IV. The Role of Ubiquitination and
Deubiquitination in Fungal
Development and Secondary
Metabolism
The importance of post-translational modifications for coordinated fungal development and
secondary metabolism is not restricted to histone modifications such as the epigenetic control in connection with transcriptional
networks. Target protein modifications by
phosphate, ubiquitin, or ubiquitin-like proteins
are also essential for the accurate adjustment of
the fungal proteome. They alter the physical
and chemical properties of a protein in
response to external or internal stimuli in
order to regulate and control its activity, halflife, transport, and subsequent cellular localization. These processes, which include the highly
conserved ubiquitin-26S proteasome pathway
(UPP) for protein stability control, are prerequisites for accurate fungal differentiation and
physiology.
A. The Ubiquitin Attachment Machinery
Influences Fungal Development and
Secondary Metabolism on Several Layers
Ubiquitin is the most prominent modifier of the
family of ubiquitin-like proteins (UBL), which
includes SUMO, the cullin modifier neural precursor cell expressed, developmentally downregulated 8 (Nedd8) or autophagy-related
modifiers (Atg8, Atg12; see Sect. V). Ubiquitin
consists of 76 amino acids and is encoded as
fusion to ribosomal proteins or as head-to-tail
fusions of many ubiquitin moieties encompassing two ubiquitin genes in filamentous fungi
such as A. nidulans or four in S. cerevisiae
(Noventa-Jorda ˜o et al. 2000; Lee et al. 2017).
These ubiquitin fusion proteins have to be
cleaved by deubiquitinating enzymes (DUBs)
to create a pool of ubiquitin monomers that
can be used for the actual ubiquitination reaction (Grou et al. 2015). Ubiquitin is essential for
fungal growth, although single deletion strains
can grow but have strong defects in fungal
growth, stress response, and development
(Leach et al. 2011; Oh et al. 2012).
About 20% of all A. nidulans proteins are
ubiquitinated during hyphal growth and are
located in the nucleus, whereas in S. cerevisiae
the biggest portion is contained in the transmembrane protein fraction (Peng et al. 2003;
Chu et al. 2016). Ubiquitin itself contains seven
conserved lysine residues (K6, K11, K27, K29,
K33, K48, K63), which can be used for ubiquitin
chain formation. The attachment of ubiquitin
chains linked through a certain lysine residue
can alter activity, localization, or stability of the
substrate. The K48-linked polyubiquitin chains
are the most abundant in yeast and usually
mark the modified protein for degradation by
the 26S proteasome (Spasser and Brik 2012;
Zuin et al. 2014).
The attachment of ubiquitin as well as other
ubiquitin-like proteins involves an enzyme cascade consisting of E1 activating, E2 conjugating, and E3 ligase enzymes (Fig. 8.4). An E1
enzyme activates ubiquitin in an ATPdependent reaction by formation of a thioester
bond. The corresponding E1 encoding UBA1
(ubiquitin activating 1) gene of S. cerevisiae is
essential for spore formation and vegetative
growth (McGrath et al. 1991). The activated
ubiquitin molecule is transferred to E2, which
can physically interact with E3 ubiquitin
ligases. Several yeast genes encoding E2
enzymes as well as the polyubiquitin encoding
locus are induced during heat stress or starvation conditions (McGrath et al. 1991; Hiraishi
et al. 2006). E3 ubiquitin ligases are classified
into the cullin-RING ligase (CRLs) and the
HECT (homologous to E6AP carboxyl terminus) ubiquitin ligase families.
Fungi such as A. nidulans express three
cullin proteins (CulA, CulC and CulD) and
humans even eight (Marı ´n 2009; von Zeska
Kress et al. 2012). CulA, corresponding to
human cullin-1, is part of the largest group of
CRLs, the SCF (SkpA, CullinA, Fbox) complexes. They are activated by the attachment
of Nedd8 to CulA, a process called neddylation.
Nedd8 and proteins of the neddylation cascade
and the SCF complex are essential for A. nidulans, whereas SUMO-deficient mutants can
grow but are impaired in multicellular development and secondary metabolite production
(von Zeska Kress et al. 2012; Harting et al.
2013). In S. cerevisiae, it is the other way
8 Coordination of Fungal Secondary Metabolism and Development
189
Deubiquitination in Fungal
Development and Secondary
Metabolism
The importance of post-translational modifications for coordinated fungal development and
secondary metabolism is not restricted to histone modifications such as the epigenetic control in connection with transcriptional
networks. Target protein modifications by
phosphate, ubiquitin, or ubiquitin-like proteins
are also essential for the accurate adjustment of
the fungal proteome. They alter the physical
and chemical properties of a protein in
response to external or internal stimuli in
order to regulate and control its activity, halflife, transport, and subsequent cellular localization. These processes, which include the highly
conserved ubiquitin-26S proteasome pathway
(UPP) for protein stability control, are prerequisites for accurate fungal differentiation and
physiology.
A. The Ubiquitin Attachment Machinery
Influences Fungal Development and
Secondary Metabolism on Several Layers
Ubiquitin is the most prominent modifier of the
family of ubiquitin-like proteins (UBL), which
includes SUMO, the cullin modifier neural precursor cell expressed, developmentally downregulated 8 (Nedd8) or autophagy-related
modifiers (Atg8, Atg12; see Sect. V). Ubiquitin
consists of 76 amino acids and is encoded as
fusion to ribosomal proteins or as head-to-tail
fusions of many ubiquitin moieties encompassing two ubiquitin genes in filamentous fungi
such as A. nidulans or four in S. cerevisiae
(Noventa-Jorda ˜o et al. 2000; Lee et al. 2017).
These ubiquitin fusion proteins have to be
cleaved by deubiquitinating enzymes (DUBs)
to create a pool of ubiquitin monomers that
can be used for the actual ubiquitination reaction (Grou et al. 2015). Ubiquitin is essential for
fungal growth, although single deletion strains
can grow but have strong defects in fungal
growth, stress response, and development
(Leach et al. 2011; Oh et al. 2012).
About 20% of all A. nidulans proteins are
ubiquitinated during hyphal growth and are
located in the nucleus, whereas in S. cerevisiae
the biggest portion is contained in the transmembrane protein fraction (Peng et al. 2003;
Chu et al. 2016). Ubiquitin itself contains seven
conserved lysine residues (K6, K11, K27, K29,
K33, K48, K63), which can be used for ubiquitin
chain formation. The attachment of ubiquitin
chains linked through a certain lysine residue
can alter activity, localization, or stability of the
substrate. The K48-linked polyubiquitin chains
are the most abundant in yeast and usually
mark the modified protein for degradation by
the 26S proteasome (Spasser and Brik 2012;
Zuin et al. 2014).
The attachment of ubiquitin as well as other
ubiquitin-like proteins involves an enzyme cascade consisting of E1 activating, E2 conjugating, and E3 ligase enzymes (Fig. 8.4). An E1
enzyme activates ubiquitin in an ATPdependent reaction by formation of a thioester
bond. The corresponding E1 encoding UBA1
(ubiquitin activating 1) gene of S. cerevisiae is
essential for spore formation and vegetative
growth (McGrath et al. 1991). The activated
ubiquitin molecule is transferred to E2, which
can physically interact with E3 ubiquitin
ligases. Several yeast genes encoding E2
enzymes as well as the polyubiquitin encoding
locus are induced during heat stress or starvation conditions (McGrath et al. 1991; Hiraishi
et al. 2006). E3 ubiquitin ligases are classified
into the cullin-RING ligase (CRLs) and the
HECT (homologous to E6AP carboxyl terminus) ubiquitin ligase families.
Fungi such as A. nidulans express three
cullin proteins (CulA, CulC and CulD) and
humans even eight (Marı ´n 2009; von Zeska
Kress et al. 2012). CulA, corresponding to
human cullin-1, is part of the largest group of
CRLs, the SCF (SkpA, CullinA, Fbox) complexes. They are activated by the attachment
of Nedd8 to CulA, a process called neddylation.
Nedd8 and proteins of the neddylation cascade
and the SCF complex are essential for A. nidulans, whereas SUMO-deficient mutants can
grow but are impaired in multicellular development and secondary metabolite production
(von Zeska Kress et al. 2012; Harting et al.
2013). In S. cerevisiae, it is the other way
8 Coordination of Fungal Secondary Metabolism and Development
189