As talked about in my previous post, bacterial degradation
of alkanes is an important step in the bioremediation of crude oil from the
environment. The key enzymes involved in the aerobic degradation of alkanes are
the alkane hydroxylases (AHs), which hydroxylate alkanes to alcohols. The most
commonly found AHs are the integral-membrane monooxygenases (AlkB) with a
substrate generally ranging from the n-alkanes C10 to C16.
However, when fused with the rubredoxin protein, AlkB enzymes have been shown
to hydrolyse n-alkanes up to C32.
Another group of enzymes, which hydrolyse short and medium chain length
alkanes, included in the AHs are the P450 CYP153. These enzymes are usually
found in alkane degrading bacteria lacking alkB although they have also been
found to coexist in some bacteria. Recent discoveries have found AH genes in
new bacterial strains. This suggests the presence of further unknown alkane
degrading bacteria and unknown AHs, which could be important to the degradation
of n-alkanes in the natural
environment and may have potential for industrial applications such as the
bioremediation of crude oil. In order to investigate alkane degrading bacteria
on a large scale, Nie et. al (2014) used microbial genome and metagonome data
deposited in GenBank and the Integrated Microbial Genomes system.
2,069 complete and 1,910 draft microbial genomes
representing 784 different genera (72 of which were Archaea) were used in this
investigation. These were used to create a microbial proteomic database
containing 15,399,030 protein sequences. In order to search for alkane
hydroxylases in these genomes 28 alkB and 18 CYP153 characterised enzymes were
used as references. Along with the ‘best
hits’ the authors also signified a hit in the protein sequence when there was a
>40% similarity to CYP153 family members. Although P450 CYP153 enzymes may
differ in their genome sequence to this extent, this seems to be a large value
to use. This may vastly increase the likelihood of false positives, with
protein sequences unable to degrade alkanes being categorised as alkane
hydroxylase enzymes. Potential enzymes would therefore need to be tested for
their ability to degrade alkanes to confirm results of this investigation. A
similar process was also conducted to search for alkane hydroxylases in
different metagenomes.
No archael genomes contained either alkB or CYP153 genes.
Although the number of archaea genera used in this investigation were
significantly lower than the amount of bacterial genera used, the lack of
protein sequences matching these enzymes may suggest the degradation of alkanes
by archaea uses a very different set of genes and enzymes. The authors did find
80 and 30 bacterial genera to contain alkB and CYP153 genes respectively. Some
of these bacteria had previously not had proven alkane hydroxylation functions.
Furthermore, their results suggested these are core genes in many genera and a
vast amount were also novel genes. Similarly to archaea many Bacillus and Geobacillus genomes did not contain alkB or CYP153 genes although
they have been shown to utilise long chain carbon sources and are found in many
oil-related environments. This again suggests that alkB and CYP153 are not the
key genes for alkane hydroxylation in these species.
Being able to understand the distribution of alkane
hydroxylases in the environment is important to understand how crude oil will
break down in different ecosystems. This could help planning the remediation of
future oil spills such as by tailoring fertilisers to increase natural bioremediation
or the addition of other bacteria to help clean up crude oil fractions which
may be less utilised. The lack of alkane hydroxylases in some major groups
indicates that some important genes involved in alkane degradation still remain
elusive. More research will be able to shed more light on these processes.
Bacteria and novel genes identified to hydrolyse alkanes in this study will
also have to be tested in order to verify these findings.
Nie, Y., Chi, C. Q., Fang, H., Liang, J. L., Lu, S. L., Lai, G. L., ... & Wu, X. L. (2014). Diverse alkane hydroxylase genes in microorganisms and environments. Scientific reports, 4.
Hi Ben, very interesting post. It would be very interesting to see what genes are responsible for alkane degradation in archeal communities and how they compare to the alkB and CYP153 genes.
ReplyDeleteHi Maria, apart from saying they didn't contain these genes, the authors didn't discuss at all about archaeel alkane degradation. From what I've seen they may be more involved in anaerobic degradation which would obviously use different enzymes. It would be interesting to see how closely related alkane degradation enzymes are in archaea and bacteria though.
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