Biology Reference
In-Depth Information
It has been postulated that a small glycopeptide secreted by fungi reduces
O
2
and Fe
3
þ
to H
2
O
2
and Fe
2
þ
(
Goodell, 2003; Hammel et al., 2002; Tanaka
et al., 1991; Wang and Gao, 2003
). CDH is involved in the formation of
Fenton's reagent, such as Fe
3
þ
reductants (
Mason et al., 2003
). Other
ligninolytic enzymes (LiP, laccase) may act as an indirect source of hydroxyl
radicals through the generation of Fe
3
þ
and O
2
reductants by formate (CO
2
.
)
and semiquinone radical formation (
Barr et al., 1992
). The principle of the
quinone redox cycling mechanism is the reduction of quinones to the
corresponding hydroquinones; this reduction can be carried out by ligninolytic
enzymes (
Gomez-Toribio et al., 2009
).
A non-enzymatic degradation mechanism in wood decay by the brown-rot
fungus S. lacrymans has been elucidated (
Eastwood et al., 2011
). This process
seems driven by an iron reductase (from a gene originally derived from a
cellobiose dehydrogenase gene) in association with a CBM. In addition,
some phenolates synthesized by the fungi, such as variegatic acid, are able
to reduce Fe
3
þ
to Fe
2
þ
, and oxidoreductases such as Gloxs and copper
radical oxidases produce the hydrogen peroxide required by the reaction.
III. PREDICTING LIGNOCELLULOLYTIC ENZYMES
USING PHYLOGENETIC INFERENCE STRATEGY
The construction and exploitation of phylogenetic trees and the elucidation of
evolutionary events are long and complex tasks, and a great deal of efforts has
been recently devoted to addressing many of the major bottlenecks. As first
proposed by
Eisen (1998)
, the general phylogenomic strategy is based on the
simple assumption that gene functions change as a result of evolution, and
reconstructing evolutionary history enables us to predict the function of new
gene products (
Eisen, 1998
). This strategy can be divided into the following
steps: (i) homology and multiple sequence alignment, (ii) construction of phy-
logenetic tree, (iii) evolutionary event detections and (iv) functional inference.
An introduction to the main tools and approaches of these steps is given in the
following sections. For more details, the strategies for reliable exploitation
of evolutionary concepts in high-throughput biology and its applications can
be found elsewhere (
Levasseur and Pontarotti, 2008; Levasseur et al., 2008a
).
A. HOMOLOGY AND MULTIPLE SEQUENCE ALIGNMENT
The presumption of homology is a prerequisite for evolutionary analysis.
The first step in any phylogenetic analysis consists in identifying sequences
closely or distantly related to the genes or sequences of interest. This delicate
