EVOLUTION OF HALOALKANE DEHALOGENASE PROTEIN
FAMILY
E.Chovancová1$, J. Kosinski2,
J. M. Bujnicki2 and J. Damborský1
1Loschmidt
Laboratories, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno,
CZ
2Laboratory of Bioinformatics and Protein Engineering,
International Institute of Molecular and Cell Biology, ul. Ks. Trojdena 4,
02-109 Warsaw, PL
$E-mail: akllupe@chemi.muni.cz
Enzymes from the haloalkane dehalogenase
protein family (EC 3.8.1.5) play an important role in bioremediation processes
for their capability to hydrolyze haloorganic compounds. Currently, this family
includes 14 experimentally characterized enzymes with proven dehalogenation
activity. In addition to them, many putative members of this family can be
found in sequence databases. In this study, we have used phylogenetic approach
to assess the origin and evolution of haloalkane dehalogenases. Knowledge of
the evolutionary history of haloalkane dehalogenases and related protein
families should provide basis to understand the evolution of enzymatic
activities and structure‑function relationships.
Over 3000 protein sequences, including
haloalkane dehalogenases and their homologs, were identified through PSI-BLAST
database searches [1]. Obtained sequences were clustered using the program
CLANS [2]. Sequences from the cluster of haloalkane dehalogenases were aligned
and used for phylogenetic reconstructions by
maximum‑likelihood [3] and neighbor‑joining [4] methods. Various evolutionary
models with different parameters were tested. For rooting of resulting trees,
three alternative outgroups were used. Phylogenetic
trees from all analyses were compared in terms of
tree topology and placement of the root. Statistical techniques including four‑cluster
likelihood mapping [5]
were further used to test phylogenetic hypotheses.
Phylogenetic
analysis of haloalkane dehalogenases indicated that the members of this family
comprise three subfamilies designated HAD‑I, HAD‑II and HAD‑III.
Most of biochemically characterized haloalkane dehalogenases (9 of 14) belong
to the subfamily HAD‑II. Calculations performed under various conditions
did not show significant differences in the results. Sister‑group
relationship was suggested for subfamilies HAD‑I and HAD‑III, while
HAD‑II subfamily appeared to be more distantly related. Preferential
grouping of HAD‑I and HAD‑III subfamilies was indicated also by
four‑cluster likelihood mapping. Based on the results, hypothesis about
evolutionary history of haloalkane dehalogenases was proposed. Results of the
analysis enabled identification of new family members and subsequent
phylogenetic classification of the whole family. Furthermore, evolutionary
studies of haloalkane dehalogenases will be useful for determination of
conserved regions. Altogether, results will lead to improved theoretical
predictions of functional, biochemical and structural properties of novel
proteins. Putative haloalkane dehalogenases with potentially interesting
properties will be cloned and biochemically characterized. This may lead to acquisition
of proteins with novel characteristics suitable for practical applications.
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This work was
supported by The European Commission 5th Framework Programme project ”Center of
Excellence in Molecular Bio-Medicine Contract no: QLK6-CT-2002-90363” and grant
from the Czech Ministry of Education no. MSM0021622412-3.