ATGs Involved in Plant Immunity and NPR1 Metabolism: Comparison
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Autophagy is an important pathway of degrading excess and abnormal proteins and organelles through their engulfment into autophagosomes that subsequently fuse with the vacuole. Autophagy-related genes (ATGs) are essential for the formation of autophagosomes. To date, about 35 ATGs have been identified in Arabidopsis, which are involved in the occurrence and regulation of autophagy. Among these, 17 proteins are related to resistance against plant pathogens. The transcription coactivator non-expressor of pathogenesis-related genes 1 (NPR1) is involved in innate immunity and acquired resistance in plants, which regulates most salicylic acid (SA)-responsive genes.

  • Arabidopsis
  • autophagy
  • NPR1
  • plant immunity

1. Roles of NPRs in Plant Immunity

1.1. The Structure of NPR1

The transcription coactivator non-expressor of pathogenesis-related genes 1 (NPR1) is a key regulatory factor of SAR, which regulates most SA-responsive genes [30,63,64,65,66][1][2][3][4][5]. NPR1 contains an N-terminal BTB/POZ (Broad-Compex, Tramtrack, and BricaBrac/POxvirus and Zinc finger) domain, an ankyrin (ANK) repeat domain, a C-terminal transactivation domain, and a nuclear localization sequence [67,68,69][6][7][8]. NPR1 interacts with TGACG motif-binding factor (TGA) through ANK or BTB/POZ domain [70,71,72][9][10][11]. In the absence of SA, the C-terminal transactivation domain of NPR1 interacts with BTB/POZ domain, which inhibits NPR1 transcriptional coactivator function. The binding of SA to NPR1 leads to conformational changes of NPR1, it functions as a coactivator of gene transcription with the release of the C-terminal transactivation domain from the N-terminal autoinhibitory domain [71,73][10][12]. A recent study provided a preliminary understanding of the structure–function relationship of NPR proteins. The SA-binding core (SBC) consisting of amino acids 373–516 in the NPR4 C-terminal domain was identified. Arabidopsis NPR4 and NPR1 share 38.1% sequence identity in their SBC region, they share the structural mechanism of SA recognition. In addition, this study also found that conformational changes of NPR4 SBC could be induced by the binding of SA to NPR1 and NPR4 [74][13].

1.2. NPR1 and Innate Immunity

NPR1 is a master regulator of plant resistance to pathogen stress, which confers immunity through multiple transcription factors [75,76,77][14][15][16]. Research over the last 20 years has revealed the potential molecular mechanism of NPR1 in different cell states. Under normal growth conditions, NPR1 is present in the cytoplasm, stabilized by intermolecular disulfide bonds. Infection by pathogens results in the accumulation of SA and NPR1 oligomer-to-monomer reaction through SA-mediated redox changes in the cell, allowing NPR1 to migrate into the nucleus [75,78,79][14][17][18]. NPR1 indirectly activates PR gene expression by interacting with TGA in the nucleus and plays an important role in regulating the PRs protein downstream [63,80,81][2][19][20]. The NPR1 in SA perception promotes TGAs transcriptional activity [82][21]. Recent studies have shown that NPR1 interacts with cyclin-dependent kinase 8 (CDK8) and enhanced disease susceptibility 1 (EDS1) to promote PR1 expression in the SA signaling pathway [83,84][22][23].
A new study found that the formation of SA-induced NPR1 condensates (SINCs) is mediated by conserved cysteine clusters in intrinsic disorder regions (IDRs) of NPR1 protein. SINCs are rich in stress-responsive proteins, including NB-NLR receptors, oxidative and DNA damage-responsive proteins, and ubiquitination-related proteins. In addition, SINCs are required to form functional NPR1-Cullin 3 RING E3 ligase (CRL3) complex in the cytoplasm. NPR1-CRL3 complex can ubiquitinate and degrade EDS1 and some important ETI regulatory factors such as WRKY transcription factors, thereby promoting cell survival in ETI [85][24].

1.3. NPR3/NPR4 and Plant Immunity

In Arabidopsis, the NPR family consists of NPR1 and five NPR1-like genes, named NPR1-like 2 (NPR2), NPR3, NPR4, BLADE-ON-PETIOLE2 (BOP2; NPR5), and BOP1 (NPR6) [86,87,88,89][25][26][27][28]. Each member of the NPR family contains a set of highly conserved cysteine residues that are thought to be involved in redox control [30][1]. It was confirmed that NPR1 and NPR3/NPR4 bind to SA and function as SA receptors, with NPR1 (Kd = 223.1 ± 38.85 nM) and NPR3 (Kd = 176.7 ± 28.31 nM) binding to SA with similar affinity. However, the affinity of NPR4 (Kd = 23.54 ± 2.743 nM) with SA is much higher [82][21]. Under normal conditions, NPR4 is a ligand of CRL3 substrate that can interact with NPR1, allowing proteasome to continuously ubiquitinate and degrade NPR1. At this time point, NPR3/NPR4 inhibits the expression of defense genes, thereby preventing an autoimmune response [90,91,92][29][30][31]. During SAR, as SA levels increase, SA binds to NPR4, induces the dissociation of NPR1 and NPR4, disrupts the NPR4-Cullin3 E3 ligase complex [90,92][29][31]. At this time point, the binding of SA to NPR3/NPR4 inhibits their transcriptional activity, while NPR1 in SA perception enhances its transcriptional activation, both of which are helpful in inducing the expression of defense genes [82][21]. In addition, studies have shown that NPR3 and NPR4 may promote PCD while NPR1 may inhibit PCD through resistance–avirulence (R-Avr) gene interaction [91][30]. Our previous study found that the expression of ATGs and the protein concentrations of ATG7 and ATG8a-PE were lower in npr3/npr4 mutants than in the wild-type. NPR3 and NPR4 may regulate the production of autophagosomes by promoting two ubiquitin-like conjugated systems [91][30].

2. ATGs Participate in the Regulation of NPR1 Metabolism

2.1. Proteasome-Mediated NPR1 Degradation

Pathogen infection causes accumulation of SA thus leads to post-translational modification of NPR1, allowing it to enter into the nucleus. NPR1 is recruited to Cullin3 (CUL3) for ubiquitination and subsequent degradation, this process requires phosphorylation of NPR1 at residues Ser11 and Ser15 [31,93,94,95,96][32][33][34][35][36]. The ubiquitination of NPR1 is a gradual process. Only when the polyubiquitination of NPR1 is enhanced by ubiquitin conjugation factor E4 (UBE4), it becomes the target of proteasome degradation [95][35]. Ubiquitin ligase activities are opposed by ubiquitin specific protease (UBP6/7). UBP6/7 are two proteasome-related deubiquitinases (DUBs) that increase NPR1 longevity [95][35]. In addition to UBP6/7, other DUBs may also play a role in regulating the expression of SA response genes, but their exact function is still unclear.
Some studies have found that the plant hormones abscisic acid (ABA) and SA antagonistically affect the level of NPR1 in cells. ABA promotes NPR1 degradation through the proteasome pathway mediated by the CUL3-NPR3/NPR4 complex, while SA protects NPR1 from ABA-induced degradation through phosphorylation [97,98,99,100][37][38][39][40]. AvrPtoB has a U-box E3 ubiquitin ligase domain at the C-terminal and shows a weak interaction with NPR1 under uninduced conditions. SA promotes the interaction between AvrPtoB and NPR1, AvrPtoB mediates NPR1 ubiquitination by E3 ligase and mediates NPR1 degradation via the proteasome pathway [101][41].

2.2. Relationship between ATGs and NPR1

Studies have found that NPR1 regulates ATGs expression. NPR1 inhibited the mRNA expression of ATG1, ATG6, and ATG8a during the early HR induced by Psm ES4326/AvrRpt2 [61][42]. SA analog benzothiadiazole (BTH) was confirmed to induce autophagy through the NPR1-dependent signaling pathway, and NPR1, NPR3, and NPR4 are jointly involved in the regulation of autophagosomes [91][30]. In addition, several studies have shown that NPR1 affects the phenotype of autophagy-deficient mutants. NPR1 could accelerate the senescence or infection-induced accumulation of ubiquitinated proteins and endoplasmic reticulum stress in atg2 [54][43]. Yoshimoto et al. found that BTH could induce senescence and cell death in atg5 mutants but could not induce senescence and cell death in atg5 npr1 double mutants, indicating that the cell death phenotype in atg5 mutants depended on NPR1 under SA induction [57][44]. Our previous study also found that ATG4 promoted NPR1 degradation by inhibiting the consumption of free SA [61][42]. In recent years, the relationship between ATGs and NPR1 has been gradually revealed (Table 1), but there are still many problems to be solved.
Table 1. Relationship between ATGs and NPR1 in Arabidopsis.
Gene Protein Relationship References
AT3G61960

AT3G53930		 ATG1a

ATG1b		 NPR1 inhibited the mRNA expression of ATG1 during Psm ES4326/AvrRpt2 infections. [61][42]
AT3G19190 ATG2 Accumulation of ubiquitinated proteins and increased ER stress in older atg2 mutants which were suppressed by mutations in NPR1. NPR1 somehow suppressed cell death in atg2 mutants upon pathogen infection. [54][43]
AT2G44140

AT3G59950		 ATG4a

ATG4b		 ATG4 inhibited the consumption of free SA and alleviated the degradation of NPR1 during Psm ES4326/AvrRpt2 induced autophagy-dependent HR. [61][42]
AT5G17290 ATG5 Pathogen-induced spread of chlorotic cell death and BTH hypersensitivity in atg5 mutants required NPR1. [57][44]
AT3G61710 ATG6 NPR1 inhibited the mRNA expression of ATG6 during Psm ES4326/AvrRpt2 infections. [61][42]
AT4G21980 ATG8a NPR1 inhibited the mRNA expression of ATG8a during Psm ES4326/AvrRpt2 infections. [61][42]

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