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Chapter 30 : Microbial Bioremediation of Chemical Pollutants: How Bacteria Cope with Multi-Stress Environmental Scenarios

Authors: VÍctor de Lorenzo1, Herminia Loza-Tavera2
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Affiliations: 1: Systems Biology Program, Centro Nacional de Biotecnología-CSIC, Campus de Cantoblanco, Madrid 28049, Spain; 2: Facultad de Química, Departamento de Bioquímica, Universidad Nacional Autónoma de México, 04510 México, México
Content Type: Monograph
Publication Year: 2011

Category: Microbial Genetics and Molecular Biology

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Abstract:

This chapter discusses the aspects of bioremediation that are related to metabolism of recalcitrant chemicals by bacteria, leaving out also detoxification and immobilization of metal ions and metalloids. The most frequent types of sites amenable to bioremediation include soil, freshwater, seawater, and sediments. The chapter talks about the instances where recalcitrant and/or xenobiotic compounds are endowed with chemical properties that cause a deleterious effect on the catalytic microorganisms present in the site-regardless of whether they can be ultimately metabolized. The chemicals at stake include metals, chaotropic agents, aromatics, and hydrophobic compounds. These stressors can be grouped based on their effect on bacterial metabolism. Heat shock-like stress and oxidative damage are certainly the two more prevalent conditions endured by environmental bacteria during in situ biodegradation of chemical waste. This is true for singular stressors as well as for mixtures of them, the most frequent bioremediation scenarios. Setting up suitable experimental systems to examine this issue is an important point in the current bioremediation research agenda. The bottleneck for the successful catabolism of a recalcitrant compound is most often not the nature of the biochemical route for its degradation, but the overcoming of the endogenous and exogenous stress associated to the working conditions.

Citation: Lorenzo V, Loza-Tavera H. 2011. Microbial Bioremediation of Chemical Pollutants: How Bacteria Cope with Multi-Stress Environmental Scenarios, p 481-492. In Storz G, Hengge R (ed), Bacterial Stress Responses, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816841.ch30
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Microbial Bioremediation of Chemical Pollutants: How Bacteria Cope with Multi-Stress Environmental Scenarios
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Citation: Lorenzo V, Loza-Tavera H. 2011. Microbial Bioremediation of Chemical Pollutants: How Bacteria Cope with Multi-Stress Environmental Scenarios, p 481-492. In Storz G, Hengge R (ed), Bacterial Stress Responses, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816841.ch30
/content/10.1128/9781555816841.ch30.ch30fig01
Figure 1.
Organization of the TOL operons of plasmid pWW0. The plasmid encodes a complete enzymatic machinery for the stepwise oxidation of one of the methyl groups of toluene, xylene and xylene (but not xylene), into the corresponding carboxylic acids (encoded by the so-called operon, driven by the σ promoter). This is followed by ring dioxygenation and cleavage of the resulting (methyl)catechol all the way down to the TCA (encoded by the or lower pathway, driven by the promoter). Expression of each of the gene clusters is subject to the interplay between host factors and plasmid-encoded regulators. The later include XylR (an xylene-responsive σ-dependent activator acting on and ) and XylS (an toluate-responsive factor acting on ). Activation of the operon requires also the concourse of either the heat shock σ or the stationary stress σ of the host (Dominguez-Cuevas et al., ; Marques et al., ). Overproduction of XylS can also activate in the absence of cognate effectors. XylR expression is autoregulated.
10.1128/9781555816841/f0484-01_thmb.gif
10.1128/9781555816841/f0484-01.gif
Image of Figure 1.
Figure 1.

Organization of the TOL operons of plasmid pWW0. The plasmid encodes a complete enzymatic machinery for the stepwise oxidation of one of the methyl groups of toluene, xylene and xylene (but not xylene), into the corresponding carboxylic acids (encoded by the so-called operon, driven by the σ promoter). This is followed by ring dioxygenation and cleavage of the resulting (methyl)catechol all the way down to the TCA (encoded by the or lower pathway, driven by the promoter). Expression of each of the gene clusters is subject to the interplay between host factors and plasmid-encoded regulators. The later include XylR (an xylene-responsive σ-dependent activator acting on and ) and XylS (an toluate-responsive factor acting on ). Activation of the operon requires also the concourse of either the heat shock σ or the stationary stress σ of the host (Dominguez-Cuevas et al., ; Marques et al., ). Overproduction of XylS can also activate in the absence of cognate effectors. XylR expression is autoregulated.

Citation: Lorenzo V, Loza-Tavera H. 2011. Microbial Bioremediation of Chemical Pollutants: How Bacteria Cope with Multi-Stress Environmental Scenarios, p 481-492. In Storz G, Hengge R (ed), Bacterial Stress Responses, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816841.ch30
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/content/10.1128/9781555816841.ch30.ch30fig02
Figure 2.
The economy of stress versus biodegradation in environmental bacteria. (a) The Gestalt (perception) chalice. This cartoon represents the notorious fact, known to the Gestalt branch of cognitive science, that it is often impossible to simultaneously perceive two different aspects of the same thing: either the faces or the chalice, but not both. This image is used here as a metaphor for the dual and altogether different notice that environmental microbes take of the presence of recalcitrant chemicals, as stressors as well as nutrients. (b) Regulatory choices in environmental bacteria. The accessible energy and reducing power in single cells is operatively represented here as ATP and NAD(P)H. Bacteria must spend a considerable share of such energy for the buildup of catabolic pathways for the dedicated metabolism of available C-sources (and to a lesser extent N, P sources and oligonutrients as well). Yet, coping with both external stress (left) or the toxicity caused by some of the C sources (right) consumes a share of the energy/reduction equivalents produced. (c) Only if the balance is positive, can biodegradation occur, as sketched.
10.1128/9781555816841/f0485-01_thmb.gif
10.1128/9781555816841/f0485-01.gif
Image of Figure 2.
Figure 2.

The economy of stress versus biodegradation in environmental bacteria. (a) The Gestalt (perception) chalice. This cartoon represents the notorious fact, known to the Gestalt branch of cognitive science, that it is often impossible to simultaneously perceive two different aspects of the same thing: either the faces or the chalice, but not both. This image is used here as a metaphor for the dual and altogether different notice that environmental microbes take of the presence of recalcitrant chemicals, as stressors as well as nutrients. (b) Regulatory choices in environmental bacteria. The accessible energy and reducing power in single cells is operatively represented here as ATP and NAD(P)H. Bacteria must spend a considerable share of such energy for the buildup of catabolic pathways for the dedicated metabolism of available C-sources (and to a lesser extent N, P sources and oligonutrients as well). Yet, coping with both external stress (left) or the toxicity caused by some of the C sources (right) consumes a share of the energy/reduction equivalents produced. (c) Only if the balance is positive, can biodegradation occur, as sketched.

Citation: Lorenzo V, Loza-Tavera H. 2011. Microbial Bioremediation of Chemical Pollutants: How Bacteria Cope with Multi-Stress Environmental Scenarios, p 481-492. In Storz G, Hengge R (ed), Bacterial Stress Responses, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816841.ch30
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/content/10.1128/9781555816841.ch30.ch30fig03
Figure 3.
Biocatalysis under endogenous and exogenous environmental stress. One key difference between chemical catalysis in the laboratory and its counterparts during bioremediation is the large number of factors at play in the process. There is first the issue of bioavailability because the substrate of the desired reaction (A) may not directly access the core catalyst (often an intracellular enzyme) because of its intrinsic lack of solubility or its adsorption to mineral matrices. In addition, the substrate is often a stressor for the live bacterial catalysts. Furthermore, the desired reactions may not be coupled to growth and can originate side products (C, F) with deleterious effects on the microorganism. Finally, the product of the process (Z) might be toxic and inhibit the progression of the whole biotransformation. The external milieu also brings in exogenous stresses that affect the course of action. This scenario provides an optimal chance to apply a systems biology approach to the design of processes of this sort (de Lorenzo, ).
10.1128/9781555816841/f0487-01_thmb.gif
10.1128/9781555816841/f0487-01.gif
Image of Figure 3.
Figure 3.

Biocatalysis under endogenous and exogenous environmental stress. One key difference between chemical catalysis in the laboratory and its counterparts during bioremediation is the large number of factors at play in the process. There is first the issue of bioavailability because the substrate of the desired reaction (A) may not directly access the core catalyst (often an intracellular enzyme) because of its intrinsic lack of solubility or its adsorption to mineral matrices. In addition, the substrate is often a stressor for the live bacterial catalysts. Furthermore, the desired reactions may not be coupled to growth and can originate side products (C, F) with deleterious effects on the microorganism. Finally, the product of the process (Z) might be toxic and inhibit the progression of the whole biotransformation. The external milieu also brings in exogenous stresses that affect the course of action. This scenario provides an optimal chance to apply a systems biology approach to the design of processes of this sort (de Lorenzo, ).

Citation: Lorenzo V, Loza-Tavera H. 2011. Microbial Bioremediation of Chemical Pollutants: How Bacteria Cope with Multi-Stress Environmental Scenarios, p 481-492. In Storz G, Hengge R (ed), Bacterial Stress Responses, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816841.ch30
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/content/10.1128/9781555816841.ch30.ch30fig04
Figure 4.
Control of the stress versus metabolism tradeoff in σ promoters. Because σ promoters, such as of the TOL plasmid, can be transcribed in vitro by just combining purified integration host factor, the sigma factor core RNAP, and activated XylR, it is plausible that the mechanism(s) in vivo that adapt transcription to environmental stresses do so by regulating the binding of one of more of these proteins to their target sites. In addition, the upstream activating sequences (UAS) of appear to be mostly unoccupied at all growth stages. This gives rise to multiple regulatory possibilities. In cases where the promoter has little intrinsic affinity for the σ -RNAP, occupation of the -12/-24 region depends exclusively on the successful competition of sigmas at the stationary phase, governed by ppGpp. In this case, physiological control mostly reflects such competition. Some sigmas, like σ, can themselves be checked by other anti-sigma proteins such as Rsd (Yuan et al., ). In the other extreme, σ promoters with a high intrinsic affinity for the enzyme may have the -12/-24 motif occupied even at the low concentrations of σ -RNAP available prior to stationary phase. In these instances, the promoter may not be subject to any physiological or stress-related inhibition, but may be active throughout all growth states. A number of extra factors (TurA, PprA) control the binding of core transcription components to their target sequences (Rescalli et al., ; Vitale et al., ).
10.1128/9781555816841/f0489-01_thmb.gif
10.1128/9781555816841/f0489-01.gif
Image of Figure 4.
Figure 4.

Control of the stress versus metabolism tradeoff in σ promoters. Because σ promoters, such as of the TOL plasmid, can be transcribed in vitro by just combining purified integration host factor, the sigma factor core RNAP, and activated XylR, it is plausible that the mechanism(s) in vivo that adapt transcription to environmental stresses do so by regulating the binding of one of more of these proteins to their target sites. In addition, the upstream activating sequences (UAS) of appear to be mostly unoccupied at all growth stages. This gives rise to multiple regulatory possibilities. In cases where the promoter has little intrinsic affinity for the σ -RNAP, occupation of the -12/-24 region depends exclusively on the successful competition of sigmas at the stationary phase, governed by ppGpp. In this case, physiological control mostly reflects such competition. Some sigmas, like σ, can themselves be checked by other anti-sigma proteins such as Rsd (Yuan et al., ). In the other extreme, σ promoters with a high intrinsic affinity for the enzyme may have the -12/-24 motif occupied even at the low concentrations of σ -RNAP available prior to stationary phase. In these instances, the promoter may not be subject to any physiological or stress-related inhibition, but may be active throughout all growth states. A number of extra factors (TurA, PprA) control the binding of core transcription components to their target sequences (Rescalli et al., ; Vitale et al., ).

Citation: Lorenzo V, Loza-Tavera H. 2011. Microbial Bioremediation of Chemical Pollutants: How Bacteria Cope with Multi-Stress Environmental Scenarios, p 481-492. In Storz G, Hengge R (ed), Bacterial Stress Responses, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816841.ch30
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References

/content/book/10.1128/9781555816841.ch30
1. Abraham, W. R.,, B. Nogales,, P. N. Golyshin,, D.H. Pieper, and, K.N. Timmis. 2002. Polychlorinated biphenyl-degrading microbial communities in soils and sediments. Curr. Opin. Microbiol. 5: 246– 253.
2. Agullo, L.,, B. Camara,, P. Martinez,, V. Latorre, and, M. Seeger. 2007. Response to (chloro)biphenyls of the polychlorobiphenyldegrader Burkholderia xenovorans LB400 involves stress proteins also induced by heat shock and oxidative stress. FEMS Microbiol. Lett. 267: 167– 175.
3. Benndorf, D., and, W. Babel. 2002. Assimilatory detoxification of herbicides by Delftia acidovorans MC1: induction of two chlorocatechol 1,2-dioxygenases as a response to chemostress. Microbiology 148: 2883– 2888.
4. Billi, D.,, D.J. Wright,, R.F. Helm,, T. Prickett,, M. Potts, and, J.H. Crowe. 2000. Engineering desiccation tolerance in Escherichia coli. Appl. Environ. Microbiol. 66: 1680– 1684.
5. Blasco, R.,, R. M. Wittich,, M. Mallavarapu,, K. N. Timmis, and, D.H. Pieper. 1995. From xenobiotic to antibiotic, formation of protoanemonin from 4–chlorocatechol by enzymes of the 3–oxoadipate pathway. J. Biol. Chem. 270: 29229– 29235.
6. Brenner, K.,, L. You, and, F.H. Arnold. 2008. Engineering microbial consortia: a new frontier in synthetic biology. Trends Biotechnol. 26: 483– 489.
7. Camara, B.,, C. Herrera,, M. Gonzalez,, E. Couve,, B. Hofer, and, M. Seeger. 2004. From PCBs to highly toxic metabolites by the biphenyl pathway. Environ. Microbiol. 6: 842– 850.
8. Carbajosa, G.,, A. Trigo,, A. Valencia, and, I. Cases. 2009. Bionemo: molecular information on biodegradation metabolism. Nucleic Acids Res. 37: D 598– 602.
9. Cases, I., and, V. de Lorenzo. 2005a. Promoters in the environment: transcriptional regulation in its natural context. Nat. Rev. Microbiol. 3: 105– 118.
10. Cases, I., and, V. de Lorenzo. 2005b. Genetically modified organisms for the environment: stories of success and failure and what we have learned from them. Int. Microbiol. 8: 213– 222.
11. Chavez, F. P.,, F. Gordillo, and, C. A. Jerez. 2006. Adaptive responses and cellular behaviour of biphenyl-degrading bacteria toward polychlorinated biphenyls. Biotechnol. Adv. 24: 309– 320.
12. Chavez, F. P.,, H. Lunsdorf, and, C.A. Jerez. 2004. Growth of polychlorinated-biphenyl-degrading bacteria in the presence of biphenyl and chlorobiphenyls generates oxidative stress and massive accumulation of inorganic polyphosphate. Appl. Environ. Microbiol. 70: 3064– 3072.
13. Chhabra, Q.,, K.H. He,, S.P. Huang,, E.J. Gaucher,, Z. Alm,, M. Z. He,, T. C. Hadi,, J. D. Hazen,, J. Wall,, A. P. Zhou,, A. K. Arkin, and, A.K. Singh. 2006. Global analysis of heat shock response in Desulfovibrio vulgaris Hildenborough. J. Bacteriol. 188: 1817– 1828.
14. Cho, Y. S.,, H.Y. Kahng,, C.K. Kim,, J. J. Kukor, and, K. H. Oh. 2002. Physiological and cellular responses of the 2,4–D degrading bacterium, Burkholderia cepacia YK-2, to the phenoxyherbicides 2,4–D and 2,4,5–T. Curr. Microbiol. 45: 415– 422.
15. Cho, Y. S.,, S.H. Park,, C.K. Kim, and, K.H. Oh. 2000. Induction of stress shock proteins DnaK and GroEL by phenoxyherbicide 2,4–D in Burkholderia sp. YK-2 isolated from rice field. Curr. Microbiol. 41: 33– 38.
16. Cytryn, E. J.,, D.P. Sangurdekar,, J.G. Streeter,, W. L. Franck,, W. S. Chang,, G. Stacey,, D. W. Emerich,, T. Joshi,, D. Xu, and, M.J. Sadowsky. 2007. Transcriptional and physiological responses of Bradyrhizobium japonicum to desiccation-induced stress. J. Bacteriol. 189: 6751– 6762.
17. De Lorenzo, V. 2006. Blueprint of an oil-eating bacterium. Nat. Biotechnol. 24: 952– 953.
18. De Lorenzo, V. 2008. Systems biology approaches to bioremediation. Curr. Opin. Biotechnol. 19: 579– 589.
19. De Lorenzo, V. and A. Danchin. 2008. Synthetic biology: discovering new worlds and new words. EMBO Rep. 9: 822– 827.
20. Dominguez-Cuevas, P.,, J.E. Gonzalez-Pastor,, S. Marques,, J. L. Ramos, and, V. de Lorenzo. 2006. Transcriptional tradeoff between metabolic and stress-response programs in Pseudomonas putida KT2440 cells exposed to toluene. J. Biol. Chem. 281: 11981– 11991.
21. Dominguez-Cuevas, P.,, J.L. Marin,, S. Ramos, and, S. Marques. 2005. RNA polymerase holoenzymes can share a single transcription start site for the Pm. J. Biol. Chem. 280: 41315– 41323.
22. Dowling, D., and, S.L. Doty. 2009. Improving phytoremediation through biotechnology. Curr. Opin. Biotechnol. 20: 204– 206.
23. Garcia De Castro, A.,, H. Bredholt,, A.R. Strom, and, A. Tunnacliffe. 2000. Anhydrobiotic engineering of gram-negative bacteria. Appl. Environ. Microbiol. 66: 4142– 4144.
24. Greated, A.,, L. Lambertsen,, P. A. Williams, and, C.M. Thomas. 2002. Complete sequence of the IncP-9 TOL plasmid pWW0 from Pseudomonas putida. Environ. Microbiol. 4: 856– 871.
25. Guazzaroni, M. E.,, M.T. Gallegos,, J.L. Ramos, and, T. Krell. 2007. Different modes of binding of mono- and biaromatic effectors to the transcriptional regulator TTGV: role in differential derepression from its cognate operator. J. Biol. Chem. 282: 16308– 16316.
26. Guazzaroni, M. E.,, T. Krell,, A. Felipe,, R. Ruiz,, C. Meng,, X. Zhang,, M. T. Gallegos, and, J.L. Ramos. 2005. The multidrug efflux regulator TtgV recognizes a wide range of structurally different effectors in solution and complexed with target DNA: evidence from isothermal titration calorimetry. J. Biol. Chem. 280: 20887– 20893.
27. Hallsworth, J. E.,, S. Heim, and, K.N. Timmis. 2003. Chaotropic solutes cause water stress in Pseudomonas putida. Environ. Microbiol. 5: 1270– 1280.
28. Hazen, T. C., and, D.A. Stahl. 2006. Using the stress response to monitor process control: pathways to more effective bioremediation. Curr. Opin. Biotechnol. 17: 285– 290.
29. Heinemann, M., and, S. Panke. 2006. Synthetic biology—putting engineering into biology. Bioinformatics 22: 2790– 2799.
30. Heipieper, H. J.,, F. Meinhardt, and, A. Segura. 2003. The cis-trans isomerase of unsaturated fatty acids in Pseudomonas and Vibrio: biochemistry, molecular biology and physiological function of a unique stress adaptive mechanism. FEMS Microbiol. Lett. 229: 1– 7.
31. Holden, P. A.,, L. J. Halverson, and, M.K. Firestone. 1997. Water stress effects on toluene biodegradation by Pseudomonas putida. Biodegradation 8: 143– 151.
32. Jishage, M.,, K. Kvint,, V. Shingler, and, T. Nystrom. 2002. Regulation of sigma factor competition by the alarmone ppGpp. Genes Dev. 1 6: 1260– 1270.
33. Kang, Y. S.,, Y. Lee,, H. Jung,, C.O. Jeon,, E. L. Madsen, and, W. Park. 2007. Overexpressing antioxidant enzymes enhances naphthalene biodegradation in Pseudomonas sp. strain As1. Microbiology 153: 3246– 3254.
34. Laurie, A. D.,, L.M. Bernardo,, C.C. Sze,, E. Skarfstad,, A. Szalewska-Palasz,, T. Nystrom, and, V. Shingler. 2003. The role of the alarmone (p)ppGpp in sigma N competition for core RNA polymerase. J. Biol. Chem. 278: 1494– 1503.
35. LeBlanc, J. C.,, E. R. Goncalves, and, W.W. Mohn. 2008. Global response to desiccation stress in the soil actinomycete Rhodococcus jostii RHA1. Appl. Environ. Microbiol. 74: 2627– 2636.
36. Macedo, A. J.,, U. Kuhlicke,, T. R. Neu,, K.N. Timmis, and, W.R. Abraham. 2005. Three stages of a biofilm community developing at the liquid-liquid interface between polychlorinated biphenyls and water. Appl. Environ. Microbiol. 71: 7301– 7309.
37. MacNaughton, S. J.,, J.R. Stephen,, A.D. Venosa,, G. A. Davis,, Y.-J. Chang, and, D.C. White. 1999. Microbial population changes during bioremediation of an experimental oil spill. Appl. Environ. Microbiol. 65: 3566– 3574.
38. Makarova, K. S.,, L. Aravind,, Y. I. Wolf,, R.L. Tatusov,, K. W. Minton,, E. V. Koonin, and, M.J. Daly. 2001. Genome of the extremely radiation-resistant bacterium Deinococcus radiodurans viewed from the perspective of comparative genomics. Microbiol. Mol. Biol. Rev. 65: 44– 79.
39. Marques, S.,, M.M. Manzanera,, M.T. Gonzalez-Perez,, J.L. Gallegos, and, J.L. Ramos. 1999. The XylS-dependent Pm promoter is transcribed in vivo by RNA polymerase with sigma 32 or sigma 38 depending on the growth phase. Mol. Microbiol. 31: 1105– 1113.
40. Martinez, P.,, L. Agullo,, M. Hernandez, and, M. Seeger. 2007. Chlorobenzoate inhibits growth and induces stress proteins in the PCB-degrading bacterium Burkholderia xenovorans LB400. Arch. Microbiol. 188: 289– 297.
41. Nogales, J.,, B.O. Palsson, and, I. Thiele. 2008. A genome-scale metabolic reconstruction of Pseudomonas putida KT244 0: iJN746 as a cell factory. BMC Syst. Biol. 2: 79.
42. Panke, S.,, V. De Lorenzo,, B. Kaiser,, B. Witholt, and, M.G. Wubbolts. 1999. Engineering of a stable whole-cell biocatalyst capable of (S)-styrene oxide. Appl. Environ. Microbiol. 65: 5619– 5623.
43. Parnell, J. j.,, J. Park,, V. Denef,, T. Tsoi,, S. Hashsham,, J. Quensen, and, J. M. Tiedje. 2006. Coping with polychlorinated biphenyl (PCB) toxicity: physiological and genome-wide responses of Burkholderia xenovorans LB400 to PCB-mediated stress. Appl. Environ. Microbiol. 72: 6607– 6614.
44. Pereira, O.,, Q. He,, A.V. Xavier,, J. Zhou,, I. Pereira, and, R.O. Louro. 2008. Transcriptional response of Desulfovibrio vulgaris Hildenborough to oxidative stress mimicking environmental conditions. Arch. Microbiol. 189: 451– 461.
45. Pieper, D. H., and, M. Seeger. 2008. Bacterial metabolism of polychlorinated biphenyls. J. Mol. Microbiol. Biotechnol. 15: 121– 138.
46. Pieper, D. H., and, W. Reineke. 2000. Engineering bacteria for bioremediation. Curr. Opin. Biotechnol. 11: 262– 270.
47. Puchalka, J.,, M.A. Oberhardt,, M. Godinho,, A. Bielecka,, D. Regenhardt,, K. N. Timmis,, J. A. Papin, and, V.A. Martins dos Santos. 2008. Genome-scale reconstruction and analysis of the Pseudomonas putida KT2440 metabolic network facilitates applications in biotechnology. PLoS Comput. Biol. 4: e1000210.
48. Ragoonanan, V.,, J. Malsam,, D.R. Bond, and, A. Aksan. 2008. Roles of membrane structure and phase transition on the hyperosmotic stress survival of Geobacter sulfurreducens. Biochim. Biophys. Acta 1778: 2283– 2290.
49. Ramos, J. L.,, E. Duque,, M. T. Gallegos,, P. Godoy,, M. I. Ramos-Gonzalez,, A. Rojas,, W. Teran, and, A. Segura. 2002. Mechanisms of solvent tolerance in gram-negative bacteria. Annu. Rev. Microbiol. 56: 743– 768.
50. Ramos, J. L.,, S. Marques, and, K.N. Timmis. 1997. Transcriptional control of the Pseudomonas TOL plasmid catabolic operons is achieved through an interplay of host factors and plasmid-encoded regulators. Annu. Rev. Microbiol. 51: 341– 373.
51. Rescalli, E.,, S. Saini,, C. Bartocci,, L. Rychlewski,, V. de Lorenzo, and, G. Bertoni. 2004. Novel physiological modulation of the Pu promoter of TOL plasmid: negative regulatory role of the TurA protein of Pseudomonas putida in the response to suboptimal growth temperatures. J. Biol. Chem. 279: 7777– 7784.
52. Reva, O. N.,, C. Weinel,, M. Weinel,, K. Bohm,, D. Stjepandic,, J. D. Hoheisel, and, B. Tummler. 2006. Functional genomics of stress response in Pseudomonas putida KT2440. J. Bacteriol. 188: 4079– 4092.
53. Reva, O. N.,, P.F. Hallin,, H. Willenbrock,, T. Sicheritz-Ponten,, B. Tummler, and, D.W. Ussery. 2008. Global features of the Alcanivorax borkumensis SK2 genome. Environ. Microbiol. 10: 614– 625.
54. Sabirova, J. S.,, T.N. Chernikova,, K.N. Timmis, and, P.N. Golyshin. 2008. Niche-specificity factors of a marine oil-degrading bacterium Alcanivorax borkumensis SK2. FEMS Microbiol. Lett. 285: 89– 96.
55. Santos, P. M.,, D. Benndorf, and, I. Sa-Correia. 2004. Insights into Pseudomonas putida KT2440 response to phenol-induced stress by quantitative proteomics. Proteomics 4: 2640– 2652.
56. Santos, P. M.,, V. Roma,, D. Benndorf,, M. von Bergen,, H. Harms, and, I. Sa-Correia. 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.
57. Schmid, A.,, J.S. Dordick,, B. Hauer,, A. Kiener,, M. Wubbolts, and, B. Witholt. 2001. Industrial biocatalysis today and tomorrow. Nature 409: 258– 268.
58. Schneiker, S.,, V.A. Martins dos Santos,, D. Bartels,, T. Bekel,, M. Brecht,, J. Buhrmester,, T. N. Chernikova,, R. Denaro,, M. Ferrer,, C. Gertler,, A. Goesmann,, O. V. Golyshina,, F. Kaminski,, A. N. Khachane,, S. Lang,, B. Linke,, A. C. McHardy,, F. Meyer,, T. Nechitaylo,, A. Puhler,, D. Regenhardt,, O. Rupp,, J. S. Sabirova,, W. Selbitschka,, M. M. Yakimov,, K. N. Timmis,, F. J. Vorholter,, S. Weidner,, O. Kaiser, and, P.N. Golyshin. 2006. Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis. Nat. Biotechnol. 24: 997– 1004.
59. Scholten, D. E.,, L. Culley,, K. J. Nie,, L. Munn, F. J. Chow,, W. Brockman, and, W. Zhang. 2007. Development and assessment of whole-genome oligonucleotide microarrays to analyze. Biochem. Biophys. Res. Commun. 358: 571– 577.
60. Skiba, A.,, V. Hecht, and, D.H. Pieper. 2002. Formation of protoanemonin from 2–chloro-cis, cis-muconate by the combined action of muconate cycloisomerase and muconolactone isomerase. J. Bacteriol. 184: 5402– 5409.
61. Tagkopoulos, I.,, Y.C. Liu, and, S. Tavazoie. 2008. Predictive behavior within microbial genetic networks. Science 320: 1313– 1317.
62. Timmis, K. N., and, D.H. Pieper. 1999. Bacteria designed for bioremediation. Trends Biotechnol. 17: 200– 204.
63. Treonis, A. M.,, N.J. Ostle,, A.W. Stott,, R. Primrose,, S. J. Grayston, and, P. Ineson. 2004. Identification of groups of metabolicallyactive rhizosphere microorganisms by stable isotope probing of PLFAs. Soil Biol. Biochem. 36: 533– 537.
64. Uchiyama, H.,, Y. Shinohara,, N. Tomioka, and, I. Kusakabe. 1999. Induction and enhancement of stress proteins in a trichloroethylene-degrading methanotrophic bacterium, Methylocystis sp. M. FEMS Microbiol. Lett. 170: 125– 130.
65. Velazquez, F., V. de Lorenzo, and, M. Valls. 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.
66. Velazquez, F.,, V. Parro, and, V. de Lorenzo. 2005. Inferring the genetic network of m- xylene metabolism through expression profiling of the xyl genes of Pseudomonas putida mt-2. Mol. Microbiol. 57: 1557– 1569.
67. Vitale, E.,, A. Milani,, F. Renzi,, E. Galli,, E. Rescalli, V. de Lorenzo, and, G. Bertoni. 2008. Transcriptional wiring of the TOL plasmid regulatory network to its host involves the submission of the sigma 54–promoter Pu to the response regulator PprA. Mol. Microbiol. 69: 698– 713.
68. Wackett, L. P. 2004. Stable isotope probing in biodegradation research. Trends Biotechnol. 22: 153– 154.
69. Yeager, C. M.,, P. J. Bottomley, and, D.J. Arp. 2001. Cytotoxicity associated with trichloroethylene oxidation in Burkholderia cepacia G4. Appl. Environ. Microbiol. 67: 2107– 2115.
70. Yuan, A. H.,, B.D. Gregory,, J.S. Sharp,, K. D. McCleary,, S. L. Dove, and, A. Hochschild. 2008. Rsd family proteins make simultaneous interactions with regions 2 and 4 of the primary sigma factor. Mol. Microbiol. 70: 1136– 1151.

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