enzyme action have been well documented by
Daniel’s laboratory (Kim et al. 2015; Daniel
2014) and are reviewed below for specific
enzymes: Relative to holocellulase-active
enzymes, white rot fungi have a complete complement of CAZymes including the endo-acting
enzymes that also are possessed by brown rot
fungi. The white rot fungi also possess processive exo-acting cellulases, also known as cellobiohydrolases (CBH). The cellulase enzymes in
white rot fungi are primarily in the glycoside
hydrolase (GH) families which attack cellulose
hydrolytically, but also include the LPMO
enzymes (auxiliary activities (AA) enzyme family 9—formerly GH61) which oxidatively cleave
cellulose. White rot fungi have many more
enzymes that are active on crystalline cellulose,
in particular enzymes in the GH6 and GH7
(CBH enzyme) families. In addition, they have
many more cellulose-binding module (CBM1)
family enzymes. For most GH enzymes to be
optimally functional, inclusion of a CBM as part
of the enzyme is important. Seven known
families of hemicellulase enzymes and eleven
pectinase enzymes are encoded in the Basidiomycota, but as discussed in the section on
brown rot fungi, there are no notable differences between white rot and brown rot species
relative to the enzyme families for hemicellulases and pectinases in the two types of decay
fungi (Riley et al. 2014).
2. White Rot Lignin Degradation Mechanisms
Because of the unique nature of the lignindegrading enzymes in white rot fungi, this section provides greater detail on these systems.
Enzymes of importance include lignin peroxidases, versatile peroxidases, manganese peroxidases, dye-decolorizing peroxidases, and
laccase. Individual white rot fungal species
will possess one or more of these enzymes.
The degradation of lignin in the white rot
fungi is biochemically complex. Lignindegrading enzymes and the biochemical
mechanisms employed by these enzymes to
oxidize lignin with LMW compounds have
been well described in a number of reviews
(Tuor et al. 1995; Leonowicz et al. 1999). A
recent review of Trametes showed that the
genome encodes for nine putative lignin peroxidases, seven putative short manganese peroxidases, and two putative versatile peroxidases;
however only one manganese peroxidase and
one versatile peroxidase isozyme were consistently expressed under different growth conditions (Vasina et al. 2017). This suggests the
importance of these particular two isozymes
but also indicates that the fungus does not
rely on these enzymes alone, and it possesses
several “back-up strategies.” Some enzymes
have the capability of reacting directly with
lignin as a substrate, while others use mediators
or LMW compounds involved in electron transfer. Some enzymes are also metal-dependent,
requiring chelated or a free transition metal to
be in close proximity to the enzyme and substrate in ways not yet fully elucidated for all
enzymes. Non-enzymatic systems in white rot
fungi generally are unable to penetrate as
deeply into the wood cell wall compared to the
non-enzymatic extracellular metabolites associated with brown rot fungi. Instead, the LMW
compounds in these systems appear to be more
intimately associated with the enzymes and
may be mediator radicals, oxygen radicals,
electron-transfer agents, or chelate-radicals
that are generated by action of the enzymes
and/or transition metal cofactors. These LMW
compounds penetrate the wood cell wall in
advance of the enzymes (Daniel 2003; Arantes
et al. 2011). In some selective white rot fungal
degradation, altered cell wall structure associated with these LMW compounds has been
observed using transmission electron microscopy (Fig. 15.5). The altered lignocellulose
structure suggests that these LMW compounds
penetrate completely through wood cell walls
including the middle lamella regions in advance
of enzymes (Messner et al. 2003; Daniel 2003,
2014). It has been reported as far back as the
1960s that the middle lamellae is often attacked
early in some types of white rot degradation of
wood, suggesting that some LMW mediators or
long-lived radicals promoted by the white rot
fungal attack are capable of penetrating deep
into cell walls in early white rot attack to preferentially attack lignin-rich zones (Cowling
1961; Daniel 2014). However, despite these
15 Fungi Involved in the Biodeterioration and Bioconversion of Lignocellulose Substrates
381
Daniel’s laboratory (Kim et al. 2015; Daniel
2014) and are reviewed below for specific
enzymes: Relative to holocellulase-active
enzymes, white rot fungi have a complete complement of CAZymes including the endo-acting
enzymes that also are possessed by brown rot
fungi. The white rot fungi also possess processive exo-acting cellulases, also known as cellobiohydrolases (CBH). The cellulase enzymes in
white rot fungi are primarily in the glycoside
hydrolase (GH) families which attack cellulose
hydrolytically, but also include the LPMO
enzymes (auxiliary activities (AA) enzyme family 9—formerly GH61) which oxidatively cleave
cellulose. White rot fungi have many more
enzymes that are active on crystalline cellulose,
in particular enzymes in the GH6 and GH7
(CBH enzyme) families. In addition, they have
many more cellulose-binding module (CBM1)
family enzymes. For most GH enzymes to be
optimally functional, inclusion of a CBM as part
of the enzyme is important. Seven known
families of hemicellulase enzymes and eleven
pectinase enzymes are encoded in the Basidiomycota, but as discussed in the section on
brown rot fungi, there are no notable differences between white rot and brown rot species
relative to the enzyme families for hemicellulases and pectinases in the two types of decay
fungi (Riley et al. 2014).
2. White Rot Lignin Degradation Mechanisms
Because of the unique nature of the lignindegrading enzymes in white rot fungi, this section provides greater detail on these systems.
Enzymes of importance include lignin peroxidases, versatile peroxidases, manganese peroxidases, dye-decolorizing peroxidases, and
laccase. Individual white rot fungal species
will possess one or more of these enzymes.
The degradation of lignin in the white rot
fungi is biochemically complex. Lignindegrading enzymes and the biochemical
mechanisms employed by these enzymes to
oxidize lignin with LMW compounds have
been well described in a number of reviews
(Tuor et al. 1995; Leonowicz et al. 1999). A
recent review of Trametes showed that the
genome encodes for nine putative lignin peroxidases, seven putative short manganese peroxidases, and two putative versatile peroxidases;
however only one manganese peroxidase and
one versatile peroxidase isozyme were consistently expressed under different growth conditions (Vasina et al. 2017). This suggests the
importance of these particular two isozymes
but also indicates that the fungus does not
rely on these enzymes alone, and it possesses
several “back-up strategies.” Some enzymes
have the capability of reacting directly with
lignin as a substrate, while others use mediators
or LMW compounds involved in electron transfer. Some enzymes are also metal-dependent,
requiring chelated or a free transition metal to
be in close proximity to the enzyme and substrate in ways not yet fully elucidated for all
enzymes. Non-enzymatic systems in white rot
fungi generally are unable to penetrate as
deeply into the wood cell wall compared to the
non-enzymatic extracellular metabolites associated with brown rot fungi. Instead, the LMW
compounds in these systems appear to be more
intimately associated with the enzymes and
may be mediator radicals, oxygen radicals,
electron-transfer agents, or chelate-radicals
that are generated by action of the enzymes
and/or transition metal cofactors. These LMW
compounds penetrate the wood cell wall in
advance of the enzymes (Daniel 2003; Arantes
et al. 2011). In some selective white rot fungal
degradation, altered cell wall structure associated with these LMW compounds has been
observed using transmission electron microscopy (Fig. 15.5). The altered lignocellulose
structure suggests that these LMW compounds
penetrate completely through wood cell walls
including the middle lamella regions in advance
of enzymes (Messner et al. 2003; Daniel 2003,
2014). It has been reported as far back as the
1960s that the middle lamellae is often attacked
early in some types of white rot degradation of
wood, suggesting that some LMW mediators or
long-lived radicals promoted by the white rot
fungal attack are capable of penetrating deep
into cell walls in early white rot attack to preferentially attack lignin-rich zones (Cowling
1961; Daniel 2014). However, despite these
15 Fungi Involved in the Biodeterioration and Bioconversion of Lignocellulose Substrates
381