Designed by: Kira Schipper and Mathias Voges   Group: iGEM10_TU_Delft   (2010-10-07)

Alkane Hydroxylase System

Figure 1:Complete Alkane degradation pathway, AlkB is one of the 1st steps herein

BBa_398014 showed an increased enzymatic activity compared the negative control. The activity of the negative control was 1.23x10-3 U/mg dry weight whereas the activity of BBa_398014 was 4.49x10-2 U/mg dry weight.


The alkane hydroxylase system from Gordonia sp. TF6 facilitates the initial step of the degradation of C5-C13 alkanes as well as that of C5-C8 cycloalkanes towards their respective alcohols. Based on the literature on this topic it is expected that the in-house mechanism of E.coli will be able to further degrade the products of this pathway.

The AH construct 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 (rubB); 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.

The AH construct was designed to harbor all four of the required coding sequences -each behind its own RBS region- sharing a constitutive promoter.


Resting-cell assays

As explained earlier the catalytic component of the alkane hydroxylase system is an integral membrane protein. Characterization must thus be done using an intact-membrane setup. An option which has been explored in literature [1] is the resting-cell assay a.k.a. biotransformation assay. These assays will indicate the presence or absence of the desired enzymes, regardless of the alkane’s utilization for growth. The logic behind this is to stall the growth of a large volume of cells by using nitrogen-deficient medium to test their alkane conversion capabilities at near-zero growth. Extraction hydrocarbons from the medium using an apolar solvent (such as ethyl acetate) after the reaction and subsequent analysis by gas chromatography would indicate the presence of the corresponding alkanol and/or the decrease of alkane. For more on the experimental setup see the following pages:

  • [ Resting-cell assays]
  • [ EtOAc extraction]
  • [ Gas chromatography program]


From the ratios hexadecane/undecane obtained from GC chromatograms we may conclude that the samples obtained from the E.coli strain, carrying the AH system, contain relatively less octane than the control strain. By comparing peak ratios we were able to estimate the specific enzymatic activity of the system, which was found to be 0.045 U/mg dry weight as can be found in figure 2.

For more information about our findings, read the [ detailed alkane hydroxylase results] page.

Figure 2: Enzyme activity [U/mg dry weight] of alkane hydroxylase system as compared to the negative control E.coli K12 strain


  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)

Sequence and Features

Assembly Compatibility:
  • 10
  • 12
    Illegal NheI site found at 7
    Illegal NheI site found at 30
  • 21
  • 23
  • 25
  • 1000