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

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Alkane Degradation Characterization

Introduction

In summary, the following strains were characterized:

E.coli K12 carrying BBa_K398014 in pSB1A2 (AH system)
E.coli K12 carrying BBa_K398017 in pSB1A2 (LadA)
E.coli TOP10 carrying BBa_K398027 in pSB1A2 (LadA)
E.coli K12 carrying BBa_K398018 in pSB1A2 (ADH)
E.coli K12 carrying BBa_K398029 in pSB1A2 (ALDH)

The characterization will generally be executed along with an 'empty' plasmid carrying strain:

E.coli K12 carrying BBa_J13002 in pSB1A2 ('empty' plasmid)

Characterization of the alkane hydroxylase system

Growth analysis

Of course, one of the first characterization experiments was to test growth of the E.coli strains carrying BBa_K398014 on alkanes. The alkanes octane and dodecane were tested as possible substrates in M9 minimal medium. The protocol can be found found [here]. The idea behind this is that E.coli might inherently contain an ADH and ALDH that, while it might be at an extremely low activity, can be able to degrade larger chain alkanes thus releasing energy for growth.

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 click [here], for the extraction method [here] and for the gas chromatography program [here].

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 ====Enzyme activity assay based on NADH absorbance====
-===Characterization of enzyme functionality===
-Parallel to this, resting-cell assays will be performed on growth-inhibited ''E.coli'' K12 strains containing the constructs described earlier. These assays will indicate the presence or absence of the desired enzymes, regardless of the alkane’s utilization for growth. The hydrocarbon compositions will be determined by gas chromatography analysis. For the intracellular enzymes, the cells were lysed and treated with the appropriate akanols and alkanals.
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