Part:BBa_K5043008

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 bacteria. 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]

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

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.