subclass of CC-type domains found in plant
NLRs (Daskalov et al. 2016; Dyrka et al. 2014).
Some fungal NLRs thus show domain architectures analogous to their plant counterparts
(except that WD/ANK/TPR-repeats are found
in place of the LRR). Similarly, nucleoside
phosphorylase domains frequent in fungal
NLRs have also been described as N-terminal
domain of NLRs in the coral Acropora digitifera
(Hamada et al. 2013), and Pkinase and a hydrolase domains (DUF676, which overlaps with our
sesB-like annotation) were found as N-terminal
domain of NLRs (with LRR-repeats) in the
mosses Physcomitrella patens and Sphagnum
fallax, respectively (Gao et al. 2018). Additionally, a number of NACHT or NB-ARC domain
STAND proteins from multicellular bacteria
(Cyanobacteria and Actinobacteria) display
domain architectures similar to fungal NLRs
(Dunin-Horkawicz et al. 2014; Koonin and Aravind 2002; Leipe et al. 2004; Urbach and Ausubel 2017) raising those question about the
evolutionary history of the protein family as
will be detailed in a following section.
IV. Evolution and Variability of NLR
Repertoires in Fungi
Work on the nwd gene family of P. anserina
which includes the het-d, het-e, and het-r
incompatibility loci and nwd2 has shown that
the WD-repeat units undergo concerted evolution within and between genes of the family
(Chevanne et al. 2010; Daskalov et al. 2015b;
Paoletti et al. 2007). Genes of the nwd family
show repeat number polymorphism and
undergo frequent rearrangements, repeat loss,
gain, and shuffling. This concerted evolution
process is both a cause and consequence of
the very high internal conservation of the
repeats (homology between repeat unit ranges
from 85 to 95%). At the same time, specific
positions of the WD-repeat units are hypervariable and under positive diversifying selection
(Paoletti et al. 2007). These positions are predicted by homology modeling to correspond to
residues forming the interaction surface of the
b-propeller structure formed cooperatively by
the WD-repeats. It was suggested that this
mechanism of concerted evolution allows for
hypervariability of the WD-repeat recognition
domain in the NWD proteins in relation with
their non-self recognition function. NLRs from
P. anserina with ANK- and TPR-repeats with
high internal conservation were also analyzed
for repeat number polymorphism and as
observed for the nwd family, and high internal
repeat conservation was correlated with frequent repeat number polymorphism in natural
isolates (Dyrka et al. 2014; Marold et al. 2015).
Again, as in the case of the WD-repeats, specific
positions of the ANK- and TPR-repeats were
hypervariable, under diversifying selection
and mapped to residues forming the interaction
surface of the ANK or TPR superstructures in
homology modeling approaches. Bioinformatic
analysis of the repeat domains in a collection of
fungal NLRs revealed that high internal repeat
conservation is also found in many other species suggesting that the proposed mechanism of
recognition domain diversification might also
be operating in a wide range of Basidiomycota
and Ascomycota species (Dyrka et al. 2014).
WD- and TPR-repeats with high internal conservation are also abundant in NACHT and NBARC proteins from Actinobacteria and Cyanobacteria (Table 6.2). In fact, WD-repeats with
high internal conservation are almost exclusively found in fungi and bacteria (Cyanobacteria and Actinobacteria in particular) (Hu et al.
2017). It is likely that, akin to the situation
described in P. anserina, concerted evolution
in WD- and TPR-repeats provides adaptive
hypervariability to other NLR-type proteins
not only in fungi but also in Actinobacteria
and Cyanobacteria. High internal conservation
of WD-repeats is also observed in an NLR-type
gene family from the red algae Chondrus crispus
where 27 out of 50 members of the gene family
display highly conserved repeats.
Of note here is the description of a highly expanded
gene family encoding NACHT-ANK proteins in Tuber
melanosporum. This gene family characterized by the
presence of a variable number of introns (from 17 to up
to 91 per gene) gives rise to codon-sized microexons
(Iotti et al. 2012). Through alternative splicing, intron
skipping, and retention, a variety of transcripts are
generated that differ in sequence at the end of the
130
A. Daskalov et al.
NLRs (Daskalov et al. 2016; Dyrka et al. 2014).
Some fungal NLRs thus show domain architectures analogous to their plant counterparts
(except that WD/ANK/TPR-repeats are found
in place of the LRR). Similarly, nucleoside
phosphorylase domains frequent in fungal
NLRs have also been described as N-terminal
domain of NLRs in the coral Acropora digitifera
(Hamada et al. 2013), and Pkinase and a hydrolase domains (DUF676, which overlaps with our
sesB-like annotation) were found as N-terminal
domain of NLRs (with LRR-repeats) in the
mosses Physcomitrella patens and Sphagnum
fallax, respectively (Gao et al. 2018). Additionally, a number of NACHT or NB-ARC domain
STAND proteins from multicellular bacteria
(Cyanobacteria and Actinobacteria) display
domain architectures similar to fungal NLRs
(Dunin-Horkawicz et al. 2014; Koonin and Aravind 2002; Leipe et al. 2004; Urbach and Ausubel 2017) raising those question about the
evolutionary history of the protein family as
will be detailed in a following section.
IV. Evolution and Variability of NLR
Repertoires in Fungi
Work on the nwd gene family of P. anserina
which includes the het-d, het-e, and het-r
incompatibility loci and nwd2 has shown that
the WD-repeat units undergo concerted evolution within and between genes of the family
(Chevanne et al. 2010; Daskalov et al. 2015b;
Paoletti et al. 2007). Genes of the nwd family
show repeat number polymorphism and
undergo frequent rearrangements, repeat loss,
gain, and shuffling. This concerted evolution
process is both a cause and consequence of
the very high internal conservation of the
repeats (homology between repeat unit ranges
from 85 to 95%). At the same time, specific
positions of the WD-repeat units are hypervariable and under positive diversifying selection
(Paoletti et al. 2007). These positions are predicted by homology modeling to correspond to
residues forming the interaction surface of the
b-propeller structure formed cooperatively by
the WD-repeats. It was suggested that this
mechanism of concerted evolution allows for
hypervariability of the WD-repeat recognition
domain in the NWD proteins in relation with
their non-self recognition function. NLRs from
P. anserina with ANK- and TPR-repeats with
high internal conservation were also analyzed
for repeat number polymorphism and as
observed for the nwd family, and high internal
repeat conservation was correlated with frequent repeat number polymorphism in natural
isolates (Dyrka et al. 2014; Marold et al. 2015).
Again, as in the case of the WD-repeats, specific
positions of the ANK- and TPR-repeats were
hypervariable, under diversifying selection
and mapped to residues forming the interaction
surface of the ANK or TPR superstructures in
homology modeling approaches. Bioinformatic
analysis of the repeat domains in a collection of
fungal NLRs revealed that high internal repeat
conservation is also found in many other species suggesting that the proposed mechanism of
recognition domain diversification might also
be operating in a wide range of Basidiomycota
and Ascomycota species (Dyrka et al. 2014).
WD- and TPR-repeats with high internal conservation are also abundant in NACHT and NBARC proteins from Actinobacteria and Cyanobacteria (Table 6.2). In fact, WD-repeats with
high internal conservation are almost exclusively found in fungi and bacteria (Cyanobacteria and Actinobacteria in particular) (Hu et al.
2017). It is likely that, akin to the situation
described in P. anserina, concerted evolution
in WD- and TPR-repeats provides adaptive
hypervariability to other NLR-type proteins
not only in fungi but also in Actinobacteria
and Cyanobacteria. High internal conservation
of WD-repeats is also observed in an NLR-type
gene family from the red algae Chondrus crispus
where 27 out of 50 members of the gene family
display highly conserved repeats.
Of note here is the description of a highly expanded
gene family encoding NACHT-ANK proteins in Tuber
melanosporum. This gene family characterized by the
presence of a variable number of introns (from 17 to up
to 91 per gene) gives rise to codon-sized microexons
(Iotti et al. 2012). Through alternative splicing, intron
skipping, and retention, a variety of transcripts are
generated that differ in sequence at the end of the
130
A. Daskalov et al.