Next Article in Journal
Evaluation of Biochemical Characteristics and Performance of the 3 Screen ICA ELISA Kit
Next Article in Special Issue
Fusarium sacchari CFEM Proteins Suppress Host Immunity and Differentially Contribute to Virulence
Previous Article in Journal
IDH1 R132H and TP53 R248Q Mutations Modulate Glioma Cell Migration and Adhesion on Different ECM Components
Previous Article in Special Issue
Fusarium sacchari Effector FsMEP1 Contributes to Virulence by Disturbing Localization of Thiamine Thiazole Synthase ScTHI2 from Sugarcane
 
 
Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
Journals
IJMS
Volume 25
Issue 22
10.3390/ijms252212187
ijms-logo
Submit to this Journal Review for this Journal Propose a Special Issue
► Article Menu

Article Menu

share Share announcement Help format_quote Cite question_answer Discuss in SciProfiles
first_page
settings
Order Article Reprints
Font Type:
Arial Georgia Verdana
Font Size:
Aa Aa Aa
Line Spacing:
Column Width:
Background:
Review

The Multifaceted Ubiquitination of BIK1 During Plant Immunity in Arabidopsis thaliana

by
Junhong Fu
†,
Huihui Wang
†,
Yuling Chen
,
Chunguang Zhang
and
Yanmin Zou
*
Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
*
Author to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Int. J. Mol. Sci. 2024, 25(22), 12187; https://doi.org/10.3390/ijms252212187
Submission received: 20 October 2024 / Revised: 10 November 2024 / Accepted: 12 November 2024 / Published: 13 November 2024
(This article belongs to the Special Issue Plant–Microbe Interactions)
Browse Figures
Versions Notes

Abstract

:
As sessile organisms, the plant immune system plays a vital role in protecting plants from the widespread pathogens in the environment. The Arabidopsis thaliana (Arabidopsis) receptor-like cytoplasmic kinase BOTRYTIS-INDUCED KINASE1 (BIK1) acts as a central regulator during plant immunity. As such, not only the BIK1 protein accumulation but also the attenuation is tightly regulated to ensure effective immune responses. Recent studies have highlighted the critical roles of ubiquitination in maintaining BIK1 homeostasis. Here, we review the latest advances in the ubiquitination of BIK1 in plant immunity, which is mediated by ubiquitin ligases PUB25/26, RHA3A/B, RGLG1/2, and PUB4. Additionally, we summarize and discuss the sites and types of BIK1 ubiquitination. Collectively, these analyses not only illustrate that the differential modifications on BIK1 by multiple ubiquitin ligases hold a crucial position in plant immunity but also provide a good example for future studies on ubiquitin-mediated modifications in plants.

1. Introduction

As sessile organisms, plants are almost challenged by various microbial pathogens in the environment; therefore, they have evolved an innate immune system to defend against the widespread pathogens. Pattern recognition receptors (PRRs)-mediated immune signaling holds a crucial position in defending against pathogen attacks. PRRs function as the first layer to recognize microbe-/pathogen-derived molecular patterns (MAMPs/PAMPs) or host-derived damage-associated molecular patterns (DAMP) and activate pattern-triggered immunity (PTI) [1,2,3,4,5]. At present, some key PRRs have been identified, such as FLAGELLIN-SENSING2 (FLS2), which perceives the bacterial flagellin (or its derived peptide flg22), EF-TU RECEPTOR (EFR), which recognizes the bacterial elongation factor EF-Tu (or its derived epitope elf18), PEP1 receptor 1 (PEPR1)/PEPR2, which perceive the AtPEPs, and CHITIN ELICITOR RECEPTOR KINASE 1 (CERK1) and LysM-RK LYSINE MOTIF RECEPTOR KINASE5 (LYK5), which recognize fungal cell wall component chitin [6,7,8,9,10]. After binding of PAMPs, PRRs form heterodimeric receptor complexes with their co-receptors, such as BRI1 ASSOCIATED RECEPTOR KINASE 1 (BAK1), and then lead to a series of auto- and trans-phosphorylation events [11,12,13]. The activated receptor complex then phosphorylates receptor-like cytoplasmic kinases (RLCKs), and then the activated RLCKs transmit the signaling to multiple downstream components.
Compared with the typical receptor-like kinases (RLKs), RLCKs only contain a cytoplasmic kinase domain but lack the ectodomain and transmembrane domain. Thereby, most of these RLCKs are localized to the plasma membrane (PM) through N-myristolation or palmitoylation and mainly function in regulating plant cellular activities. In Arabidopsis thaliana (Arabidopsis), there are 149 RLCKs, which are divided into 17 subgroups based on the sequence homology [14,15]. Most of these RLCKs play key roles in the regulation of developmental processes, hormone signaling, biotic and abiotic stresses, and so on [16,17,18]. For instance, some of the Arabidopsis RLCK-XII subfamily members regulate BR signaling [15,19,20,21], and many of the RLCK-VII subfamily members are shown to have functions during PRR-mediated immunity, such as PBS1-LIKE (PBL1), PATTERN-TRIGGERED IMMUNITY COMPROMISED RECEPTOR-LIKE CYTOPLASMIC KINASE1 (PCRK1), and PCRK2 [22,23,24,25,26,27].
BOTRYTIS-INDUCED KINASE 1 (BIK1) is one of the RLCK-VII subfamily members [27,28]. In Arabidopsis, BIK1 and other closely RLCKs work as central regulators between multiple receptor complexes and downstream signaling components (Figure 1) [22,23,24,25,26,27,28,29,30,31,32]. The BIK1 gene is initially identified to be significantly induced during Botrytis cinerea (Botrytis) infection using an Arabidopsis microarray, thus named BOTRYTIS-INDUCED KINASE 1 (BIK1) [23]. There are six exons and five introns in the BIK1 genomic region (Figure 2A). In agreement with most RLCKs, the coding DNA sequence (CDS) of BIK1 encodes a ser/thr protein kinase, which contains a plant consensus N-myristoylation motif and a kinase catalytic domain (Figure 2B) [23]. In addition, loss of function of the BIK1 gene leads to severe susceptibility to necrotrophic fungal pathogens Botrytis and Alternaria brassicicola (A. brassicicola), but enhances the resistance to the bacterial pathogen Pseudomonas syringae pv. tomato (Pst) DC3000, which may be due to the increased salicylic acid (SA) accumulation in the bik1 mutant [23]. With or without Botrytis infection, the level of SA is all higher than wildtype, suggesting that BIK1 acts as a negative regulator of SA accumulation. Moreover, BIK1 is required for normal plant growth and development as well. For example, bik1 mutant plants exhibit early flowering, reduced fertility, shorter primary roots, longer and more root hairs and lateral roots, and the leaves of bik1 have serrated margins and wrinkled surfaces compared to wild-type plants, respectively [23]. Subsequently, it is also confirmed that BIK1 functions in ethylene (ET) signaling. Flg22, ACC, and pathogen-induced expression of BIK1 is dependent on EIN3, which is one of the master transcription factors in the ethylene signaling pathway, and bik1 mutant plants display altered expression of ET-regulated genes [33]. Additionally, BIK1 negatively regulates BR signaling. The bik1 mutant plants are hypersensitive to brassinosteroids (BR) compared to wild-type plants. Furthermore, upon BR treatment, a leucine-rich repeat (LRR)-receptor kinase BRASSINOSTEROID INSENSITIVE 1 (BRI1), which recognizes the polyhydroxylated growth hormone BR, associates with and phosporylates BIK1, thereby leading to the release of BIK1 from the BRI1 receptor [34]. Recently, BIK1 is reported to interact with and phosphorylate SNF1-related protein kinase 2.6 (SnRK2.6) and controls multiple osmotic stress responses [35].
A series of studies of BIK1 have further demonstrated its important roles in plant immunity. BIK1 protein is required for immune signaling mediated by multiple PRRs, such as FLS2, EFR, PEPR1/2, BAK1, CERK1, and LYK5 (Figure 1) [22,24,25,28,36,37]. Upon PAMPs perception, BIK1 is phosphorylated and released from the PRR complex, leading to the phosphorylation and activation of multiple membrane components, such as the NADPH oxidase RESPIRATORY BURST OXIDASE HOMOLOG D (RbohD), which catalyzes the production of reactive oxygen species (ROS), the Ca2+-permeable channel OSCA1.3, two CYCLIC NUCLEOTIDE-GATED CHANNEL (CNGC) proteins, CNGC2 and CNGC4, both of which result in cytosolic calcium influx, and the DIACYLGLYCEROL KINASE 5 (DGK5) which mediate the phosphorylation of diacylglycerol (DAG), leading to phosphatidic acid (PA) burst [22,25,26,28,38,39,40,41,42]. In addition to the plasma membrane (PM) localization through N-myristoylation, BIK1 also localizes to the nucleus to phosphorylate transcription factors WRKY33, WRKY50, and WRKY57, which function in jasmonic acid (JA) and SA regulation, and the phosphorylation of these WRKYs is impaired while BIK1 is phosphorylated at S89/T90 residues by EFR [29]. However, how BIK1 is released from PM and translocated to the nucleus is yet unclear. Furthermore, BIK1 is directly targeted by some bacterial effector proteins, such as the cysteine protease Pseudomonas phaseolicola B (AvrPphB), which cleaves BIK1, and the Xanthomonas campestris effector AvrAC, which adds uridine 5′-monophosphate to BIK1 for reducing its kinase activity, also indicating the key roles of BIK1 in immune signaling [28,43]. Therefore, it seems that BIK1 serves as a ‘signaling hub’ to connect the PRR complex and the downstream components, thereby transmitting the PAMP signaling to intracellular signaling and inducing distinct defenses (Figure 1). As such, both the BIK1 protein stability and activation must be tightly regulated to prevent plant autoimmunity and ensure proper responses to pathogens.
Protein ubiquitination is one of the most abundant post-translational modifications in plant immunity. The ubiquitination process involves covalently linking ubiquitins (Ubs) to the target protein through three main reaction sequences: activation, conjugation, and ligation, which are catalyzed by 3 enzymes, respectively: E1 (Ub-activating enzyme, UBA), E2 (Ub-conjugating enzyme, UBC), and E3 (Ub ligase enzyme) [44,45,46]. Firstly, free Ub, which contains 76 amino-acid residues, is activated by the E1 enzyme in an ATP-dependent manner and then transferred from E1 to the catalytic cysteine (cys) of E2. Finally, the E3 cooperates with the E2-Ub conjugate to catalyze the transfer of Ub to the lysine (Lys, K) residues of the substrate proteins [46,47]. Among the 3 enzymes, E3s are the most abundant enzymes in the ubiquitination system and majorly determine the specificity of the substrate for ubiquitination modification. To date, a great deal of studies focus on the importance of E3s involved in plant immunity for avoiding excessive immune responses or regulating the activity of immune components. For instance, during PTI in Arabidopsis, PLANT U-BOX domain-containing E3 ligases PUB12/13 directly polyubiquitinate FLS2 and promote flagellin-induced FLS2 degradation. Moreover, PUB12/13 are phosphorylated by BAK1, which is essential for FLS2-PUB12/13 association, and loss of function of the PUB12/13 genes leads to enhanced immune responses to flagellin treatment [48]. In addition, PUB22, PUB23, and PUB24 are shown to be negative regulators of PTI, and PUB22 mediates the ubiquitination and degradation of Exo70B2, which is one of the exocyst complex subunits [49,50]. Furthermore, PUB22 is phosphorylated and stabilized by the activated MPK3 upon flg22 perception [51]. PBL13 also belongs to the RLCK-VII subfamily; however, it negatively regulates PTI responses through phosphorylating the C terminus of NADPH oxidase RbohD and then leading to the increased polyubiquitination of RbohD, which is catalyzed by PBL13-interacting E3 ligase (PIRE) with and without flg22 perception [52].
BIK1 protein is regulated by multiple mechanisms, such as transcription, phosphorylation, de-phosphorylation, S-nitrosylation, UMPylation, and ubiquitination, or the interplay between them (Figure 3A and Table 1) [33,43,53,54,55,56,57,58,59,60,61,62,63]. Among them, ubiquitination is one of the most abundant types of protein post-translational modification in plant immunity, and multiple studies have demonstrated the key roles of ubiquitination in regulating BIK1 homeostasis. In this review, we aim to summarize and discuss the functions of the differential ubiquitination of BIK1 mediated by seven ubiquitin ligases in PAMP-triggered immune responses. In addition, these advances not only demonstrate that the differential modifications on BIK1 by ubiquitin hold a crucial position in plant immunity but also provide a good example for future research in the insight into the understanding of ubiquitin-mediated modifications in plants.

2. Ubiquitin-Mediated Modifications on BIK1

To date, multiple ubiquitin ligases have been identified to ubiquitinate BIK1 since 2018, when the first pair of ubiquitin ligases PLANT U-BOX domain-containing PROTEIN 25 (PUB25) and PUB26 were identified, hence opening a new chapter for the understanding of BIK1 protein stability [56].

2.1. PUB25/26 Mediated Polyubiquitination of BIK1

Through a liquid chromatography–tandem mass spectrometry (LC-MS/MS) assay, Wang et al. first identified PUB25 as an interacting protein of BIK1. Then, split-luciferase complementation assays in Nicotiana benthamiana and co-immunoprecipitation (coIP) in Arabidopsis protoplasts further confirmed the association of PUB25 with BIK1. PUB26 is the closest homolog of PUB25, and the subsequent works demonstrated that both PUB25/26 directly interacted with and polyubiquitinated BIK1, which led to the proteasome-mediated degradation of BIK1. In line with this, the BIK1 protein level was greatly reduced and accumulated in the PUB25-OE line and pub25/26 double mutant compared to Col-0 plants, respectively. Furthermore, pub25/26 mutant plants displayed more resistance to Botrytis and the nonvirulent type III secretion mutant strain Pst DC3000 hrcC–, while PUB25-OE transgenic plants showed increased susceptibility to Botrytis and Pst DC3000 hrcC– compared to wild-type plants, suggesting that PUB25/26 negatively regulated immunity in Arabidopsis. Interestingly, Wang et al. found that PUB25/26 specifically targeted the hypophosphorylated BIK1 for degradation, thereby preventing excessive immune signaling and maintaining homeostasis of immunity [56]. On the other hand, this also reveals that the interplay between phosphorylation and ubiquitination of BIK1 is essential for BIK1 homeostasis.
Additionally, Wang et al. reported that CALCIUM-DEPENDENT PROTEIN KINASE 28 (CPK28) phosphorylated and activated PUB25/26, while the heterotrimeric G proteins directly inhibited PUB25/26 activity to stabilize BIK1. Thus, Wang et al. demonstrated that PUB25/26, the G proteins, and CPK28 formed a signaling module to regulate the non-activated BIK1 protein accumulation [56]. Moreover, CPK28 is also directly associated with BIK1 in vivo and phosphorylates BIK1 in vitro but does not affect BIK1-PUB25 interaction [56,61]. Liu et al. subsequently found that two closely related RING-finger E3 ubiquitin ligases, ARABIDOPSIS TOXICOS EN LEVADURA31 (ATL31) and ATL6 polyubiquitinated and degraded CPK28, which led to the enhanced accumulation of BIK1 [64]. Bai et al. reported recently that another ubiquitin ligase, RING DOMAIN LIGASE 2 (RGLG2), repressed the ubiquitin ligase activity of PUB25 to maintain BIK1 protein homeostasis [57], collectively suggesting that the regulation of BIK1 homeostasis is more complicated.

2.2. RGLG1/2 Mediated Monoubiquitination of BIK1

Apart from regulating the ubiquitin ligase activity of PUB25, RGLG2 also directly ubiquitinates BIK1 [57]. By an RNA sequencing screening, Bai et al. first identified that RING DOMAIN LIGASE 1 (RGLG1), the closest homolog of RGLG2, exhibited a similar expression pattern to BIK1 upon flg22 treatment. Split-luciferase complementation assay in Nicotiana benthamiana indicated the association of RGLG1 with BIK1, which was reduced after flg22 treatment. Subsequently, the authors confirmed that, similar to PUB25/26, both RGLG1 and RGLG2 directly interacted with and ubiquitinated the hypophosphorylated proportion of BIK1. Interestingly, rglg1/2 mutant plants were more susceptible to Pst DC3000 hrcC– compared to wild-type plants, suggesting that RGLG1/2 positively regulated immune signaling. Further studies showed that RGLG1/2 mediated the monoubiquitination of BIK1 to promote the BIK1 protein accumulation and its association with BAK1, which differed from the actions of PUB25/26 [56,57]. Consistent with this, the overexpression of RGLG1/2 in Arabidopsis protoplasts resulted in increased accumulation of BIK1, while the BIK1 protein level was reduced in transgenic plants BIK1 OE/rglg1/2 compared to BIK1 OE/Col-0. In addition, the authors also demonstrated that RGLG1/2 competed with PUB25 for binding to BIK1 to maintain an appropriate BIK1 protein level in the resting stage. Upon flg22 perception, the association of RGLG1/2 with either PUB25/26 or BIK1 was reduced, thereby resulting in the degradation of the hypophosphorylated BIK1 by PUB25/26 to prevent further accumulation of activated BIK1. Collectively, Bai et al. demonstrated that RGLG1/2 and PUB25/26 form a module to regulate the homeostasis of hypophosphorylated BIK1. However, it remains unclear how the two pairs of ubiquitin ligases compete for association with BIK1.

2.3. RHA3A/3B Mediated Monoubiquitination of BIK1

In addition to RGLG1/2, two transmembrane ubiquitin ligases RING-H2 FINGER A3A (RHA3A) and RHA3B also mediate monoubiquitination of BIK1, but the mechanism is distinct [58]. Given that the disassociation of activated BIK1 from the PRR complex is crucial for subsequent immune responses, the exact mechanism of how to regulate the activated BIK1 remains to be fully elucidated. Ma et al. found that BIK1 was ubiquitinated upon PAMP treatments (flg22, elf18, pep1, and chitin) through an in vivo ubiquitination assay conducted in Arabidopsis protoplasts. The PAMP-induced ubiquitination of BIK1, which was about 8 kDa larger than that of unmodified BIK1, appeared to be monoubiquitination. The authors identified RHA3A as an interacting protein of BIK1 by a yeast two-hybrid screen. RHA3B is the closest homologue of RHA3A. And the subsequent works demonstrated that RHA3A/3B directly interacted with and monoubiquitinated BIK1. Additionally, the rha3a/b mutants and the transgenic plants pBIK1::BIK19KR-HA/bik1, in which monoubiquitination but not phosphorylation is blocked, exhibited reduced flg22-induced ROS bust and were more susceptible to Pst DC3000 hrcC−, compared to Col-0 and pBIK1::BIK1-HA/bik1 transgenic plants, respectively. Subsequent studies demonstrated that the monoubiquitination of BIK1 by RHA3A/3B promoted the release of BIK1 from the FLS2-BAK1 complex. This mechanism differs from that of RGLG1/2, which mediate the monoubiquitination of hypophosphorylated BIK1 and promote the BAK1-BIK1 interaction. Hitherto, RGLG1/2 and PUB25/26 target the hypophosphorylated BIK1 for its accumulation and degradation, respectively, while RHA3A/3B target hyperphosphorylated BIK1 for its dissociation from the PRR complex [56,57,58]. Notably, Ma et al. also revealed that the monoubiquitination of BIK1 mediated by RHA3A/3B contributes to its internalization from the plasma membrane to endocytic vesicles for signaling activation, and this flg22-triggered BIK1 endocytosis is distinct from that of FLS2, which is internalized for degradation and signaling attenuation [48,65,66].

2.4. PUB4 Mediated Polyubiquitination of BIK1

Besides PUB25/26, there are some other PUBs playing crucial roles in BIK1-mediated immune signaling. For example, two PUB proteins, PUB2 and PUB4, physically associate with FLS2, BIK1, PBL27, and RbohD and enhance BIK1-FLS2 and BIK1-RbohD associations independent of flg22 [59]. PUB4 catalyzes the polyubiquitination of BIK1 as well [60]. However, the regulation of BIK1 homeostasis mediated by PUB4 is more complicated [59,60]. Firstly, Wang et al. found that the pub2/4 mutant plants exhibited reduced ROS generation, callose deposition, and MAPK activation after PAMP treatment and were more susceptible to the pathogen Pst DC3000 hrcC−, indicating that PUB2/4 play positive roles in the PAMP-triggered immune responses [59,60]. RipAC, which is a type III effector protein from Ralstonia solanacearum, suppresses pattern-triggered immunity. Yu et al. identified PUB4 as an interacting protein of RipAC by a yeast two-hybrid screen, and the subsequent works revealed the positive role of PUB4. For example, pub4 mutant plants exhibited reduced ROS burst, compromised stomatal closure in response to multiple PAMPs, and displayed more susceptibility to Pst DC3000 hrcC− and Pst DC3000 COR−, which is a coronatine (COR) deficient mutant of DC3000. However, the MAPK activation was not affected in pub4 mutants, which is different from what Wang et al. demonstrated [59,60]. Notably, the PUB4 protein possesses a U-box domain and six armadillo (ARM) repeats, which are reported to mediate E3 ligase activity and protein–protein interactions, respectively. Intriguingly, Wang et al. unveiled that, although PUB4 was shown to have autoubiquitination activity, the ARM repeats region but not the U-box domain was essential for its function in plant immunity, while Yu et al. discovered that PUB4 mediated the polyubiquitination of non-activated BIK1 for degradation at the resting state. Furthermore, Yu et al. revealed that PUB4 promoted the accumulation of activated BIK1 after PAMP treatment; however, the mechanism is not yet clear [59,60].

3. Ubiquitination Sites on BIK1

Typically, ubiquitination of the target proteins occurs on the lysine residues of the substrate proteins to form stable isopeptide (or peptide) linkages with ubiquitin [45,67,68]. There are 30 lysine (K) residues in BIK1 protein, and two residues, K105 and K106, are located in the ATP-binding pocket, which is critical for ATP binding and required for kinase activity [58].
By MS analyses and mutational analyses, Ma et al. and Grubb et al. identified 15 potential ubiquitination sites on BIK1: three in the N-terminal variable domain (K31, K41, K61), seven in the canonical kinase domain (K95, K106, K155, K170, K186, K286, K337), and five in the C-terminal region (K358, K366, K369, K374, K388) [58,69] (Figure 2B). Among them, nine ubiquitination residues of BIK1 (K31, K41, K95, K170, K186, K286, K337, K358, K366) are targeted by RHA3A/B (Figure 2B). Ma et al. demonstrated that individual lysine mutations did not affect monoubiquitination of BIK1 by mutational analyses in vivo, thus the monoubiquitination may not be restricted to a single lysine; once a single site is mutated, the alternative sites could still be ubiquitylated [31,58]. Moreover, the mutant variant BIK1(9KR) largely blocks flg22-induced BIK1 monoubiquitination and the dissociation from the PRR complex. Apart from the BIK1(9KR), the mutant variant of the N-terminal five lysine residues (BIK1(N5KR)) or C-terminal four lysine residues (BIK1(C4KR)) partially affects the BIK1 ubiquitination [58]. However, RGLG1/2 still promotes the protein accumulation of BIK1C4KR, and PUB25 also mediates the degradation of BIK1C4KR, suggesting that the C-terminal ubiquitination sites of BIK1 mediated by RHA3A/B may not be targeted by RGLG1/2 and PUB25/26 [57].
Notably, the materials used for MS analyses in the studies of Ma et al. and Grubb et al. were treated with PAMP, flg22, or elf18, respectively [58,69]. However, RGLGs and PUBs target the non-activated proportion of BIK1, so it is possible that there are some new ubiquitination sites of BIK1 that have not been discovered. Therefore, it is important to develop new methods to identify the respective sites of BIK1 mediated by RGLGs and PUBs, thereby elucidating how these E3 ligases synergistically regulate the protein stability of BIK1.

4. Ubiquitination Types

With respect to the ubiquitination types, there are monoubiquitination and polyubiquitination with at least eight different linkages [45,47]. Monoubiquitination is formed by the transfer of a single Ub to the lysine residue of a substrate protein. When multiple lysine residues become modified with one ubiquitin, leading to multimonoubiquitylation. Furthermore, if ubiquitination occurs on lysine residues of a ubiquitin, which is already attached to the substrate protein, leading to the formation of polymeric chains. Moreover, the C-terminus of Ub can be attached to any of the seven internal lysine residues (K6, K11, K27, K29, K33, K48, and K63) or the N-terminal methionine (Met1) of ubiquitins that are already substrate-bound, thereby leading to at least eight different linkages. During the Ub elongation, if the same lysine residue of Ub is modified, the formed polyubiquitin chains are homogenous, as in the K48- or K63-linked chains. If different residues link alternately, the chains are heterotypic, mixed, and branched polyubiquitin chains, as in the K63/Met-linked chain [45,47,67,70,71,72,73,74,75]. Different types of ubiquitin modification may result in distinct fates for the substrate proteins [45,76]. Of the various modes of ubiquitination, K48- and K63-linked polyubiquitination are the best-known types. Proteins marked by K48-linked polyubiquitination are always targeted to the 26S proteasome for degradation, while monoubiquitination, K63-, or Met1-linked ubiquitination usually leads to a non-degradative fate for regulating the substrate’s activity, localization, protein trafficking, DNA repair, endocytosis, and so on [76,77].
The types of BIK1 ubiquitination mediated by these ubiquitin ligases are different. For example, PUB25/26 and PUB4 trigger the polyubiquitination of BIK1 [56,60]. RGLG1/2 and RHA3A/B mediate the monoubiquitination of BIK1 [57,58]. Recent advances revealed that RGLG1/2 and PUB25/26 could catalyze multiple types of ubiquitin modification. For instance, RGLG1/2 is shown to catalyze K48, K63-linked polyubiquitination, and monoubiquitination [57,78,79]. K63-linked ubiquitination has been shown to regulate the internalization and endocytotic trafficking of membrane-localized receptors. As reported, RGLG1/2 could catalyze K63-linked polyubiquitylation of the auxin transport protein PIN-FORMED 2 (PIN2) to modulate apical dominance and function in endosomal sorting decisions [78,79]. Notably, RGLG1/2 also mediates the degradation of MAPKKK18 and transcription factor ERF53 to control drought responses likely via K48-linked polyubiquitylation [80,81]. Moreover, RGLG2 could move to the nucleus from the plasma membrane under drought stress; however, the mechanism is not yet clear. RGLG1 and RGLG5 are found to ubiquitinate PP2CA, a negative regulator of abscisic acid (ABA) signaling, and lead to proteasome-mediated degradation.
PUB25/26 have been reported recently that they could catalyze both K48- and K63-linked polyubiquitination as well. For example, PUB25/26 interact and mediate the polyubiquitination of the transcriptional regulator INDUCER OF C-REPEAT BINDING FACTOR EXPRESSION1 (ICE1) and MYB15 via K48-linked polyubiquitylation for protein degradation, while catalyzing K63-linked polyubiquitylation of them to enhance their stability, thus dynamically modulating the stability of ICE1 and MYB15 at different stages of the cold response [82]. However, does PUB25 or PUB26 mediate both K48- and K63-linked polyubiquitination of BIK1 in plant immunity? And how do RGLG1/2 or PUB25/26 catalyze the ubiquitination of multiple substrates with different ubiquitin modifications? Although E3 ubiquitin ligases hold key roles in the specificity of substrate recognition and subsequent protein fate, the ubiquitin conjugate E2-E3 pairs mainly determine the types of ubiquitination [45,76]. As reported, RGLG2 has been shown to interact with E2 ubiquitin-conjugating enzyme UBC35, a plant homolog of the yeast ubiquitin conjugation enzyme UBC13, which is known to be capable of catalyzing the formation of K63-linked ubiquitin chains [79,83]. Thus, it will be interesting to identify which E2 interacts with the seven ubiquitin ligases for mediating the BIK1 ubiquitination and whether the E2s are the same or different ones to interact with distinct E3s of BIK1.

5. Conclusions and Perspectives

Taken together, this study reviews the multifaceted regulations of BIK1 homeostasis by ubiquitination in plant immunity. BIK1 serves as an essential component of plant immunity; as such, not only the BIK1 protein accumulation but also the attenuation is tightly regulated to ensure proper immunity. The present studies altogether suggest that PUB25/26, RHA3A/3B, PUB4, and RGLG1/2 form a regulatory network to regulate BIK1 homeostasis via different ubiquitination types (Figure 3B). In the resting stage, BIK1 is monoubiquitinated by RGLG1/2 and polyubiquitinated by PUB25/26 and PUB4 to dynamically maintain the BIK1 protein level. RGLG1/2 and PUB25 negatively regulate each other and antagonistically control the accumulation of non-activated BIK1 protein. And PUB4 targets and degrades non-activated BIK1 as well. Upon flg22 treatment, BIK1 is activated by the PRR complex and then monoubiquitinated by RHA3A/3B, leading to the disassociation of activated BIK1 from the PRR complex, ultimately resulting in the activation of multiple downstream components. Meanwhile, flg22 also induces the disassociation of PUB25/26 with RGLG1/2 and the phophorylation of PUB25/26 by CPK28, both of which enhance the E3 ligase activity of PUB25/26. This leads to the degradation of the hypophosphorylated portion of BIK1, indirectly limiting the pool of the activated BIK1 pool and preventing excessive immune activation. Moreover, PUB4 could enhance the accumulation of activated BIK1 following PAMP treatment with an unclear mechanism.
Despite these breakthroughs in the understanding of BIK1 ubiquitination, many important questions remain unclear. For example, (1) since CPK28-mediated phosphorylation positively regulates the activity of PUB25/26, is the activity of RGLGs or RHA3A/3B regulated by the phosphorylation of kinases? Such as CPK28, BIK1, or other kinases? (2) How do these ubiquitin ligases function orchestrally to maintain BIK1 homeostasis? (3) Given that seven ubiquitin ligases regulate the homeostasis of BIK1, what is the biological significance of this kind of regulation? Furthermore, do these regulations differ at different tissues, distinct developmental stages, or under various stress conditions? (4) Considering that the monoubiquitination of activated BIK1 mediated by RHA3A/3B plays a role in endocytosis, what are the exact outcomes of RGLG1/2-mediated BIK1 monoubiquitination? Are there other E3 ubiquitin ligases that target and degrade hyperphosphorylated BIK1? What is the ultimate fate of hyperphosphorylated BIK1? (5) How are the orthologs of AtBIK1 regulated in other crops, and do they also undergo regulation by multiple ubiquitin ligases? Answers to these questions will shed new light on our understanding of ubiquitination in plant immunity.

Author Contributions

Conceptualization, J.F., H.W. and Y.Z.; writing, Y.C., C.Z. and Y.Z. All authors have read and agreed to the published version of the manuscript.

Funding

The work was funded by the National Natural Science Foundation of China (32070291).

Conflicts of Interest

The authors declare no conflicts of interest.

References

  1. Jones, J.D.G.; Dangl, J.L. The plant immune system. Nature 2006, 444, 323–329. [Google Scholar] [CrossRef]
  2. Chisholm, S.T.; Coaker, G.; Day, B.; Staskawicz, B.J. Host-microbe interactions: Shaping the evolution of the plant immune response. Cell 2006, 124, 803–814. [Google Scholar] [CrossRef]
  3. Tsuda, K.; Katagiri, F. Comparing signaling mechanisms engaged in pattern-triggered and effector-triggered im-munity. Curr. Opin. Plant Biol. 2010, 13, 459–465. [Google Scholar] [CrossRef]
  4. Huffaker, A.; Pearce, G.; Ryan, C.A. An endogenous peptide signal in Arabidopsis activates components of the innate immune response. Proc. Natl. Acad. Sci. USA 2006, 103, 10098–10103. [Google Scholar] [CrossRef]
  5. Yamaguchi, Y.; Huffaker, A.; Bryan, A.C.; Tax, F.E.; Ryan, C.A. PEPR2 is a second receptor for the Pep1 and Pep2 peptides and contributes to defense responses in Arabidopsis. Plant Cell 2010, 22, 508–522. [Google Scholar] [CrossRef]
  6. Gomez-Gomez, L.; Boller, T. FLS2: An LRR receptor-like kinase involved in the perception of the bacterial elicitor flagellin in Arabidopsis. Mol. Cell 2000, 5, 1003–1011. [Google Scholar] [CrossRef]
  7. Zipfel, C.; Kunze, G.; Chinchilla, D.; Caniard, A.; Jones, J.D.; Boller, T.; Felix, G. Perception of the bacterial PAMP EF-Tu by the receptor EFR restricts Agrobacterium-mediated trans-formation. Cell 2006, 125, 749–760. [Google Scholar] [CrossRef]
  8. Zou, Y.; Wang, S.; Zhou, Y.; Bai, J.; Huang, G.; Liu, X.; Zhang, Y.; Tang, D.; Lu, D. Transcriptional regulation of the immune receptor FLS2 controls the ontogeny of plant innate immunity. Plant Cell 2018, 30, 2779–2794. [Google Scholar] [CrossRef]
  9. Liu, T.; Liu, Z.; Song, C.; Hu, Y.; Han, Z.; She, J.; Fan, F.; Wang, J.; Jin, C.; Chang, J.; et al. Chitin-induced dimerization activates a plant immune receptor. Science 2012, 336, 1160–1164. [Google Scholar] [CrossRef] [PubMed]
  10. Cao, Y.; Liang, Y.; Tanaka, K.; Nguyen, C.T.; Jedrzejczak, R.P.; Joachimiak, A.; Stacey, G. The kinase LYK5 is a major chitin receptor in Arabidopsis and forms a chitin-induced complex with related kinase CERK1. eLife 2014, 3, e03766. [Google Scholar] [CrossRef] [PubMed]
  11. Chinchilla, D.; Zipfel, C.; Robatzek, S.; Kemmerling, B.; Nürnberger, T.; Jones, J.D.G.; Felix, G.; Boller, T. A flagellin-induced complex of the receptor FLS2 and BAK1 initiates plant defence. Nature 2007, 448, 497–500. [Google Scholar] [CrossRef] [PubMed]
  12. Heese, A.; Hann, D.R.; Gimenez-Ibanez, S.; Jones, A.M.; He, K.; Li, J.; Schroeder, J.I.; Peck, S.C.; Rathjen, J.P. The receptor-like kinase SERK3/BAK1 is a central regulator of innate immunity in plants. Proc. Natl. Acad. Sci. USA 2007, 104, 12217–12222. [Google Scholar] [CrossRef] [PubMed]
  13. Sun, Y.; Li, L.; Macho, A.P.; Han, Z.; Hu, Z.; Zipfel, C.; Zhou, J.-M.; Chai, J. Structural basis for flg22-induced activation of the Arabidopsis FLS2-BAK1 immune complex. Science 2013, 342, 624–628. [Google Scholar] [CrossRef] [PubMed]
  14. Shiu, S.-H.; Karlowski, W.M.; Pan, R.; Tzeng, Y.-H.; Mayer, K.F.X.; Li, W.-H. Comparative analysis of the receptor-like kinase family in Arabidopsis and rice. Plant Cell 2004, 16, 1220–1234. [Google Scholar] [CrossRef]
  15. Liang, X.; Zhou, J.-M. Receptor-like cytoplasmic kinases: Central players in plant receptor kinase–mediated signaling. Annu. Rev. Plant Biol. 2018, 69, 267–299. [Google Scholar] [CrossRef]
  16. Lin, W.; Ma, X.; Shan, L.; He, P. Big roles of small kinases: The complex functions of receptor-like cytoplasmic kinases in plant immunity and development. J. Integr. Plant Biol. 2013, 55, 1188–1197. [Google Scholar] [CrossRef]
  17. Tang, D.; Wang, G.; Zhou, J.-M. Receptor kinases in plant-pathogen interactions: More than pattern recognition. Plant Cell 2017, 29, 618–637. [Google Scholar] [CrossRef]
  18. Yu, X.; Feng, B.; He, P.; Shan, L. From chaos to harmony: Responses and signaling upon microbial pattern recognition. Annu. Rev. Phytopathol. 2017, 55, 109–137. [Google Scholar] [CrossRef]
  19. Kim, T.-W.; Guan, S.; Sun, Y.; Deng, Z.; Tang, W.; Shang, J.-X.; Sun, Y.; Burlingame, A.L.; Wang, Z.-Y. Brassinosteroid signal transduction from cell-surface receptor kinases to nuclear transcription factors. Nat. Cell Biol. 2009, 11, 1254–1260. [Google Scholar] [CrossRef]
  20. Sreeramulu, S.; Mostizky, Y.; Sunitha, S.; Shani, E.; Nahum, H.; Salomon, D.; Hayun, L.B.; Gruetter, C.; Rauh, D.; Ori, N.; et al. BSKs are partially redundant positive regulators of brassinosteroid signaling in Arabidopsis. Plant J. 2013, 74, 905–919. [Google Scholar] [CrossRef]
  21. Tang, W.; Kim, T.W.; Oses-Prieto, J.A.; Sun, Y.; Deng, Z.; Zhu, S.; Wang, R.; Burlingame, A.L.; Wang, Z.Y. BSKs mediate signal transduction from the receptor kinase BRI1 in. Science 2008, 321, 557–560. [Google Scholar] [CrossRef]
  22. Lu, D.; Wu, S.; Gao, X.; Zhang, Y.; Shan, L.; He, P. A receptor-like cytoplasmic kinase, BIK1, associates with a flagellin receptor complex to initiate plant innate immunity. Proc. Natl. Acad. Sci. USA 2010, 107, 496–501. [Google Scholar] [CrossRef] [PubMed]
  23. Veronese, P.; Nakagami, H.; Bluhm, B.; AbuQamar, S.; Chen, X.; Salmeron, J.; Dietrich, R.A.; Hirt, H.; Mengiste, T. The membrane-anchored BOTRYTIS-INDUCED KINASE1 plays distinct roles in Arabidopsis resistance to necrotrophic and biotrophic pathogens. Plant Cell 2006, 18, 257–273. [Google Scholar] [CrossRef] [PubMed]
  24. Liu, Z.; Wu, Y.; Yang, F.; Zhang, Y.; Chen, S.; Xie, Q.; Tian, X.; Zhou, J.-M. BIK1 interacts with PEPRs to mediate ethylene-induced immunity. Proc. Natl. Acad. Sci. USA 2013, 110, 6205–6210. [Google Scholar] [CrossRef]
  25. Kadota, Y.; Sklenar, J.; Derbyshire, P.; Stransfeld, L.; Asai, S.; Ntoukakis, V.; Jones, J.D.; Shirasu, K.; Menke, F.; Jones, A.; et al. Direct regulation of the NADPH oxidase RBOHD by the PRR-associated kinase BIK1 during plant immunity. Mol. Cell 2014, 54, 43–55. [Google Scholar] [CrossRef] [PubMed]
  26. Li, L.; Li, M.; Yu, L.; Zhou, Z.; Liang, X.; Liu, Z.; Cai, G.; Gao, L.; Zhang, X.; Wang, Y.; et al. The FLS2-associated kinase BIK1 directly phosphorylates the NADPH oxidase RbohD to control plant im-munity. Cell Host Microbe 2014, 15, 329–338. [Google Scholar] [CrossRef]
  27. Rao, S.; Zhou, Z.; Miao, P.; Bi, G.; Hu, M.; Wu, Y.; Feng, F.; Zhang, X.; Zhou, J.-M. Roles of receptor-like cytoplasmic kinase VII members in pattern-triggered immune signaling. Plant Physiol. 2018, 177, 1679–1690. [Google Scholar] [CrossRef]
  28. Zhang, J.; Li, W.; Xiang, T.; Liu, Z.; Laluk, K.; Ding, X.; Zou, Y.; Gao, M.; Zhang, X.; Chen, S.; et al. Receptor-like cytoplasmic kinases integrate signaling from multiple plant immune receptors and are targeted by a pseudomonas syringae effector. Cell Host Microbe 2010, 7, 290–301. [Google Scholar] [CrossRef]
  29. Lal, N.K.; Nagalakshmi, U.; Hurlburt, N.K.; Flores, R.; Bak, A.; Sone, P.; Ma, X.; Song, G.; Walley, J.; Shan, L.; et al. The receptor-like cytoplasmic kinase BIK1 localizes to the nucleus and regulates defense hormone ex-pression during plant innate immunity. Cell Host Microbe 2018, 23, 485–497. [Google Scholar] [CrossRef]
  30. Liu, J.; Liu, B.; Chen, S.; Gong, B.-Q.; Chen, L.; Zhou, Q.; Xiong, F.; Wang, M.; Feng, D.; Li, J.-F.; et al. A Tyrosine Phosphorylation Cycle Regulates Fungal Activation of a Plant Receptor Ser/Thr Kinase. Cell Host Microbe 2018, 23, 241–253.e6. [Google Scholar] [CrossRef]
  31. Kong, L.; Rodrigues, B.; Kim, J.H.; He, P.; Shan, L. More than an on-and-off switch: Post-translational modifications of plant pattern recognition receptor complexes. Curr. Opin. Plant Biol. 2021, 63, 102051. [Google Scholar] [CrossRef]
  32. Yu, X.Q.; Niu, H.Q.; Liu, C.; Wang, H.L.; Yin, W.; Xia, X. PTI-ETI synergistic signal mechanisms in plant immunity. Plant Biotechnol. J. 2024, 22, 2113–2128. [Google Scholar] [CrossRef]
  33. Laluk, K.; Luo, H.; Chai, M.; Dhawan, R.; Lai, Z.; Mengiste, T. Biochemical and genetic requirements for function of the immune response regulator BOTRY-TIS-INDUCED KINASE1 in plant growth, ethylene signaling, and PAMP-triggered immunity in Arabidopsis. Plant Cell 2011, 23, 2831–2849. [Google Scholar] [CrossRef] [PubMed]
  34. Lin, W.; Lu, D.; Gao, X.; Jiang, S.; Ma, X.; Wang, Z.; Mengiste, T.; He, P.; Shan, L. Inverse modulation of plant immune and brassinosteroid signaling pathways by the receptor-like cytoplasmic kinase BIK1. Proc. Natl. Acad. Sci. USA 2013, 110, 12114–12119. [Google Scholar] [CrossRef]
  35. Li, G.-J.; Chen, K.; Sun, S.; Zhao, Y. Osmotic signaling releases PP2C-mediated inhibition of Arabidopsis SnRK2s via the receptor-like cytoplasmic kinase BIK1. EMBO J. 2024, 43, 1–28. [Google Scholar] [CrossRef] [PubMed]
  36. Shinya, T.; Yamaguchi, K.; Desaki, Y.; Yamada, K.; Narisawa, T.; Kobayashi, Y.; Maeda, K.; Suzuki, M.; Tanimoto, T.; Takeda, J.; et al. Selective regulation of the chitin-induced defense response by the Arabidopsis receptor-like cytoplasmic kinase PBL27. Plant J. 2014, 79, 56–66. [Google Scholar] [CrossRef] [PubMed]
  37. Huang, W.R.; Joosten, M.H. Immune signaling: Receptor-like proteins make the difference. Trends Plant Sci. 2024, 29, 1360–1385. [Google Scholar] [CrossRef]
  38. Thor, K.; Jiang, S.; Michard, E.; George, J.; Scherzer, S.; Huang, S.; Dindas, J.; Derbyshire, P.; Leitão, N.; DeFalco, T.A.; et al. The calcium-permeable channel OSCA1.3 regulates plant stomatal immunity. Nature 2020, 588, 569–573. [Google Scholar] [CrossRef]
  39. Tian, W.; Hou, C.; Ren, Z.; Wang, C.; Zhao, F.; Dahlbeck, D.; Hu, S.; Zhang, L.; Niu, Q.; Li, L.; et al. A calmodulin-gated calcium channel links pathogen patterns to plant immunity. Nature 2019, 572, 131–135. [Google Scholar] [CrossRef]
  40. Kong, L.; Ma, X.; Zhang, C.; Kim, S.-I.; Li, B.; Xie, Y.; Yeo, I.-C.; Thapa, H.; Chen, S.; Devarenne, T.P.; et al. Dual phosphorylation of DGK5-mediated PA burst regulates ROS in plant immunity. Cell 2024, 187, 609–623.e21. [Google Scholar] [CrossRef]
  41. Qi, F.; Li, J.; Ai, Y.; Shangguan, K.; Li, P.; Lin, F.; Liang, Y. DGK5β-derived phosphatidic acid regulates ROS production in plant immunity by stabilizing NADPH oxidase. Cell Host Microbe 2024, 32, 425–440.e7. [Google Scholar] [CrossRef] [PubMed]
  42. Hou, S.; Rodrigues, O.; Liu, Z.; Shan, L.; He, P. Small holes, big impact: Stomata in plant- pathogen-climate epic trifecta. Mol. Plant 2024, 17, 26–49. [Google Scholar] [CrossRef] [PubMed]
  43. Feng, F.; Yang, F.; Rong, W.; Wu, X.; Zhang, J.; Chen, S.; He, C.; Zhou, J.-M. A Xanthomonas uridine 5′-monophosphate transferase inhibits plant immune kinases. Nature 2012, 485, 114–118. [Google Scholar] [CrossRef]
  44. Vierstra, R.D. The ubiquitin-26S proteasome system at the nexus of plant biology. Nat. Rev. Mol. Cell Biol. 2009, 10, 385–397. [Google Scholar] [CrossRef]
  45. Komander, D.; Rape, M. The ubiquitin code. Annu. Rev. Biochem. 2012, 81, 203–229. [Google Scholar] [CrossRef]
  46. Dittmar, G.; Selbach, M. Deciphering the ubiquitin code. Mol. Cell 2017, 65, 779–780. [Google Scholar] [CrossRef] [PubMed]
  47. Patel, R.S.; Pannala, N.M.; Das, C. Reading and writing the ubiquitin code using genetic code expansion. ChemBioChem 2024, 25, e202400190. [Google Scholar] [CrossRef]
  48. Lu, D.; Lin, W.; Gao, X.; Wu, S.; Cheng, C.; Avila, J.; Heese, A.; Devarenne, T.P.; He, P.; Shan, L. Direct ubiquitination of pattern recognition receptor FLS2 attenuates plant innate immunity. Science 2011, 332, 1439–1442. [Google Scholar] [CrossRef]
  49. Trujillo, M.; Ichimura, K.; Casais, C.; Shirasu, K. Negative regulation of PAMP-triggered immunity by an E3 ubiquitin ligase triplet in Arabidopsis. Curr. Biol. 2008, 18, 1396–1401. [Google Scholar] [CrossRef]
  50. Stegmann, M.; Anderson, R.G.; Ichimura, K.; Pecenkova, T.; Reuter, P.; Žárský, V.; McDowell, J.M.; Shirasu, K.; Trujillo, M. The ubiquitin ligase PUB22 targets a subunit of the exocyst complex required for PAMP-triggered responses in Arabidopsis. Plant Cell 2012, 24, 4703–4716. [Google Scholar] [CrossRef]
  51. Furlan, G.; Nakagami, H.; Eschen-Lippold, L.; Jiang, X.; Majovsky, P.; Kowarschik, K.; Hoehenwarter, W.; Lee, J.; Trujillo, M. Changes in PUB22 ubiquitination modes triggered by MITOGEN-ACTIVATED PROTEIN KINASE3 dampen the immune response. Plant Cell 2017, 29, 726–745. [Google Scholar] [CrossRef] [PubMed]
  52. Lee, D.; Lal, N.K.; Lin, Z.-J.D.; Ma, S.; Liu, J.; Castro, B.; Toruño, T.; Dinesh-Kumar, S.P.; Coaker, G. Regulation of reactive oxygen species during plant immunity through phosphorylation and ubiquitination of RBOHD. Nat. Commun. 2020, 11, 1838. [Google Scholar] [CrossRef] [PubMed]
  53. Jiang, Y.; Han, B.; Zhang, H.; Mariappan, K.G.; Bigeard, J.; Colcombet, J.; Hirt, H. MAP 4K4 associates with BIK 1 to regulate plant innate immunity. EMBO Rep. 2019, 20, e47965. [Google Scholar] [CrossRef] [PubMed]
  54. Cui, B.; Pan, Q.; Cui, W.; Wang, Y.; Loake, V.I.P.; Yuan, S.; Liu, F.; Loake, G.J. S-nitrosylation of a receptor-like cytoplasmic kinase regulates plant immunity. Sci. Adv. 2024, 10, eadk3126. [Google Scholar] [CrossRef] [PubMed]
  55. Zhang, M.; Chiang, Y.-H.; Toruño, T.Y.; Lee, D.; Ma, M.; Liang, X.; Lal, N.K.; Lemos, M.; Lu, Y.-J.; Ma, S.; et al. The MAP4 kinase SIK1 ensures robust extracellular ROS burst and antibacterial immunity in plants. Cell Host Microbe 2018, 24, 379–391.e5. [Google Scholar] [CrossRef]
  56. Wang, J.; Grubb, L.E.; Wang, J.; Liang, X.; Li, L.; Gao, C.; Ma, M.; Feng, F.; Li, M.; Li, L.; et al. A regulatory module controlling homeostasis of a plant immune kinase. Mol. Cell 2018, 69, 493–504. [Google Scholar] [CrossRef]
  57. Bai, J.; Zhou, Y.; Sun, J.; Chen, K.; Han, Y.; Wang, R.; Zou, Y.; Du, M.; Lu, D. BIK1 protein homeostasis is maintained by the interplay of different ubiquitin ligases in immune signaling. Nat. Commun. 2023, 14, 4624. [Google Scholar] [CrossRef]
  58. Ma, X.; Claus, L.A.N.; Leslie, M.E.; Tao, K.; Wu, Z.; Liu, J.; Yu, X.; Li, B.; Zhou, J.; Savatin, D.V.; et al. Ligand-induced monoubiquitination of BIK1 regulates plant immunity. Nature 2020, 581, 199–203. [Google Scholar] [CrossRef]
  59. Wang, Y.; Wu, Y.; Zhong, H.; Chen, S.; Wong, K.; Xia, Y. Arabidopsis PUB2 and PUB4 connect signaling components of pattern-triggered immunity. New Phytol. 2022, 233, 2249–2265. [Google Scholar] [CrossRef]
  60. Yu, G.; Derkacheva, M.; Rufian, J.S.; Brillada, C.; Kowarschik, K.; Jiang, S.; Derbyshire, P.; Ma, M.; A DeFalco, T.; Morcillo, R.J.L.; et al. The Arabidopsis E3 ubiquitin ligase PUB4 regulates BIK1 and is targeted by a bacterial type-III effector. EMBO J. 2022, 41, e107257. [Google Scholar] [CrossRef]
  61. Monaghan, J.; Matschi, S.; Shorinola, O.; Rovenich, H.; Matei, A.; Segonzac, C.; Malinovsky, F.G.; Rathjen, J.P.; MacLean, D.; Romeis, T.; et al. The calcium-dependent protein kinase CPK28 buffers plant immunity and regulates BIK1 turnover. Cell Host Microbe 2014, 16, 605–615. [Google Scholar] [CrossRef] [PubMed]
  62. Couto, D.; Niebergall, R.; Liang, X.; Bücherl, C.A.; Sklenar, J.; Macho, A.P.; Ntoukakis, V.; Derbyshire, P.; Altenbach, D.; Maclean, D.; et al. The Arabidopsis protein phosphatase PP2C38 negatively regulates the central immune kinase BIK1. PLoS Pathog. 2016, 12, e1005811. [Google Scholar] [CrossRef]
  63. Liu, Y.; Jackson, E.; Liu, X.; Huang, X.; van der Hoorn, R.A.L.; Zhang, Y.; Li, X. Proteolysis in plant immunity. Plant Cell 2024, 36, 3099–3115. [Google Scholar] [CrossRef] [PubMed]
  64. Liu, X.; Zhou, Y.; Du, M.; Liang, X.; Fan, F.; Huang, G.; Zou, Y.; Bai, J.; Lu, D. The calcium-dependent protein kinase CPK28 is targeted by the ubiquitin ligases ATL31 and ATL6 for proteasome-mediated degradation to fine-tune immune signaling in Arabidopsis. Plant Cell 2022, 34, 679–697. [Google Scholar] [CrossRef]
  65. Robatzek, S.; Chinchilla, D.; Boller, T. Ligand-induced endocytosis of the pattern recognition receptor FLS2 in Arabidopsis. Genes Dev. 2006, 20, 537–542. [Google Scholar] [CrossRef]
  66. Zhou, J.; Liu, D.; Wang, P.; Ma, X.; Lin, W.; Chen, S.; Mishev, K.; Lu, D.; Kumar, R.; Vanhoutte, I.; et al. Regulation of brassinosteroid receptor BRI1 endocytosis and degradation by plant U-box PUB12/PUB13-mediated ubiquitination. Proc. Natl. Acad. Sci. USA 2018, 115, 1906–1915. [Google Scholar] [CrossRef]
  67. Asmamaw, M.D.; Liu, Y.; Zheng, Y.C.; Shi, X.J.; Liu, H.M. Skp2 in the ubiquitin-proteasome system: A comprehensive review. Med. Res. Rev. 2020, 40, 1920–1949. [Google Scholar] [CrossRef]
  68. Nakamura, N. Ubiquitin system. Int. J. Mol. Sci. 2018, 19, 1080. [Google Scholar] [CrossRef] [PubMed]
  69. Grubb, L.E.; Derbyshire, P.; E Dunning, K.; Zipfel, C.; Menke, F.L.H.; Monaghan, J. Large-scale identification of ubiquitination sites on membrane-associated proteins in Arabidopsis thaliana seedlings. Plant Physiol. 2021, 185, 1483–1488. [Google Scholar] [CrossRef]
  70. Damgaard, R.B. The ubiquitin system: From cell signalling to disease biology and new therapeutic opportunities. Cell Death Differ. 2021, 28, 423–426. [Google Scholar] [CrossRef]
  71. Tracz, M.; Bialek, W. Beyond K48 and K63: Non-canonical protein ubiquitination. Cell. Mol. Biol. Lett. 2021, 26, 1. [Google Scholar] [CrossRef] [PubMed]
  72. Varshavsky, A. The ubiquitin system, autophagy, and regulated protein degradation. Annu. Rev. Biochem. 2017, 86, 123–128. [Google Scholar] [CrossRef] [PubMed]
  73. Deshaies, R.J.; Joazeiro, C.A. RING domain E3 ubiquitin ligases. Annu. Rev. Biochem. 2009, 78, 399–434. [Google Scholar] [CrossRef] [PubMed]
  74. Schmukle, A.C.; Walczak, H. No one can whistle a symphony alone—How different ubiquitin linkages cooperate to orchestrate NF-κB activity. J. Cell Sci. 2012, 125, 549–559. [Google Scholar] [CrossRef] [PubMed]
  75. Shabek, N.; Herman-Bachinsky, Y.; Buchsbaum, S.; Lewinson, O.; Haj-Yahya, M.; Hejjaoui, M.; Lashuel, H.A.; Sommer, T.; Brik, A.; Ciechanover, A. The size of the proteasomal substrate determines whether its degradation will be mediated by mono- or polyubiquitylation. Mol. Cell 2012, 48, 87–97. [Google Scholar] [CrossRef]
  76. Zhou, B.; Zeng, L. Conventional and unconventional ubiquitination in plant immunity. Mol. Plant Pathol. 2017, 18, 1313–1330. [Google Scholar] [CrossRef]
  77. Sadowski, M.; Sarcevic, B. Mechanisms of mono- and poly-ubiquitination: Ubiquitination specificity depends on compatibility between the E2 catalytic core and amino acid residues proximal to the lysine. Cell Div. 2010, 5, 19. [Google Scholar] [CrossRef]
  78. Retzer, K.; Moulinier-Anzola, J.; Lugsteiner, R.; Konstantinova, N.; Schwihla, M.; Korbei, B.; Luschnig, C. Endosomally localized RGLG-type E3 RING-finger ligases modulate sorting of ubiquitylation-mimic PIN2. Int. J. Mol. Sci. 2022, 23, 6767. [Google Scholar] [CrossRef]
  79. Yin, X.J.; Volk, S.; Ljung, K.; Mehlmer, N.; Dolezal, K.; Ditengou, F.; Hanano, S.; Davis, S.J.; Schmelzer, E.; Sandberg, G.; et al. Ubiquitin lysine 63 chain-forming ligases regulate apical dominance in Arabidopsis. Plant Cell 2007, 19, 1898–1911. [Google Scholar] [CrossRef]
  80. Yu, J.; Kang, L.; Li, Y.; Wu, C.; Zheng, C.; Liu, P.; Huang, J. RING finger protein RGLG1 and RGLG2 negatively modulate MAPKKK18 mediated drought stress tolerance in Arabidopsis. J. Integr. Plant Biol. 2021, 63, 484–493. [Google Scholar] [CrossRef]
  81. Cheng, M.-C.; Hsieh, E.-J.; Chen, J.-H.; Chen, H.-Y.; Lin, T.-P. Arabidopsis RGLG2, functioning as a RING E3 ligase, interacts with AtERF53 and negatively regulates the plant drought stress response. Plant Physiol. 2012, 158, 363–375. [Google Scholar] [CrossRef] [PubMed]
  82. Wang, X.; Zhang, X.; Song, C.-P.; Gong, Z.; Yang, S.; Ding, Y. PUB25 and PUB26 dynamically modulate ICE1 stability via differential ubiquitination during cold stress in Arabidopsis. Plant Cell 2023, 35, 3585–3603. [Google Scholar] [CrossRef] [PubMed]
  83. Pan, I.C.; Schmidt, W. Functional implications of K63-linked ubiquitination in the iron deficiency response of Arabidopsis roots. Front. Plant Sci. 2014, 4, 542. [Google Scholar] [CrossRef] [PubMed]
Ijms 25 12187 g001
Figure 1. BIK1 acts downstream of multiple PRR complexes and transmits the PAMP/DAMP signaling downstream to induce distinct defenses.
Figure 1. BIK1 acts downstream of multiple PRR complexes and transmits the PAMP/DAMP signaling downstream to induce distinct defenses.
Ijms 25 12187 g001
Ijms 25 12187 g002
Figure 2. The structures of the BIK1 gene and BIK1 protein. (A). Gene structure of BIK1. Blue box indicates exon; white box indicates intron. (B). Protein structure and ubiquitylation sites of BIK1. N, N-terminal domain; K, kinase catalytic domain; C, carboxy-terminal domain. Ubiquitinated lysines, which are shown in blue: RHA3A/B ubiquitylation sites.
Figure 2. The structures of the BIK1 gene and BIK1 protein. (A). Gene structure of BIK1. Blue box indicates exon; white box indicates intron. (B). Protein structure and ubiquitylation sites of BIK1. N, N-terminal domain; K, kinase catalytic domain; C, carboxy-terminal domain. Ubiquitinated lysines, which are shown in blue: RHA3A/B ubiquitylation sites.
Ijms 25 12187 g002
Ijms 25 12187 g003
Figure 3. A model of the multifaceted ubiquitination of BIK1 in plant immunity. (A) BIK1 is regulated by multiple mechanisms. (B) Differential ubiquitination of BIK1 by PUB25/26, RGLG1/2, RHA3A/3B, and PUB4.
Figure 3. A model of the multifaceted ubiquitination of BIK1 in plant immunity. (A) BIK1 is regulated by multiple mechanisms. (B) Differential ubiquitination of BIK1 by PUB25/26, RGLG1/2, RHA3A/3B, and PUB4.
Ijms 25 12187 g003
Table 1. The post-translational modifications of BIK1.
Table 1. The post-translational modifications of BIK1.
Post-Translational ModificationResponsible RegulatorsMolecular FunctionFunctionReference
UbiquitinationPUB25/26Hypophosphorylated BIK1 degradationImmune signalling[56]
RGLG1/2Hypophosphorylated BIK1 accumulationImmune signalling[57]
RHA3A/3BBIK1 release; BIK1 endocytosisImmune signalling[58]
PUB4Hypophosphorylated BIK1 degradation; activated BIK1 accumulationImmune signalling[59,60]
PhosphorylationBAK1BIK1 activation and stabilizationImmune signalling[22]
EFRBIK1 activationImmune signalling[29]
PEPR1/2BIK1 activationImmune signalling[4,5,24]
CERK1/LYK5BIK1 activationImmune signalling[9,10]
BRI1BIK1 activationBR signaling[34]
CPK28Negative regulator of BIK1Immune signalling[61]
MAP4K3/4BIK1 stabilityImmune signalling[53,55]
De-phosphorylationPP2C38Negative regulator of BIK1Immune signalling[62]
S-nitrosylation BIK1 activation and stabilizationImmune signalling[54]
UMPylationAvrACReducing BIK1 kinase activityImmune signalling[43]
Disclaimer/Publisher’s Note: The statements, opinions and data contained in all publications are solely those of the individual author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to people or property resulting from any ideas, methods, instructions or products referred to in the content.

Share and Cite

MDPI and ACS Style

Fu, J.; Wang, H.; Chen, Y.; Zhang, C.; Zou, Y. The Multifaceted Ubiquitination of BIK1 During Plant Immunity in Arabidopsis thaliana. Int. J. Mol. Sci. 2024, 25, 12187. https://doi.org/10.3390/ijms252212187

AMA Style

Fu J, Wang H, Chen Y, Zhang C, Zou Y. The Multifaceted Ubiquitination of BIK1 During Plant Immunity in Arabidopsis thaliana. International Journal of Molecular Sciences. 2024; 25(22):12187. https://doi.org/10.3390/ijms252212187

Chicago/Turabian Style

Fu, Junhong, Huihui Wang, Yuling Chen, Chunguang Zhang, and Yanmin Zou. 2024. "The Multifaceted Ubiquitination of BIK1 During Plant Immunity in Arabidopsis thaliana" International Journal of Molecular Sciences 25, no. 22: 12187. https://doi.org/10.3390/ijms252212187

APA Style

Fu, J., Wang, H., Chen, Y., Zhang, C., & Zou, Y. (2024). The Multifaceted Ubiquitination of BIK1 During Plant Immunity in Arabidopsis thaliana. International Journal of Molecular Sciences, 25(22), 12187. https://doi.org/10.3390/ijms252212187

Note that from the first issue of 2016, this journal uses article numbers instead of page numbers. See further details here.

Article Metrics

Back to TopTop