Ames BN (1990) Bacterial defenses against oxidative stress. Trends Genet 6: 363–368. doi: 10.1016/0168-9525(90)90278-e
|
| [44] | Storz G, Imlay JA (1999) Oxidative stress. Curr Opin Microb 2: 188–194.
|
| [45] | Singh R, Mailloux RJ, Puiseux-Dao S, Appanna VD (2007) Oxidative stress evokes a metabolic adaptation that favors increased NADPH synthesis and decreased NADH production in Pseudomonas fluorescens. J Bacteriol 189: 6665–6675. doi: 10.1128/jb.00555-07
|
| [46] | Kr？mer JO, Bolten CJ, Heinzle E, Schr？der H, Wittmann C (2008) Physiological response of Corynebacterium glutamicum to oxidative stress induced by deletion of the transcriptional repressor McbR. Microbiology 154: 3917–3930. doi: 10.1099/mic.0.2008/021204-0
|
| [47] | Chen PR, Brugarolas P, He C (2011) Redox signaling in human pathogens. Antioxid & Redox Sign 14: 1107–1118. doi: 10.1089/ars.2010.3374
|
| [48] | Hogardt M, Heesemann J (2010) Adaptation of Pseudomonas aeruginosa during persistence in the cystic fibrosis lung. Int J Med Microbiol 300: 557–562. doi: 10.1016/j.ijmm.2010.08.008
|
| [49] | Le Gac M, Plucain J, Hindré T, Lenski RE, Schneider D (2012) Ecological and evolutionary dynamics of coexisting lineages during a long-term experiment with Escherichia coli. Proc Natl Acad Sci U S A 109: 9487–9492. doi: 10.1073/pnas.1207091109
|
| [50] | Hindré T, Knibbe C, Beslon G, Schneider D (2012) New insights into bacterial adaptation through in vivo and in silico experimental evolution. Nat Rev Microbiol 10: 352–365. doi: 10.1038/nrmicro2750
|
| [51] | Kondrashov FA, Koonin EV, Morgunov IG, Finogenova TV, Kondrashova MN (2006) Evolution of glyoxylate cycle enzymes in Metazoa: Evidence of multiple horizontal transfer events and pseudogene formation. Biol Direct 1: 31.
|
| [52] | Smith RA, Gunsalus IC (1957) Isocitritase; enzyme properties and reaction equilibrium. J Biol Chem 229: 305–319.
|
| [53] | Wittmann C, Weber J, Betiku E, Kr？mer J, B？hm D, et al. (2007) Response of fluxome and metabolome to temperature-induced recombinant protein synthesis in Escherichia coli. J Biotechnol 132: 375–384. doi: 10.1016/j.jbiotec.2007.07.495
|
| [54] | Reinscheid DJ, Eikmanns BJ, Sahm H (1994) Characterization of the isocitrate lyase gene from Corynebacterium glutamicum and biochemical analysis of the enzyme. J Bacteriol 176: 3474–3483. doi: 10.1099/13500872-140-11-3099
|
| [55] | Dunn MF, Ramirez-Trujillo JA, Hernandez-Lucas I (2009) Major roles of isocitrate lyase and malate synthase in bacterial and fungal pathogenesis. Microbiology 155: 3166–3175. doi: 10.1099/mic.0.030858-0
|
| [56] | Son MS, Matthews WJ, Kang Y, Nguyen DT, Hoang TT (2007) In vivo evidence of Pseudomonas aeruginosa nutrient acquisition and pathogenesis in the lungs of cystic fibrosis patients. Infection and Immunity 75: 5313–5324. doi: 10.1128/iai.01807-06
|
| [57] | Lindsey TL, Hagins JM, Sokol PA, Silo-Suh LA (2008) Virulence determinants from a cystic fibrosis isolate of Pseudomonas aeruginosa include isocitrate lyase. Microbiology 154: 1616–1627. doi: 10.1099/mic.0.2007/014506-0
|
| [58] | McKinney JD, Bentrup KHzu, Mu？oz-Elías EJ, Miczak A, Chen B, et al. (2000) Persistence of Mycobacterium tuberculosis in macrophages and mice requires the glyoxylate shunt enzyme isocitrate lyase. Nature 406: 735–738.
|
| [59] | Fang FC, Libby SJ, Castor ME, Fung AM (2005) Isocitrate lyase (AceA) is required for Salmonella persistence but not for acute lethal infection in mice. Infect Immun 73: 2547–2549. doi: 10.1128/iai.73.4.2547-2549.2005
|
| [60] | Wall DM, Duffy PS, DuPont C, Prescott JF, Meijer WG (2005) Isocitrate lyase activity is required for virulence of the intracellular pathogen Rhodococcus equi. Infect Immun 73: 6736–6741. doi: 10.1128/iai.73.10.6736-6741.2005
|
| [61] | Hamood AN, Griswold JA, Duhan CM (1996) Production of extracellular virulence factors by Pseudomonas aeruginosa isolates obtained from tracheal, urinary tract, and wound infections. J Surg Res 61: 425–432. doi: 10.1006/jsre.1996.0140
|
| [62] | Rumbaugh K, Griswold J, Hamood A (1999) Pseudomonas aeruginosa strains obtained from patients with tracheal, urinary tract and wound infection: variations in virulence factors and virulence genes. J Hosp Infect 43: 211–218. doi: 10.1053/jhin.1999.0252
|
| [63] | Rosenbloom J, Koo H, Howard PS, Mecham R, Macarak EJ (1995) Elastic fibers and their role in bladder extracellular matrix. Adv Exp Med Biol 385: 161–72. doi: 10.1007/978-1-4899-1585-6_19
|
| [64] | Hellerstein MK (2008) A critique of the molecular target-based drug discovery paradigm based on principles of metabolic control: Advantages of pathway-based discovery. Metab Eng 10: 1–9. doi: 10.1016/j.ymben.2007.09.003
|
| [65] | Fuhrer T, Fischer E, Sauer U (2005) Experimental identification and quantification of glucose metabolism in seven bacterial species. J Bacteriol 187: 1581–1590. doi: 10.1128/jb.187.5.1581-1590.2005
|
| [66] | Marx A, Graaf AAde, Wiechert W, Eggeling L, Sahm H (1996) Determination of the fluxes in the central metabolism of Corynebacterium glutamicum by nuclear magnetic resonance spectroscopy combined with metabolite balancing. Biotechnol Bioeng 49: 111–129. doi: 10.1002/(sici)1097-0290(19960120)49:2<111::aid-bit1>3.3.co;2-u
|
