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A Genomic View of the Catabolism of Aromatic Compounds in Pseudomonas

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Handbook of Hydrocarbon and Lipid Microbiology

Abstract:

The genetic, and the more recent genomic, proteomic, and metabolomic, approaches that have been undertaken to study the catabolism of aromatic compounds in different Pseudomonas strains have contributed significantly to the acceleration and completion of our understanding on different aspects of the physiology, ecology, biochemistry, and regulatory mechanisms underlying a secondary metabolism that allows the use of this highly abundant carbon source by some bacteria. Comparative genomics suggests that the overall organization of catabolic clusters is conserved across the Pseudomonas genus. However, species-specific and strain-specific variations account for differences in gene arrangements, substrate specificities, and regulatory elements. Moreover, genomic analyses point to the existence of parologous genes likely involved in the degradation of aromatic compounds, suggesting that our current knowledge about the degradative potential of Pseudomonas is still far from complete. On the other hand, many aromatic compounds, e.g., hydrocarbons and phenolic compounds, simultaneously serve as potential nutrients to be metabolized by bacteria but also as cellular stressors. The transcriptomic and proteomic approaches carried out with some Pseudomonas strains provide some light on the biodegradation versus stress dilemma. The increased use of the “omic” techniques, together with the genome-scale metabolic reconstructions developed for some Pseudomonas strains, will certainly contribute significantly to unravel the intricate regulatory and metabolic networks that govern the biodegradation of aromatic compounds, as well as their distribution and ecophysiological relevance. All the basic knowledge generated so far about the metabolism of aromatic compounds in Pseudomonas paves the way for a wealth of biotechnological applications, e.g., bioremediation, biotransformations, biosensors, etc., and it is of great potential in Synthetic Biology. Therefore, Pseudomonas becomes a paradigmatic bacterial genus both for increasing basic knowledge and for applied research within the field of aromatic compounds degradation.

†J. I. Jiménez and J. Nogales attributed equally to this work

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References

  • Agulló L, Cámara B, Martínez P, Latorre V, Seeger M (2007) Response to (chloro)biphenyls of the polychlorobiphenyl-degrader Burkholderia xenovorans LB400 involves stress proteins also induced by heat shock and oxidative stress. FEMS Microbiol Lett 267: 167–175.

    Article  PubMed  Google Scholar 

  • Alonso S, Navarro-Llorens JM, Tormo A, Perera J (2003) Construction of a bacterial biosensor for styrene. J Biotechnol 102: 301–306.

    PubMed  CAS  Google Scholar 

  • Arias S, Olivera ER, Arcos M, Naharro G, Luengo JM (2008) Genetic analyses and molecular characterization of the pathways involved in the conversion of 2-phenylethylamine and 2-phenylethanol into phenylacetic acid in Pseudomonas putida U. Environ Microbiol 10: 413–432.

    Article  PubMed  CAS  Google Scholar 

  • Arias-Barrau E, Olivera ER, Luengo JM, Fernández C, Galán B, García JL, Díaz E, Miñambres B (2004) The homogentisate pathway: a central catabolic pathway involved in the degradation of L-phenylalanine, L-tyrosine, and 3-hydroxyphenylacetate in Pseudomonas putida. J Bacteriol 186: 5062–5077.

    Article  PubMed  CAS  Google Scholar 

  • Blasco R, Ramos JL, Wittich RM (2008) Pseudomonas aeruginosa strain RW41 mineralizes 4-chlorobenzenesulfonate, the major polar by-product from DDT manufacturing. Environ Microbiol 10: 1591–1600.

    Article  PubMed  CAS  Google Scholar 

  • Bundy BM, Campbell AL, Neidle EL (1998) Similarities between the antABC-encoded anthranilate dioxygenase and the benABC-encoded benzoate dioxygenase of Acinetobacter sp. strain ADP1. J Bacteriol 180: 4466–4474.

    PubMed  CAS  Google Scholar 

  • Carmona M, Prieto MA, Galán B, García JL, Díaz E (2008) Signaling networks and design of pollutant biosensors. In: Microbial Biodegradation. Genomics and Molecular Biology. Díaz E (ed.). Norkfolk, UK: Caister Academic Press, 97–143.

    Google Scholar 

  • Cases I, de Lorenzo V (2005) Promoters in the environment: transcriptional regulation in its natural context. Nat Rev Microbiol 3: 105–118.

    Article  PubMed  CAS  Google Scholar 

  • Choi EN, Cho MC, Kim Y, Kim C-K, Lee K (2003) Expansion of growth substrate range in Pseudomonas putida F1 by mutations in both cymR and todS, which recruit a ring-fission hydrolase CmtE and induce the tod catabolic operon, respectively. Microbiology 149: 795–805.

    Article  PubMed  CAS  Google Scholar 

  • Cuskey SM, Olsen RH (1988) Catabolism of aromatic biogenic amines by Pseudomonas aeruginosa PAO1 via meta cleavage of homoprotocatechuic acid. J Bacteriol 170: 393–399.

    PubMed  CAS  Google Scholar 

  • Dejonghe W, Goris J, El Fantroussi S, Hofte M, De Vos P, Verstraete W, Top EM (2000) Effect of dissemination of 2,4-dichlorophenoxyacetic acid (2,4-D) degradation plasmids on 2,4-D degradation and on bacterial community structure in two different soil horizons. Appl Environ Microbiol 66: 3297–3304.

    Article  PubMed  CAS  Google Scholar 

  • De las Heras A, Carreño CA, De Lorenzo V (2008) Stable implantation of orthogonal sensor circuits in Gram-negative bacteria for environmental release. Environ Microbiol 10: 3305–3316.

    Google Scholar 

  • del Castillo T, Ramos JL (2007) Simultaneous catabolite repression between glucose and toluene metabolism in Pseudomonas putida is channeled through different signaling pathways. J Bacteriol 189: 6602–6610.

    Article  PubMed  CAS  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  PubMed  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Dunaway-Mariano D, Babbitt PC (1994) On the origins and functions of the enzymes of the 4-chlorobenzoate to 4-hydroxybenzoate converting pathway. Biodegradation 5: 259–276.

    Article  PubMed  CAS  Google Scholar 

  • Duque E, Rodríguez-Herva JJ, de la Torre J, Domínguez-Cuevas P, Muñoz-Rojas J, Ramos JL (2007) The RpoT regulon of Pseudomonas putida DOT-T1E and its role in stress endurance against solvents. J Bacteriol 189: 207–219.

    Article  PubMed  CAS  Google Scholar 

  • Eaton RW (1997) p-Cymene catabolic pathway in Pseudomonas putida F1: cloning and characterization of DNA encoding conversion of p-cymene to p-cumate. J Bacteriol 179: 3171–3180.

    PubMed  CAS  Google Scholar 

  • Erb RW, Eichner CA, Wagner-Döbler I, Timmis KN (1997) Bioprotection of microbial communities from toxic phenol mixtures by a genetically designed pseudomonad. Nat Biotech 15: 378–382.

    Article  CAS  Google Scholar 

  • Farrow JM 3rd, Pesci EC (2007) Two distinct pathways supply anthranilate as a precursor of the Pseudomonas quinolone signal. J Bacteriol 189: 3425–3433.

    Article  PubMed  CAS  Google Scholar 

  • Gaillard M, Vallaeys T, Vorhölter FJ, Minoia M, Werlen C, Sentchilo V, Pühler A, van der Meer JR (2006) The clc element of Pseudomonas sp. strain B13, a genomic island with various catabolic properties. J Bacteriol 188: 1999–2013.

    Article  PubMed  CAS  Google Scholar 

  • Galán B, Díaz E, García JL (2000) Enhancing desulphurization by engineering a flavin reductase-encoding gene cassette in recombinant biocatalysts. Environ Microbiol 2: 687–694.

    Article  PubMed  Google Scholar 

  • Galvão TC, de Lorenzo V (2006) Transcriptional regulators à la carte: engineering new effector specificities in bacterial regulatory proteins. Curr Opin Biotechnol 17: 34–42.

    Article  PubMed  Google Scholar 

  • Gao X, Tan CL, Yeo CC, Poh CL (2005) Molecular and biochemical characterization of the xlnD-encoded 3-hydroxybenzoate 6-hydroxylase involved in the degradation of 2,5-xylenol via the gentisate pathway in Pseudomonas alcaligenes NCIMB 9867. J Bacteriol 187: 7696–7702.

    Article  PubMed  CAS  Google Scholar 

  • García B, Olivera ER, Miñambres B, Fernández-Valverde, M, Canedo LM, Prieto MA, García JL, Martínez M, Luengo JM (1999) Novel biodegradable aromatic plastics from a bacterial source. Genetic and biochemical studies on a route of the phenylacetyl-CoA catabolon. J Biol Chem 274: 29228–29241.

    Article  PubMed  Google Scholar 

  • Gescher J, Ismail W, Ölgeschläger E, Eisenreich W, Wörth J, Fuchs G (2006) Aerobic benzoyl-coenzyme A (CoA) catabolic pathway in Azoarcus evansii: conversion of ring cleavage product by 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase. J Bacteriol 188: 2919–2927.

    Article  PubMed  CAS  Google Scholar 

  • Harayama S, Timmis KN (1992) Aerobic biodegradation of aromatic hydrocarbons by bacteria. In: Metal Ions in Biological Systems, vol. 28. Sigel H, Sigel A (eds.). New York: Marcel Dekker Inc., 99–156.

    Google Scholar 

  • Harwood CS, Parales RE (1996) The β-ketoadipate pathway and the biology of self-identity. Ann Rev Microbiol 50: 553–590.

    Article  CAS  Google Scholar 

  • Iwaki H, Muraki T, Ishihara S, Hasegawa Y, Rankin KN, Sulea T, Boyd J, Lau PCK (2007) Characterization of a Pseudomonad 2-nitrobenzoate nitroreductase and its catabolic pathway-associated 2-hydroxylaminobenzoate mutase and a chemoreceptor involved in 2-nitrobenzoate chemotaxis. J Bacteriol 189: 3502–3514.

    Article  PubMed  CAS  Google Scholar 

  • Jenal U, Malone J (2006) Mechanisms of cyclic-di-GMP signaling in bacteria. Annu Rev Genet 40: 385–407.

    Article  PubMed  CAS  Google Scholar 

  • Jiménez JI, Canales Á, Jiménez-Barbero J, Ginalski K, Rychlewski L, García JL, Díaz E (2008) Deciphering the genetic determinants for aerobic nicotinic acid degradation: The nic cluster from Pseudomonas putida KT2440. Proc Nat Acad Sci USA 105: 11329–11334.

    Article  PubMed  Google Scholar 

  • Jiménez JI, Miñambres B, García JL, Díaz E (2004) Genomic insights in the metabolism of aromatic compounds in Pseudomonas. In: Pseudomonas, vol. 3. Ramos JL (ed.). New York: Kluwer Academic, 425–462.

    Google Scholar 

  • Kallastu A, Hörak R, Kivisaar M (1998) Identification and characterization of IS1411, a new insertion sequence which causes transcriptional activation of the phenol degradation genes in Pseudomonas putida. J Bacteriol 180: 5306–5312.

    PubMed  CAS  Google Scholar 

  • Kim YH, Cho K, Yun S-H, Kim JY, Kwon K-H, Yoo JS, Kim SI (2006) 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 6: 1301–1318.

    Article  PubMed  CAS  Google Scholar 

  • Kivistik PA, Putrins M, Püvi K, Ilves H, Kivisaar M, Hörak R (2006) The ColRS two-component system regulates membrane functions and protects Pseudomonas putida against phenol. J Bacteriol 188: 8109–8117.

    Article  PubMed  CAS  Google Scholar 

  • Klemba M, Jakobs B, Wittich R-M, Pieper D (2000) Chromosomal integration of tcb chlorocatechol degradation pathway genes as a means of expanding the growth substrate range of bacteria to include haloaromatics. Appl Environ Microbiol 66: 3255–3261.

    Article  PubMed  CAS  Google Scholar 

  • Kuiper I, Bloemberg GV, Lugtenberg BJJ (2001) Selection of a plant-bacterium pair as a novel tool for rhizostimulation of polycyclic aromatic hydrocarbon-degrading bacteria. Mol Plant Microb Interact 14: 1197–1205.

    Article  CAS  Google Scholar 

  • Kurbatov L, Albrecht D, Herrmann H, Petruschka L (2006) Analysis of the proteome of Pseudomonas putida KT2440 grown on different sources of carbon and energy. Environ Microbiol 8: 466–478.

    Article  PubMed  CAS  Google Scholar 

  • Kurnasov O, Jablonski L, Polanuyer B, Dorrestein P, Begley T, Osterman A (2003) Aerobic tryptophan degradation pathway in bacteria: novel kynurenine formamidase. FEMS Lett 227: 219–227.

    Article  CAS  Google Scholar 

  • Leahy JG, Batchelor PJ, Morcomb SM (2003) Evolution of the soluble diiron monooxygenases. FEMS Microbiol Rev 27:449–479.

    Article  PubMed  CAS  Google Scholar 

  • Liu M, Durfee T, Cabrera JE, Zhao K, Jin DJ, Blattner FR (2005) Global transcriptional programs reveal a carbon source foraging strategy by Escherichia coli. J Biol Chem 280:15921–15927.

    PubMed  CAS  Google Scholar 

  • Lorenzo P, Alonso S, Velasco A, Díaz E, García JL, Perera J (2004) Design of catabolic cassettes for styrene biodegradation. Antonie van Leeuwenhoek 84: 17–24.

    Article  Google Scholar 

  • Luengo JM, García JL, Olivera ER (2001) The phenylacetyl-CoA catabolon: a complex catabolic unit with broad biotechnological applications. Mol Microbiol 39: 1434–1442.

    Article  PubMed  CAS  Google Scholar 

  • Luengo JM, García B, Sandoval A, Naharro G, Olivera ER (2003) Bioplastics from microorganisms. Curr Opin Microbiol 6: 251–260.

    Article  PubMed  CAS  Google Scholar 

  • Maruyama K, Shibayama T, Ichikawa A, Sakou Y, Yamada S, Sugisaki H (2004) Cloning and characterization of the genes encoding enzymes for the protocatechuate meta-degradation pathway of Pseudomonas ochraceae NGJ1. Biosci Biotechnol Biochem 68: 1434–1441.

    Article  PubMed  CAS  Google Scholar 

  • Miyakoshi M, Shintani M, Terabayashi T, Kai S, Yamane H, Nojiri H (2007) Transcriptome analysis of Pseudomonas putida KT2440 harboring the completely sequenced IncP-7 plasmid pCAR1. J Bacteriol 189: 6849–6860.

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Moonen MJH, Kamerbeek NM, Westphal AH, Boeren SA, Janssen DB, Fraaije MW, van Berkel WJH (2008a) Elucidation of the 4-hydroxyacetophenone catabolic pathway in Pseudomonas fluorescens ACB. J Bacteriol 190: 5190–5198.

    Article  PubMed  CAS  Google Scholar 

  • Moonen MJH, Synowsky SA, van den Berg WAM, Westphal AH, Heck AJR, van den Heuvel RHH, Fraaije MW, van Berkel WJH (2008b) Hydroquinone dioxygenase from Pseudomonas fluorescens ACB: a novel member of the family of nonheme-iron(II)-dependent dioxygenases. J Bacteriol 190: 5199–5209.

    Article  PubMed  CAS  Google Scholar 

  • Munthali MT, Timmis KN, Díaz E (1996) Use of colicin E3 for biological containment of microorganisms. Appl Environ Microbiol 62: 1805–1807.

    PubMed  CAS  Google Scholar 

  • Nogales J, Canales A, Jiménez-Barbero J, García JL, Díaz E (2005) Molecular characterization of the gallate dioxygenase from Pseudomonas putida KT2440. The prototype of a new subgroup of extradiol dioxygenases. J Biol Chem 280:35382–35390.

    Article  PubMed  CAS  Google Scholar 

  • Nogales J, Macchi R, Franchi F, Barzaghi D, Fernández C, García JL, Bertoni G, Díaz E (2007) Characterization of the last step of the aerobic phenylacetic acid degradation pathway. Microbiology 153: 357–365.

    Article  PubMed  CAS  Google Scholar 

  • Nogales J, Palsson BO, Thiele I (2008) A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory. BMC Syst Biol doi: 10.1186/1752–0509–2–79.

    Google Scholar 

  • Oberhardt MA, Puchalka J, Fryer KE, Martins dos Santos VAP, Papin JA (2008) Genome-scale metabolic network analysis of the opportunistic pathogen Pseudomonas aeruginosa PAO1. J Bacteriol 190: 2790–2803.

    Article  PubMed  CAS  Google Scholar 

  • O'Leary ND, O'Connor KE, Ward P, Goff M, Dobson ADW (2005) Genetic characterization of accumulation of polyhydroxyalkanoate from styrene in Pseudomonas putida CA-3. Appl Environ Microbiol 71: 4380–4387.

    Article  PubMed  Google Scholar 

  • Olivera ER, Carnicero D, García B, Miñambres B, Moreno MA, Cañedo L, DiRusso CC, Naharro G, Luengo JM (2001) Two different pathways are involved in the β-oxidation of n-alkanoic and n-phenylalkanoic acids in Pseudomonas putida U: genetic studies and biotechnological applications. Mol Microbiol 39: 863–874.

    Article  PubMed  CAS  Google Scholar 

  • Olivera ER, Miñambres B, García B, Muñiz C, Moreno MA, Ferrández A, Díaz E, García JL, Luengo JM (1998) Molecular characterization of the phenylacetic acid catabolic pathway in Pseudomonas putida U: the phenylacetyl-CoA catabolon. Proc Natl Acad Sci USA 95:6419–6424.

    Article  PubMed  CAS  Google Scholar 

  • Ouyang SP, Liu Q, Sun SY, Chen JC, Chen GQ (2007) Genetic engineering of Pseudomonas putida KT2442 for biotransformation of aromatic compounds to chiral cis-diols. J Biotechnol 132: 246–250.

    Article  PubMed  CAS  Google Scholar 

  • Parales RE, Ju K-S, Rollefson JB, Ditty JL (2008) Bioavailability, chemotaxis, and transport of organic pollutants. In: Microbial Biodegradation. Genomics and Molecular Biology. Díaz E (ed.). Norkfolk, UK: Caister Academic, 145–187.

    Google Scholar 

  • Park SH, Oh KH, Kim CK (2001) Adaptive and cross-protective responses of Pseudomonas sp. DJ-12 to several aromatics and other stress shocks. Curr Microbiol 43: 176–181.

    Article  PubMed  CAS  Google Scholar 

  • Phoenix P, Keane A, Patel A, Bergeron H, Ghoshal S, Lau PCK (2003) Characterization of a new solvent-responsive gene locus in Pseudomonas putida F1 and its functionalization as a versatile biosensor. Environ Microbiol 5: 1309–1327.

    Article  PubMed  CAS  Google Scholar 

  • Powlowski J, Shingler V (1994) Genetics and biochemistry of phenol degradation by Pseudomonas sp. CF600. Biodegradation 5: 219–236.

    Article  PubMed  CAS  Google Scholar 

  • Priefert H, Rabenhorst J, Steinbüchel A (2001) Biotechnological production of vanillin. Appl Microbiol Biotechnol 56: 296–314.

    Article  PubMed  CAS  Google Scholar 

  • Prieto MA, de Eugenio LI, Galán B, Luengo JM, Witholt B (2007) Synthesis and degradation of polyhydroxyalkanoates. In: Pseudomonas, vol. 5. Ramos JL, Filloux A (eds.). The Netherlands: Springer, 397–428.

    Chapter  Google Scholar 

  • Puchalka 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(10): e1000210. doi:10.1371/journal.pcbi.1000210.

    Article  PubMed  Google Scholar 

  • Reardon KF, Mosteller DC, Bull Rogers JD (2000) Biodegradation kinetics of benzene, toluene, and phenol as single and mixed substrates for Pseudomonas putida F1. Biotechnol Bioeng 69: 385–400.

    Article  PubMed  CAS  Google Scholar 

  • Reineke W (1998) Development of hybrid strains for the mineralization of chloroaromatics by patchwork assembly. Annu Rev Microbiol 52: 287–331.

    Article  PubMed  CAS  Google Scholar 

  • Resnick SM, Lee K, Gibson DT (1996) Diverse reactions catalyzed by napthalene dioxygenase from Pseudomonas sp. strain NCIB9816. J Ind Microbiol 17: 438–457.

    Google Scholar 

  • Rodríguez-Herva JJ, García V, Hurtado A, Segura A, Ramos JL (2007) The ttgGHI solvent efflux pump operon of Pseudomonas putida DOT-T1E is located on a large self-transmissible plasmid. Environ Microbiol 9: 1550–1561.

    Article  PubMed  Google Scholar 

  • Rojas A, Duque E, Schmid A, Hurtado A, Ramos JL, Segura A (2004) Biotransformation in double-phase systems: physiological responses of Pseudomonas putida DOT-T1E to a double phase made of aliphatic alcohols and biosynthesis of substituted catechols. Appl Environ Microbiol 70: 3637–3643.

    Article  PubMed  CAS  Google Scholar 

  • Ronchel MC, Ramos JL (2001) Dual system to reinforce biological containment of recombinant bacteria designed for rhizoremediation. Appl Environ Microbiol 67: 2649–2656.

    Article  PubMed  CAS  Google Scholar 

  • Rosenberg SL, Hegeman GD (1971) Genetics of the mandelate pathway in Pseudomonas aeruginosa. J Bacteriol 108: 1257–1269.

    PubMed  CAS  Google Scholar 

  • Santos PM, Benndorf D, Sá-Correia I (2004) Insights into Pseudomonas putida KT2440 response to phenol-induced stress by quantitative proteomics. Proteomics 4: 2640–2652.

    Article  PubMed  CAS  Google Scholar 

  • Santos PM, Roma V, Benndorf D, von Bergen M, Harms H, Sá-Correia I (2007) Mechanistic insights into the global response to phenol in the phenol-biodegrading strain Pseudomonas sp. M1 revealed by quantitative proteomics. OMICS 11: 233–251.

    Article  PubMed  CAS  Google Scholar 

  • Santos PM, Sá-Correia I (2007) Characterization of the unique organization and co-regulation of a gene cluster required for phenol and benzene catabolism in Pseudomonas sp. M1. J Biotechnol 131: 371–378.

    Article  PubMed  CAS  Google Scholar 

  • Sarand I, Österberg S, Holmqvist S, Holmfeldt P, Skärfstad E, Parales RE, Shingler V (2008) Metabolism-dependent taxis towards (methyl)phenols is coupled through the most abundant of three polar localized Aer-like proteins of Pseudomonas putida. Environ Microbiol 10: 1320–1334.

    Article  PubMed  CAS  Google Scholar 

  • Segura A, Godoy P, van Dillewijn P, Hurtado A, Arroyo N, Santacruz S, Ramos, JL (2005) Proteomic analysis reveals the participation of energy- and stress-related proteins in the response of Pseudomonas putida DOT-T1E to toluene. J Bacteriol 187: 5937–5945.

    Article  PubMed  CAS  Google Scholar 

  • Sikkema J, de Bont JA, Poolman B (1995) Mechanisms of membrane toxicity of hydrocarbons. Microbiol Rev 59: 201–222.

    PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Song B, Ward BB (2005) Genetic diversity of benzoyl coenzyme A reductase genes detected in denitrifying isolates and estuarine sediment communities. Appl Environ Microbiol 71: 2036–2045.

    Article  PubMed  CAS  Google Scholar 

  • Spain JC (1995) Biodegradation of nitroaromatic compounds. Annu Rev Microbiol 49: 523–555.

    Article  PubMed  CAS  Google Scholar 

  • Taira K, Hirose J, Hayashida S, Furukawa K (1992) Analysis of bph operon from the polychlorinated biphenyl-degrading strain of Pseudomonas pseudoalcaligenes KF707. J Biol Chem 267: 4844–4853.

    PubMed  CAS  Google Scholar 

  • Takenaka S, Murakami S, Kim YJ, Aoki K (2000) Complete nucleotide sequence and functional analysis of the genes for 2-aminophenol metabolism from Pseudomonas sp. AP-3. Arch Microbiol 174: 265–272.

    Article  PubMed  CAS  Google Scholar 

  • Tang H, Wang S, Ma L, Meng X, Deng Z, Zhang D, Ma C, Xu P (2008) A novel gene, encoding 6-hydroxy-3-succinoylpyridine hydroxylase, involved in nicotine degradation by Pseudomonas putida strain S16. Appl Environ Microbiol 74: 1567–1574.

    Article  PubMed  CAS  Google Scholar 

  • Trautwein K, Kuhner S, Wöhlbrand L, Halder T, Kuchta K, Steinbüchel A, Rabus R (2008) Solvent stress response of the denitrifying bacterium “Aromatoleum aromaticum” strain EbN1. Appl Environ Microbiol 74: 2267–2274.

    Article  PubMed  CAS  Google Scholar 

  • Tsoi TV, Plotnikova EG, Cole JR, Guerin WF, Bagdasarian M, Tiedje JM (1999) Cloning, expression, and nucleotide sequence of the Pseudomonas aeruginosa 142 ohb genes coding for oxygenolytic ortho dehalogenation of halobenzoates. Appl Environ Microbiol 65: 2151–2162.

    PubMed  CAS  Google Scholar 

  • Van der Meer JR (2008) A genomic view on the evolution of catabolic pathways and bacterial adaptation to xenobiotic compounds. In: Microbial Biodegradation. Genomics and Molecular Biology. Díaz E (ed.). Norkfolk, UK: Caister Academic, 219–267.

    Google Scholar 

  • Van Dillewijn P, Caballero A, Paz JA, Gonzalez-Pérez MM, Oliva JM, Ramos JL (2007) Bioremediation of 2,4,6-trinitrotoluene under field conditions. Environ Sci Technol 41: 1378–1383.

    Article  PubMed  CAS  Google Scholar 

  • Velázquez F, de Lorenzo V, Valls M (2006) The m-xylene biodegradation capacity of Pseudomonas putida mt-2 is submitted to adaptation to abiotic stresses: evidence from expression profiling of xyl genes. Environ Microbiol 8: 591–602.

    Article  PubMed  Google Scholar 

  • Villacieros M, Whelan C, Mackova M, Molgaard J, Sánchez-Contreras M, Lloret J Aguirre de Cárcer D, Oruezábal RI, Bolaños L, Macek T, Karlson U, Dowling DN, Martín M, Rivilla R (2005) Polychlorinated biphenyl rhizoremediation by Pseudomonas fluorescens F113 derivatives, using a Sinorhizobium meliloti nod system to drive bph gene expression. Appl Environ Microbiol 71: 2687–2694.

    Article  PubMed  CAS  Google Scholar 

  • Volkers RJM, de Jong AL, Hulst AG, van Baar BLM, de Bont JAM, Wery J (2006) Chemostat-based proteomic analysis of toluene-affected Pseudomonas putida S12. Environ Microbiol 8: 1674–1679.

    Article  PubMed  CAS  Google Scholar 

  • Wackett LP (2003) Pseudomonas putida, a versatile biocatalyst. Nat Biotech 21: 136–138.

    Article  CAS  Google Scholar 

  • Werlen C, Jaspers MCM, van der Meer JR (2004) Measurement of biologically available naphthalene in gas and aqueous phases by use of a Pseudomonas putida biosensor. Appl Environ Microbiol 70: 43–51.

    Article  PubMed  CAS  Google Scholar 

  • Wierckx NJP, Ballerstedt H, de Bont JAM, de Winde JH, Ruijssenaars HJ, Wery J (2008) Transcriptome analysis of a phenol-producing Pseudomonas putida S12 construct: genetic and physiological basis for improved production. J Bacteriol 190: 2822–2830.

    Article  PubMed  CAS  Google Scholar 

  • Williams PA, Sayers JR (1994) The evolution of pathways for aromatic hydrocarbon oxidation in Pseudomonas. Biodegradation 5: 195–217.

    Article  PubMed  CAS  Google Scholar 

  • Yan Y, Yang J, Dou Y, Chen M, Ping S, Peng J, Lu W, Zhang W, Yao Z, Li H, Liu W, He S, Geng L, Zhang X, Yang F, Yu H, Zhan Y, Li D, Lin Z, Wang Y, Elmerich C, Lin M, Jin Q (2008) Nitrogen fixation island and rhizosphere competence traits in the genome of root-associated Pseudomonas stutzeri A1501. Proc Nat Acad Sci USA 105: 7564–7569.

    Article  PubMed  CAS  Google Scholar 

  • You IS, Ghosal D, Gunsalus IC (1991) Nucleotide sequence analysis of the Pseudomonas putida PpG7 salicylate hydroxylase gene (nahG) and its 3’-flanking region. Biochemistry 30:1635–1641.

    Article  PubMed  CAS  Google Scholar 

  • Young DM, Parke D, Ornston LN (2005) Opportunities for genetic investigation afforded by Acinetobacter baylyi, a nutritionally versatile bacterial species that is highly competent for natural transformation. Annu Rev Microbiol 59: 519–551.

    Article  PubMed  CAS  Google Scholar 

  • Zhao B, Yeo CC, Lee CC, Geng A, Chew FT, Poh CL (2004) Proteome analysis of gentisate-induced response in Pseudomonas alcaligenes NCIB 9867. Proteomics 4: 2028–2036.

    Article  PubMed  CAS  Google Scholar 

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Acknowledgments

Work in our laboratory was supported by grants from the Comisión Interministerial de Ciencia y Tecnología (GEN2006-27750-C5-3-E, BIO2006-05957, BFU2006-15214-CO3-01, MMA-PR21/06-039/2006/3-11.2, and CSD2007-00005) and Comunidad Autónoma de Madrid (P-AMB-259-0505).

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Authors and Affiliations

  1. Department of Microbial Biotechnology, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas, Madrid, Spain

    J. I. Jiménez

  2. Department of Molecular Microbiology, Centro de Investigaciones Biológicas-Consejo Superior de Investigaciones Científicas, Madrid, Spain

    J. Nogales, J. L. García & E. Díaz

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  1. J. I. Jiménez
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  2. J. Nogales
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  3. J. L. García
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  4. E. Díaz
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Editors and Affiliations

  1. Environmental Microbiology Laboratory, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Braunschweig, Germany

    Kenneth N. Timmis (Professor) (Professor)

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Jiménez, J.I., Nogales, J., García, J.L., Díaz, E. (2010). A Genomic View of the Catabolism of Aromatic Compounds in Pseudomonas . In: Timmis, K.N. (eds) Handbook of Hydrocarbon and Lipid Microbiology. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-77587-4_91

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