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Revision as of 08:53, 13 September 2024


Pyrene degradation operon

Encodes an operon with in total nine protein coding sequences. These encode enzymes, forming a complete metabolic pathway which degrades pyrene to 3,4-dihydroxy-phenanthrene, a phenanthrene degradation intermediate. [1, 2] In this way this part shall enable bacteria, already able to degrade phenanthrene (like Pseudomonas vancouverensis DSM8368 [3, 4]), to degrade pyrene, too.


Usage and Biology

Genes were chosen based on Mycobacterium vanbaalenii Pyr-1’s pyrene degradation pathway and mainly derived from this bacterium. As shown in fig. 1 pyrene gets subsequently degraded to 3,4-dihydroxy-phenanthrene by the different enzymes/enzyme complexes in the operon. [2] The resulting 3,4-dihydroxy-phenanthrene shall be channelled into phenanthrene degradation pathway. [1]

Resizable Image


Figure 1. Schematic design of this part, generated by SnapGene.


Sequence and Features


Assembly Compatibility:
  • 10
    INCOMPATIBLE WITH RFC[10]
    Illegal EcoRI site found at 3199
    Illegal EcoRI site found at 7727
    Illegal PstI site found at 719
    Illegal PstI site found at 4703
    Illegal PstI site found at 5754
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal EcoRI site found at 3199
    Illegal EcoRI site found at 7727
    Illegal NheI site found at 7
    Illegal NheI site found at 30
    Illegal PstI site found at 719
    Illegal PstI site found at 4703
    Illegal PstI site found at 5754
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal EcoRI site found at 3199
    Illegal EcoRI site found at 7727
    Illegal BglII site found at 390
    Illegal BglII site found at 4695
    Illegal BamHI site found at 1259
    Illegal BamHI site found at 3644
    Illegal XhoI site found at 54
    Illegal XhoI site found at 931
    Illegal XhoI site found at 1880
    Illegal XhoI site found at 2362
    Illegal XhoI site found at 3909
    Illegal XhoI site found at 8073
  • 23
    INCOMPATIBLE WITH RFC[23]
    Illegal EcoRI site found at 3199
    Illegal EcoRI site found at 7727
    Illegal PstI site found at 719
    Illegal PstI site found at 4703
    Illegal PstI site found at 5754
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal EcoRI site found at 3199
    Illegal EcoRI site found at 7727
    Illegal PstI site found at 719
    Illegal PstI site found at 4703
    Illegal PstI site found at 5754
    Illegal NgoMIV site found at 749
    Illegal NgoMIV site found at 854
    Illegal NgoMIV site found at 1957
    Illegal NgoMIV site found at 2637
    Illegal NgoMIV site found at 4039
    Illegal NgoMIV site found at 4342
    Illegal NgoMIV site found at 8108
    Illegal AgeI site found at 1350
    Illegal AgeI site found at 1408
  • 1000
    COMPATIBLE WITH RFC[1000]

References

[1] W. C. EVANS, H. N. FERNLEY, and E. GRIFFITHS, "OXIDATIVE METABOLISM OF PHENANTHRENE AND ANTHRACENE BY SOIL PSEUDOMONADS. THE RING-FISSION MECHANISM," The Biochemical journal, vol. 95, no. 3, pp. 819–831, 1965, doi: 10.1042/bj0950819.
[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] W. W. Mohn, A. E. Wilson, P. Bicho, and E. R. Moore, "Physiological and phylogenetic diversity of bacteria growing on resin acids," Systematic and applied microbiology, vol. 22, no. 1, pp. 68–78, 1999, doi: 10.1016/S0723-2020(99)80029-0.
[4] Y. Yang, R. F. Chen, and M. P. Shiaris, "Metabolism of naphthalene, fluorene, and phenanthrene: preliminary characterization of a cloned gene cluster from Pseudomonas putida NCIB 9816," Journal of bacteriology, vol. 176, no. 8, pp. 2158–2164, 1994, doi: 10.1128/jb.176.8.2158-2164.1994.
[5] 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.