showing that the β3-strand and, specifically, the motif WKATGTDK (Fig. 2) contact
the major groove of the DNA. This region, which is localized in the C subdomain, is
highly conserved, except for the second threonine, and an important structural and
functional role has been proposed for the conserved glycine residue (Yoshiyama et al.
2009; Welner et al. 2016). To gain further insights into the structural feature of
the NAC domain, additional X-ray crystallography and nuclear magnetic resonance
spectroscopy studies would be required.
2.2 The Regulatory Region Is Placed in the C-Terminal
Domain
The C-terminal domain plays an essential role in the regulation of transcription (Olsen
et al. 2005), but it has also been shown to be involved in protein–protein interactions
(Kim et al. 2007a; Jeong et al. 2009; Kjaersgaard et al. 2011). Despite being a highly
variable and mostly disordered region with a high content of low-complexity amino
acid repeats (Jensen et al. 2010), specific motifs have been identified in several NAC
subgroups that have been evolutionarily maintained (Nuruzzaman et al. 2012). The
W-motif (WNY) and L-motif (SLPPL) have been identified in NAC proteins from
Arabidopsis, Picea abies and P. pinaster and seem to be associated with organ initiation and differentiation (Takada et al. 2001; Larsson et al. 2012; Pascual et al. 2015).
The W-motif proved to be essential for transcriptional activation, but the function of the
L-motif remains unknown. In the C-terminal region of stress-related NAC genes from
Arabidopsis and P. abies, specifically those of subgroup III (ANAC019, ANAC055,
ANAC072, ATAF1, ATAF2 and PaNAC03), a motif with a high negative charge
density, SEKEE (V/I) QSSFRLE, that forms the transactivation domain has been
identified (Jensen et al. 2010; Dalman et al. 2017). In silico analyses indicated that
several NAC proteins, such as NAP, a positive regulator of senescence (Guo and Gan
2006), and SHYG (Speedy Hyponastic Growth), which regulates flooding-induced
leaf movement in Arabidopsis (Rauf et al. 2013), have highly conserved intrinsic
disorder profiles immediately behind the NAC domain (Stender et al. 2015). Bioinformatic analyses have, in some NAC proteins, identified a sequence motif that is
substrate-specific for hydrolases and proteases. However, other members of the NAC
family contain transmembrane motifs in the C-terminal region that are mostly formed
by polar and negatively charged residues with conserved hydrophobic residues embedded in the polar matrix (Jensen et al. 2010). These NAC TFs are bound to the plasma
membrane or endoplasmic reticulum and activated by proteases during stress responses (Seo et al. 2008, 2010; Chi et al. 2017). In summary, our knowledge of the function
of these protein motifs is very limited, and further research is required to elucidate their
biological importance. The combination of computational methods with experimental
data could help identify regulatory motifs with high confidence for a particular TF that
can be used to recognize interacting proteins (Stender et al. 2015). This approach could
be used to reconstruct regulatory networks that are involved in the control of important
processes in trees.
NAC Transcription Factors in Woody Plants
201
the major groove of the DNA. This region, which is localized in the C subdomain, is
highly conserved, except for the second threonine, and an important structural and
functional role has been proposed for the conserved glycine residue (Yoshiyama et al.
2009; Welner et al. 2016). To gain further insights into the structural feature of
the NAC domain, additional X-ray crystallography and nuclear magnetic resonance
spectroscopy studies would be required.
2.2 The Regulatory Region Is Placed in the C-Terminal
Domain
The C-terminal domain plays an essential role in the regulation of transcription (Olsen
et al. 2005), but it has also been shown to be involved in protein–protein interactions
(Kim et al. 2007a; Jeong et al. 2009; Kjaersgaard et al. 2011). Despite being a highly
variable and mostly disordered region with a high content of low-complexity amino
acid repeats (Jensen et al. 2010), specific motifs have been identified in several NAC
subgroups that have been evolutionarily maintained (Nuruzzaman et al. 2012). The
W-motif (WNY) and L-motif (SLPPL) have been identified in NAC proteins from
Arabidopsis, Picea abies and P. pinaster and seem to be associated with organ initiation and differentiation (Takada et al. 2001; Larsson et al. 2012; Pascual et al. 2015).
The W-motif proved to be essential for transcriptional activation, but the function of the
L-motif remains unknown. In the C-terminal region of stress-related NAC genes from
Arabidopsis and P. abies, specifically those of subgroup III (ANAC019, ANAC055,
ANAC072, ATAF1, ATAF2 and PaNAC03), a motif with a high negative charge
density, SEKEE (V/I) QSSFRLE, that forms the transactivation domain has been
identified (Jensen et al. 2010; Dalman et al. 2017). In silico analyses indicated that
several NAC proteins, such as NAP, a positive regulator of senescence (Guo and Gan
2006), and SHYG (Speedy Hyponastic Growth), which regulates flooding-induced
leaf movement in Arabidopsis (Rauf et al. 2013), have highly conserved intrinsic
disorder profiles immediately behind the NAC domain (Stender et al. 2015). Bioinformatic analyses have, in some NAC proteins, identified a sequence motif that is
substrate-specific for hydrolases and proteases. However, other members of the NAC
family contain transmembrane motifs in the C-terminal region that are mostly formed
by polar and negatively charged residues with conserved hydrophobic residues embedded in the polar matrix (Jensen et al. 2010). These NAC TFs are bound to the plasma
membrane or endoplasmic reticulum and activated by proteases during stress responses (Seo et al. 2008, 2010; Chi et al. 2017). In summary, our knowledge of the function
of these protein motifs is very limited, and further research is required to elucidate their
biological importance. The combination of computational methods with experimental
data could help identify regulatory motifs with high confidence for a particular TF that
can be used to recognize interacting proteins (Stender et al. 2015). This approach could
be used to reconstruct regulatory networks that are involved in the control of important
processes in trees.
NAC Transcription Factors in Woody Plants
201