enzymes are secreted to depolymerize or
hydrolyze specific chemical linkages in substrates. Glycosyl hydrolase (GH) enzymes, for
example, are enzymes that hydrolyze glycosidic
bonds in either cellulose or hemicellulose.
There are many different types of GHs and
many families of this types of enzyme are now
known (Williams 2017). Other enzymes that
may be present in some fungal species will
target specific linkages in lignin or hemicellulose, such as fungal esterases, that have high
affinity for acetylated carbohydrates as found
in some hemicelluloses. Some fungal enzymes
are also specific for deconstruction of specific
types of pectin in the bordered pits or middle
lamella, while other enzymes in white rot fungi
have broad specificity in degrading aromatic
compounds.
White rot fungi primarily employ extracellular degradative enzymatic systems in the degradation of lignocellulose substrates, but in
some cases LMW mediators or metal radical
ions are known, or have been proposed, to
work in conjunction with white rot enzymes
to explain the types of degradation patterns
observed at the nanoscale. Brown rot fungi
decaying wood use a combination of a LMW
catalytic system, that can penetrate into the
wood cell wall in early stages of attack by the
fungus, together with a more limited suite of
cellulase enzymes. The pattern of attack by this
LMW catalytic system is consistent with attack
by hydroxyl radicals (
l OH), and the most prominent theory on the LMW degradation mechanism involves a mechanism for hydroxyl
radical attack (Goodell et al. 2017; Suzuki et al.
2006), which is known as the chelator-mediated
Fenton (CMF) system (Kent et al. 2018; Goodell
et al. 2017; Arantes and Milagres 2006; Nurika
et al. 2019). Brown rot fungi discarded their
machinery for production of most peroxidases
(lignin degrading enzymes) and also many of
their carbohydrate active enzymes (CAZymes)
and oxidoreductases as they evolved the LMW
non-enzymatic system to biocatalytically
deconstruct cellulose and lignin. Although as
noted previously, there is intergradation
between brown rot and white rot fungi (Riley
et al. 2014), this chapter will maintain traditional definitions of the two for convenience,
to allow the reader to understand the differences at either end of the spectra.
Basidiomycota fungi evolved approximately 295 million years ago to produce Class
II—peroxidase enzymes (PODs); enzymes
which allowed these particular progenitors of
current day white rot fungi to deconstruct lignin. Basidiomycota species prior to this possessed enzymes capable of depolymerizing and
metabolizing cellulose, and therefore they were
able to decompose grasses and sedges. However, as tracheophytes evolved as the first plants
to incorporate lignin into to their cell walls
about 375 million years ago, the fungal species
at that time were unable to deconstruct this new
lignified plant cellular material. Lignification
allowed plants to grow larger and taller.
Researchers have suggested that the gap of
approximately 90 million years between lignin
production in plants and the ability of fungi to
decay those plants is in-part responsible for the
buildup of vegetation which resulted in
current-day coal seams in many locations on
earth (Floudas et al. 2012; Eastwood 2014).
It is important to note the different roles of
enzymes and LMW catalytic systems in the
wood degradation process. Although extracellular enzymes are often casually discussed in
the scientific literature as being capable of
penetrating lignified plant cell walls, there is a
large body of literature that demonstrates that,
although enzymes can erode the surfaces of
plant cell walls at the molecular level, they are
too large to penetrate the intact structure of
secondary plant cell walls for more than a nanometer at best (Tepfer and Taylor 1981; Flournoy
et al. 1991). In plants such as corn and Arabidopsis, where secondary walls do not exist, and
in particular when delignification procedures
have been used (Ding et al. 2012), enzymatic
erosion and penetration of one to a few elementary microfibril layers have been observed.
However, in intact, heavily lignified, secondary
cell walls of wood, enzymes do not readily penetrate. This has been demonstrated in white rot
fungi and brown rot fungi, via the use of many
different probes of sizes simulating those of
enzymes (Stone and Scallan 1967; Tepfer and
Taylor 1981; Kleman-Leyer et al. 1992; Arantes
et al. 2012). In the soft rot Ascomycota, it has
15 Fungi Involved in the Biodeterioration and Bioconversion of Lignocellulose Substrates
373
hydrolyze specific chemical linkages in substrates. Glycosyl hydrolase (GH) enzymes, for
example, are enzymes that hydrolyze glycosidic
bonds in either cellulose or hemicellulose.
There are many different types of GHs and
many families of this types of enzyme are now
known (Williams 2017). Other enzymes that
may be present in some fungal species will
target specific linkages in lignin or hemicellulose, such as fungal esterases, that have high
affinity for acetylated carbohydrates as found
in some hemicelluloses. Some fungal enzymes
are also specific for deconstruction of specific
types of pectin in the bordered pits or middle
lamella, while other enzymes in white rot fungi
have broad specificity in degrading aromatic
compounds.
White rot fungi primarily employ extracellular degradative enzymatic systems in the degradation of lignocellulose substrates, but in
some cases LMW mediators or metal radical
ions are known, or have been proposed, to
work in conjunction with white rot enzymes
to explain the types of degradation patterns
observed at the nanoscale. Brown rot fungi
decaying wood use a combination of a LMW
catalytic system, that can penetrate into the
wood cell wall in early stages of attack by the
fungus, together with a more limited suite of
cellulase enzymes. The pattern of attack by this
LMW catalytic system is consistent with attack
by hydroxyl radicals (
l OH), and the most prominent theory on the LMW degradation mechanism involves a mechanism for hydroxyl
radical attack (Goodell et al. 2017; Suzuki et al.
2006), which is known as the chelator-mediated
Fenton (CMF) system (Kent et al. 2018; Goodell
et al. 2017; Arantes and Milagres 2006; Nurika
et al. 2019). Brown rot fungi discarded their
machinery for production of most peroxidases
(lignin degrading enzymes) and also many of
their carbohydrate active enzymes (CAZymes)
and oxidoreductases as they evolved the LMW
non-enzymatic system to biocatalytically
deconstruct cellulose and lignin. Although as
noted previously, there is intergradation
between brown rot and white rot fungi (Riley
et al. 2014), this chapter will maintain traditional definitions of the two for convenience,
to allow the reader to understand the differences at either end of the spectra.
Basidiomycota fungi evolved approximately 295 million years ago to produce Class
II—peroxidase enzymes (PODs); enzymes
which allowed these particular progenitors of
current day white rot fungi to deconstruct lignin. Basidiomycota species prior to this possessed enzymes capable of depolymerizing and
metabolizing cellulose, and therefore they were
able to decompose grasses and sedges. However, as tracheophytes evolved as the first plants
to incorporate lignin into to their cell walls
about 375 million years ago, the fungal species
at that time were unable to deconstruct this new
lignified plant cellular material. Lignification
allowed plants to grow larger and taller.
Researchers have suggested that the gap of
approximately 90 million years between lignin
production in plants and the ability of fungi to
decay those plants is in-part responsible for the
buildup of vegetation which resulted in
current-day coal seams in many locations on
earth (Floudas et al. 2012; Eastwood 2014).
It is important to note the different roles of
enzymes and LMW catalytic systems in the
wood degradation process. Although extracellular enzymes are often casually discussed in
the scientific literature as being capable of
penetrating lignified plant cell walls, there is a
large body of literature that demonstrates that,
although enzymes can erode the surfaces of
plant cell walls at the molecular level, they are
too large to penetrate the intact structure of
secondary plant cell walls for more than a nanometer at best (Tepfer and Taylor 1981; Flournoy
et al. 1991). In plants such as corn and Arabidopsis, where secondary walls do not exist, and
in particular when delignification procedures
have been used (Ding et al. 2012), enzymatic
erosion and penetration of one to a few elementary microfibril layers have been observed.
However, in intact, heavily lignified, secondary
cell walls of wood, enzymes do not readily penetrate. This has been demonstrated in white rot
fungi and brown rot fungi, via the use of many
different probes of sizes simulating those of
enzymes (Stone and Scallan 1967; Tepfer and
Taylor 1981; Kleman-Leyer et al. 1992; Arantes
et al. 2012). In the soft rot Ascomycota, it has
15 Fungi Involved in the Biodeterioration and Bioconversion of Lignocellulose Substrates
373