Skip to main content
SpringerLink
Log in

Systems and Synthetic Biology Approaches for Metabolic Engineering of Pseudomonas putida

  • Chapter
  • First Online:
Microbial Models: From Environmental to Industrial Sustainability

Part of the book series: Microorganisms for Sustainability ((MICRO,volume 1))

Abstract

Pseudomonas putida is increasingly attracting attention as a bacterial host of reference both for basic and applied research. Over the years, this Gram-negative soil bacterium has been considered a potential agent for environmental bioremediation of industrial wastes and xenobiotic compounds and also a promising colonizer of the rhizosphere. However, the potential biotechnological applications of P. putida were enormously multiplied by the advent of contemporary synthetic biology which, together with the wealth of information provided by systems-level analysis of its genome, transcriptome, proteome, metabolome, and fluxome, enabled the implementation of targeted metabolic engineering approaches. This chapter summarizes the main discoveries within this context that mediated the transition of P. putida from its humble origin in the soil to modern biotechnology setups, where it excels in a number of practical applications for which other traditional microbial cell factories cannot be used (e.g., in hosting harsh oxidative reactions for the production of valuable chemicals).

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Bagdasarian M, Lurz R, Rückert B, Franklin FCH, Bagdasarian MM, Frey J, Timmis KN (1981) Specific purpose plasmid cloning vectors. II. Broad host range, high copy number, RSF1010-derived vectors, and a host-vector system for gene cloning in Pseudomonas. Gene 16:237–247

    Article  CAS  PubMed  Google Scholar 

  • Belda E, van Heck RGA, López-Sánchez MJ, Cruveiller S, Barbe V, Fraser C, Klenk HP, Petersen J, Morgat A, Nikel PI, Vallenet D, Rouy Z, Sekowska A, Martins dos Santos VAP, de Lorenzo V, Danchin A, Médigue C (2016) The revisited genome of Pseudomonas putida KT2440 enlightens its value as a robust metabolic chassis. Environ Microbiol 18:3403–3424

    Google Scholar 

  • Cabiscol E, Tamarit J, Ros J (2000) Oxidative stress in bacteria and protein damage by reactive oxygen species. Int Microbiol 3:3–8

    CAS  PubMed  Google Scholar 

  • Chavarría M, Kleijn RJ, Sauer U, Pflüger-Grau K, de Lorenzo V (2012) Regulatory tasks of the phosphoenolpyruvate-phosphotransferase system of Pseudomonas putida in central carbon metabolism. mBio 3:e00012–e00028

    Article  CAS  Google Scholar 

  • Chavarría M, Nikel PI, Pérez-Pantoja D, de Lorenzo V (2013) The Entner-Doudoroff pathway empowers Pseudomonas putida KT2440 with a high tolerance to oxidative stress. Environ Microbiol 15:1772–1785

    Article  CAS  PubMed  Google Scholar 

  • Choi KH, Schweizer HP (2006) Mini-Tn7 insertion in bacteria with single attTn7 sites: example Pseudomonas aeruginosa. Nat Protoc 1:153–161

    Article  CAS  PubMed  Google Scholar 

  • Clarke PH (1982) The metabolic versatility of pseudomonads. Antonie van Leeuwenhoek 48:105–130

    Google Scholar 

  • Conway T (1992) The Entner-Doudoroff pathway: history, physiology and molecular biology. FEMS Microbiol Rev 103:1–27

    Article  CAS  Google Scholar 

  • Danchin A (2012) Scaling up synthetic biology: do not forget the chassis. FEBS Lett 586:2129–2137

    Article  CAS  PubMed  Google Scholar 

  • Daniel R (2004) The soil metagenome–a rich resource for the discovery of novel natural products. Curr Opin Biotechnol 15:199–204

    Article  CAS  PubMed  Google Scholar 

  • Daniels C, Godoy P, Duque E, Molina-Henares MA, de la Torre J, del Arco JM, Herrera C, Segura A, Guazzaroni ME, Ferrer M, Ramos JL (2010) Global regulation of food supply by Pseudomonas putida DOT-T1E. J Bacteriol 192:2169–2181

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • de Lorenzo V (2008) Systems biology approaches to bioremediation. Curr Opin Biotechnol 19:579–589

    Article  CAS  PubMed  Google Scholar 

  • de Lorenzo V, Danchin A (2008) Synthetic biology: discovering new worlds and new words. EMBO Rep 9:822–827

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • de Lorenzo V, Timmis KN (1994) Analysis and construction of stable phenotypes in gram-negative bacteria with Tn5- and Tn10-derived minitransposons. Methods Enzymol 235:386–405

    Article  CAS  PubMed  Google Scholar 

  • de Lorenzo V, Herrero M, Jakubzik U, Timmis KN (1990) Mini-Tn5 transposon derivatives for insertion mutagenesis, promoter probing, and chromosomal insertion of cloned DNA in Gram-negative eubacteria. J Bacteriol 172:6568–6572

    Article  PubMed  PubMed Central  Google Scholar 

  • de Lorenzo V, Eltis L, Kessler B, Timmis KN (1993a) Analysis of Pseudomonas gene products using lacI q /Ptrp-lac plasmids and transposons that confer conditional phenotypes. Gene 123:17–24

    Article  PubMed  Google Scholar 

  • de Lorenzo V, Fernández S, Herrero M, Jakubzik U, Timmis KN (1993b) Engineering of alkyl- and haloaromatic-responsive gene expression with mini-transposons containing regulated promoters of biodegradative pathways of Pseudomonas. Gene 130:41–46

    Article  PubMed  Google Scholar 

  • del Castillo T, Ramos JL, Rodríguez-Herva JJ, Fuhrer T, Sauer U, Duque E (2007) Convergent peripheral pathways catalyze initial glucose catabolism in Pseudomonas putida: genomic and flux analysis. J Bacteriol 189:5142–5152

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • den Dooren de Jong LE (1926) Bijdrage Tot de Kennis van het Mineralisatieproces, Thesis, Rotterdam, The Netherlands

    Google Scholar 

  • Domínguez-Cuevas P, González-Pastor JE, Marqués S, Ramos JL, de Lorenzo V (2006) Transcriptional tradeoff between metabolic and stress-response programs in Pseudomonas putida KT2440 cells exposed to toluene. J Biol Chem 281:11981–11991

    Article  CAS  PubMed  Google Scholar 

  • Durante-Rodríguez G, de Lorenzo V, Martínez-García E (2014) The Standard European Vector Architecture (SEVA) plasmid toolkit. Methods Mol Biol 1149:469–478

    Article  CAS  PubMed  Google Scholar 

  • Ebert BE, Kurth F, Grund M, Blank LM, Schmid A (2011) Response of Pseudomonas putida KT2440 to increased NADH and ATP demand. Appl Environ Microbiol 77:6597–6605

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Endy D (2005) Foundations for engineering biology. Nature 438:449–453

    Article  CAS  PubMed  Google Scholar 

  • Escapa IF, García JL, Bühler B, Blank LM, Prieto MA (2012) The polyhydroxyalkanoate metabolism controls carbon and energy spillage in Pseudomonas putida. Environ Microbiol 14:1049–1063

    Article  CAS  PubMed  Google Scholar 

  • Follonier S, Escapa IF, Fonseca PM, Henes B, Panke S, Zinn M, Prieto MA (2013) New insights on the reorganization of gene transcription in Pseudomonas putida KT2440 at elevated pressure. Microb Cell Fact 12:30

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fonseca P, Moreno R, Rojo F (2011) Growth of Pseudomonas putida at low temperature: global transcriptomic and proteomic analyses. Environ Microbiol Rep 3:329–339

    Article  CAS  PubMed  Google Scholar 

  • Frank S, Klockgether J, Hagendorf P, Geffers R, Schöck U, Pohl T, Davenport CF, Tümmler B (2011) Pseudomonas putida KT2440 genome update by cDNA sequencing and microarray transcriptomics. Environ Microbiol 13:1309–1326

    Article  CAS  PubMed  Google Scholar 

  • Hayaishi O, Katagiri M, Rothberg S (1955) Mechanism of the pyrocatechase reaction. J Am Chem Soc 77:5450–5451

    Article  CAS  Google Scholar 

  • Heim S, Ferrer M, Heuer H, Regenhardt D, Nimtz M, Timmis KN (2003) Proteome reference map of Pseudomonas putida strain KT2440 for genome expression profiling: distinct responses of KT2440 and Pseudomonas aeruginosa strain PAO1 to iron deprivation and a new form of superoxide dismutase. Environ Microbiol 5:1257–1269

    Article  CAS  PubMed  Google Scholar 

  • Herbst FA, Danielsen HN, Wimmer R, Nielsen PH, Dueholm MS (2015) Label-free quantification reveals major proteomic changes in Pseudomonas putida F1 during the exponential growth phase. Proteomics 15:3244–3252

    Article  CAS  PubMed  Google Scholar 

  • Hervás AB, Canosa I, Santero E (2008) Transcriptome analysis of Pseudomonas putida in response to nitrogen availability. J Bacteriol 190:416–420

    Article  CAS  PubMed  Google Scholar 

  • Jendrossek D (2009) Polyhydroxyalkanoate granules are complex subcellular organelles (carbonosomes). J Bacteriol 191:3195–3202

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kahl LJ, Endy D (2013) A survey of enabling technologies in synthetic biology. J Biol Eng 7:13

    Article  PubMed  PubMed Central  Google Scholar 

  • Kim J, Park W (2014) Oxidative stress response in Pseudomonas putida. Appl Microbiol Biotechnol 98:6933–6946

    Article  CAS  PubMed  Google Scholar 

  • Kim J, Oliveros JC, Nikel PI, de Lorenzo V, Silva-Rocha R (2013) Transcriptomic fingerprinting of Pseudomonas putida under alternative physiological regimes. Environ Microbiol Rep 5:883–891

    Article  CAS  PubMed  Google Scholar 

  • Kim J, Pérez-Pantoja D, Silva-Rocha R, Oliveros JC, de Lorenzo V (2015) High-resolution analysis of the m-xylene/toluene biodegradation subtranscriptome of Pseudomonas putida mt-2. Environ Microbiol 18:3327–3341

    Google Scholar 

  • La Rosa R, Nogales J, Rojo F (2015) The Crc/CrcZ-CrcY global regulatory system helps the integration of gluconeogenic and glycolytic metabolism in Pseudomonas putida. Environ Microbiol 17:3362–3378

    Article  CAS  PubMed  Google Scholar 

  • Ladisch MR, Mosier NS (2009) Modern Biotechnology: connecting innovations in microbiology and biochemistry to engineering fundamentals. Wiley-AIChE, Hoboken

    Google Scholar 

  • Latrach-Tlemçani L, Corroler D, Barillier D, Mosrati R (2008) Physiological states and energetic adaptation during growth of Pseudomonas putida mt-2 on glucose. Arch Microbiol 190:141–150

    Article  CAS  PubMed  Google Scholar 

  • Lehrbach PR, Zeyer J, Reineke W, Knackmuss HJ, Timmis KN (1984) Enzyme recruitment in vitro: use of cloned genes to extend the range of haloaromatics degraded by Pseudomonas sp. strain B13. J Bacteriol 158:1025–1032

    CAS  PubMed  PubMed Central  Google Scholar 

  • Lessie TG, Phibbs PV (1984) Alternative pathways of carbohydrate utilization in pseudomonads. Annu Rev Microbiol 38:359–388

    Google Scholar 

  • Li SS, Hu X, Zhao H, Li YX, Zhang L, Gong LJ, Guo J, Zhao HB (2015) Quantitative analysis of cellular proteome alterations of Pseudomonas putida to naphthalene-induced stress. Biotechnol Lett 37:1645–1654

    Article  CAS  PubMed  Google Scholar 

  • Loeschcke A, Thies S (2015) Pseudomonas putida–a versatile host for the production of natural products. Appl Microbiol Biotechnol 99:6197–6214

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • López NI, Pettinari MJ, Nikel PI, Méndez BS (2015) Polyhydroxyalkanoates: much more than biodegradable plastics. Adv Appl Microbiol 93:93–106

    Google Scholar 

  • Loza-Tavera H, de Lorenzo V (2011) Microbial bioremediation of chemical pollutants: how bacteria cope with multi-stress environmental scenarios. In: Storz G, Hengge R (eds) Bacterial stress responses. ASM Press, Washington, DC, pp 481–492

    Google Scholar 

  • Lu J, Holmgren A (2014) The thioredoxin antioxidant system. Free Radic Biol Med 66:75–87

    Article  CAS  PubMed  Google Scholar 

  • Manara A, DalCorso G, Baliardini C, Farinati S, Cecconi D, Furini A (2012) Pseudomonas putida response to cadmium: changes in membrane and cytosolic proteomes. J Proteome Res 11:4169–4179

    Article  CAS  PubMed  Google Scholar 

  • Martínez-García E, de Lorenzo V (2012) Transposon-based and plasmid-based genetic tools for editing genomes of gram-negative bacteria. Methods Mol Biol 813:267–283

    Article  CAS  PubMed  Google Scholar 

  • Martínez-García E, Calles B, Arévalo-Rodríguez M, de Lorenzo V (2011) pBAM1: an all-synthetic genetic tool for analysis and construction of complex bacterial phenotypes. BMC Microbiol 11:38

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Martínez-García E, Aparicio T, Goñi-Moreno A, Fraile S, de Lorenzo V (2014a) SEVA 2.0: an update of the Standard European Vector Architecture for de-/re-construction of bacterial functionalities. Nucleic Acids Res 43:D1183–D1189

    Article  PubMed  PubMed Central  Google Scholar 

  • Martínez-García E, Aparicio T, de Lorenzo V, Nikel PI (2014b) New transposon tools tailored for metabolic engineering of gram-negative microbial cell factories. Front Bioeng Biotechnol 2:46

    PubMed  PubMed Central  Google Scholar 

  • Martínez-García E, Benedetti I, Hueso A, de Lorenzo V (2015) Mining environmental plasmids for synthetic biology parts and devices. Microbiol Spectr 3, PLAS-0033-2014

    Google Scholar 

  • Martins dos Santos VAP, Heim S, Moore ER, Strätz M, Timmis KN (2004) Insights into the genomic basis of niche specificity of Pseudomonas putida KT2440. Environ Microbiol 6:1264–1286

    Article  CAS  Google Scholar 

  • Medico E, Gambarotta G, Gentile A, Comoglio PM, Soriano P (2001) A gene trap vector system for identifying transcriptionally responsive genes. Nat Biotechnol 19:579–582

    Article  CAS  PubMed  Google Scholar 

  • Mohn WW, Garmendia J, Galvão TC, de Lorenzo V (2006) Surveying biotransformations with à la carte genetic traps: translating dehydrochlorination of lindane (γ-hexachlorocyclohexane) into lacZ-based phenotypes. Environ Microbiol 8:546–555

    Article  CAS  PubMed  Google Scholar 

  • Moreno R, Rojo F (2013) The contribution of proteomics to the unveiling of the survival strategies used by Pseudomonas putida in changing and hostile environments. Proteomics 13:2822–2830

    CAS  PubMed  Google Scholar 

  • Neidhardt FC, Ingraham JL, Schaechter M (1990) Physiology of the bacterial cell: a molecular approach. Sinauer Associates, Sunderland

    Google Scholar 

  • Nelson KE, Weinel C, Paulsen IT, Dodson RJ, Hilbert H, Martins dos Santos VAP, Fouts DE, Gill SR, Pop M, Holmes M, Brinkac L, Beanan M, DeBoy RT, Daugherty S, Kolonay J, Madupu R, Nelson W, White O, Peterson J, Khouri H, Hance I, Chris Lee P, Holtzapple E, Scanlan D, Tran K, Moazzez A, Utterback T, Rizzo M, Lee K, Kosack D, Moestl D, Wedler H, Lauber J, Stjepandic D, Hoheisel J, Straetz M, Heim S, Kiewitz C, Eisen JA, Timmis KN, Düsterhöft A, Tümmler B, Fraser CM (2002) Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440. Environ Microbiol 4:799–808

    Article  CAS  PubMed  Google Scholar 

  • Nikel PI (2012) A brief guide to Pseudomonas putida as a microbial cell factory. BioEssays Available on line at http://goo.gl/DXF1y

  • Nikel PI, Chavarría M (2015) Quantitative physiology approaches to understand and optimize reducing power availability in environmental bacteria. In: McGenity TJ, Timmis KN, Nogales Fernández B (eds) Hydrocarbon and lipid microbiology protocols. Humana Press, Heidelberg, pp 1–32

    Google Scholar 

  • Nikel PI, de Lorenzo V (2013) Implantation of unmarked regulatory and metabolic modules in gram-negative bacteria with specialised mini-transposon delivery vectors. J Biotechnol 163:143–154

    Article  CAS  PubMed  Google Scholar 

  • Nikel PI, Pérez-Pantoja D, de Lorenzo V (2013) Why are chlorinated pollutants so difficult to degrade aerobically? Redox stress limits 1,3-dichloroprop-1-ene metabolism by Pseudomonas pavonaceae. Philos Trans R Soc Lond B Biol Sci 368:20120377

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nikel PI, Martínez-García E, de Lorenzo V (2014a) Biotechnological domestication of pseudomonads using synthetic biology. Nat Rev Microbiol 12:368–379

    Article  CAS  PubMed  Google Scholar 

  • Nikel PI, Silva-Rocha R, Benedetti I, de Lorenzo V (2014b) The private life of environmental bacteria: pollutant biodegradation at the single cell level. Environ Microbiol 16:628–642

    Article  CAS  PubMed  Google Scholar 

  • Nikel PI, Chavarría M, Fuhrer T, Sauer U, de Lorenzo V (2015) Pseudomonas putida KT2440 strain metabolizes glucose through a cycle formed by enzymes of the Entner-Doudoroff, Embden-Meyerhof-Parnas, and pentose phosphate pathways. J Biol Chem 290:25920–25932

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nikodinovic-Runic J, Flanagan M, Hume AR, Cagney G, O’Connor KE (2009) Analysis of the Pseudomonas putida CA-3 proteome during growth on styrene under nitrogen-limiting and non-limiting conditions. Microbiology 155:3348–3361

    Article  CAS  PubMed  Google Scholar 

  • Nogales J, Palsson BØ, Thiele I (2008) A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory. BMC Syst Biol 2:79

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Oliver RW (2000) The coming biotech age: the business of bio-materials. McGraw-Hill, New York

    Google Scholar 

  • Panikov NS, Mandalakis M, Dai S, Mulcahy LR, Fowle W, Garrett WS, Karger BL (2015) Near-zero growth kinetics of Pseudomonas putida deduced from proteomic analysis. Environ Microbiol 17:215–228

    Article  CAS  PubMed  Google Scholar 

  • Park SJ, Choi JS, Kim BC, Jho SW, Ryu JW, Park D, Lee KA, Bhak J, Kim SI (2009) PutidaNET: interactome database service and network analysis of Pseudomonas putida KT2440. BMC Genomics 10:S18

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Peters JE, Craig NL (2001) Tn7: smarter than we thought. Nat Rev Mol Cell Biol 2:806–814

    Article  CAS  PubMed  Google Scholar 

  • Poblete-Castro I, Becker J, Dohnt K, Martins dos Santos VAP, Wittmann C (2012a) Industrial biotechnology of Pseudomonas putida and related species. Appl Microbiol Biotechnol 93:2279–2290

    Article  CAS  PubMed  Google Scholar 

  • Poblete-Castro I, Escapa IF, Jäger C, PuchaÅ‚ka J, Lam CMC, Schomburg D, Prieto MA, Martins dos Santos VAP (2012b) The metabolic response of P. putida KT2442 producing high levels of polyhydroxyalkanoate under single- and multiple-nutrient-limited growth: highlights from a multi-level omics approach. Microb Cell Fact 11:34

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Prieto MA, Escapa IF, Martínez V, Dinjaski N, Herencias C, de la Peña F, Tarazona N, Revelles O (2014) A holistic view of polyhydroxyalkanoate metabolism in Pseudomonas putida. Environ Microbiol 18:341–357

    Google Scholar 

  • PuchaÅ‚ka J, Oberhardt MA, Godinho M, Bielecka A, Regenhardt D, Timmis KN, Papin JA, Martins dos Santos VAP (2008) Genome-scale reconstruction and analysis of the Pseudomonas putida KT2440 metabolic network facilitates applications in biotechnology. PLoS Comput Biol 4:e1000210

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ramos JL, Sol Cuenca M, Molina-Santiago C, Segura A, Duque E, Gómez-García MR, Udaondo Z, Roca A (2015) Mechanisms of solvent resistance mediated by interplay of cellular factors in Pseudomonas putida. FEMS Microbiol Rev 39:555–566

    Article  PubMed  Google Scholar 

  • Reva ON, Weinel C, Weinel M, Böhm K, Stjepandic D, Hoheisel JD, Tümmler B (2006) Functional genomics of stress response in Pseudomonas putida KT2440. J Bacteriol 188:4079–4092

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rojo F, Pieper DH, Engesser KH, Knackmuss HJ, Timmis KN (1987) Assemblage of ortho cleavage route for simultaneous degradation of chloro- and methylaromatics. Science 238:1395–1398

    Article  CAS  PubMed  Google Scholar 

  • Ruiz JA, de Almeida A, Godoy MS, Mezzina MP, Bidart GN, Méndez BS, Pettinari MJ, Nikel PI (2012) Escherichia coli redox mutants as microbial cell factories for the synthesis of reduced biochemicals. Comput Struct Biotechnol J 3:e201210019

    Article  PubMed  Google Scholar 

  • Schweizer HP, de Lorenzo V (2004) Molecular tools for genetic analysis of pseudomonads. In: Ramos JL (ed) The pseudomonads: genomics, life style and molecular architecture. Kluwer Academic/Plenum, New York, pp 317–350

    Chapter  Google Scholar 

  • Silva-Rocha R, Martínez-García E, Calles B, Chavarría M, Arce-Rodríguez A, de las Heras A, Páez-Espino AD, Durante-Rodríguez G, Kim J, Nikel PI, Platero R, de Lorenzo V (2013) The Standard European Vector Architecture (SEVA): a coherent platform for the analysis and deployment of complex prokaryotic phenotypes. Nucleic Acids Res 41:D666–D675

    Article  CAS  PubMed  Google Scholar 

  • Sohn SB, Kim TY, Park JM, Lee SY (2010) In silico genome-scale metabolic analysis of Pseudomonas putida KT2440 for polyhydroxyalkanoate synthesis, degradation of aromatics and anaerobic survival. Biotechnol J 5:739–750

    Article  CAS  PubMed  Google Scholar 

  • Sudarsan S, Dethlefsen S, Blank LM, Siemann-Herzberg M, Schmid A (2014) The functional structure of central carbon metabolism in Pseudomonas putida KT2440. Appl Environ Microbiol 80:5292–5303

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Timmis KN (2002) Pseudomonas putida: a cosmopolitan opportunist par excellence. Environ Microbiol 4:779–781

    Article  PubMed  Google Scholar 

  • Udaondo Z, Molina L, Segura A, Duque E, Ramos JL (2016) Analysis of the core genome and pangenome of Pseudomonas putida. Environ Microbiol 18:3268–3283

    Google Scholar 

  • Vallon T, Simon O, Rendgen-Heugle B, Frana S, Mückschel B, Broicher A, Siemann-Herzberg M, Pfannenstiel J, Hauer B, Huber A, Breuer M, Takors R (2015) Applying systems biology tools to study n-butanol degradation in Pseudomonas putida KT2440. Eng Life Sci 15:760–771

    Article  CAS  Google Scholar 

  • van der Werf MJ, Overkamp KM, Muilwijk B, Koek MM, van der Werff-van der Vat BJ, Jellema RH, Coulier L, Hankemeier T (2008) Comprehensive analysis of the metabolome of Pseudomonas putida S12 grown on different carbon sources. Mol Biosyst 4:315–327

    Article  CAS  PubMed  Google Scholar 

  • van Duuren JB, PuchaÅ‚ka J, Mars AE, Bücker R, Eggink G, Wittmann C, Martins dos Santos VAP (2013) Reconciling in vivo and in silico key biological parameters of Pseudomonas putida KT2440 during growth on glucose under carbon-limited condition. BMC Biotechnol 13:93

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wijte D, van Baar BL, Heck AJ, Altelaar AF (2011) Probing the proteome response to toluene exposure in the solvent tolerant Pseudomonas putida S12. J Proteome Res 10:394–403

    Article  CAS  PubMed  Google Scholar 

  • Williams PA, Murray K (1974) Metabolism of benzoate and the methylbenzoates by Pseudomonas putida (arvilla) mt-2: evidence for the existence of a TOL plasmid. J Bacteriol 120:416–423

    CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang W, Li F, Nie L (2010) Integrating multiple ‘omics’ analysis for microbial biology: application and methodologies. Microbiology 156:287–301

    Article  CAS  PubMed  Google Scholar 

  • Zobel S, Benedetti I, Eisenbach L, de Lorenzo V, Wierckx N, Blank LM (2015) Tn7-Based device for calibrated heterologous gene expression in Pseudomonas putida. ACS Synth Biol 4:1341–1351

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgment

The author is indebted to Prof. Víctor de Lorenzo (CNB-CSIC), the enlightening tutelage and continuous support of whom has been instrumental to develop many of the studies on which this chapter is based. The works by the author have been financed by the European Molecular Biology Organization and the Marie Skłodowska-Curie Actions from the European Commission. There is no conflict of interest related to the contents of this chapter.

Author information

Authors and Affiliations

  1. Systems and Synthetic Biology Program, National Spanish Center for Biotechnology (CNB-CSIC), 28049, Madrid, Spain

    Pablo I. Nikel

Authors
  1. Pablo I. Nikel
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Pablo I. Nikel .

Editor information

Editors and Affiliations

  1. Biochemistry and Molecular Biology Section, Faculty of Sciences, Universidad de la República, Montevideo, Uruguay

    Susana Castro-Sowinski

Rights and permissions

Reprints and permissions

Copyright information

© 2016 Springer Science+Business Media Singapore

About this chapter

Cite this chapter

Nikel, P.I. (2016). Systems and Synthetic Biology Approaches for Metabolic Engineering of Pseudomonas putida . In: Castro-Sowinski, S. (eds) Microbial Models: From Environmental to Industrial Sustainability. Microorganisms for Sustainability, vol 1. Springer, Singapore. https://doi.org/10.1007/978-981-10-2555-6_1

Download citation

Publish with us

Policies and ethics

Search

Navigation