Crosstalk between Ubiquitination and Other Post-translational Protein Modifications in Plant Immunity

Abstract

Post-translational modifications (PTMs) are central to the modulation of protein activity, stability, subcellular localization, and interaction with partners. They greatly expand the diversity and functionality of the proteome and have taken the center stage as key players in regulating numerous cellular and physiological processes. Increasing evidence indicates that in addition to a single regulatory PTM, many proteins are modified by multiple different types of PTMs in an orchestrated manner to collectively modulate the biological outcome. Such PTM crosstalk creates a combinatorial explosion in the number of proteoforms in a cell and greatly improves the ability of plants to rapidly mount and fine-tune responses to different external and internal cues. While PTM crosstalk has been investigated in depth in humans, animals, and yeast, the study of interplay between different PTMs in plants is still at its infant stage. In the past decade, investigations showed that PTMs are widely involved and play critical roles in the regulation of interactions between plants and pathogens. In particular, ubiquitination has emerged as a key regulator of plant immunity. This review discusses recent studies of the crosstalk between ubiquitination and six other PTMs, i.e., phosphorylation, SUMOylation, poly(ADP-ribosyl)ation, acetylation, redox modification, and glycosylation, in the regulation of plant immunity. The two basic ways by which PTMs communicate as well as the underlying mechanisms and diverse outcomes of the PTM crosstalk in plant immunity are highlighted.

Keywords: PTM crosstalk; S-nitrosylation; SUMOylation; phosphorylation; plant immunity; ubiquitination.

Figure 1

Interplay between Ubiquitination and Other PTMs. (A) Crosstalk between ubiquitination and phosphorylation. The ubiquitination of kinase causes its degradation (e.g., FLS2) or change in subcellular localization (e.g., BRI1). The phosphorylation of E3 ligase affects its pattern of interaction with the substrate (e.g., PUB12/13) or enzymatic activity (e.g., PUB25/26). (B) Interplay between ubiquitination and SUMOylation. Ubiquitination and SUMOylation may antagonistically compete for the attaching site (K) of the substrate. The SUMOylation of the Ub E3 ligase COP1 enhances its trans-ubiquitination activity. The ubiquitination of the SUMO E3 ligase SIZ1 mediates its degradation. STUbL (SUMO-targeted ubiquitin ligase) specifically ubiquitinates the SUMOylated substrate for degradation. (C) Crosstalk between ubiquitination and Poly(ADP-ribosyl)ation. PTUbL (PAR-targeted ubiquitin ligase) specifically ubiquitinates PARylated substrate for degradation. (D) Crosstalk between ubiquitination and acetylation. The NTA of the first Met in SNC1 sequence (Ac-MMD), which is catalyzed by NatA, acts as a signal for degradation. The degradation might be ubiquitination dependent. (E) Interplay between ubiquitination and S-nitrosylation. S-nitrosylation of the substrate promotes its ubiquitination and degradation. The S-nitrosylation at Cys37 and Cys118 of ASK1 is required for assembly of the SCF^TIR1/AFB2 complex. (F) Crosstalk between ubiquitination and glycosylation. The special F-box protein Fbs (F-box protein-recognizing sugar chain 1) of the SCF type E3 ligase recognizes glycans of the substrate and mediates ubiquitination and degradation. The red arrows denote the outcomes of the modification and the black arrows indicate the enzymatic reaction. Ub, ubiquitin; P, phosphogroup; S, SUMO; ADPr, ADP-ribose; Ac-, CH₃CO; -SNO, S-nitrosothiol; K, lysine.

Figure 2

The Activation and Signaling of FLS2/BAK1- and CERK1/LYK5-Mediated Plant PTI Are Modulated by the Interplay of Phosphorylation, Ubiquitination, and SUMOylation. (A) In the absence of PAMPs, the PRRs BAK1 and FLS2 as well as LYK5 and CERK1 are dissociated. BAK1, PUB12/13, the heterotrimeric G proteins, CPK28, and PUB25/26 form a complex. FLS2 is complexed with the deSUMOylating enzyme, Desi3a. The non-phosphorylated (non-activated) form of BIK1 associates with the BAK1 and FLS2 complex, respectively. PUB25/26 specifically ubiquitinates non-activated BIK1 and mediates its degradation but the G proteins inhibit the E3 activity of PUB25/26. The Desi3a interacts with FLS2 and inhibits its SUMOylation. In addition, PUB13 mediates the ubiquitination and degradation of another PRR, LYK5 and PUB22 form a dimer/oligomer and catalyze self-ubiquitination for degradation. (B) The presence of PAMP flg22 induces mutual phosphorylation and association of FLS2 and BAK1 as well as phosphorylation of PUB12/13 by BAK1 and their association. flg22 also induces phosphorylation of BIK1 by phosphorylated BAK1, which results in the activated form of BIK1 that is resistant to PUB25/26-mediated ubiquitination, and in turn phosphorylates BAK1 and FLS2 and dissociation of the activated BIK1 from the BAK1–FLS2 complex. The release of activated BIK1 from the BAK1–FLS2 complex triggers the downstream PTI signaling that culminates in PTI. The flg22 also induces (1) the degradation of Desi3a, which promotes the SUMOylation of FLS2 that is essential for activation of downstream immune signaling and (2) the release of the G proteins from the complex, and promotes the phosphorylation of PUB25/26 by CPK28, which increases the E3 ligase activity of PUB25/26 and speeds up the degradation of the non-activated BIK1. Meanwhile, the phosphorylated PUB12/13 ubiquitinates FLS2 for degradation to attenuate plant immune signaling. Upon challenge of chitin, CERK1 interacts with LYK5 but PUB13 dissociates from LYK5, which activates the chitin-induced immunity. CERK1 is suggested to be ubiquitinated by PUB12 for degradation. The presence of PAMPs activates the MAPK cascades including MPK3 as part of the immune signaling pathway. The activated MPK3 phosphorylates PUB22 to inhibit its oligomerization and autoubiquitination, which promotes the ubiquitination of the immune-essential component Exo70B2 by PUB22 for degradation.

Figure 3

The Stability, Activity, and Subcellular Localization of NPR1 Are Regulated by Multiple PTMs. In resting cells, S-nitrosylation of NPR1 promotes its oligomerization. Upon pathogen challenge, SA (salicylic acid) induces a change from oligomer to monomer, which is catalyzed by thioredoxins (TRXs). Monomeric NPR1 is phosphorylated by SnRK2.8 at S589, which is required for its nuclear entry. In the nucleus, NPR1 is phosphorylated at S55/59, which inhibits its SUMOylation. The stable and inactive NPR1 represses the transcription of downstream defense genes. Upon SA induction, S55/59 phosphorylation sites are likely dephosphorylated, which facilitates its SUMOylation. The SUMOylation of NPR1 is essential for S11/15 phosphorylation that activates transcription of defense genes. S11/15 phosphorylation is required for its ubiquitination and degradation mediated by NPR3–CUL3 E3 ubiquitin ligase complexes.