Composite parts
Name
Part
Description
Pyrene degradation operon
Complete operon, containing all nine protein coding sequences
for complete pyrene degradation as well as regulatory elements.
Coding sequences for pyrene degradation pathway
Name
Part
Description
nidA
nidA forms together with nidB, phtAc and phtAd pyrene dioxygenase
enzyme
complex. This complex catalyzes the oxidation of pyrene to
cis-4,5-dihydro-4,5-dihydroxypyrene.
This is the first step in biodegradation of pyrene.[1]
nidB
nidB forms together with nidA, phtAc and phtAd pyrene dioxygenase
enzyme
complex. This complex catalyzes the oxidation of pyrene to
Cis-4,5-Dihydro-4,5-dihydroxypyrene.
This is the first step in biodegradation of pyrene.[1]
phdE
Encodes dihydrodiol dehydrogenase presumably catalyzing reaction of
Cis-4,5-Dihydro-4,5-dihydroxypyrene to 4,5-dihydroxypyrene. This is the second step in
pyrene
biodegradation.[2]
phdF
Encodes ring cleavage dioxygenase presumably catalyzing reaction of
4,5-dihydroxypyrene to Phenanthrene-4,5-Dicarboxylate. This is the third step in pyrene
biodegradation[2].
phtC
Encodes decarboxylase presumably catalyzing reaction of
Phenanthrene-4,5-Dicarboxylate to Phenanthrene-4-carboxylate. This is the fourth step in
pyrene
biodegradation[2].
pdoA2
Encodes Phenanthrene ring-hydroxylating oxygenase, α subunit.
Presumably
catalyzes as complex with pdoB2, phtAc and phtAd oxidation of Phenanthrene-4-carboxylate
to
cis-phenanthrene-3,4-dihydrodiol-4-carboxylate [2].
pdoB2
Encodes Phenanthrene ring-hydroxylating oxygenase, β subunit.
Presumably
catalyzes as complex with pdoA2, phtAc and phtAd oxidation of Phenanthrene-4-carboxylate
to
cis-phenanthrene-3,4-dihydrodiol-4-carboxylate [2].
Regulatory elements
Backbones
Name
Resistance marker
Length
Description
pUPD
Ampicillin
3640bp
For domestication of ordered gBlocks [3].
pDGB2_alpha1
Kanamycin
6943bp
For GoldenBraid Assembly [3].
pDGB3_alpha2
Kanamycin
6967bp
For GoldenBraid Assembly [3].
pDGB1_alpha2_SF
Kanamycin
2768bp
For GoldenBraid Assembly [3].
pDGB3_omega1
Spectinomycin
7295bp
For GoldenBraid Assembly [3].
pDGB3_omega2
Spectinomycin
7295bp
For GoldenBraid Assembly [3].
pSEVA231
Kanamycin
3123bp
Used as shuttle vector for E. Coli and Pseudomonads [4].
pQE
Ampicillin
5317bp
Used to produce proteins in E. Coli BL21.
References
[1] O. Kweon, S.-J. Kim, J. P. Freeman, J. Song, S. Baek, and C. E. Cerniglia, "Substrate specificity and
structural characteristics of the novel Rieske nonheme iron aromatic ring-hydroxylating oxygenases nidAB and
nidA3B3 from Mycobacterium vanbaalenii PYR-1," mBio, vol. 1, no. 2, 2010, doi: 10.1128/mBio.00135-10.
[2] S.-J. Kim, O. Kweon, R. C. Jones, J. P. Freeman, R. D. Edmondson, and C. E. Cerniglia, "Complete and integrated pyrene degradation pathway in Mycobacterium vanbaalenii PYR-1 based on systems biology," Journal of bacteriology, vol. 189, no. 2, pp. 464–472, 2007, doi: 10.1128/jb.01310-06.
[3] M. Vazquez-Vilar et al., "GB3.0: a platform for plant bio-design that connects functional DNA elements with associated biological data," Nucleic acids research, vol. 45, no. 4, pp. 2196–2209, 2017, doi: 10.1093/nar/gkw1326.
[4] R. Silva-Rocha et al., "The Standard European Vector Architecture (SEVA): a coherent platform for the analysis and deployment of complex prokaryotic phenotypes," Nucleic acids research, vol. 41, Database issue, D666-75, 2013, doi: 10.1093/nar/gks1119.
[2] S.-J. Kim, O. Kweon, R. C. Jones, J. P. Freeman, R. D. Edmondson, and C. E. Cerniglia, "Complete and integrated pyrene degradation pathway in Mycobacterium vanbaalenii PYR-1 based on systems biology," Journal of bacteriology, vol. 189, no. 2, pp. 464–472, 2007, doi: 10.1128/jb.01310-06.
[3] M. Vazquez-Vilar et al., "GB3.0: a platform for plant bio-design that connects functional DNA elements with associated biological data," Nucleic acids research, vol. 45, no. 4, pp. 2196–2209, 2017, doi: 10.1093/nar/gkw1326.
[4] R. Silva-Rocha et al., "The Standard European Vector Architecture (SEVA): a coherent platform for the analysis and deployment of complex prokaryotic phenotypes," Nucleic acids research, vol. 41, Database issue, D666-75, 2013, doi: 10.1093/nar/gks1119.