Biology Reference
In-Depth Information
Cryptococcus neoformans involved in the biosynthesis of melanin as a viru-
lence factor. Additionally, in the Ascomycota group, laccase-like multi-
copper oxidases can be functionally assigned as lignin degraders in addition
to other functions, such as iron metabolism, pathogenic interactions, pig-
ment synthesis in conidiospores, induction of fruiting bodies and offensive/
defensive strategies during interactions of fungi (
Askwith et al., 1994;
Assavanig et al., 1992; H ¨ lker et al., 2002; K¨ es and Liu, 2000; Nosanchuk
and Casadevall, 2003; Score et al., 1997
). Thus, phylogenetic functional
inference approaches may facilitate future functional annotation in different
clades, for example, particularly in the Ascomycota group.
F. TOWARDS A DEDICATED DATABASE FOR LIGNINOLYTIC ENZYMES
Besides modern annotation procedures, one of the main conditions for
predicting the function of lignocellulolytic enzymes is the availability of
expert databases in which full information is provided. The current reference
database for carbohydrate-active enzymes is the integrated database CAZy
(
http://www.cazy.org
)
in which carbohydrate-active enzymes are classified
into several sequence- and structure-based family schemes (
Cantarel et al.,
2009; Coutinho and Henrissat, 1999; Henrissat, 1991
). CAZy describes
families of structurally related functional modules of enzymes that degrade,
modify, or create glycosidic bonds and their ancillary CBMs. Today, CAZy
enables us to describe and elucidate major aspects of the carbohydrate
metabolism not only in fungi but also in other organisms from different
kingdoms, with implications for both theoretical and applied knowledge.
In 2008, a dedicated database, FOLy, was designed exclusively for fungal
oxidative lignin enzymes (
Levasseur et al., 2008b
). Initially, ligninolytic
enzymes and related sequences were classified on their sequence/structure,
and ligninolytic families of FOLy were divided into the categories of lignin
oxidases (LOs) and lignin-degrading auxiliary (LDA) enzymes, according to
whether their action on lignin degradation was respectively direct or indirect.
The main objective of this database was to gain new insights obtained by
global analyses of interactions between the different enzymes potentially
involved in lignin degradation. In further development, phylogenomic stud-
ies will be pursued to refine the specific families into subfamilies using the
strategies and approaches developed above. To date a full original classifica-
tion of ligninolytic enzymes is in progress to extend the families covered and
to use finer methods and tools to address the future fungal comparative
genomics of lignolysis. A new database release of FOLy is also planned in
the next future (Levasseur, Personal communication).
