Team:TU Delft/Project/alkane-degradation/parts


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Alkane Degradation Parts


The Alkanivore E.coli strain has been designed to carry the genes required for the conversion of medium (C5-C13) and long chain (C15-C36) alkanes. A general scheme for the oxidation of the alkanes is illustrated in figure 1.

Figure 1 – Schematic description of the alkane degradation pathway with the corresponding genes.

To create the alkane degradation constructs a number of genes encoding for alkane degradation enzymes were synthesized and combined with promoters and ribosome binding sites obtained from the BioBrick distribution plates. Combination of these genes resulted in the following BioBrick constructs (the intermediates have also been submitted to the registry).

BBa_K398014 - Medium-chain (C5-13) alkane conversion

Our medium-chain hydrocarbon degrading strain contains the alkane hydroxylase (AH) native to Gordonia sp. TF6 [1]. This system facilitates the initial oxidation step of C5-C13 alkanes along with that of C5-C8 cycloalkanes towards their respective alcohols. Based on the literature on this topic [ref] it is expected that the in-house mechanism of E.coli will be able to further degrade the products of this pathway.

The AH gene cluster consists of the sequences encoding for:

  • alkane 1-monooxygenase (alkB2); an integral cytoplasmic membrane monooxygenase of which homologs have been reported for varying genus and species. This is the catalytic component of the AH system and as such oxidizes (cyclo)alkanes to their respective (cyclo)alkanols by transferring one oxygen atom from molecular oxygen to the alkane.
  • Rubredoxin reductase (rubR); catalyzes the reduction of the second oxygen atom released from molecular oxygen using electrons supplied by NADH.
  • Rubredoxin (rubA3); facilitates the transfer of electrons from NADH to rubredoxin reductase.
  • Rubredoxin (rubA4); an electron-carrier protein required by the AH system.

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BBa K398014 AlkB2 RubA3 RubA4 RubR.png

BBa_K398017 - Long-chain (C15-36) alkane conversion

For the first step in the long-chain alkane degradation pathway the apoprotein ladA was implemented [2]; an alkane monooxygenase from ‘’Geobacillus thermodenitrificans’’ NG80-2. This protein facilitates the conversion of long-chain alkanes (from C15 up to at least C36) to their corresponding primary alcohols in the presence of flavin mononucleotide, oxygen and NADH.

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TUDelft BBa K398017.png

BBa_K398018 - Long-chain alkanol conversion

The next step is catalyzed by a zinc-independent alcohol dehydrogenase from Bacillus thermoleovorans B23; a thermophilic bacterium [3-4]. The enzyme converts long-chain alkanols into their respective alkanals by oxidation of NADH.

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TUDelft BBa K398018.png

BBa_K398029 - Long-chain alkanal conversion

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  1. Fujii, T., Narikawa, T., Takeda, K., Kato, J., Biotransformation of various alkanes using the Escherichia coli expressing an alkane hydroxylase system from Gordonia sp. TF6. Bioscience, biotechnology, and biochemistry, 68(10) 2171-2177 (2004)
  2. Liu Li, Xueqian Liu, Wen Yang, Feng Xu, Wei Wang, Lu Feng, Mark Bartlam, Lei Wang and Zihe Rao. Crystal Structure of Long-Chain Alkane Monooxygenase (LadA) in Complex with Coenzyme FMN: Unveiling the Long-Chain Alkane Hydroxylase. Journal of molecular biology, 376: 453–465 (2008)
  3. Tomohisa Kato, Asuka Miyanaga, Mitsuru Haruki, Tadayuki Imanaka, Masaaki Morikawa & Shigenori Kanaya. Gene Cloning of an Alcohol Dehydrogenase from Thermophilic Alkane-Degrading Bacillus thermoleovorans B23. Journal of Bioscience and Bioengineering 91(1):100-102 (2001)
  4. Tomohisa Kato, Asuka Miyanaga, Shigenori Kanaya, Masaaki Morikawa. Gene cloning and characterization of an aldehyde dehydrogenase from long-chain alkane-degrading Geobacillus thermoleovorans B23. Extremophiles 14:33-39 (2010)