Biology Reference
In-Depth Information
sub-functionalization, or one of the duplicates evolves towards a new func-
tion (neo-functionalization;
Force et al., 1999; Levasseur and Pontarotti,
2011
). For functional inference, orthologs are considered to share a similar
function compared with paralogs (
Collette et al., 2003
). By contrast, paralogs
can be either biochemically sub-functionalized or neo-functionalized. If so,
they will have diverse biochemical functions, although in the case of neo-
functionalization one of the copies may retain the ancestral function. Paralogy
is therefore closely associated with functional diversification and/or specializa-
tion. Duplications can be deciphered by a phylogenetic study, and information
can be used for functional annotation. When phylogenetic trees are con-
structed, specific algorithms are applied to distinguish orthologs from paralogs
(
Dufayard et al., 2005; Zmasek and Eddy, 2002
). By superimposition of the
gene tree and the function tree, some nodes can be annotated for a specific
function and hold throughout the lineages (
Levasseur and Pontarotti, 2008
).
D. PHYLOGENY-BASED INFERENCE STRATEGIES
Genome annotation projects use a standard strategy to infer the function of
gene models by seeking best similarity (homologs) with known sequences and
by propagating the structural and functional annotation. However, the top
reciprocal best hits are not reliable and can lead to many errors. As phylo-
genomic analysis combines phylogenetic tree construction, integrates experi-
mental information and differentiates orthologs from paralogs, it could
greatly facilitate our ability to address these errors. The gene genealogy
and function genealogy can be superimposed on phylogenetic tree and
sequence shift information reported. After the construction of a reliable
phylogenetic tree, the tree topology is analysed to localize speciation or
gene duplication events at particular branch points. Finally, the phylogenetic
tree is overlaid with experimental data, and changes in structure or function
can be traced along the evolutionary tree. Based on evolutionary biology
concepts and resulting functional consequences on duplicates, the functional
inference will be more accurate and reliable. In previous work, a dedicated
software based on a Bayesian approach was developed by
Engelhardt et al.
(2005)
to identify the evolutionary gene history and infer gene function by
superimposing experimental information on the phylogenetic tree.
E. THE EXAMPLE OF LACCASES
As previously discussed, laccases are attractive and environmental-friendly
multi-copper oxidases that have shown potential for many biotechnological
applications. In 2010, all homologs of laccase proteins were selected from
