Biomedical Aspect
Page 1 of 6
Review
Bacterial group III alcohol dehydrogenases–function,
evolution and biotechnological applications
Abstract
Introduction
Introduction
Living organisms have developed
strategies to cope with alcoholic
substrates. Due to the manifold
appearance of alcoholic compounds,
enzymes that are capable of decomposing or processing such molecules
have emerged several times during
evolution. These proteins are the
so-called alcohol dehydrogenases,
a group of ubiquitous enzymes that
catalyse the interconversion between
alcohols and aldehydes or ketones. In
addition to several other co-factors
that are used by alcohol dehydrogenases, three non-homologous protein
families exclusively use NAD(P)/
NAD(P)H. Two of the three protein
families have been predominantly
and extensively studied in animals;
this short review focuses on bacterial group III alcohol dehydrogenases
and sheds some light on their functionality, distribution and potential
biotechnological applications.
Conclusion
In contrast to other NAD(P)-dependent ADHs, there is only little information on group III ADHs, however,
recent investigations have shown
some promise for some of these
enzymes. The continuous evaluation of such biocatalysts will aid in
the development of environment
friendly approaches for the production of fine chemicals, which could
provide an alternative to traditional
petrochemical routes.
Alcohol dehydrogenases (ADHs;
EC 1.1.1.1 and EC 1.1.1.2), an omnipresent group of enzymes, catalyse
the interconversion between alcoholic compounds and their corresponding aldehydes or ketones,
an activity essential for different
processes in living organisms. These
enzymes are abundant in animals,
plants, fungi, algae, bacteria and
the Archaea domain. They are
present in diverse tissues, such as
the liver, kidney, gastric mucosa and
mammary glands, as well as in microorganisms thriving in extreme environments, such as solfataric fields or
hot vents1-3. To catalyse the reduction of aldehydes or oxidation of alcohols, ADHs are in need of a co-factor
which is used as an electron acceptor.
Based on the utilisation of a specific
co-factor, it is possible to group
these proteins into three different
categories: (1) nicotinamide adenine
dinucleotide- (NAD-) or nicotinamide adenine dinucleotide phosphate- (NADP-) dependent ADHs,
(2) pyrroloquinolinequinone-, haemgroup and F420-dependent enzymes
and (3) flavin adenine dinucleotidedependent isozymes4.
So far, there are three distantly
related types of ADHs, which can
be grouped as NAD(P)-dependent
ADHs. The zinc-containing, long/
medium chain ADHs (group I) are
the most studied and can be distinguished from the superfamilies of the
metal-free, short chain ADHs (group
II) and the metal-containing ADHs
(group III). Several organisms such
as mosquitoes and flies have been
described to contain ADHs of all the
three different types. In contrast, the
human genome comprises of at least
seven genes encoding group I ADHs,
* Corresponding author
skander.elleuche@tuhh.de
Institute of Technical Microbiology, Hamburg
University of Technology (TUHH), Kasernenstr. 12, D-21073 Hamburg, Germany
and a single open reading frame
which codes for an ADH belonging
to group III1,5. Furthermore, the
mammalian enzyme horse liver
alcohol dehydrogenase is a prototype of the first group, while a group
II isozyme was first studied from the
fruit fly Drosophila melanogaster4,6.
The third group of ADHs was first
discovered in micro-organisms,
and the first isozyme that has been
studied in detail is a microbial ADH
from the ethanol producing bacterium Zymomonas mobilis7. In this
review, we have briefly focused on
the function, evolution and possible
applications of the highly diverse
group III of ADHs.
Discussion
The authors have referenced some of
their own studies in this review. The
protocols of these studies have been
approved by the relevant ethics
committees related to the institutions in which these studies were
performed.
Function of group III ADHs
ADHs fulfil multiple physiological
roles and display a wide variety
of substrate specificities by exhibiting great substrate promiscuity4,8.
However, not every isozyme is
capable of oxidising short chain alcoholic compounds, such as ethanol.
This can also be illustrated by the
transcriptional expression profile of
ADH encoding genes. While the
expression of group II ADH genes is
usually induced by ethanol exposure,
this is not true for other NAD(P)dependent ADHs. They often show
low affinity and catalytic efficiency
towards ethanol as a substrate, indicating again that these enzymes
mainly resume versatile roles in the
cell without participating in ethanol
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F
: Elleuche S, Antranikian G. Bacterial group III alcohol dehydrogenases – function, evolution and
biotechnological applications. OA Alcohol 2013 Mar 01;1(1):3.
CompeƟng interests: none declared. Conflict of Interests: none declared.
All authors contributed to the concepƟon, design, and preparaƟon of the manuscript, as well as read and approved the final manuscript.
All authors abide by the AssociaƟon for Medical Ethics (AME) ethical rules of disclosure.
S Elleuche*, G Antranikian
Page 2 of 6
Figure 1: Reaction mechanism of alcohol dehydrogenases. These enzymes catalyse the NAD(P)-dependent interconversion of aldehydes or ketones and enantiomerically pure alcoholic compounds. The complete structure of NAD+/NADH
is indicated by a red H-atom, while the additional phosphate-group of NADP+/
NADPH is indicated in green.
metabolism1. Nevertheless, there is a
reaction mechanism that is common
for all NAD(P)-dependent ADHs: the
reduction of an aldehyde or ketone
results in the production of an alcoholic compound and an oxidised
co-factor. The regeneration of
NAD(P) is often essential for other
coupled physiological reactions,
especially in microorganisms. In
agreement with this reaction, the
oxidation of an alcohol results in the
production of an aldehyde or ketone
and supplies reduced NAD(P)H
(Figure 1).
ADHs are capable of processing a
wide variety of substrates including
linear, branched, primary, secondary
and circular alcohols in addition to
their corresponding aldehydes and
ketones. Within the third group of
NAD(P)-dependent ADHs, some
members are described and characterised as lactaldehyde dehydrogenases, butanol dehydrogenases,
1,3-propanediol (1,3-PD) dehydro-
genases, while other isozymes exclusively catalyse the reduction of aldehydes without oxidising alcohols at
all9-12. Therefore, it has been speculated, that some group III ADHs are
mainly involved in aldehyde reduction in bacterial species rather than
alcohol turnover.
The prototype enzyme YqhD from
Escherichia coli, shows a rather
high affinity to aldehydes coupled
with low alcohol oxidation activity,
which is in good agreement with
group III ADHs from other microorganisms8,12,13. Due to the substrate
looseness of group III ADHs, detailed
characterisation of various candidate
genes is necessary to fully understand their function-evolution relationships. For this reason, it is often
hard to disentangle the physiological
functions of these enzymes. Isozymes
that have mainly been characterised
so far include those from the family
of Enterobacteriaceae, such as E. coli
and Klebsiella pneumoniae and from
the hemiascomycetous yeast Saccharomyces cerevisiae. Members from
extremophilic micro-organisms, such
as (hyper-) thermophilic archaeal
and bacterial species, have also been
investigated in detail2,3,9,14,15.
Distantly related members of
group III ADHs were encoded as pairs
in enterobacterial species and characterised in detail. The enzyme FucO
from E. coli is a lactaldehyde: propanediol oxidoreductase catalysing the
NADH-dependent reduction of lactaldehyde to produce 1,2-propanediol
(1,2-PD)10,14. The closely related
protein DhaT from K. pneumoniae
has been shown to be capable of
converting 3-hydroxypropionaldehyde into 1,3-PD, which is important
for NAD+-production under physiological conditions. Adh3.1 from
the plant pathogenic enterobacterium Dickeya zeae, showed highest
activity on short chain primary alcohols, but was unable to act on 1,2-PD
or 1,3-PD9,13. These members are
clustered together and named as
lactaldehydes: propanediol oxidoreductase-like enzymes or named on
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: Elleuche S, Antranikian G. Bacterial group III alcohol dehydrogenases – function, evolution and
biotechnological applications. OA Alcohol 2013 Mar 01;1(1):3.
CompeƟng interests: none declared. Conflict of interests: none declared.
All authors contributed to the concepƟon, design, and preparaƟon of the manuscript, as well as read and approved the final manuscript.
All authors abide by the AssociaƟon for Medical Ethics (AME) ethical rules of disclosure.
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Page 3 of 6
Table 1. Substrate and cofactor specificiƟes of group III ADHs.
DhaT-like
E. coli
FucO14
Co-factor
YqhD-like
K. pneuK. pneuD. zeae
E. coli
moniae
moniae
13
8,12
Adh3.1
YqhD
DhaT15
YqhD23
D. zeae
Adh3.213
NAD(H) NAD(H)
NAD(H)
NADPH
NADPH
NADPH
Ethanol
+
-
+
-
n.d.
-
Propanol
+
+
+
-
n.d.
-
Butanol
n.d.
-
-
-
n.d.
-
Methanol
-
-
-
-
n.d.
-
Glycerol
+
-
-
-
n.d.
-
1,2-PD
+
-
-
-
n.d.
-
1,3-PD
n.d.
+
-
-
n.d.
-
Acetaldehyde
+
n.d.
+
+
n.d.
-
Propanal
+
+
+
+
n.d.
-
Butanal
n.d.
n.d.
-
+
n.d.
+
3-HPA
n.d.
+
n.d.
+
+
n.d.
Glyoxal
n.d.
n.d.
-
+
n.d.
+
Methylglyoxal
n.d.
n.d.
+
+
n.d.
+
Glycoaldehyde
+
n.d.
+
+
n.d.
+
Alcohols
Aldehydes
NAD, nicotinamide adenine dinucleotide; NADP, nicotinamide adenine dinucleotide phosphate; n.d., not determined; 1,2-PD, 1,2-propanediol; 1,3-PD,
1,3-propanediol; 3-HPA, 3-hydroxypropionaldehyde.
the basis of the most studied prototype as DhaT-like enzymes. They can
be opposed to the YqhD-like enzymes
within the group III ADHs, which
are mostly annotated as butanol
dehydrogenases. Both groups show
functionally overlapping as well as
diverse properties (Table 1). Instead
of NADH, YqhD-like enzymes exclusively use NADPH as a co-factor
and prefer to catalyse the reduction of aldehydes to the oxidation of
alcohols. This enzyme is of industrial importance due to its ability to
produce 1,3-PD (see below). YqhD
from E. coli and Adh3.2 from D. zeae
are useful in detoxifying glyoxals13,16.
It is hypothesised that E. coli YqhD
might be involved in protecting the
cells from the toxic effects of lipidoxidation derived aldehydes. Addi-
tionally, the physiological role of
DhaT from K. pneumoniae is speculated to be the regeneration of NAD+,
which is needed as a co-factor in
the oxidative glycerol degradation
pathway12,17.
Evolution of group III ADHs
Enzyme evolution is mainly determined by functional convergence
and functional diversification18. The
fact that different non-homologous
ADHs are capable of catalysing the
interconversion of aldehydes and
alcohols, although they are structurally distinct, makes these groups
of enzymes an excellent candidate
for functional convergent evolution. However, the ability to act on
different substrates and/or to be
involved in different metabolic pathways of orthologous ADHs within a
specific group, may be the result of
gene duplications and/or functional
diversification.
Group III ADHs are not related
to other NAD(P)-dependent ADHs,
which means that they arose independently during the course of
evolution. The complex and long
evolutionary history of this group
of enzymes reflects its physiological
versatility. While only a single mitochondrial group III ADH has been
identified in animal genomes, there
have been several enzymes found
in prokaryotes, executing multiple
physiological roles and exhibiting
diverse substrate specificities1,13.
These enzyme variants might be the
result of ancient gene duplications
and functional diversification events.
Gene duplications followed by functional innovation have been shown
to appear very often in enzymes13,1921. As a result of functional diversification within the third group of
ADHs, these enzymes can be further
subdivided and show substantially
distinct substrate specificities and
functions10,11,13-15,22. Moreover, it
has been hypothesised that group III
ADHs were distributed throughout
the horizontal gene transfer between
the Archaea and Bacteria domains,
which might have involved functional
diversification and non-orthologous
gene displacement3.
The third group of ADHs contains
enzymes that exhibit a size of around
385 amino acid residues (Figure 2).
Pairs of the functionally characterised
DhaT-like and YqhD-like members of
the group III ADHs, show a low identity of approximately 20% over the
complete length of the proteins, but
show an overall structural similarity.
Pairs of these enzymes were found
and characterised in several bacterial species, such as K. pneumoniae,
E. coli or D. zeae9,10,13-15,23. However,
this was not the case in all of the
members of the Enterobacteriaceae
family. It was shown that another
species of the genus Klebsiella,
namely K. oxytoca, does not encode a
DhaT-like ADH, but a protein that is
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: Elleuche S, Antranikian G. Bacterial group III alcohol dehydrogenases – function, evolution and
biotechnological applications. OA Alcohol 2013 Mar 01;1(1):3.
CompeƟng interests: none declared. Conflict of Interests: none declared.
All authors contributed to the concepƟon, design, and preparaƟon of the manuscript, as well as read and approved the final manuscript.
All authors abide by the AssociaƟon for Medical Ethics (AME) ethical rules of disclosure.
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Page 4 of 6
Figure 2: Schematic illustration depicting the gene structure of group III ADHs including a multiple sequence alignment of the co-factor binding and metal-ion coordinating region. ClustalX was used with the following sequences: D.
zeae Adh3.1 (HF546061), Adh3.2 (HF546062); E. coli FucO (AAA23825.1), YqhD (NP_417484.1); K. pneumonia DhaT
(YP_005956552.1), KpYqhD (ABR78827.1); O. oeni Adh3 (HE974350) and Z. mobilis ZmAdh2 (BAF76066.1). A black line
indicates the co-factor binding region and asterisks highlight the conserved amino acid residues involved in metal-ion coordination. Protein lengths are indicated beside the alignment. Members of the DhaT-like proteins are boxed in light blue
and a light grey box illustrates members of the YqhD-like isozymes.
>80% identical to the YqhD enzyme
from E. coli. Interestingly, this
enzyme, YqhD-1, seems to compensate for the loss or the non-existence
of the DhaT-like ADH by exhibiting
low activity towards several alcoholic
compounds24. Although metal-ion
containing ADHs appear alike in their
tertiary structure, they differ in their
quaternary structure. Dimeric, tetrameric, octameric and decameric
states have been described in
this superfamily9-11,22,25,26. Moreover,
there is a difference in the presence
of the metal-ion in the conserved
catalytic region of the group III ADHs.
While iron or zinc were predominantly identified as catalytic ions,
the recently solved structure of Adh3
from the gram-positive bacterium
Oenococcus oeni, revealed the presence of a nickel ion in the dimeric
structure of this protein25. Another
striking difference was found within
the primary structure of the order
Lactobacillales (including O. oeni),
where the coordinating amino acid
residues are asparagine, two histidines and an atypical glutamine
which is replaced by a third histidine in well-characterised structures
from other members of the group
III ADHs (Figure 2). In addition, the
metal ions of DhaT-like members of
the group III ADHs were bound more
tightly in comparison to the YqhDlike isozymes9,24,25. Nevertheless,
the great diversity within this group
of enzymes complicates the functional annotation of newly identified
sequences that are neither expressed
nor characterised in detail.
Applications of group III ADHs
The history of the biotechnological
applications of ADHs commenced
more than 100 years ago when noble
prize laureate Eduard Buchner established the process of alcohol fermentation without the utilisation of yeast
cells27. Group III ADHs do not play
a role in the production of alcoholic
beverages, but are mainly of industrial importance as biocatalysts for
the synthesis of fine chemicals.
A well-known example for the
industrial utilisation of group III
ADHs in the production of chemical
compounds (e.g. 1,3-PD), is the application of DhaT and YqhD in recombinant E. coli. This small molecule
can be used as a monomer for the
production of a variety of products,
such as synthetic polymers, drugs,
fibres or cosmetics28. A lot of effort
has been made to generate multimutated, engineered, expression
strains to increase the titre of 1,3-PD
produced from glycerol. Moreover, it
has been shown that ADHs YqhD and
FucO are important for the production of 1,2-PD from glycerol in E. coli
with YqhD exhibiting the additional
advantage of reducing methylglyoxal to acetol; the latter compound
has the ability of being converted to
1,2-PD by another enzyme, namely
the D-aminopropanol dehydrogenase GldA8.
As mentioned above, the physiological role of YqhD might be to
act as an aldehyde scavenger, which
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: Elleuche S, Antranikian G. Bacterial group III alcohol dehydrogenases – function, evolution and
biotechnological applications. OA Alcohol 2013 Mar 01;1(1):3.
CompeƟng interests: none declared. Conflict of interests: none declared.
All authors contributed to the concepƟon, design, and preparaƟon of the manuscript, as well as read and approved the final manuscript.
All authors abide by the AssociaƟon for Medical Ethics (AME) ethical rules of disclosure.
Review
Page 5 of 6
prompted Lee and Park29 to develop
another interesting application of
YqhD. In a recent publication, these
authors came up with a suicidal
vector-cloning system which is based
on the toxic effects of butanal and
propanal in the host E. coli29. It has
been shown that E. coli is sensitive to
butanal and other aldehydes, when
yqhD-encoding genes are overexpressed in a recombinant form and
these aldehydes are reduced to give
alcoholic compounds13,16,29. In the
presented system, the lacZ-gene in
vector pUC19 is replaced by a yqhDvariant with a preceding multiple
cloning site (MCS). The expression
of yqhD leads to lethality when E.
coli transformants are incubated
on butanal- or propanal-containing
plates. The insertion of a foreign
DNA-fragment into the MCS interferes with the expression of yqhD,
which results in transformants that
survive on aldehyde-containing
growth plates29.
Conclusion
ADHs are a family of proteins with a
complex and interesting evolutionary
history. This has led to the generation of enzymes with broad substrate
promiscuity. These proteins can be
involved in either a variety of distinct
pathways or an exclusive catalysation
of well-balanced specific reactions,
often producing enantiomerically
pure products. In contrast to other
NAD(P)-dependent ADHs, there is
only little information on group III
ADHs so far. However, some recent
investigations have proven the promising applicability of some of these
enzymes. The continuous evaluation
of such biocatalysts will open new
avenues for environmentally friendly
production of fine chemicals, which
can effectively compete with traditional petrochemical routes. Moreover, there is a need for a diverse
portfolio of novel, efficient and characterised ADHs to cover the industrial demand of these highly versatile
enzymes.
Abbreviations list
ADH, alcohol dehydrogenase; MCS,
multiple cloning site; NAD, nicotinamide adenine dinucleotide; NADP,
nicotinamide adenine dinucleotide
phosphate; 1,2-PD, 1,2-propanediol;
1,3-PD, 1,3-propanediol.
Acknowledgement
The work in our laboratory was
funded by the Excellence Cluster
in the Excellence Initiative by the
State of Hamburg ‘Fundamentals
of Synthetic Biological Systems
(SynBio)’.
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F
: Elleuche S, Antranikian G. Bacterial group III alcohol dehydrogenases – function, evolution and
biotechnological applications. OA Alcohol 2013 Mar 01;1(1):3.
CompeƟng interests: none declared. Conflict of interests: none declared.
All authors contributed to the concepƟon, design, and preparaƟon of the manuscript, as well as read and approved the final manuscript.
All authors abide by the AssociaƟon for Medical Ethics (AME) ethical rules of disclosure.
Review