the cluster are used to predict the type of secondary metabolite that may be produced,
although this is currently still rather inaccurate.
The wide diversity among members of the
fungal kingdom is also reflected in the wide
range of natural products they produce, making
fungi an interesting source for novel drugs.
Genome sequencing has resulted in a large catalog of biosynthetic gene clusters (Keller 2019).
Unfortunately, most natural products are not
produced under lab conditions, complicating
their identification in high-throughput screens
(Keller et al. 2005). Several companies (e.g.,
Hexagon Bio, USA) are currently using highthroughput genome sequencing to identify
novel natural products, purely based on their
gene content. Interesting candidate gene clusters are then heterologously expressed in production species using a synthetic biology
approach, thus circumventing the problem of
low production of the natural products in their
natural host. S. cerevisiae and Aspergillus nidulans are examples of production species (Billingsley et al. 2016; Clevenger et al. 2017; Harvey
et al. 2018). This approach illustrates the power
of large-scale genome sequencing and analysis.
B. Carbohydrate-Active Enzymes
Fungi are heterotrophs: they feed on organic
matter. A large source of organic matter is
plant biomass, or, more specifically, polysaccharides in lignocellulose (including cellulose,
hemicellulose, and pectin). Fungi have evolved
a wide range of extracellular enzymes to break
down these recalcitrant polysaccharides into
smaller compounds (monosaccharides and oligosaccharides) that can be transported over the
cell membrane. Collectively, these enzymes are
known as carbohydrate-active enzymes
(CAZymes) and are organized in a special database, the CAZy database. CAZy describes the
families of structurally related catalytic and
carbohydrate-binding modules (or functional
domains) of enzymes that degrade, modify, or
create glycosidic bonds (Lombard et al. 2014).
More generally, CAZymes are enzymes
involved in the breakdown, biosynthesis, and
modification of carbohydrates.
Based on their domain structure CAZymes
are classified into glycoside hydrolases (GH),
glycosyl transferases (GT), polysaccharide
lyases (PL), carbohydrate esterases (CE), and
enzymes with auxiliary activities (AA). Each of
these categories is subdivided into numerous
families with predicted enzyme activities (Lombard et al. 2014). Although their identification
is based on sequence homology (and therefore
relatively straightforward), it is important to
note that even within families there can be a
range of predicted enzyme activities. It may
therefore be necessary to confirm the enzyme
activity of the predicted CAZyme with lab
experiments.
From a biotechnology perspective,
CAZymes are interesting due to their ability to
break down (unfermentable) polysaccharides
into oligosaccharides and monosaccharides
that can be fermented into ethanol by S. cerevisiae. As such, CAZymes play an important role
in converting plant biomass into biofuel. Moreover, fungal pathogens of plants use CAZymes
as an important weapon in their arsenal to
attack their host. In the case of pathogens of
important agricultural crops, the CAZyme content of fungal genome can lead to important
insights (discussed below).
Initial genome sequencing efforts focused
on established model systems used to study
CAZymes. Examples include Aspergillus niger
(Pel et al. 2007) and Neurospora crassa (Galagan
et al. 2003). This resulted in a wide range of
well-characterized enzymes (Coutinho et al.
2009). Furthermore, several key regulators
involved in the regulation of CAZyme gene
expression were identified (Benocci et al.
2017). Later, large-scale sequencing efforts
focused on fungi that break down plant polysaccharides. An important sequencing effort is
the 1000 Fungal Genomes Project by the Joint
Genome Institute (Grigoriev et al. 2014), resulting in a large number of genomes from across
the fungal kingdom, including many plant biomass degrading fungi. More targeted sequencing efforts have focused on groups of fungi,
such as the genus Aspergillus (Vesth et al.
2018) or the class Agaricomycetes (Floudas
et al. 2012; Ohm et al. 2014), which includes
potent degraders of lignocellulose.
9 Fungal Genomics
213
although this is currently still rather inaccurate.
The wide diversity among members of the
fungal kingdom is also reflected in the wide
range of natural products they produce, making
fungi an interesting source for novel drugs.
Genome sequencing has resulted in a large catalog of biosynthetic gene clusters (Keller 2019).
Unfortunately, most natural products are not
produced under lab conditions, complicating
their identification in high-throughput screens
(Keller et al. 2005). Several companies (e.g.,
Hexagon Bio, USA) are currently using highthroughput genome sequencing to identify
novel natural products, purely based on their
gene content. Interesting candidate gene clusters are then heterologously expressed in production species using a synthetic biology
approach, thus circumventing the problem of
low production of the natural products in their
natural host. S. cerevisiae and Aspergillus nidulans are examples of production species (Billingsley et al. 2016; Clevenger et al. 2017; Harvey
et al. 2018). This approach illustrates the power
of large-scale genome sequencing and analysis.
B. Carbohydrate-Active Enzymes
Fungi are heterotrophs: they feed on organic
matter. A large source of organic matter is
plant biomass, or, more specifically, polysaccharides in lignocellulose (including cellulose,
hemicellulose, and pectin). Fungi have evolved
a wide range of extracellular enzymes to break
down these recalcitrant polysaccharides into
smaller compounds (monosaccharides and oligosaccharides) that can be transported over the
cell membrane. Collectively, these enzymes are
known as carbohydrate-active enzymes
(CAZymes) and are organized in a special database, the CAZy database. CAZy describes the
families of structurally related catalytic and
carbohydrate-binding modules (or functional
domains) of enzymes that degrade, modify, or
create glycosidic bonds (Lombard et al. 2014).
More generally, CAZymes are enzymes
involved in the breakdown, biosynthesis, and
modification of carbohydrates.
Based on their domain structure CAZymes
are classified into glycoside hydrolases (GH),
glycosyl transferases (GT), polysaccharide
lyases (PL), carbohydrate esterases (CE), and
enzymes with auxiliary activities (AA). Each of
these categories is subdivided into numerous
families with predicted enzyme activities (Lombard et al. 2014). Although their identification
is based on sequence homology (and therefore
relatively straightforward), it is important to
note that even within families there can be a
range of predicted enzyme activities. It may
therefore be necessary to confirm the enzyme
activity of the predicted CAZyme with lab
experiments.
From a biotechnology perspective,
CAZymes are interesting due to their ability to
break down (unfermentable) polysaccharides
into oligosaccharides and monosaccharides
that can be fermented into ethanol by S. cerevisiae. As such, CAZymes play an important role
in converting plant biomass into biofuel. Moreover, fungal pathogens of plants use CAZymes
as an important weapon in their arsenal to
attack their host. In the case of pathogens of
important agricultural crops, the CAZyme content of fungal genome can lead to important
insights (discussed below).
Initial genome sequencing efforts focused
on established model systems used to study
CAZymes. Examples include Aspergillus niger
(Pel et al. 2007) and Neurospora crassa (Galagan
et al. 2003). This resulted in a wide range of
well-characterized enzymes (Coutinho et al.
2009). Furthermore, several key regulators
involved in the regulation of CAZyme gene
expression were identified (Benocci et al.
2017). Later, large-scale sequencing efforts
focused on fungi that break down plant polysaccharides. An important sequencing effort is
the 1000 Fungal Genomes Project by the Joint
Genome Institute (Grigoriev et al. 2014), resulting in a large number of genomes from across
the fungal kingdom, including many plant biomass degrading fungi. More targeted sequencing efforts have focused on groups of fungi,
such as the genus Aspergillus (Vesth et al.
2018) or the class Agaricomycetes (Floudas
et al. 2012; Ohm et al. 2014), which includes
potent degraders of lignocellulose.
9 Fungal Genomics
213