A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: i JN746 as a cell factory
Tóm tắt
Pseudomonas putida is the best studied pollutant degradative bacteria and is harnessed by industrial biotechnology to synthesize fine chemicals. Since the publication of P. putida KT2440's genome, some in silico analyses of its metabolic and biotechnology capacities have been published. However, global understanding of the capabilities of P. putida KT2440 requires the construction of a metabolic model that enables the integration of classical experimental data along with genomic and high-throughput data. The constraint-based reconstruction and analysis (COBRA) approach has been successfully used to build and analyze in silico genome-scale metabolic reconstructions. We present a genome-scale reconstruction of P. putida KT2440's metabolism, i JN746, which was constructed based on genomic, biochemical, and physiological information. This manually-curated reconstruction accounts for 746 genes, 950 reactions, and 911 metabolites. i JN746 captures biotechnologically relevant pathways, including polyhydroxyalkanoate synthesis and catabolic pathways of aromatic compounds (e.g., toluene, benzoate, phenylacetate, nicotinate), not described in other metabolic reconstructions or biochemical databases. The predictive potential of i JN746 was validated using experimental data including growth performance and gene deletion studies. Furthermore, in silico growth on toluene was found to be oxygen-limited, suggesting the existence of oxygen-efficient pathways not yet annotated in P. putida's genome. Moreover, we evaluated the production efficiency of polyhydroxyalkanoates from various carbon sources and found fatty acids as the most prominent candidates, as expected. Here we presented the first genome-scale reconstruction of P. putida, a biotechnologically interesting all-surrounder. Taken together, this work illustrates the utility of i JN746 as i) a knowledge-base, ii) a discovery tool, and iii) an engineering platform to explore P. putida's potential in bioremediation and bioplastic production.
Tài liệu tham khảo
Clarke P, Richmond MH: Genetics and Biochemistry of Pseudomonas. 1975, New York, USA: John Wiley & Sons
Clarke P: The metabolic versatility of pseudomonads. Antonie Van Leeuwenhoek. 1982, 48 (2): 105-130. 10.1007/BF00405197
Franklin FC, Bagdasarian M, Bagdasarian MM, Timmis K: Molecular and functional analysis of the TOL plasmid pWWO from Pseudomonas putida and cloning of genes for the entire regulated aromatic ring meta cleavage pathway. Proc Natl Acad Sci USA. 1981, 78 (12): 7458-7462. 10.1073/pnas.78.12.7458
Bayley SA, Duggleby CJ, Worsey MJ, Williams PA, Hardy KG, Broda aP: Two modes of loss of the Tol function from Pseudomonas putida mt-2. Mol Gen Genet. 1977, 154 (2): 203-204. 10.1007/BF00330838
Mermod N, Harayama S, Timmis K: New route to bacterial production of indigo. Bio/Technology. 1986, 4: 321-324. 10.1038/nbt0486-321.
Ramos J, Wasserfallen A, Rose K, Timmis K: Redesigning metabolic routes: manipulation of TOL plasmid pathway for catabolism of alkylbenzoates. Science. 1987, 235 (4788): 593-596. 10.1126/science.3468623
Cases I, de Lorenzo V: Expression systems and physiological control of promoter activity in bacteria. Curr Opin Microbiol. 1998, 1 (3): 303-310. 10.1016/S1369-5274(98)80034-9
Gilbert ES, Walker AW, Keasling J: A constructed microbial consortium for biodegradation of the organophosphorus insecticide parathion. Appl Microbiol Biotechnol. 2003, 61: 77-81.
Timmis KN, Steffan RJ, Unterman R: Designing microorganisms for the treatment of toxic wastes. Annu Rev Microbiol. 1994, 48: 525-557. 10.1146/annurev.mi.48.100194.002521
Dejonghe W, Boon N, Seghers D, Top EM, Verstraete W: Bioaugmentation of soils by increasing microbial richness: missing links. Environ Microbiol. 2001, 3 (10): 649-657. 10.1046/j.1462-2920.2001.00236.x
Galán B, Díaz E, García JL: Enhancing desulphurization by engineering a flavin reductase-encoding gene cassette in recombinant biocatalysts. Environ Microbiol. 2000, 2 (6): 687-669. 10.1046/j.1462-2920.2000.00151.x
Zeyer J, Lehrbach PR, Timmis KN: Use of cloned genes of Pseudomonas TOL plasmid to effect biotransformation of benzoates to cis-dihydrodiols and catechols by Escherichia coli cells. Appl Environ Microbiol. 1985, 50 (6): 1409-1413.
Wubbolts MG, Timmis KN: Biotransformation of substituted benzoates to the corresponding cis-diols by an engineered strain of Pseudomonas oleovorans producing the TOL plasmid-specified enzyme toluate-1, 2-dioxygenase. Appl Environ Microbiol. 1990, 56 (2): 569-571.
Schmid A, Dordick JS, Hauer B, Kiener A, Wubbolts M, Witholt B: Industrial biocatalysis today and tomorrow. Nature. 2001, 409 (6817): 258-268. 10.1038/35051736
Olivera ER, Carnicero D, Jodra R, Minambres B, Garcia B, Abraham GA, Gallardo A, Roman JS, Garcia JL, Naharro G, et al: Genetically engineered Pseudomonas: a factory of new bioplastics with broad applications. Environmental Microbiology. 2001, 3 (10): 612-618. 10.1046/j.1462-2920.2001.00224.x
Ouyang SP, Luo RC, Chen SS, Liu Q, Chung A, Wu Q, Chen GQ: Production of Polyhydroxyalkanoates with High 3-Hydroxydodecanoate Monomer Content by fadB and fadA Knockout Mutant of Pseudomonas putida KT2442. Biomacromolecules. 2007, 8 (8): 2504-2511. 10.1021/bm0702307
Huijberts GN, Eggink G, de Waard P, Huisman GW, Witholt B: Pseudomonas putida KT2442 cultivated on glucose accumulates poly(3-hydroxyalkanoates) consisting of saturated and unsaturated monomers. Appl Environ Microbiol. 1992, 58 (2): 536-544.
O'Sullivan DJ, O'Gara F: Traits of fluorescent Pseudomonas spp. involved in suppression of plant root pathogens. Microbiol Rev. 1992, 56 (4): 662-676.
Walsh UF, Morrissey JP, O'Gara F: Pseudomonas for biocontrol of phytopathogens: from functional genomics to commercial exploitation. Curr Opin Biotechnol. 2001, 12 (3): 289-295. 10.1016/S0958-1669(00)00212-3
Nelson KE, Weinel C, Paulsen IT, Dodson RJ, Hilbert H, Martins dos Santos VAP, Fouts DE, Gill SR, Pop M, Holmes M, et al: Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440. Environmental Microbiology. 2002, 4 (12): 799-808. 10.1046/j.1462-2920.2002.00366.x
Ramos JL: Pseudomonas. 2004, New York Kluwer: Academic/Plenum Publishers
Yuste L, Hervas AB, Canosa I, Tobes R, Jimenez JI, Nogales J, Perez-Perez MM, Santero E, Diaz E, Ramos J-L, et al: Growth phase-dependent expression of the Pseudomonas putida KT2440 transcriptional machinery analysed with a genome-wide DNA microarray. Environmental Microbiology. 2006, 8 (1): 165-177. 10.1111/j.1462-2920.2005.00890.x
Dominguez-Cuevas P, Gonzalez-Pastor J-E, Marques S, Ramos J-L, de Lorenzo V: Transcriptional Tradeoff between Metabolic and Stress-response Programs in Pseudomonas putida KT2440 Cells Exposed to Toluene. J Biol Chem. 2006, 281 (17): 11981-11991. 10.1074/jbc.M509848200
Kim Hwan Young, Sung-Ho Cho Kun, Young Jin Yun, Kyung-Hoon Kim, Shin Jong Kwon, YSI Kim: Analysis of aromatic catabolic pathways in Pseudomonas putida KT 2440 using a combined proteomic approach: 2-DE/MS and cleavable isotope-coded affinity tag analysis. PROTEOMICS. 2006, 6 (4): 1301-1318. 10.1002/pmic.200500329
del Castillo T, Ramos JL, Rodriguez-Herva JJ, Fuhrer T, Sauer U, Duque E: Convergent Peripheral Pathways Catalyze Initial Glucose Catabolism in Pseudomonas putida: Genomic and Flux Analysis. J Bacteriol. 2007, 189 (14): 5142-5152. 10.1128/JB.00203-07
del Castillo T, Ramos JL: Simultaneous Catabolite Repression between Glucose and Toluene Metabolism in Pseudomonas putida Is Channeled through Different Signaling Pathways. J Bacteriol. 2007, 189 (18): 6602-6610. 10.1128/JB.00679-07
Jimenez JI, Minambres B, Garcia JL, Diaz E: Genomic analysis of the aromatic catabolic pathways from Pseudomonas putida KT2440. Environmental Microbiology. 2002, 4 (12): 824-841. 10.1046/j.1462-2920.2002.00370.x
dos Santos VAPM, Heim S, Moore ERB, Stratz M, Timmis KN: Insights into the genomic basis of niche specificity of Pseudomonas putida KT2440. Environmental Microbiology. 2004, 6 (12): 1264-1286. 10.1111/j.1462-2920.2004.00734.x
Palsson BØ: In silico biotechnology. Era of reconstruction and interrogation. Curr Opin Biotechnol. 2004, 15 (1): 50-51. 10.1016/j.copbio.2004.01.006
Reed JL, Famili I, Thiele I, Palsson BO: Towards multidimensional genome annotation. Nat Rev Genet. 2006, 7 (2): 130-141. 10.1038/nrg1769
Palsson BO: Two-dimensional annotation of genomes. Nat Biotechnol. 2004, 22 (10): 1218-1219. 10.1038/nbt1004-1218
Price ND, Reed JL, Palsson BO: Genome-scale models of microbial cells: evaluating the consequences of constraints. Nat Rev Micro. 2004, 2 (11): 886-897. 10.1038/nrmicro1023.
Becker SA, Feist AM, Mo ML, Hannum G, Palsson BO, Herrgard MJ: Quantitative Prediction of Cellular Metabolism with Constraint-based Models: The COBRA Toolbox. Nat Protoc. 2007, 2 (3): 727-738. 10.1038/nprot.2007.99
Price ND, Reed JL, Palsson BO: Genome-scale models of microbial cells: evaluating the consequences of constraints. Nat Rev Microbiol. 2004, 2 (11): 886-897. 10.1038/nrmicro1023
Feist AM, Scholten JCM, Palsson BO, Brockman FJ, Ideker T: Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri. Mol Syst Biol. 2006, 2:
Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO: A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Mol Syst Biol. 2007, 3:
Oh Y-K, Palsson BO, Park SM, Schilling CH, Mahadevan R: Genome-scale Reconstruction of Metabolic Network in Bacillus subtilis Based on High-throughput Phenotyping and Gene Essentiality Data. J Biol Chem. 2007, 282 (39): 28791-28799. 10.1074/jbc.M703759200
Thiele I, Vo TD, Price ND, Palsson B: An Expanded Metabolic Reconstruction of Helicobacter pylori (i IT341 GSM/GPR): An in silico genome-scale characterization of single and double deletion mutants. J Bacteriol. 2005, 187 (16): 5818-5830. 10.1128/JB.187.16.5818-5830.2005
Jamshidi N, Palsson B: Investigating the metabolic capabilities of Mycobacterium tuberculosis H37Rv using the in silico strain iNJ661 and proposing alternative drug targets. BMC Systems Biology. 2007, 1 (1): 26- 10.1186/1752-0509-1-26
Beste DJ, Hooper T, Stewart G, Bonde B, Avignone-Rossa C, Bushell ME, Wheeler P, Klamt S, Kierzek AM, McFadden J: GSMN-TB: a web-based genome-scale network model of Mycobacterium tuberculosis metabolism. Genome Biol. 2007, 8 (5): R89- 10.1186/gb-2007-8-5-r89
Becker SA, Palsson BO: Genome-scale reconstruction of the metabolic network in Staphylococcus aureus N315: an initial draft to the two-dimensional annotation. BMC Microbiol. 2005, 5 (1): 8- 10.1186/1471-2180-5-8
Heinemann M, Kummel A, Ruinatscha R, Panke S: In silico genome-scale reconstruction and validation of the Staphylococcus aureus metabolic network. Biotechnol Bioeng. 2005, 92 (7): 850-864. 10.1002/bit.20663
Oliveira AP, Nielsen J, Forster J: Modeling Lactococcus lactis using a genome-scale flux model. BMC Microbiol. 2005, 5: 39- 10.1186/1471-2180-5-39
Duarte NC, Becker SA, Jamshidi N, Thiele I, Mo ML, Vo TD, Srivas R, Palsson BO: Global reconstruction of the human metabolic network based on genomic and bibliomic data. Proceedings of the National Academy of Sciences. 2007, 104 (6): 1777-1782. 10.1073/pnas.0610772104.
Reed JL, Patel TR, Chen KH, Joyce AR, Applebee MK, Herring CD, Bui OT, Knight EM, Fong SS, Palsson BO: Systems approach to refining genome annotation. Proceedings of the National Academy of Sciences. 2006, 103 (46): 17480-17484. 10.1073/pnas.0603364103.
Ibarra RU, Edwards JS, Palsson BO: Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth. Nature. 2002, 420 (6912): 186-189. 10.1038/nature01149
Joyce AR, Fong SS, Palsson BO: Adaptive Evolution of E. coli on Either Lactate or Glycerol Leads to Convergent, Generalist Phenotypes. International E Coli Alliance Second Annual Meeting: 2004; Banff, Alberta. 2004
Fong SS, Palsson BO: Metabolic gene deletion strains of Escherichia coli evolve to computationally predicted growth phenotypes. Nature Genetics. 2004, 36 (10): 1056-1058. 10.1038/ng1432
Park JH, Lee KH, Kim TY, Lee SY: Metabolic engineering of Escherichia coli for the production of L-valine based on transcriptome analysis and in silico gene knockout simulation. Proceedings of the National Academy of Sciences. 2007, 104 (19): 7797-7802. 10.1073/pnas.0702609104.
Thiele I, Price ND, Vo TD, Palsson BO: Candidate metabolic network states in human mitochondria: Impact of diabetes, ischemia, and diet. J Biol Chem. 2005, 280 (12): 11683-11695. 10.1074/jbc.M409072200
Ravasz E, Somera AL, Mongru DA, Oltvai ZN, Barabasi AL: Hierarchical organization of modularity in metabolic networks. Science. 2002, 297 (5586): 1551-1555. 10.1126/science.1073374
Barabasi AL, Oltvai ZN: Network biology: understanding the cell's functional organization. Nature reviews. 2004, 5 (2): 101-113. 10.1038/nrg1272
Almaas E, Kovacs B, Vicsek T, Oltvai ZN, Barabasi AL: Global organization of metabolic fluxes in the bacterium Escherichia coli. Nature. 2004, 427 (6977): 839-843. 10.1038/nature02289
Feist AM, Palsson BO: Metabolic Flux Balancing: Basic concepts, Scientific and Practical Use – 13 Years Later. Nat Biotechnol. 2008, 26 (6): 659-667. 10.1038/nbt1401
Reed JL, Vo TD, Schilling CH, Palsson BO: An expanded genome-scale model of Escherichia coli K-12 (i JR904 GSM/GPR). Genome Biology. 2003, 4 (9): R54.51-R54.52. 10.1186/gb-2003-4-9-r54.
Varma A, Palsson BO: Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110. Appl Environ Microbiol. 1994, 60 (10): 3724-3731.
Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita KF, Itoh M, Kawashima S, Katayama T, Araki M, Hirakawa M: From genomics to chemical genomics: new developments in KEGG. Nucl Acids Res. 2006, 34 (suppl_1): D354-357. 10.1093/nar/gkj102.
Romero P, Karp P: PseudoCyc, A Pathway-Genome Database for Pseudomonas aeruginosa. Journal of Molecular Microbiology and Biotechnology. 2003, 5 (4): 230-239. 10.1159/000071075.
Choi C, Munch R, Leupold S, Klein J, Siegel I, Thielen B, Benkert B, Kucklick M, Schobert M, Barthelmes J, et al: SYSTOMONAS – an integrated database for systems biology analysis of Pseudomonas. Nucl Acids Res. 2007, 35 (suppl_1): D533-537. 10.1093/nar/gkl823.
Revelles O, Wittich R-M, Ramos JL: Identification of the Initial Steps in D-Lysine Catabolism in Pseudomonas putida. J Bacteriol. 2007, 189 (7): 2787-2792. 10.1128/JB.01538-06
Huijberts GN, de Rijk TC, de Waard P, Eggink G: 13C nuclear magnetic resonance studies of Pseudomonas putida fatty acid metabolic routes involved in poly(3-hydroxyalkanoate) synthesis. J Bacteriol. 1994, 176 (6): 1661-1666.
Hazer B, Steinbüchel A: Increased diversification of polyhydroxyalkanoates by modification reactions for industrial and medical applications. Appl Microbiol Biotechnol. 2007, 74 (1): 1-12. 10.1007/s00253-006-0732-8
Madison LL, Huisman GW: Metabolic Engineering of Poly(3-Hydroxyalkanoates): From DNA to Plastic. Microbiol Mol Biol Rev. 1999, 63 (1): 21-53.
Oberhardt MA, Puchalka J, Fryer KE, Martins dos Santos VAP, Papin JA: Genome-Scale Metabolic Network Analysis of the Opportunistic Pathogen Pseudomonas aeruginosa PAO1. J Bacteriol. 2008, 190 (8): 2790-2803. 10.1128/JB.01583-07
Janssen P, Goldovsky L, Kunin V, Darzentas N, Ouzounis CA: Genome coverage, literally speaking. The challenge of annotating 200 genomes with 4 million publications. EMBO Rep. 2005, 6 (5): 397-399. 10.1038/sj.embor.7400412
Ryan PR, Delhaize E, Jones DL: Function and mechanism Of Organic anion exudation from plant roots. Annual Review of Plant Physiology and Plant Molecular Biology. 2001, 52 (1): 527-560. 10.1146/annurev.arplant.52.1.527.
Espinosa-Urgel M, Ramos J-L: Expression of a Pseudomonas putida Aminotransferase Involved in Lysine Catabolism Is Induced in the Rhizosphere. Appl Environ Microbiol. 2001, 67 (11): 5219-5224. 10.1128/AEM.67.11.5219-5224.2001
Stanier RY, Palleroni N, Doudoroff M: The aerobic pseudomonads: a taxonomic study. J Gen Microbiol. 1966, 43 (2): 159-271.
Galvao TC, de Lorenzo V, Canovas D: Uncoupling of choline-O-sulphate utilization from osmoprotection in Pseudomonas putida. Molecular Microbiology. 2006, 62 (6): 1643-1654. 10.1111/j.1365-2958.2006.05488.x
Vicente M, Canovas JL: Glucolysis in Pseudomonas putida: Physiological Role of Alternative Routes from the Analysis of Defective Mutants. J Bacteriol. 1973, 116 (2): 908-914.
Reed JL, Famili I, Thiele I, Palsson BO: Towards multidimensional genome annotation. Nat Rev Genet. 2006, 7 (2): 130-141. 10.1038/nrg1769
Worsey MJ, Williams PA: Metabolism of toluene and xylenes by Pseudomonas (putida (arvilla) mt-2: evidence for a new function of the TOL plasmid. J Bacteriol. 1975, 124 (1): 7-13.
Assinder SJ, PA W: The TOL plasmids: determinants of the catabolism of toluene and the xylenes. Adv Microb Physiol. 1990, 31 (1–69):
Harayama S, Rekik M, Wubbolts M, Rose K, Leppik RA, Timmis KN: Characterization of five genes in the upper-pathway operon of TOL plasmid pWW0 from Pseudomonas putida and identification of the gene products. J Bacteriol. 1989, 171 (9): 5048-5055.
Harayama S, Rekik M: The meta cleavage operon of TOL degradative plasmid pWW0 comprises 13 genes. Mol Gen Genet. 1990, 221 (1): 113-120. 10.1007/BF00280375
Ramos JL, Marques S, Timmis KN: Transcriptional control of the pseudomonas tol plasmid catabolic operons is achieved through an interplay of host factors and plasmid-encoded regulators. Annual Review of Microbiology. 1997, 51 (1): 341-373. 10.1146/annurev.micro.51.1.341
Ramakrishna R, Edwards JS, McCulloch A, Palsson BO: Flux-balance analysis of mitochondrial energy metabolism: consequences of systemic stoichiometric constraints. American journal of physiology. 2001, 280 (3): R695-704.
Fischer E, Zamboni N, Sauer U: High-throughput metabolic flux analysis based on gas chromatography-mass spectrometry derived 13C constraints. Anal Biochem. 2004, 325 (2): 308-316. 10.1016/j.ab.2003.10.036
Alagappan G, Cowan RM: Effect of temperature and dissolved oxygen on the growth kinetics of Pseudomonas putida F1 growing on benzene and toluen. Chemosphere. 2004, 54 (8): 1255-1265. 10.1016/j.chemosphere.2003.09.013
Denef VJ, Klappenbach JA, Patrauchan MA, Florizone C, Rodrigues JLM, Tsoi TV, Verstraete W, Eltis LD, Tiedje JM: Genetic and Genomic Insights into the Role of Benzoate-Catabolic Pathway Redundancy in Burkholderia xenovorans LB400. Appl Environ Microbiol. 2006, 72 (1): 585-595. 10.1128/AEM.72.1.585-595.2006
Fridovich I: Superoxide radicals, superoxide dismutases and the aerobic lifestyle. Photochem Photobiol. 1978, 28 (4–5): 733-741. 10.1111/j.1751-1097.1978.tb07009.x
Jacobs MA, Alwood A, Thaipisuttikul I, Spencer D, Haugen E, Ernst S, Will O, Kaul R, Raymond C, Levy R, et al: Comprehensive transposon mutant library of Pseudomonas aeruginosa. Proceedings of the National Academy of Sciences. 2003, 100 (24): 14339-14344. 10.1073/pnas.2036282100.
Liberati NT, Urbach JM, Miyata S, Lee DG, Drenkard E, Wu G, Villanueva J, Wei T, Ausubel FM: An ordered, nonredundant library of Pseudomonas aeruginosa strain PA14 transposon insertion mutants. Proceedings of the National Academy of Sciences. 2006, 103 (8): 2833-2838. 10.1073/pnas.0511100103.
Ward PG, de Roo G, O'Connor KE: Accumulation of Polyhydroxyalkanoate from Styrene and Phenylacetic Acid by Pseudomonas putida CA-3. Appl Environ Microbiol. 2005, 71 (4): 2046-2052. 10.1128/AEM.71.4.2046-2052.2005
Timm A, Steinbuchel A: Formation of polyesters consisting of medium-chain-length 3-hydroxyalkanoic acids from gluconate by Pseudomonas aeruginosa and other fluorescent pseudomonads. Appl Environ Microbiol. 1990, 56 (11): 3360-3367.
Burgard AP, Pharkya P, Maranas CD: Optknock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization. Biotechnol Bioeng. 2003, 84 (6): 647-657. 10.1002/bit.10803
Pharkya P, Burgard AP, Maranas CD: OptStrain: a computational framework for redesign of microbial production systems. Genome Res. 2004, 14 (11): 2367-2376. 10.1101/gr.2872004
Hua Q, Joyce AR, Fong SS, Palsson BO: Metabolic analysis of adaptive evolution for in silico designed lactate-producing strains. Biotechnol Bioeng. 2006
Lee SY, Lee DY, Kim TY: Systems biotechnology for strain improvement. Trends Biotechnol. 2005, 23 (7): 349-358. 10.1016/j.tibtech.2005.05.003
Abril MA, Michan C, Timmis KN, Ramos JL: Regulator and enzyme specificities of the TOL plasmid-encoded upper pathway for degradation of aromatic hydrocarbons and expansion of the substrate range of the pathway. J Bacteriol. 1989, 171 (12): 6782-6790.
Fuhrer T, Fischer E, Sauer U: Experimental Identification and Quantification of Glucose Metabolism in Seven Bacterial Species. J Bacteriol. 2005, 187 (5): 1581-1590. 10.1128/JB.187.5.1581-1590.2005
Becker SA, Feist AM, Mo ML, Hannum G, Palsson BO, Herrgard MJ: Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox. Nat Protocols. 2007, 2 (3): 727-738. 10.1038/nprot.2007.99.
Neidhardt FC, Ingraham JL, Schaechter M: Physiology of the bacterial cell: a molecular approach. 1990, Sunderland, Mass.: Sinauer Associates
Pinkart HC, White DC: Lipids of pseudomonas. 111-138. Pseudomonas. Plenum Press
Edwards JS, Ibarra RU, Palsson B: In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data. Nat Biotechnol. 2001, 19 (2): 125-130. 10.1038/84379
Schilling CH, Edwards JS, Letscher D, Palsson BO: Combining pathway analysis with flux balance analysis for the comprehensive study of metabolic systems. Biotechnol Bioeng. 2000, 71 (4): 286-306. 10.1002/1097-0290(2000)71:4<286::AID-BIT1018>3.0.CO;2-R
Edwards JS, Ibarra RU, Palsson BO: In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data. Nat Biotechnol. 2001, 19: 125-130. 10.1038/84379
Riley M, Abe T, Arnaud MB, Berlyn MK, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Keseler IM, Kosuge T, et al: Escherichia coli K-12: a cooperatively developed annotation snapshot-2005. Nucleic Acids Res. 2006, 34 (1): 1-9. 10.1093/nar/gkj405
Nogales J, Canales A, Jimenez-Barbero J, Garcia JL, Diaz E: Molecular Characterization of the Gallate Dioxygenase from Pseudomonas putida KT2440: The prototype of a new subgroup of extradiol dioxygenases. J Biol Chem. 2005, 280 (42): 35382-35390. 10.1074/jbc.M502585200
Fan CL, Miller DL, Rodwell VW: Metabolism of Basic Amino Acids in Pseudomonas putida. Transport of lysine, ornithine, and arginine. J Biol Chem. 1972, 247 (8): 2283-2288.
Vilchez S, Molina L, Ramos C, Ramos JL: Proline Catabolism by Pseudomonas putida: Cloning, Characterization, and Expression of the put Genes in the Presence of Root Exudates. J Bacteriol. 2000, 182 (1): 91-99.
Haywood GW, Anderson AJ, Ewing DF, Dawes EA: Accumulation of a Polyhydroxyalkanoate Containing Primarily 3-Hydroxydecanoate from Simple Carbohydrate Substrates by Pseudomonas sp. Strain NCIMB 40135. Appl Environ Microbiol. 1990, 56 (11): 3354-3359.
Huisman GW, de Leeuw O, Eggink G, Witholt B: Synthesis of poly-3-hydroxyalkanoates is a common feature of fluorescent pseudomonads. Appl Environ Microbiol. 1989, 55 (8): 1949-1954.