Membrane-bound enzymes produced by the bacteria Pseudomonas putida produce energy from trapped hydrocarbon-based substrates by producing oxygen free radicals that break down the substrates.

Hydrocarbon-based substances like gasoline and parrafin wax do not spontaneously combust with air under normal circumstances. An intense, focused energy input (e.g., a spark) is required to overcome the activation energy for the overall energy-releasing reaction. In some organisms, the oxygen-mediated break down of hydrocarbons and the accompanying release of energy is not activated by intense, focused heat; instead it is activated by enzymes and oxygen free-radicals.

The bacterium Pseudomonas putida oxidizes various alkanes primarily with a membrane-bound enzyme called AlkB that forms a hydrophobic pocket attractive to hydrocarbon-based substrates. The enzyme converts oxygen to free radicals to break down the trapped substrates. This process is capable of providing net energy input for the bacteria. Potential substrates include propane, n-butane, and other alkanes with carbon lengths between 5 and 13. That includes many hydrocarbon components of crude oil.


"As alkanes are apolar molecules that are chemically very inert, their metabolism by microorganisms poses challenges related to their low water solubility, their tendency to accumulate in cell membranes, and the energy needed to activate the molecule." (Rojo 2009:2477)

"Aerobic alkane degraders use O2 as a reactant for the activation of the alkane molecule. The alkane-activating enzymes, which are monooxygenases, overcome the low chemical reactivity of the hydrocabon by generating reactive oxygen species." (Rojo 2009:2478)

"In the case of n-alkanes containing two or more carbon atoms, aerobic degradation usually starts by the oxidation of a terminal methyl group to render a primary alcohol, which is further oxidized to the corresponding aldehyde, and finally converted into a fatty acid. Fatty acids are conjugated to CoA and further processed by b-oxidation to generate acetyl-CoA." (Rojo 2009:2478-9)

"The best-characterized alkane-degradation pathway is that encoded by the OCT plasmid of P. [Pseudomonas] putida GPo1...The first enzyme of this pathway is an integral-membrane non-haem diiron monooxygenase, named AlkB, that hydroxylates alkanes at the terminal position. AlkB requires two soluble electron transfer proteins named rubredoxin (AlkG) and rubredoxin reductase (AlkT). Rubredoxin reductase, via its cofactor FAD, transfers electrons from NADH to the rubredoxin, which in turn transfers the electrons to AlkB." (Rojo 2009:2479-80)

"[AlkB has] six transmembrane segments and a catalytic site that faces the cytoplasm. The active site includes four His-containing sequence motives...which chelate two iron atoms...The diiron cluster allows the O2-dependent activation of the alkane through a substrate radical intermediate...One of the O2 atoms is transferred to the terminal methyl group of the alkane, rendering an alcohol, while the other one is reduced to H2O by electrons transferred by the rubredoxin...The P. putida GPo1 AlkB alkane hydroxylase can oxidize propane, n-butane, as well as C5 to C13 alkanes...All these alkanes can also support growth. Methane, ethane, or alkanes longer than C13, are not oxidized...AlkB has been proposed to contain a deep hydrophobic pocket formed by the six transmembrane helices; the alkane molecule should slide into this pocket until the terminal methyl group is correctly positioned relative to the His residues that chelate the iron atoms. Amino acids with bulky side-chains protruding into the hydrophobic pocket can impose a limit to the size of the alkane molecule that can slide into the pocket and still allow a proper alignment of the terminal methyl group with the catalytic His residues. Substitution of these amino acids by residues with less bulky side-chains allows larger alkanes to fit in place into the hydrophobic pocket." (Rojo 2009:2480)

Journal article
Degradation of alkanes by bacteriaEnvironmental MicrobiologyAugust 5, 2009
Fernando Rojo

Degradation of alkanes by bacteria

Pseudomonas putidaSpecies