oxygenated system would be present in
most active fungal environments.
Research suggests that early upregulation
of a large group of LMW compounds and
enzymes that may generate LMW catalysis
occurs prior to upregulation of glycoside
hydrolase enzymes (Zhang et al. 2016). The
upregulation of these metabolites is timed so
that subsequent upregulation of CAZymes follows in a staggered manner (Zhang et al. 2016).
These findings are consistent with both glycopeptide and CMF working theories, and the
staggered upregulation hypothesis also does
not preclude mechanisms that allow spatial diffusion of LMW metabolites as has been
described for the CMF mechanism. Polyketide
synthases (PKS) have also been found to be
upregulated in the brown rot fungi (Riley et al.
2014), and this may be important due to the
role these synthases play in the production of
LMW metabolites ranging from siderophores
to fungal antibiotics. Some of these LMW metabolites derived from polyketide pathways are
structurally related to the LMW compounds
isolated from brown rot fungi that have been
proposed for redox chemistries involved in
non-enzymatic degradation schemes (Paszczynski et al. 1999; Kerem et al. 1999; Goodell
et al. 1997).
The generation of hydroxyl radicals is a
consistent feature that is recognized in the
LMW catalytic system in brown rots and that
is also proposed to occur in the glycopeptide
hypothesis in these fungi. The hydroxyl radical
is the most potent oxidant known in biological
systems, and it is therefore important that it be
generated in a location where it cannot damage
fungal hyphae. Relative to the CMF mechanism,
hydroquinones, catecholates, and similar
redox-cycling compounds are greatly affected
by pH, and under low pH conditions with free
iron, they can be expected to reduce multiple
moles of iron which is then able to generate
hydroxyl radicals (Tamaru et al. 2019; Goodell
et al. 1997) as has been demonstrated in the
CMF mechanism. Further exploration which
advances our understanding of how hydroxyl
radicals are generated by CMF or other
mechanisms must take into account either
how the fungus is protected from hydroxyl radical action (Zhu et al. 2016) or how hydroxyl
radical generation is spatially controlled to
react within the wood cell wall (Goodell et al.
2017). More research is needed in this area to
explore non-enzymatic catalytic mechanisms in
the brown rot fungi and in microorganisms in
general. This type of mechanism for the nonenzymatic generation of hydroxyl radicals at a
distance from the organism to solubilize a substrate while also preventing oxidative damage
to the microorganism itself is so far unknown
outside of the brown rot fungi.
2. Enzymatic Degradation in the Brown Rot
Fungi
Riley et al. (Riley et al. 2014) published a
paradigm-shifting paper discussing a new
approach to the classification of brown rot
and white rot fungi. As might be expected for
fungi that do not metabolize lignin, lignindegrading peroxidase enzymes have been lost
in the brown rots, although the genomes of
some brown rot species have been shown to
encode for laccases. Brown rot fungi have a
reduced number of enzymes acting on crystalline cellulose, with cellobiohydrolase enzymes
absent or lacking a critical cellulose-binding
domain (Riley et al. 2014). Lytic polysaccharide
monooxygenase (LPMO) enzymes are generally
also reduced in the brown rot fungi compared
to white rot species. The Gloeophyllales and
Boletales families have one and two cellobiose
dehydrogenase enzymes, respectively, but other
brown rot families and genera analyzed have
lost these enzymes completely. Endoglucanases
are considered to be one of the most important
enzymes in brown rot fungi, yet they are
reduced in number compared to the white
rots. A clean division between the brown rots
and white rots cannot be drawn relative to the
number and types of hemicellulase and pectinase enzymes that are produced by these species (Riley et al. 2014). Additional research
must still confirm particular aspects of the
research demonstrating the interaction
between non-enzymatic and enzymatic brown
378
B. Goodell
most active fungal environments.
Research suggests that early upregulation
of a large group of LMW compounds and
enzymes that may generate LMW catalysis
occurs prior to upregulation of glycoside
hydrolase enzymes (Zhang et al. 2016). The
upregulation of these metabolites is timed so
that subsequent upregulation of CAZymes follows in a staggered manner (Zhang et al. 2016).
These findings are consistent with both glycopeptide and CMF working theories, and the
staggered upregulation hypothesis also does
not preclude mechanisms that allow spatial diffusion of LMW metabolites as has been
described for the CMF mechanism. Polyketide
synthases (PKS) have also been found to be
upregulated in the brown rot fungi (Riley et al.
2014), and this may be important due to the
role these synthases play in the production of
LMW metabolites ranging from siderophores
to fungal antibiotics. Some of these LMW metabolites derived from polyketide pathways are
structurally related to the LMW compounds
isolated from brown rot fungi that have been
proposed for redox chemistries involved in
non-enzymatic degradation schemes (Paszczynski et al. 1999; Kerem et al. 1999; Goodell
et al. 1997).
The generation of hydroxyl radicals is a
consistent feature that is recognized in the
LMW catalytic system in brown rots and that
is also proposed to occur in the glycopeptide
hypothesis in these fungi. The hydroxyl radical
is the most potent oxidant known in biological
systems, and it is therefore important that it be
generated in a location where it cannot damage
fungal hyphae. Relative to the CMF mechanism,
hydroquinones, catecholates, and similar
redox-cycling compounds are greatly affected
by pH, and under low pH conditions with free
iron, they can be expected to reduce multiple
moles of iron which is then able to generate
hydroxyl radicals (Tamaru et al. 2019; Goodell
et al. 1997) as has been demonstrated in the
CMF mechanism. Further exploration which
advances our understanding of how hydroxyl
radicals are generated by CMF or other
mechanisms must take into account either
how the fungus is protected from hydroxyl radical action (Zhu et al. 2016) or how hydroxyl
radical generation is spatially controlled to
react within the wood cell wall (Goodell et al.
2017). More research is needed in this area to
explore non-enzymatic catalytic mechanisms in
the brown rot fungi and in microorganisms in
general. This type of mechanism for the nonenzymatic generation of hydroxyl radicals at a
distance from the organism to solubilize a substrate while also preventing oxidative damage
to the microorganism itself is so far unknown
outside of the brown rot fungi.
2. Enzymatic Degradation in the Brown Rot
Fungi
Riley et al. (Riley et al. 2014) published a
paradigm-shifting paper discussing a new
approach to the classification of brown rot
and white rot fungi. As might be expected for
fungi that do not metabolize lignin, lignindegrading peroxidase enzymes have been lost
in the brown rots, although the genomes of
some brown rot species have been shown to
encode for laccases. Brown rot fungi have a
reduced number of enzymes acting on crystalline cellulose, with cellobiohydrolase enzymes
absent or lacking a critical cellulose-binding
domain (Riley et al. 2014). Lytic polysaccharide
monooxygenase (LPMO) enzymes are generally
also reduced in the brown rot fungi compared
to white rot species. The Gloeophyllales and
Boletales families have one and two cellobiose
dehydrogenase enzymes, respectively, but other
brown rot families and genera analyzed have
lost these enzymes completely. Endoglucanases
are considered to be one of the most important
enzymes in brown rot fungi, yet they are
reduced in number compared to the white
rots. A clean division between the brown rots
and white rots cannot be drawn relative to the
number and types of hemicellulase and pectinase enzymes that are produced by these species (Riley et al. 2014). Additional research
must still confirm particular aspects of the
research demonstrating the interaction
between non-enzymatic and enzymatic brown
378
B. Goodell