Chapter 16 : Degradative Plasmids

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Ebook: Choose a downloadable PDF or ePub file. Chapter is a downloadable PDF file. File must be downloaded within 48 hours of purchase

Buy this Chapter
Digital (?) $15.00

Preview this chapter:
Zoom in

Degradative Plasmids, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555817732/9781555812652_Chap16-1.gif /docserver/preview/fulltext/10.1128/9781555817732/9781555812652_Chap16-2.gif


Degradative plasmids carry genes that confer on the host bacteria the ability to degrade recalcitrant organic compounds not commonly found in nature. Many plasmid-encoded degradative gene clusters are also discrete regulons if they have regulators specialized for the regularion of the genes encoding degradative enzymes. The degradation pathway is composed of two segments when it is delimited by substrates for growth and the integrity as transcriptional units, each of which has a wide range of enzymatic substrate specificity toward alkyl-substituted aromatic compounds. The recent completion of the nucleotide sequencing of the whole pWWO plasmid revealed open reading frames (ORFs) related to plasmid replication, maintenance, and transfer. Other toluene-degradative (TOL) plasmid, such as pWW53 and pDK1 , have been found to have upper and lower pathways at different relative locations on the plasmids, although the organizations of the structural genes for the degradative enzymes in the respective cluster are highly conserved. Most of the 2,4-D plasmids were found in strains isolated by enrichment on 2,4-D as the sole source of carbon and energy, and some of them were found to take part in the degradation of a herbicide with a similar structure, 2-methyI-4-chlorophenoxyacetic acid. The lower pathway includes cleavage of the aromatic ring by dioxygenases with formation of (chloro)maleylacetates. The genes on TOL plasmids, including pWWO, and the related and genes have enabled comparative studies, as described. Transposon Tn5271 on plasmid pBRC60 is not flanked by target-site duplications on both sides, which are supposed to be generated during transposition.

Citation: Ogawa N, Chakrabarty A, Zaborina O. 2004. Degradative Plasmids, p 341-376. In Funnell B, Phillips G (ed), Plasmid Biology. ASM Press, Washington, DC. doi: 10.1128/9781555817732.ch16

Key Concept Ranking

Gene Expression and Regulation
Highlighted Text: Show | Hide
Loading full text...

Full text loading...


Image of Figure 1.
Figure 1.

The catabolic pathways/genes involved in the degradation of xylene encoded by TOL plasmids and the corresponding genes in the degradative pathway for naphthalene and dimethylphcnol on NAH7 and pVI 150, respectively. The structure of the compound numbered 1 that serves as growth substrate for strain mt-2 is (Rl = R2 = H, toluene), (Rl = CH, R2 = H, -xylene), (Rl = H, R2 = CH, -xylene), (Rl = CH, R2 = H, 3-ethyltoluene), and (Rl = CH , R2 = CH, 1,2,4-trimethylbenzene). The metabolites numbered 2 to 11 in the case where the substrate is toluene are: 2, benzyl alcohol; 3, benzaldehyde; 4, benzoate; 5, benzoate dihydrodiol (l,2-dihydrocyclohexa-3,5-diene carboxylate); 6, catechol; 7, 2-hydroxymuconic semialdehyde; 8, 4-oxalocrotonate (enol); 9, 4-oxalocrotonate (keto); 10, 2-oxopentenoate (enol) or 2-hydroxypent-2,4-dienoate; and 11, 4-hydroxy-2-oxovalerate. Enzyme abbreviations are: XO, xylene oxygenase; BADH, benzyl alcohol dehydrogenase; BZDH, benzaldehyde dehydrogenase; TO, toluate 1,2-dioxygenase; DHCDH, 1,2-dihydroxycyclohexa-3,5-dicne carboxylate (benzoatc dihydrodiol) dehydrogenase; C230, catechol 2,3-dioxygenase; HMSH, 2-hydroxymuconic-scmialdehyde hydrolase; HMSD, 2-hydroxymuconic-semialdehyde dehydrogenase; 4OI, 4-oxalocrotonate isomerase; 4OD, 4-oxalocrotonate decarboxylase; OEH, 2-oxo-4-pemenoate (or 2-hydroxy-2,4-dienoate) hydratase; and HOA, 4-hydroxy-2-oxovalerate aldolase. The TOL pathway was adapted from that of Assindcr and Williams ( ) with permission from Elsevier. Respective pathways are described elsewhere ( ).

Citation: Ogawa N, Chakrabarty A, Zaborina O. 2004. Degradative Plasmids, p 341-376. In Funnell B, Phillips G (ed), Plasmid Biology. ASM Press, Washington, DC. doi: 10.1128/9781555817732.ch16
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 2.
Figure 2.

(a) Regulatory circuits of the catabolic genes that degrade xylene/toluene on pWW0. Reproduced with permission from the ( ), © 1997 by Annual Reviews, (b) Relative locations of the catabolic and regulatory genes and the transposons on TOL and NAH plasmids. These plasmids share homologous catechol -cleavage pathway genes. The incongruity of relative locations of the genes and transposons suggests independent recruitment of the genes by the transposons. The figure is not drawn to scale. Precise maps are available elsewhere ( ).

Citation: Ogawa N, Chakrabarty A, Zaborina O. 2004. Degradative Plasmids, p 341-376. In Funnell B, Phillips G (ed), Plasmid Biology. ASM Press, Washington, DC. doi: 10.1128/9781555817732.ch16
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 3.
Figure 3.

The catabolic pathways/genes involved in the degradation of 2,4-D, and the schematic representation of the catabolic gene region on pJP4 and pMAB1. The metabolites of 2,4-D (numbered 1, 2,4-dichlorophcnoxyacetate) arc numbered 2 to 7; 2, 2,4-dichlorophenol; 3, 3,5-dichlorocatechol; 4, 2,4-dichloro--muconate; 5,2-chlorodienelactone; 6, 2-chloromaleylacetate; and 7, β-ketoadipate. The genes and the corresponding enzymes are; , 2,4-dichloro phenoxyacetate/α-ketoglutarate dioxygenase; , 2,4-dichlorophcnol hydroxylase; , 3,5-dichlorocatechol 1,2-dioxygenase; , chloromuconatc cycloisomerasc; , dienlactone hydrolase; and , (chloro)maleylacetate reductase. An asterisk indicates ca. 200-bp intergenic region containing 71-bp sequence identical to downward extremity of ISJP4.

Citation: Ogawa N, Chakrabarty A, Zaborina O. 2004. Degradative Plasmids, p 341-376. In Funnell B, Phillips G (ed), Plasmid Biology. ASM Press, Washington, DC. doi: 10.1128/9781555817732.ch16
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 4.
Figure 4.

The catabolic pathways/genes of benzoic acid, phenol, and 3-chlorobenzoic acid via -deavage pathways.

Citation: Ogawa N, Chakrabarty A, Zaborina O. 2004. Degradative Plasmids, p 341-376. In Funnell B, Phillips G (ed), Plasmid Biology. ASM Press, Washington, DC. doi: 10.1128/9781555817732.ch16
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 5.
Figure 5.

Organization of the gene clusters of intradiol-cleavage pathways that degrade (chloro)catechol or (chloro)hydroxyquinol. Identities at amino acid sequence level between the corresponding genes are indicated numerically (%).

Citation: Ogawa N, Chakrabarty A, Zaborina O. 2004. Degradative Plasmids, p 341-376. In Funnell B, Phillips G (ed), Plasmid Biology. ASM Press, Washington, DC. doi: 10.1128/9781555817732.ch16
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 10.
Figure 10.

The schematic representation of the catabolic gene regions on pENH91 and pP51. Reproduced from reference . The map of pP51 is based on references . , and .

Citation: Ogawa N, Chakrabarty A, Zaborina O. 2004. Degradative Plasmids, p 341-376. In Funnell B, Phillips G (ed), Plasmid Biology. ASM Press, Washington, DC. doi: 10.1128/9781555817732.ch16
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 6.
Figure 6.

Replicons of AC1100. The sizes of rhe replicons are not drawn proportionally. The locations of the relevant genes are indicated by arrowheads.

Citation: Ogawa N, Chakrabarty A, Zaborina O. 2004. Degradative Plasmids, p 341-376. In Funnell B, Phillips G (ed), Plasmid Biology. ASM Press, Washington, DC. doi: 10.1128/9781555817732.ch16
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 7.
Figure 7.

Pathway of 2,4,5-T degradation. The and genes encode two subunits of the 2,4,5-T oxygenase that convert 2,4,5-T into 2,4,5-TCP. A two-component flavin-containing monooxygenase encoded by the and genes catalyzes the para-hydroxylation of 2,4,5-TCP to yield 2,5-DCHQ. A second hydroxylation step by the same enzyme converts 2,5-DCHQ into 5-CHQ. The gene product, a dechlorinase, catalyzes dechlorination of 5-CHQ to yield HQox. An HBQ reductase reduces HQ-ox to HQ before HQDO, encoded by the gene, can catalyze ring cleavage to yield maleylacetate. Maleylacetate reductase, encoded by the gene, catalyzes the reduction of maleylacetate to β-ketoadipate, which ultimately is converted into tricarboxylic acid (TCA) cycle intermediates.

Citation: Ogawa N, Chakrabarty A, Zaborina O. 2004. Degradative Plasmids, p 341-376. In Funnell B, Phillips G (ed), Plasmid Biology. ASM Press, Washington, DC. doi: 10.1128/9781555817732.ch16
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 8.
Figure 8.

A model of evolution of catechol weta-clcavage pathways and recruitment of other genes to form the lower pathways on NAH7, pWWO, and pVII50. Adapted from original by Harayama and Rekik ( ) with permission of the publisher.

Citation: Ogawa N, Chakrabarty A, Zaborina O. 2004. Degradative Plasmids, p 341-376. In Funnell B, Phillips G (ed), Plasmid Biology. ASM Press, Washington, DC. doi: 10.1128/9781555817732.ch16
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 9.
Figure 9.

A model for the acquisition of the genes by a prototype plasmid of pENH91. The model is drawn based on the model of chromosome mobilization by IS proposed by Wyndham et al. ( ). While class II transposable elements to which IS belongs transfer by a replicative mechanism ( ), IS could transpose via a cut-and-paste (nonreplicative) mechanism in analogy with IS ( ). ( ) A prototype plasmid of pENH91 containing a single copy of IS. ( ) Tandem formation of IS on the plasmid, which facilitates the formation of cointegrate. ( ) Bacterial chromosome with a cbnRABCD gene cluster. The target sites (1 and 2) are written arbitrarily. No consensus target sequence is apparent for IS ( ). ( ) Cointegrate formation by the plasmid with the chromosome. Two to three nucleotides in the junction of IS tandem are lost during the reaction. ( ) Further insertion of another copy of IS beyond the catabolic region and subsequent deletion by homologous recombination beween the two distal copies of IS result in the formation of a plasmid with a composite transposon structure.

Citation: Ogawa N, Chakrabarty A, Zaborina O. 2004. Degradative Plasmids, p 341-376. In Funnell B, Phillips G (ed), Plasmid Biology. ASM Press, Washington, DC. doi: 10.1128/9781555817732.ch16
Permissions and Reprints Request Permissions
Download as Powerpoint


1. Abril, M.-A.,, M. Buck,, and J. L. Ramos. 1991. Activation of the Pseudomonas TOL plasmid upper pathway operon. Identification of binding sites for the positive regulator XylR and for integration host factor protein. J. Biol. Chem. 266:1583215838.
2. Abril, M.-A.,, C. Michan,, K. N. Timmis,, and J. L. Ramos. 1989. 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. 171:67826790. (Erratum, 172:3534, 1990.).
3.Anipe, V.y and N. D. Lindley. 1995. Acetate utilization is inhibited by benzoate in Alcaligenes eutrophus: evidence for transcriptional control of the expression of acoE coding for acetyl coenzyme A synthetase. J. Bacteriol. 177:58265833.
4. Amy, P. S.,, J .W. Schulke,, L. M. Frazier,, and R. J . Seidler. 1985. Characterization of aquatic bacteria and cloning of genes specifying partial degradation of 2,4-dichlorophenoxyacetic acid. Appl. Environ. Microbiol. 49:12371245.
5.Aramaki, H,, Y, Sagara, M. Hosoi, and T. Horiuchi. 1993. Evidence for autoregulation of camR, which encodes a repressor for the cytochrome P-450cam hydroxylase operon on the Pseudomonas putida CAM plasmid. J. Bacteriol. 175:78287833.
6. Aramaki, H.,, Y. Sagara,, H. Kobata,, N. Shimamoto,, and T. Horiuchi. 1995. Purification and characterization of a cam repressor (CamR) for the cytochrome P-450cam hydroxylase operon on the Pseudomonas putida CAM plasmid. J. Bacteriol. 177:31203127.
7. Arensdorf, J.J.,, and D. D, Focht. 1994. Formation of chlorocatechol meta cleavage products by a pseudomonad during metabolism of monochlorobiphenyls. Appl. Environ. Microbiol. 60:28842889.
8. Armengaud, J.,, K. N. Timmis,, and R. -M. Wittich. 1999. A functional 4-hydroxysalicylate/hydroxyquinol degradative pathway gene cluster is linked to the initial dibenzo-p-dioxin pathway genes in Sphingomonas sp. strain RWI. J. Bacteriol. 181:34523461.
9. Assinder, S. J.,, P. De Marco,, D. J. Osborne, C L. Poh, L. E. Shaw, M. K. Winson, and P. A. Williams. 1993. A comparison of the multiple alleles of xylS carried by TOL plasmids pWW53 and pDK 1 and its implications for their evolutionary relationship. J. Gen. Microbiol. 139:557568.
10. Assinder, S.J.,, and P. A. Williams. 1990. The TOL plasmids: determinants of the catabolism of toluene and the xylenes. Adv. Microb. Physiol. 31:169.
11. Bartels, I.,, H.-J. Knackmuss, and W, Reineke. 1984. Suicide inactivation of catechol 2,3-dioxygenasc from Pseudomonas putida mt-2 by 3-halocatechols. Appl. Environ. Microbiol. 47:500505.
12. Bartilson, M.,, I. Nordlund,, and V. Shingler. 1990. Location and organization of the dimethylphenol catabolic genes of Pseudomonas CF600. Mol Gen. Genet. 220:294300.
13. Batic, C. J ., , D. P. Ballou, and C. J . Correll. 1991. Phthalate dioxygenase reductase and related flavin-iron-sulfur containing electron transferases, p. 543556. In F. Muller (ed.), Chemistry and Biochemistry of Flavoenzymes, CRC Press, Boca Raton, Fla..
14. Bayley, S. A.,, D. W. Morris,, and P. Broda. 1979. The relationship of degradative and resistance plasmids of Pseudomonas belonging to the same incompatibility group. Nature 280:338339.
15. Beil, S.,, K. N. Timmis,, and D. H. Pieper. 1999. Genetic and biochemical analyses of the tec operon suggest a route for evolution of chlorobcnzene degradation genes, J. Bacteriol. 181:341346.
16. Benson, S.,, M. Fennewald,, J. Shapiro,, and C. Huettner. 1977. Fractionation of inducible alkane hydroxylase activity in Pseudomonas putida and characterization of hydroxylascnegative plasmid mutations.J. Bacteriol. 132:614621.
17. Benson, S.,, and J. Shapiro. 1976. Plasmid-determined alcohol dehydrogenase activity in alkane-utilizing strains of Pseudomonas putida. J. Bacteriol. 126:794798.
18. Benson, S.,, and J. Shapiro. 1978. TOL is a broad-host-range plasmid. J Bacteriol. 135:278280.
19. Berger, B.,, and D. Haas. 2001. Transposase and cointegrase: specialized transposition proteins of the bacterial insertion sequence IS21 and related elements. Cell. Mol Life. Sci. 58:403419.
20. Bertoni, G.,, N. Fujita,, A. Ishihama,, and V. de Lorenzo. 1998. Active recruitment of σ54-RNA polymerase to the Pu promoter of Pseudomonas putida: role of IHF and aCTD. EMBO J. 17:51205128.
21. Bertoni, G.,, S. Marques,, and V. de Lorenzo. 1998. Activation of the toluene-responsive regulator XylR causes a transcriptional switch between α54and σ70 promoters at the divergent PrIPs region of the TOL plasmid. Mol. Microbiol. 27:651659.
22. Bhat, M. A.,, M. Tsuda,, K. Horiike,, M. Nozaki,, C. S. Vaidyanathan,, and T. Nakazawa. 1994. Identification and characterization of a new plasmid carrying genes for degradation of 2,4-dichlorophenoxyacetatc from Pseudomonas cepacia CSV90. Appl. Environ. Microbiol. 60:307312.
23. Blasco, R.,, M. Mallavarapu,, R.-M. Wittich,, K. N. Timmis,, and D. H. Pieper, 1997. Evidence that formation of protoanemonin from metabolites of 4-chlorobiphenyl degradation negatively affects the survival of 4-chlorobiphenylcomctabolizing microorganisms. Appl. Environ. Microbiol. 63:427434.
24. 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. 270:2922929235.
25.Bradley, D, E., and P. A. Williams. 1982. The TOL plasmid is naturally derepressed for transfer. J. Gen. Microbiol. 128:30193024.
26. Brenner, V.,, J. J. Arensdorf,, and D. D. Focht. 1994. Genetic construction of PCB degraders. Biodegradation 5:359377.
27. Brenner, V.,, B. S. Hernandez,, and D. D. Focht. 1993. Variation in chlorobenzoate catabolism by Pseudomonas putida Pill as a consequence of genetic alterations. Appl. Environ. Microbiol 59:27902794.
28. Brückmann, M.,, R. Blasco,, K. N. Timmis,, and D. H. Pieper. 1998. Detoxification of protoanemonin by dienclactone hydrolase. J. Bacteriol. 180:400402.
29. Brühlmann, F., and W, Chen. 1999. Tuning biphenyl dioxygenase for extended substrate specificity. Biotechnol. Bioeng. 63:544551.
30. Bundy, B. M.,, L. S. Collier,, T. R. Hoover,, and E. L. Ncidle. 2002. Synergistic transcriptional activation by one regulatory protein in response to two metabolites. Proc. Natl. Acad. Sci. USA 99:76937698.
31. Burlage, R. S.,, L. A. Bemis,, A. C. Layton,, G. S. Sayler,, and F. Larimer. 1990. Comparative genetic organization of incompatibility group P degradative plasmids. J. Bacteriol. 172:68186825.'
32. Butler, C. S.,, and J . R, Mason. 1997. Structure-function analysis of the bacterial aromatic ring-hydroxylating dioxygenases. Adv. Microb. Physiol. 38:4784.
33. Cai, M.,, and L. Xun, 2002. Organization and regulation of pentachlorophenol-degrading genes in Sphingobium cblorophenoficum ATCC 39723. J. Bacteriol. 184:46724680.
34.Canosa, I, J. M. Sánchez-Romero, L. Yuste, and F, Rojo. 2000. A positive feedback mechanism controls expression of AlkS. the transcriptional regulator of the Pseudomonas oleovorans alkane degradation pathway. Mol. Microbiol. 35:791799.
35. Cases, I.,, and V. de Lorenzo. 2001. The black cat/white cat principle of signal integration in bacterial promoters. EMBO J. 20:111.
36. Cavalca, L.,, A. Hartmann,, N. Rouard,, and G. Soulas. 1999. Diversity of tfdC genes: distribution and polymorphism among 2,4-dichlorophenoxyacetic acid degrading soil bacteria. FEMS Microbiol. Ecol. 29:4558.
37. Cebolla, A.,, C. Sousa,, and V. de Lorenzo. 1997. Effector specificity mutants of the transcriptional activator NahR of naphthalene degrading Pseudomonas define protein sites involved in binding of aromatic inducers. J Biol. Chem. 272:39863992.
38. Chakrabarty, A. M. 1972. Genetic basis of the biodegradation of salicylate in Pseudomonas. J. Bacteriol 112:815823.
39. Chakrabarty, A. M. 1973. Genetic fusion of incompatible plasmids in Pseudomonas. Proc. Natl. Acad. Sci. USA 70:16411644.
40. Chakrabarty, A. M.,, G. Chou,, and I. C. Gunsalus. 1973. Genetic regulation of octane dissimilation plasmid in Pseudomonas. Proc. Natl. Acad. Sci. USA 70:11371140.
41. Chakrabarty, A. M.,, D. A. Friello,, and L. H. Bopp. 1978. Transposition of plasmid DNA segments specifying hydrocarbon degradation and their expression in various microorganisms. Proc. Natl. Acad. Sci. USA 75:31093112.
42. Chatfield, L. K.,, and P. A. Williams. 1986. Naturally occurring TOL plasmids in Pseudomonas strains carry either two homologous or two nonhomologous catechol 2,3-oxygenase genes. J. Bacteriol. 168:878885.
43. Chatterjee, D. K.,, and A. M. Chakrabarty. 1982. Genetic rearrangements in plasmids specifying total degradation of chlorinated benzoic acids. Mol. Gen. Genet. 188:279285.
44. Chatterjee, D. K.,, and A. M. Chakrabarty. 1983. Genetic homology between independently isolated chlorobenzoate-degradative plasmids. J. Bacteriol. 153:532534.
45. Chatterjee, D. K.,, S. T. Kellogg,, S. Hamada,, and A. M. Chakrabarty. 1981. Plasmid specifying total degradation of 3-chlorobenzoate by a modified ortbo pathway. J. Bacteriol. 146:639646.
46. Chaudhry, G. R. and G. H. Huang. 1988. Isolation and characterization of a new plasmid from a Flavobacterium sp. which carries the genes for degradation of 2,4-dichlorophenoxyacetate.J. Bacteriol. 170:38973902.
47. Christensen, B. B.,, C. Sternberg,, and S. Molin. 1996. Bacterial plasmid conjugation on semi-solid surfaces monitored with the green fluorescent protein (GFP) from Aequorea victoria as a marker. Gene 173:5965.
48. Chugani, S. A.,, M. R. Parsek,, C. D. Hershberger,, K. Murakami,, A. Ishihama,, and A. M. Chakrabarty. 1997. Activation of the catBCA promoter: probing the interaction of CatR and RNA polymerase through in vitro transcription. J. Bacteriol 179:22212227.
49. Clément, P.,, D. H. Pieper,, and B. Gonzalez. 2001. Molecular characterization of a deletion/duplication rearrangement in tfd genes from Ralstonia eutropha JMP134(pJP4) that improves growth on 3-chlorobenzoic acid but abolishes growth on 2,4-dichlorophcnoxyacetic acid. Microbiology 147:21412148.
50. Coco, W. M.,, R. K, Rothmel, S. Henikoff, and A. M. Chakrabarty. 1993. Nucleotide sequence and initial functional characterization of the clcR gene encoding a LysR family activator of the clcABD chlorocatechol operon in Pseudomonas putida. J. Bacteriol. 175:417427.
51. Collier, L. S.,, G. L. Gaines III,, and E. L. Neidle. 1998. Regulation of benzoate degradation in Acinetobacter sp. strain ADP1 by BenM, a LysR-type transcriptional activator. J. Bacteriol. 180:24932501.
52. Cowles, C. E.,, N. N. Nichols,, and C. S. Harwood. 2000. BenR, a XylS homologue, regulates three different pathways of aromatic acid degradation in Pseudomonas putida. J. Bacteriol. 182:63396346.
53. Daane, L. L.,, J. A. E. Molina,, E. C. Berry,, and M. J. Sadowsky. 1996. Influence of earthworm activity on gene transfer from Pseudomonas fluorescens to indigenous soil bacteria. Appl. Environ. Microbiol. 62:515521.
54. Dabrock, B.,, M. Kesseler,, B. Averhoff,, and G. Gottschalk. 1994. Identification and characterization of a transmissible linear plasmid from Rhodococcus erytbropolis BD2 that encodes isopropylbenzene and trichloroethene catabolism. Appl. Environ. Microbiol. 60:853860.
55. Daubaras, D. L.,, C. E. Danganan,, A. Hübner,, R. W. Ye,, W. Hendrickson,, and A. M. Chakrabarty. 1996. Biodegradation of 2,4,5-trichlorophenoxyacetic acid by Burkholderia cepacia strain AC 1100: evolutionary insight. Gene 179:18.
56. Daubaras, D. L.,, C. D. Hershberger,, K. Kitano,, and A. M. Chakrabarty. 1995. Sequence analysis of a gene cluster involved in metabolism of 2,4,5- trichlorophcnoxyacetic acid by Burkholderia cepacia AC1100. Appl. Environ. Microbiol. 61:12791289.
57. Daubaras, D. L.,, K. Saido,, and A. M. Chakrabarty. 1996. Purification of hydroxyquinol 1,2-dioxygenase and maleyl-acetate reductase: the lower pathway of 2,4,5-trichlorophenoxyacctic acid metabolism by Burkholderia cepacia A O 100, Appl. Environ. Microbiol. 62:42764279.
58. Dejonghe, W.,, J. Goris,, S. El Famroussi,, M. Höfte,, P. De Vos,, W. Verstraete,, and E. M. Top. 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. 66:32973304.
59. de Lorenzo, V.,, M. Herrero,, M. Metzke,, and K. N. Timmis. 1991. An upstream XylR- and IHF-induced nucleoprotein complex regulates the σ54-dependent Pu promoter of TOL plasmid. EMBO J. 10:11591167.
60. de Lorenzo, V.,, and J. Perez-Martin. 1996. Regulatory noise in prokaryotic promoters: how bacteria learn to respond to novel environmental signals. Mol. Microbiol. 19:11771184.
61. de Souza, M. L.,, L. P. Wackett,, and M. J. Sadowsky. 1998. The atzABC genes encoding atrazine catabolism are located on a self-transmissible plasmid in Pseudomonas sp. strain ADP. Appl. Environ. Microbiol. 64:23232326.
62. Díaz, E., and M, A. Prieto. 2000. Bacterial promoters triggering biodegradation of aromatic pollutants. Curr. Opin. Biotechnol. 11:467475.
63. Diaz-Aroca, E.,, M. V. Mendiola,, J . C. Zabala,, and F. de la Cruz. 1987. Transposition of IS91 docs not generate a target duplication. J. Bacteriol. 169:442443.
64. Di Gioia, D.,, M. Peel,, F. Fava,, and R. C. Wyndham. 1998. Structures of homologous composite transposons carrying cbaABC genes from Europe and North America. Appl. Environ. Microbiol. 64:19401946.
65. DiGiovanni, G. D.,, J. W. Neilson,, I. L. Pepper,, and N. A. Sinclair. 1996. Gene transfer of Alcaligenes eutropbus JMP134 plasmid pJP4 to indigenous soil recipients. Appl. Environ. Microbiol. 62:25212526.
66. Don, R. H.,, and J. M. Pemberton. 1981. Properties of six pesticide degradation plasmids isolated from Alcaligenes paradoxus and Alcaligenes eutropbus. J. Bacteriol. 145:681686.
67. Don, R. H.,, and J. M. Pemberton. 1985. Genetic and physical map of the 2,4-dichlorophenoxyacetic acid-degradative plasmid pJP4. J. Bacteriol. 161:466468.
68. Dorn, E., M, Hellwig, W. Reineke, and H.-J. Knackmuss. 1974. Isolation and characterization of a 3-chlorobenzoate degrading pseudomonad. Arch. Microbiol. 99:6170.
69. Dorn, E.,, and H.-J. Knackmuss. 1978. Chemical structure and biodegradability of halogenated aromatic compounds. Substituent effects on 1,2-dioxygenation of catechol. Biochem. J. 174:8594.
70. Duetz, W. A.,, J. B. van Beilen, and B, Witholt. 2001. Using proteins in their natural environment: potential and limitations of microbial whole-cell hydroxylations in applied biocatalysis. Curr. Opin. Biotechnol. 12:419425.
71. Duetz, W. A.,, M. K. Winson,, J. G. van Andel,, and P. A. Williams. 1991. Mathematical analysis of catabolic function loss in a population of Pseudomonas putida mt-2 during non-limited growth on benzoate. J. Gen. Microbiol. 137:13631368.
72. Duggleby, C. J.,, S. A. Bayley,, M. J. Worsey,, P. A. Williams,, and P. Broda. 1977. Molecular sizes and relationships of TOL plasmids in Pseudomonas. J. Bacteriol. 130:12741280.
73. Dunaway-Mariano, D.,, and P. C. Babbitt. 1994. On the origins and functions of the enzymes of the 4-chlorobenzoate to 4-hydroxybenzoate converting pathway. Biodegradation 5:259276.
74. Dunn, N. W.,, and I. C. Gunsalus. 1973. Transmissible plasmid coding early enzymes of naphthalene oxidation in Pseudomonas putida. J. Bacteriol. 114:974979.
75. Dunning Hotopp, J. C.,, and R. P. Hausinger. 2001. Alternative substrates of 2,4-dichlorophenoxyacetate/?-ketoglutarate dioxygenase. J. Mol Catal. B: Enzym. 15:155162.
76. Dunning Hotopp, J. C.,, and R. P. Hausinger. 2002. Probing the 2,4-dichlorophcnoxyacetate/α-ketoglutarate dioxyge nase substrate-binding site by site-directed mutagenesis and mechanism-based inactivation. Biochemistry 41:97879794.
77. Eggink, G.,, H. Engel,, W. G. Meijer,, J. Otten,, J. Kingma,, and B. Witholt. 1988. Alkane utilization in Pseudomonas oleovorans. Structure and function of the regulatory locus alkR. J. Biol. Chem. 263:1340013405.
78. Eggink, G.,, H. Engel,, G. Vriend,, P. Terpstra,, and B. Witholt. 1990. Rubredoxin reductase of Pseudomonas oleovorans. Structural relationship to other flavoprotein oxidorcductases based on one NAD and two HAD fingerprints, J. Mol. Biol 212:135142.
79. Eggink, G.,, P. H. van Lelyveld,, A. Arnberg,, N. Arfman,, C. Witteveen,, and B. Witholt. 1987. Structure of the Pseudomonas putida alkBAC operon. Identification of transcription and translation products, J Biol. Chem. 262:64006406.
80. Eichhorn, E.,, J. R. van der Ploeg,, M. A. Kertesz,, and T. Leisinger. 1997. Characterization of α-ketoglutarate-dependent taurine dioxygenase from Escherichia coli. J. Biol. Chem. 272:2303123036.
81. Elkins, J. M.,, M. J. Ryle,, I. J. Clifton,, J. C. Dunning Hotopp,, J. S. Lloyd. N. I. Burzlaff, J. E. Baldwin, R. P. Hausinger, and P. L. Roach. 2002. X-ray crystal structure of Escherichia coli taurine/α-ketoglutarate dioxygenase complexed to ferrous iron and substrates. Biochemistry 41:51855192.
82. Erickson, B. D.,, and F. J. Mondello. 1992. Nucleotide sequencing and transcriptional mapping of the genes encoding biphenyl dioxygenase, a multicomponent polychlorinated- biphenyl-degrading enzyme in Pseudomonas strain LB400. J. Bacteriol 174:29032912.
83. Erickson, B. IX, and F. J. Mondello. 1993. Enhanced biodegradation of polychlorinated biphenyls after site-directed mutagenesis of a biphenyl dioxygenase gene. Appl. Environ. Microbiol. 59:38583862.
84. Farhana, L.,, and P. B. New. 1997. The 2,4-dichlorophcnol hydroxylase of Alcaligenes eutrophus JMP134 is a homote-tramer. Can. J. Microbiol. 43:202205.
85. Fennewald, M.,, S. Benson,, M. Oppici,, and J. Shapiro. 1979. Insertion element analysis and mapping of the Pseudomonas plasmid alk regulon. J. Bacteriol. 139:940952.
86. Fennewald, M.,, and J. Shapiro. 1977. Regulatory mutations of the Pseudomonas plasmid alk regulon. J. Bacteriol 132:622627.
87. Fernández, S.,, V. Shingler,, and V. de Lorenzo. 1994. Cross-regulation by XylR and DmpR activators of Pseudomonas putida suggests that transcriptional control of biodegradative operons evolves independently of catabolic genes. J. Bacteriol 176:50525058.
88. Fetzner, S.,, R. Muller,, and F. Lingens. 1989. Degradation of 2-chlorobenzoate by Pseudomonas cepacia 2CBS. Biol. Chem. Hoppe-Seyler 370:1731182.
89. Fetzner, S.,, R. Müller,, and F. Lingens. 1992. Purification and some properties of 2-halobenzoate 1,2-dioxygcnase, a two-component enzyme system from Pseudomonas cepacia 2CBS. J. Bacteriol. 174:279290.
90. Filer, K., and A, R. Harker. 1997. Identification of the inducing agent of the 2,4-dichlorophcnoxyaccrie acid pathway encoded by plasmid pJP4. Appl. Environ. Microbiol. 63:317320.
91. Fong, K. P. Y.,, C. B. H. Goh,, and H.-M. Tan. 2000. The genes for benzene catabolism in Pseudomonas putida Ml.2 are flanked by two copies of the insertion element IS1489, forming a class-l-type catabolic transposon, Tn5542. Plasmid 43:103110.
92. Francisco, P. B.Jr.,, N. Ogawa,, K. Suzuki,, and K. Miyashita. 2001. The chlorobenzoate dioxygenase genes of Burkholderia sp. strain NK8 involved in the catabolism of chlorobenzoates. Microbiology 147:121133.
93. Frantz, B.,, and A. M. Chakrabarty. 1987. Organization and nucleotide sequence determination of a gene cluster involved in 3-chlorocatechol degradation. Proc. Natl. Acad. Sci. USA 84:44604464.
94. Fujita, M.,, H. Aramaki, T, Horiuchi, and A. Amemura. 1993. Transcription of the cam operon and camR genes in Pseudomonas putida PpG1. J Bacteriol. 175:69536958.
95. Fukumori, F.,, and R. P. Hausinger. 1993. Alcaligenes eutrophus JMPI34 “2,4-dichlorophenoxyacetatc monooxygenase” is an α-ketoglutarate-dependent dioxygenase. J. Bacteriol 175:20832086.
96. Fukumori, F.,, and C. P. Saint. 1997. Nucleotide sequences and regulational analysis of genes involved in conversion of aniline to catechol in Pseudomonas putida UCC22(pTDN1). J. Bacteriol. 179:399408.
97. Fulthorpe, R. R., C McGowan, O. V. Maltseva, W. E. Holben, and J. M. Tiedic. 1995. 2,4-Dichlorophenoxyacetic acid-degrading bacteria contain mosaics of catabolic genes. Appl. Environ. Microbiol. 61:32743281.
98. Furukawa, K. 1994. Molecular genetics and evolutionary relationship of PCB-degrading bacteria. Biodegradation 5:289300.
99. Furukawa, K.,, and A. M. Chakrabarty. 1982. Involvement of plasmids in total degradation of chlorinated biphenyls. Appl. Environ. Microbiol. 44:619626.
100. Furukawa, K.,, N. Tomizuka,, and A. Kamibayashi. 1979. Effect of chlorine substitution on the bacterial metabolism of various polychlorinated biphenyls. Appl. Environ. Microbiol. 38:301310.
101. Furukawa, K.,, K. Tonumura,, and A. Kamibayashi. 1979. Metabolism of 2,4,4'-trichlorobiphenyl by Acinetobacter sp. P6. Agric. Biol. Chem. 43:15771583.
102. Galas, D. J.,, and M. Chandler,. 1989. Bacterial insertion sequences, p. 109162. In D. E. Berg, and M. M. Howe (ed.), Mobile DNA, 1st ed. ASM Press, Washington, D.C..
103. Gallegos, M.-T.,, R. Schleif,, A. Bairoch,, K. Hofmann,, and J . L. Ramos. 1997. AraC/XylS family of transcriptional regulators. Microbiol. Mol. Biol. Rev. 61:393410.
104. Gallegos, M.-T.,, P. A. Williams,, and J. L. Ramos. 1997. Transcriptional control of the multiple catabolic pathways encoded on the TOL plasmid pWW53 of Pseudomonas putida MT53J. Bacteriol. 179:50245029.
105. Garrec, G.,, M.-L., 1. Artaud, and C. Capcillere-Blandin. 2001. Purification and catalytic properties of the chlorophenol 4-monooxygenase from Burkholderia cepacia strain AC1100. Biochim. Biopbys. Acta 1547:288301.
106. Genka, H.,, Y. Nagata,, and M. Tsuda. 2002. Site-specific recombination system encoded by toluene catabolic transposon Tn4651. J. Bacteriol. 184:47574766.
107. Ghosal, D.,, and I.-S. You. 1988. Nucleotide homology and organization of chlorocatechol oxidation genes of plasmids pJP4 and pAC27. Mol. Gen. Genet. 211:113120.
108.Ghosal, D, I.-S. You, D. K. Chatterjee, and A. M. Chakrabarty. 1985. Genes specifying degradation of 3- cblorobenzoic acid in plasmids pAC27 and pJP4. Proc. Natl. Acad. Set. USA 82:16381642.
109. Gibello, A.,, M. Suarez,, J . L. Allende,, and M. Martin. 1997. Molecular cloning and analysis of the genes encoding the 4- hydroxyphenylacetatc hydroxylase from Klebsiella pneumoniae. Arch. Microbiol. 167:160166.
110.Gibson, IX T., and R. E. Parales. 2000. Aromatic hydrocarbon dioxygenases in environmental biotechnology. Curr. Opin. Biotechnol. 11:236243.
111. Golovleva, L. A.,, O. Zaborina,, R. Pertsova,, B. Baskunov, Y, Schurukhin, and S. Kuzmin. 1992. Degradation of polychlorinated phenols by Streptomyces rocbei 303. Biodegradation 2:201208.
112. Gomada, M.,, H. Imaishi,, K. Miura,, S. Inouye,, T. Nakazawa,, and A. Nakazawa. 1994. Analysis of DNA bend structure of promoter regulatory regions of xylene-metabolizing genes on the Pseudomonas TOL plasmid. J. Biochem. (Tokyo) 116:10961104.
112a.. Created, A.,, L. Lambertsen,, P. A. Williams,, and C. M. Thomas. 2002. Complete sequence of the IncP9 TOL plasmid pWW0 from Pseudomonas putida. Environ. Microbiol 4:856871.
113. Grimm, A. C.,, and C. S. Harwood. 1999. NahY, a catabolic plasmid-encoded receptor required for chemotaxis of Pseudomonas putida to the aromatic hydrocarbon naphthalene. J. Bacteriol 181:33103316.
114. Haak, B.,, S. Fetzner,, and F. Lingens. 1995. Cloning, nucleotide sequence, and expression of the plasmid-encoded genes for the two-component 2-halobenzoatc 1,2-dioxygenase from Pseudomonas cepacia 2CBS. J. Bacteriol 177:667675.
115. Harayama, S.,, and M. Rekik. 1990. The meta cleavage operon of TOL degradative plasmid pWW0 comprises 13 genes. Mol Gen. Genet. 221:113120.
116. Harayama, S.,, and M. Rekik. 1993. Comparison of the nucleotide sequences of the meta-cleavage pathway genes of TOL plasmid pWW0 from Pseudomonas putida with other meta-cleavage genes suggests that both single and multiple nucleotide substitutions contribute to enzyme evolution. Mol. Gen. Genet. 239:8189.
117. Harayama, S.,, M. Rekik,, A. Bairoch,, E. L. Neidle,, and L. N. Ornston. 1991. Potential DNA slippage structures acquired during evolutionary divergence of Acinetobacter calcoaccticus chromosomal ben ABC and Pseudomonas putida TOL pWW0 plasmid xy/XYZ, genes encoding benzoate dioxygenases. J. Bacteriol 173:75407548.
118. Harayama, S.,, M. Rekik,, M. Wubbolts,, K. Rose,, R. A. Leppik,, and K. N. Timmis. 1989. Characterization of five genes in the upper-pathway operon of TOL plasmid pWW0 from Pseudomonas putida and identification of the gene products. J. Bacteriol 171:50485055.
119. Harayama, S.,, and K. N. Timmis,. 1989. Catabolism of aromatic hydrocarbons by Pseudomonas, p. 151174. In D. A. Hopwood, and K. F. Chater (ed.), Genetics of Bacterial Diversity. Academic Press Inc., London, United Kingdom.
120. Harwood, C. S.,, and R. E. Parales. 1996. The β-ketoadipate pathway and the biology of self-identity. Annu. Rev. Microbiol 50:553590.
121. Hauschild, J . E.,, M. Seto,, E. Masai,, T. Hatta,, K. Kimbara,, M. Fukuda,, and K. Yano,. 1997. Multiple metabolic pathways involved in polychlorinated biphenyl (PCB) degradation in Rhodococcus sp. strain RHA1, p. 2133 . In K. Horikoshi,, M. Fukuda,, and T. Kudo (ed.), Microbial Diversity and Genetics of Biodegradation. Japan Scientific Societies Prcss/Kargcr, Tokyo, Japan.
122. Hausinger, R. P.,, F. Fukumori,, D. A. Hogan,, T. M. Sassanella,, Y. Kamagata,, H. Takami,, and R. E. Saari,. 1997. Biochemistry of 2,4-doichIorophenoxyacetic acid (2,4-D) degradation: evolutionary implications, p. 3551 . In K. Horikoshi,, M. Fukuda,, and T. Kudo (ed.), Microbial Diversity and Genetics of Biodegradation. Japan Scientific Societies Press/Karger, Tokyo, Japan.
123. Hawkins, A. C., and C, S. Harwood. 2002. Chemotaxis of Ralstonia eutropha JMP134(pJP4) to the herbicide 2,4- dichlorophenoxyacetate. Appl Environ. Microbiol. 68:968972.
124. Hayatsu, M.,, M. Hirano,, and T. Nagata. 1999. Involvement of two plasmids in the degradation of carbaryl by Arthrobacter sp. strain RC100. Appl Environ. Microbiol. 65:10151019.
125. Heinaru, A. L.,, C. J. Dugglcby,, and P. Broda. 1978. Molecular relationships of degradative plasmids determined by in situ hybridisation of their endonuclease-generated fragments. Mol Gen. Genet. 160:347351.
126. Higson, F. K.,, and D. D. Focht. 1992. Utilization of 3- chloro-2-methylbenzoic acid by Pseudomonas cepacia MB2 through the meta fission pathway. Appl Environ. Microbiol 58:25012504.
127. Hofer, B.,, L. D. Eltis,, D. N. Dowling,, and K. N. Timmis. 1993. Genetic analysis of a Pseudomonas locus encoding a pathway for biphenyl/polychlorinated biphenyl degradation. Gene 130:4755.
128. Hogan, D. A.,, S. R. Smith,, E. A. Saari,, J. McCracken,, and R. P. Hausinger. 2000. Site-directed mutagenesis of 2,4- dichlorophenoxyacetic acid/α-ketoglutarate dioxygenase. Identification of residues involved in metallocenter formation and substrate binding. J. Biol. Chem. 275:1240012409.
129. Holtel, A.,, D. Goldenberg,, H. Giladi,, A. B. Oppenheim,, and K. N. Timmis. 1995. Involvement of IHF protein in expression of the Ps promoter of the Pseudomonas putida TOL plasmid. J. Bacteriol 177:33123315.
130. Holtel, A.,, K. N. Timmis,, and J . L. Ramos. 1992. Upstream binding sequences of the XylR activator protein and integration host factor in the xylS gene promoter region of the Pseudomonas TOL plasmid. Nucleic Acids Res. 20:17551762.
131. Horak, R.,, and M. Kivisaar. 1998. Expression of the transposase gene tnpA of Tn4652 is positively affected by integration host factor. J. Bacteriol 180:28222829.
132. Hübncr, A.,. C. E. Danganan,, L. Xun,, A. M. Chakrabarty,, and W. Hendrickson. 1998. Genes for 2,4,5-trichlorophenoxyacetic acid metabolism in Burkholderia cepacia AC 1100: characterization of the tftC and tftD genes and locations of the tft operons on multiple replicons. Appl. Environ. Microbiol. 64:20862093.
133. Hübner, A.,, and W. Hendrickson. 1997. A fusion promoter created by a new insertion sequence, IS1490, activates transcription of 2,4,5-trichlorophenoxyacetic acid catabolic genes in Burkholderia cepacia AC 1100. J. Bacteriol 179:27172723.
134. Hugo, N.,, J . Armcngaud,, J . Gaillard,, K. N. Timmis,, and Y. Jouanneau. 1998. A novel [2Fe-2S] ferredoxin from Pseudomonas putida mt2 promotes the reductive reactivation of catechol 2,3-dioxygenase. J. Biol. Chem. 273:96229629.
135. Inoue, J.,, J. P. Shaw,, M. Rekik,, and S. Harayama. 1995. Overlapping substrate specificities of benzaldehyde dehydrogenase (thexylC gene product) and 2-hydroxymuconic semialdehyde dehydrogenase (the xylG gene product) encoded by TOL plasmid pWW0 of Pseudomonas putida. J. Bacteriol. 177:11961201.
136. Inouye, S., 1998. Plasmids, p. 133. In T. C. Montie (ed.), Pseudomonas, Biotechnology Handbooks, vol. 10. Plenum Press, New York, N.Y..
137. Inouye, S.,, M. Gomada,, U. M. Sangodkar,, A. Nakazawa,, and T. Nakazawa. 1990. Upstream regulatory sequence for transcriptional activator XylR in the first operon of xylene metabolism on theTOL plasmid. J. Mol Biol. 216:251260.
138. Inouye, S.,, A. Nakazawa,, and T. Nakazawa. 1981. Molecular cloning of gene xylS of the TOL plasmid: evidence for positive regulation of the xylDEGF operon by xylS. J . Bacteriol. 148:413418.
139. Inouye, S.,, A. Nakazawa,, and T. Nakazawa. 1986. Nucleotide sequence of the regulatory gene xylS on the Pseudomonas putida TOL plasmid and identification of the protein product. Gene 44:235242.
140. Inouye, S., A, Nakazawa, and T. Nakazawa. 1987. Overproduction of the xylS gene product and activation of the xylDLEGF operon on the TOL plasmid. J. Bacteriol 169:35873592.
141. Inouye, S.,, A. Nakazawa,, and T. Nakazawa. 1987. Expression of the regulatory gene xylS on the TOL plasmid is positively controlled by the xylR gene product. Proc. Natl Acad. Sci. USA 84:51825186.
142. Inouye, S.,, A. Nakazawa,, and T. Nakazawa. 1988. Nucleotide sequence of the regulatory gene xylR of the TOL plasmid from Pseudomonas putida. Gene 66:301306.
143. Jacoby, G. A.,, J. E. Rogers,, A. E. Jacob,, and R. W. Hedges. 1978. Transposition of Pseudomonas toluene-degrading genes and expression in Escherichia coli. Nature 274:179180.
144. Jeenes, D. J.,, and P. A. Williams. 1982. Excision and integration of degradative pathway genes from TOL plasmid pWW0. J. Bacteriol. 150:188194.
145.Jeffrey, W, H., S. M. Cuskey, P. J. Chapman, S. Resnick, and R. H. Olsen. 1992. Characterization of Pseudomonas putida mutants unable to catabolize benzoate: cloning and characterization of Pseudomonas genes involved in benzoate catabolism and isolation of a chromosomal DNA fragment able to substitute for xylS in activation of the TOL lower-pathway promoter. J. Bacteriol. 174:49864996.
146. Joset, F.,, and J. Guespin-Michel. 1993. Transposable elements, p. 132164. In Prokaryotic Genetics. Blackwell Scientific Publications, Oxford, United Kingdom.
147. Junker, F.,, and A. M. Cook. 1997. Conjugative plasmids and the degradation of arylsulfonates in Comamonas testosteroni. Appl. Environ. Microbiol. 63:24032410.
148. Junker, F.,, R. Kicwitz,, and A. M. Cook. 1997. Characterization of the p-toluenesulfonatc operon tsaMBCD and tsaR in Comamonas testosteroni T-2. J. Bacteriol. 179:919927.
149. Ka, J. O.,, W. E. Holben,, and J. M. Tiedje. 1994. Genetic and phenotypic diversity of 2,4-dichlorophcnoxyacetic acid (2,4- D)-degrading bacteria isolated from 2,4-D-treated field soils. Appl. Environ. Microbiol. 60:11061115.
150. Ka, J. O.,, W. E. Holben,, and J. M. Tiedje. 1994. Use of gene probes to aid in recovery and identification of functionally dominant 2,4-dichlorophenoxyacetic acid-degrading populations in soil. Appl. Environ. Microbiol. 60:11161120.
151. Ka, J. O.,, W. E. Holben,, and J. M. Tiedje. 1994. Analysis of competition in soil among 2,4-dichlorophenoxyacetic acid-degrading bacteria. Appl. Environ. Microbiol. 60:11211128.
152. Ka, J . O., and J, M, Tiedje. 1994. Integration and excision of a 2,4-dichlorophenoxyacetic acid-degradative plasmid in Alcaligenes paradoxus and evidence of its natural intergeneric transfer. J. Bacteriol 176:52845289.
153. Kasak, L.,, R. Horak,, A. Nurk,, K. Talvik,, and M. Kivisaar. 1993. Regulation of the catechol 1,2-dioxygenase- and phenol monooxygenase-encoding pheBA operon in Pseudomonas putida PaW85. J. Bacteriol. 175:80388042.
154. Kasberg, T., V, Seibert, M. Schlömann, and W. Reineke. 1997. Cloning, characterization, and sequence analysis of the clcE gene encoding the maleylacetate reductase of Pseudomonas sp. strain B13. J. Bacteriol. 179:38013803.
155. Kaschabek, S. R.,, T. Kasbcrg,, D. Muller,, A. E. Mars,, D. B. Janssen,, and W. Rcinekc 1998. Degradation of chloroaromatics: purification and characterization of a novel type of chlorocatechol 2,3-dioxygenase of Pseudomonas putida GJ31. J. Bacteriol. 180:296302.
156. Kaschabek, S. R.,, B. Kuhn,, D. Muller,, E. Schmidt,, and W. Rcinekc. 2002. Degradation of aromatics and chloroaromatics by Pseudomonas sp. strain B13: purification and characterization of 3-oxoadipatc:succinyl-coenzymc A (CoA) transferase and 3-oxoadipyl-CoA thiolasc. J. Bacteriol. 184:207215.
157. Kato, K.,, K. Ohtsuki,, Y. Koda,, T. Maekawa,, T. Yomo,, S. Negoro,, and I. Urabc. 1995. A plasmid encoding enzymes for nylon oligomer degradation: nucleotide sequence and analysis of pOAD2. Microbiology 141:25852590.
158. Kauppi, B.,, K. Lee,, E. Carredano,, R. E. Parales,, D. T. Gibson,, H. Eklund,, and S. Ramaswamy. 1998. Structure of an aromatic-ring-hydroxylating dioxygenase-naphthalcne 1,2- dioxygenase. Structure 6:571586.
159. Kawasaki, H.,, H. Yahara,, and K. Tonomura, 1981. Isolation and characterization of plasmid pUO1 mediating dehalogenation of haloacetate and mercury resistance in Moraxetta sp. B. Agric. Biol. Chem. 45:14771481.
160. Keil, H.,, S. Keil,, R. W. Pickup,, and P. A. Williams. 1985. Evolutionary conservation of genes coding for meta pathway enzymes within TOL plasmids pWW0 and pWW53. J. Bacteriol. 164:887895.
161.Keil. H., M. R. Lebens, and P. A. Williams. 1985. TOL plasmid pWW15 contains two nonhomologous, independently regulated catechol 2,3-oxygenase genes. J. Bacteriol 163:248255.
162. Kellogg, S. T.,, D. K. Chatterjee,, and A. M. Chakrabarty. 1981. Plasmid-assisted molecular breeding: new technique for enhanced biodegradation of persistent toxic chemicals. Science 214:11331135.
163. Kesseler, M.,, E. R. Dabbs,, B. Averhoff,, G. Gottschalk. 1996. Studies on the isopropylbenzene 2,3-dioxygenase and the 3- isopropylcatechol 2,3-dioxygenase genes encoded by the linear plasmid of Rhodococcus erythropolis BD2. Microbiology 142:32413251.
164. Kessler, B.,, M. Herrero, K, N. Timmis, and V. de Lorenzo. 1994. Genetic evidence that rhe XylS regulator of the Pseudomonas TOL meta operon controls the Pm promoter through weak DNA-protein interactions. J. Bacteriol. 176:31713176.
165. Kessler, B.,, S. Marques,, T. Köhler,, J. L. Ramos,, K. N. Timmis,, and V. de Lorenzo. 1994. Cross talk between catabolic pathways in Pseudomonas putida: XylS-dependent and -independent activation of the TOL meta operon requires the same f/5-acting sequences within the Pm promoter. J. Bacteriol 176:55785582.
166. Kimura, N.,, A. Nishi,, M. Goto,, and K. Furukawa. 1997. Functional analyses of a variety of chimeric dioxygenases constructed from two biphenyl dioxygenases that are similar structurally but different functionally. J. Bacteriol 179:39363943.
167. Kinkle, B. K. M. J. Sadowsky, E. L. Schmidt, and W. C. Kokskinen. 1993. Plasmids pJP4 and R68.45 can be transferred between populations of Bradyrbizobia in nonsterile soil. Appl. Environ. Microbiol 59:17621766.
168. Kivisaar, M.,, R. Horak,, L. Kasak,, A. Heinaru,, and J. Habicht. 1990. Selection of independent plasmids determining phenol degradation in Pseudomonas putida and the cloning and expression of genes encoding phenol monooxygenase and catechol 1,2-dioxygenase. Plasmid 24:2536.
169.Klečka, G, M., and D. T. Gibson. 1981. Inhibition of catechol 2,3-dioxygenase from Pseudomonas putida by 3- chlorocatechol. Appl. Environ. Microbiol. 41:11591165.
170. Kleinstcuber, S.,, R. H. Muller,, and W. Babel. 2001. Expression of the 2,4-D degradative pathway of pJP4 in an alkaliphilic, moderately halophilic soda lake isolate, Halomottas sp. E R 3 . Extremophiles 5:375384.
171. Klemba, M.,, B. Jakobs,, R.-M. Wittich,, and D. Pieper. 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. 66:32553261.
172. Koga, H.,, H. Aramaki,, E. Yamaguchi,, K. Takcuchi,, T. Horiuchi,, and I. C. Gunsalus. 1986. camRy a negative regulator locus of the cytochrome P-450cam hydroxylase operon. J. Bacteriol. 166:10891095.
173.Koga, H,, E, Yamaguchi, K. Matsunaga, H. Aramaki, and T. Horiuchi. 1989. Cloning and nucleotide sequences of NADHputidaredoxin reductase gene [camA) and putidaredoxin gene {cam ft) involved in cytochrome P-450cam hydroxylase of Pseudomonas putida. J. Biochem. (Tokyo) 106:831836.
174. Köhler, T.,, S. Harayama,, J. - L . Ramos, and K. N. Timmis. 1989. Involvement of Pseudomonas putida RpoN σ factor in regulation of various metabolic functions. J. Bacteriol. 171:43264333.
175. Kok, M.,, R. Oldenhuis,, M. P. G. van der Linden,, C. H. C. Mculenberg,, J. Kingma,, and B. Witholt. 1989. The Pseudomonas oleovorans alkBAC operon encodes two structurally related rubredoxins and an aldehyde dehydrogenase. J Biol. Chem. 264:54425451.
176. Kok, M.,, R. Oldenhuis,, M. P. G. van der Linden,, P. Raatjes,, J. Kingma,, P. H. vanLelyveld,, and B. Witholt. 1989. The Pseudomonas oleovorans alkane hydroxylase gene. Sequence and expression. J. Biol Chem. 264:54355441.
177. Kozyreva, L. P.,, Y. V. Shurukhin, Z, I. FinkePshtein, B. P. Baskunov, and L. A, Golovleva. 1993. Metabolism of the herbicide 2,4-D by a Nocardioides simplex strain. Mikrobiologiya 62:7885.
178. Kumamaru, T.,, H. Suenaga,, M. Mitsuoka,, T. Watanabe,, and K. Furukawa. 1998. Enhanced degradation of polychlorinated biphenyls by directed evolution of biphenyl dioxygenase. Nat. Biotechnol 16:663666.
179. Kunz, D. A.,, and P. J. Chapman. 1981. Isolation and characterization of spontaneously occurring TOL plasmid mutants of Pseudomotias putida HSl. J. Bacteriol. 146:952964.
180. Laemmli, C. M.,, J. H. J. Leveau,, A. J. B. Zehnder,, and J. R. van der Meer. 2000. Characterization of a second tfd gene cluster for chlorophenol and chlorocatechol metabolism on plasmid pJP4 in Ralstonia eutropha JMP134(pJP4). J. Bacteriol. 182:41654172.
181. Laemmli, C. M.,, R. Schönenberger,, M. Suter,, A. J. B. Zehnder,, and J. R. van der Meer. 2002. TfdDII, one of the two chloromuconate cycloisomerases of Ralstonia eutropha JMP134 (pJP4), cannot efficiently convert 2-chloro-cis, cis-muconate to tranms-dienelactone to allow growth on 3- chlorobenzoate. Arch. Microbiol. 178:1325.
182. Lange, C. C , B. J . Schneider, and C S. Orser. 1996. Verification of the role of PCP 4-monooxygenase in chlorine elimination from pentachlorophenol by Flavobacterium sp. strain ATCC 39723. Biochem. Biophys. Res. Commun. 219:146149.
183. Larkin, M. J.,, R. De Mot,, L. A. Kulakov,, and I. Nagy. 1998. Applied aspects of Rhodococcus genetics. Anionie Leeuwenhoek 74:133153.
184. Latus, M. J.,, H.-J. Seitz,, J. Eberspacher,, and F. Lingens. 1995. Purification and characterization of hydroxyquinol 1,2-dioxygenase from Azotobacter sp. strain GP1. Appl. Environ. Microbiol. 61:24532460.
185. Lau, E. Y.,, and T. C Bruce. 2001. The active site dynamics of 4-chlorobenzoyl-CoA dehalogenase. Proc. Natl. Acad. Sci. USA. 98:95279532.
186. Lawrence, J. G.,, and J. R. Roth. 1996. Selfish operons: horizontal transfer may drive the evolution of gene clusters. Genetics 143:18431860.
187. Lehrbach, P. R.,, I. McGregor,, J. M, Ward, and P. Broda. 1983. Molecular relationships between Pseudomonas INC P-9 degradative plasmids TOL, NAH, and SAL. Plasmid 10:164174.
188. Lehrbach, P. R.,, J. Ward,, P. Meulien,, and P. Broda. 1982. Physical mapping of TOL plasmids pWW0 and pND2 and various R plasmid-TOL derivatives from Pseudomonas spp. J. Bacteriol. 152:12801283.
189. Leveau, J. H. J, F. König, H. Füchslin, C. Werlen, and J. R. van der Meer. 1999. Dynamics of multigene expression during catabolic adaptation of Ralstonia eutropha JMP134 (pJP4) to the herbicide 2, 4-dichlorophenoxyacetatc. Mol. Microbiol. 33:396406.
190. Leveau, J. H. J.,. and J. R. van der Meer. 1996. The tfdR gene product can successfully take over the role of the insertion element-inactivated TfdT protein as a transcriptional activator of the tfdCDEF gene cluster, which encodes chlorocatechol degradation in Ralstonia eutropha JMP134(pJP4). J. Bacteriol. 178:68246832. (Erratum, 179:2096, 1997).
191. Leveau, J. H. J.,, and J. R. van der Meer. 1997. Genetic characterization of insertion sequence ISJP4 on plasmid pJP4 from Ralstonia eutropha JMP134. Gene 202:103114.
192. Leveau, J. H. J.,, A. J. B. Zehnder,, and J. R. van der Meer. 1998. The tfdK gene product facilitates uptake of 2,4- dichlorophcnoxyacetate by Ralstonia eutropha JMP134 (pJP4). J. Bacteriol. 180:22372243.
193. Liu, S.,, N. Ogawa, and K, Miyashita. 2001. The chlorocatechol degradative genes, tfdT-CDEFy of Burkholderia sp. strain NK8 arc involved in chlorobenzoate degradation and induced by chlorobenzoates and chlorocatechols. Gene 268:207214.
194. Lloyd-Jones, G.,, C. de Jong,, R. C. Ogden,, W. A, Duetz, and P. A, Williams. 1994. Recombination of the bph (biphenyl) catabolic genes from plasmid pWW100 and their deletion during growth on benzoate. Appl. Environ. Microbiol. 60:691696.
195.Löffler, F,, F. Lingens, and R. Müller. 1995. Dehalogenation of 4-chlorobcnzoate. Characterisation of 4-chlorobenzoylcoenzyme A dehalogenase from Pseudomonas sp. CBS3. Biodegradation 6:203212,
196.Luo, L. K, L. Taylor, H. Xiang, Y. Wei, W. Zhang, and D. Dunaway-Mariano. 2001. Role of active site binding interactions in 4-chlorobenzoyl-coenzymc A dehalogenase catalysis. Biochemistry 40:1568415692.
197. Mäe, A. A.,, R. O. Marks,, N. R. Ausmees,, V. M. Kôiv,, and A. L. Heinaru. 1993. Characterization of a new 2,4- dichlorophenoxyacetic acid degrading plasmid pEST4011: physical map and localization of catabolic genes. J. Gen. Microbiol. 139:31653170.
197a.. Maeda, K.,, H. Nojiri,, M. Shintani,, T. Yoshida,, H. Habe,, and T. Omori. 2003. Complete nucleotide sequence of carbazole/ dioxin-degrading plasmid pCARl in Pseudomonas resinovorans strain CA10. J Mol. Biol. 326:2133.
198. Marqués, S.,, M. T. Gallegos,, and J. L. Ramos. 1995. Role of σ4 in transcription from the positively controlled Pm promoter of the TOL plasmid of Pseudomonas putida. Mol. Microbiol. 18:851857.
199. Marqués, S.,, M. Manzanera,, M.-M. Gonzalez-Perez,, M. T. Gallegos,, and J. L. Ramos. 1999. The XylS-dependent Pm promoter is transcribed in vivo by RNA polymerase with σ32 or σ38depending on the growth phase. Mol. Microbiol. 31:11051103.
200. Mars, A. E.,, J. Kingma,, S. R. Kaschabek,, W. Reineke,, and D. B. Janssen. 1999. Conversion of 3-chlorocatechol by var ious catechol 2,3-dioxygenascs and sequence analysis of the chlorocatechol dioxygenase region of Pseudomonas putida GJ31. J. Bacteriol. 181:13091318.
201. Martinez, B.,, J. Tomkins,, L. P. Wackett,, R. Wing,, and M. J. Sadowsky. 2001. Complete nucleotide sequence and organization of the atrazine catabolic plasmid pADP-1 from Pseudomonas sp. strain ADP. J. Bacteriol. 183:56845697.
202. Masai, E.,, K. Sugiyama,, N. Iwashita,, S. Shimizu,, J. E. Hauschild,, T. Hatta,, K. Kimbara,, K. Yano,, and M. Fukuda 1997. The bpbDEF meta-cleavage pathway genes involved in biphenyl/polychlorinated biphenyl degradation are located on a linear plasmid and separated from the initial bpbACB genes in Rhodococcus sp. strain RHAI. Gene 187:141149.
203. Mathys, R. G.,, A. Schmid,, and B. Witholt. 1999. Integrated two-liquid phase bioconversion and product-recovery processes for the oxidation of alkanes: process design and economic evaluation. Biotechnol. Bioeng. 64:459477.
204. Matrubutham, U.,, and A. R. Harker. 1994. Analysis of duplicated gene sequences associated with tfdR and tfdS in Alcaligenes eutropbus JMP134. J. Bacteriol. 176:23482353.
205. McFall, S. M.,, B. Abraham,, C. G. Narsolis,, and A. M. Chakrabarty. 1997. A tricarboxylic acid cycle intermediate regulating transcription of a chloroaromatic biodegradativc pathway: fumarate-mediated repression of the clcABD operon. J . Bacteriol. 179:67296735.
206. McFall, S. M.,, S. A. Chugani,, and A. M. Chakrabarty. 1998. Transcriptional activation of the catechol and chlorocatechol operons: variations on a theme. Gene 223:257267.
207. McFall, S. M.,, T. J. Klem,, N. Fujita,, A. Ishihama,, and A. M. Chakrabarty. 1997. DNase I footprinting, DNA bending and in vitro transcription analyses of CIcR and CatK interactions with the clcABD promoter: evidence of a conserved transcriptional activation mechanism. Mol. Microbiol. 24:965976,
208. McFall, S. M.,, M. R. Parsek,, and A. M. Chakrabarty. 1997. 2-Chloromuconate and CIcR-mediated activation of the clcABD operon: in vitro transcriptional and DNase I foot- print analyses. J. Bacteriol. 179:36553663.
209.McGowan, C, R, Fulthorpe, A. Wright, and J. M. Tiedje. 1998. Evidence for interspecies gene transfer in the evolution of 2,4-dichlorophenoxyacetic acid degraders. Appl Environ. Microbiol. 64:40894092.
210.Merlin, C, D. Springael, and A. Toussaint. 1999. Tn4371: a modular structure encoding a phage-like integrase, a Pseudomonas-Wkv catabolic pathway, and RP4/Ti-like transfer functions. Plasmid 41:4054.
211. Mermod, N.,, J. L. Ramos,, A. Bairoch,, and K. N. Timmis. 1987. The xylS gene positive regulator of TOL plasmid pWWO: identification, sequence analysis and overproduction leading to constitutive expression of meta cleavage operon. Mol Gen. Genet. 207:349354.
212. Miura, K.,, S. Inouye,, and A. Nakazawa. 1998. Protein bind- ing in vivo to OP2 promoter of the Pseudomonas putida TOL plasmid. Biochem. Mol. Biol. Int. 46:933941.
213. Miyauchi, K.,, H.-S. Lee,. M. Fukuda,, M. Takagi,, and Y. Nagata. 2002. Cloning and characterization of linR, involved in regulation of the downstream pathway for γ-hexachloro- cyclohexane degradation in Spbingomonas paucimobilis UT26. Appl. Environ. Microbiol. 68:18031807.
214. Muller, R.,, J . Thiele, U, Klagcs, and F. Lingcns. 1984. Incorporation of [18O] water into 4-hydroxybenzoic acid in the reaction of 4-chlorobenzoate dehalogenase from Pseudomonas spec. CBS3. Biochem. Biopbys. Res. Commun. 124:178182.
215. Murray, K.,, C. J. Duggleby,, J. M. Sala-Trepat,, and P. A. Williams. 1972. The metabolism of benzoate and methylbenzoates via the meta-cleavagc pathway by Pseudomonas arvilla mt-2. J. Biol. Chem. 28:301310.
216. Nakai, C.,, H. Kagamiyama,, M. Nozaki,, T. Nakazawa,, S. Inouye,, Y. Ebina,, and A. Nakazawa. 1983. Complete nucleotide sequence of the metapyrocatechase gene on the TOL plasmid of Pseudomonas putida mt-2. J. Biol. Chem. 258:29232928.
217. Nakatsu, C. H.,, R. R. Fulthorpe,, B. A. Holland,, M. C. Peel,, and R. C Wyndham. 1995. The phylogenetic distribution of a transposable dioxygenase from the Niagara River watershed. Mol Ecol. 4:593603.
218.Nakatsu, C, J . Ng, R. Singh, N. Straus, and C. Wyndham. 1991. Chlorobenzoate catabolic transposon Tn5271 is a composite class 1 element with flanking class II insertion sequences. Proc. Natl Acad. Sci. USA 88:83128316.
219. Nakatsu, C. H.,, M. Providenti,, and R. C. Wyndham. 1997. The cis-diol dehydrogenase cbaC gene of Tn5271 is required for growth on 3-chlorobenzoate but not 3,4-dichlorobenzoate. Gene 196:209218.
220. Nakatsu, C. H.,, and R. C Wyndham. 1993. Cloning and expression of the transposablc chlorobenzoate-3,4-dioxygenasc genes of Alcaligenes sp. strain BR60. Appl. Environ. Microbiol. 59:36253633.
221. Nakazawa, T.,, E. Hayashi,, T. Yokota,, Y. Ebina,, and A. Nakazawa. 1978. Isolation of TOL and RP4 recombinants by integrative suppression.J. Bacteriol. 134:270277.
222. Nakazawa, T.,, and T. Yokota. 1973. Benzoate metabolism in Pseudomonas putida (arvilla) mt-2: demonstration of two benzoate pathways. J. Bacteriol. 115:262267.
223. Nam, J. W.,, H. Nojiri,, T. Yoshida,, H. Habe,, H. Yamane,, and T. Omori. 2001. New classification system for oxygenase components involved in ring-hydroxylating oxygenations. Biosci. Biotechnol. Biochem. 65:254263.
224. Negoro, S.,, T. Taniguchi,, M. Kanaoka,, H. Kimura,, and H. Okada. 1