2025/01/06 by Yuqing Yan, Hui Wang, Yan Bi +2 · 1 voice
Agricultural and Biological Sciences · Biochemistry, Genetics and Molecular Biology · #Cocoa and Sweet Potato Agronomy #Plant tissue culture and regeneration #Ubiquitin and proteasome pathways
paper · doi:10.1111/jipb.13831
openalex publication_date 2025/01/06 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
The rice E3 ubiquitin ligases OsCIE1 and IPI7 mediate the non-proteolytic polyubiquitination of the pattern-recognition receptor kinase OsCERK1 and the transcription factor IPA1, respectively, in response to Magnaporthe oryzae infection, thereby fine-tuning rice growth-immunity trade-offs. To defend against pathogen attacks, plants have evolved a sophisticated immune system comprising pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) and effector-triggered immunity (ETI). Upon recognizing invading pathogens, plant cells rapidly initiate a series of immune signaling events, including a burst of reactive oxygen species (ROS), activation of mitogen-activated protein kinase (MAPK) cascades, calcium flux, phytohormone signaling, and post-translational modifications (PTMs) of target proteins. Since immunity activation is energetically costly and often associated with growth, development, and yield penalties, plants have evolved effective strategies to finely tune immune responses. These strategies maintain a low level of basal immunity that prevents autoimmunity during plant growth and development under normal conditions, while enabling plants to initiate rapid, robust, and effective immune responses upon pathogen infection (Wang et al., 2021). Protein ubiquitination is a major type of PTM that is involved in a wide range of cellular programs, including plant growth, development, abiotic stress responses, and immunity. Ubiquitination involves the sequential activation of an E1 ubiquitin-activating enzyme, an E2 ubiquitin conjugating enzyme, and an E3 ubiquitin ligase, and modulates different fates of ubiquitinated proteins by influencing their stability, activity, and protein–protein interactions. Extensive studies have demonstrated that E3 ligases, key components of the ubiquitination cascade, play pivotal roles in the immunity of rice (Oryza sativa) plants as either positive or negative regulators. Moreover, most of the identified E3 ligases to date exert their immune functions by ubiquitinating their downstream substrates for eventual degradation through the ubiquitin–26S proteasome system (Yan et al., 2024). Emerging evidence suggests that several E3 ligases also participate in balancing rice immunity with growth, development, and yield. For instance, the E3 ubiquitin ligase IDEAL PLANT ARCHITECTURE 1 (IPA1)-INTERACTING PROTEIN 1 (IPI1) precisely modulates rice immunity and flowering by targeting the rice orthologs of Arabidopsis (Arabidopsis thaliana) EARLY FLOWERING 3 (ELF3) for degradation (Xu et al., 2024; Yi et al., 2024). However, the underlying biochemical and molecular mechanisms by which E3 ligases fine-tune rice immunity and yield remain largely unknown. Two recent articles published in Nature and Nature Communications offered clues. Indeed, two rice E3 ligases, namely CHITIN ELICITOR RECEPTOR KINASE 1 (OsCERK1)-INTERACTING-E3 1 (OsCIE1) and IPA1 INTERACTOR 7 (IPI7; also reported as AvrPiz-t INTERACTING PROTEIN 6 (APIP6)), were shown to balance rice immunity and yield by facilitating non-proteolytic ubiquitination of the pattern-recognition receptor kinase OsCERK1 and the transcription factor IPA1, respectively (Shi et al., 2024; Wang et al., 2024). Wang et al. (2024) demonstrated that OsCIE1 preferentially interacted with the active phosphorylated form of OsCERK1 and negatively regulated OsCERK1-activated immunity. Notably, the ubiquitination of OsCERK1 by OsCIE1 did not mark it for proteasomal degradation, but instead inhibited its kinase activity, thereby suppressing OsCERK1-activated downstream immune responses, including MAPK activation and the ROS burst (Wang et al., 2024). This notion is supported by the observation that the Oscie1 mutant exhibited phenotypes similar to those of OsCERK1-overexpressing lines, while Oscerk1 Oscie1 double mutant plants showed largely wild-type phenotypes (Wang et al., 2024). Likewise, Shi et al. (2024) uncovered that IPI7 promoted the non-proteolytic polyubiquitination of IPA1 at lysine 29 (K29) and fine-tuned its transcriptional activation of WRKY45 expression for initiation of immune responses. Notably, ipi7 knockout plants exhibited compromised resistance to Magnaporthe oryzae, suggesting that IPI7 contributes positively to rice immunity. Moreover, knockout of IPI7 neutralized the immunity-boosting effect seen in plants overexpressing the phosphomimic IPA1 variant IPA1S163D, underscoring the beneficial role of IPI7 in IPA1-triggered immunity (Shi et al., 2024). These findings on OsCIE1 and IPI7 provide insight into how rice E3 ligases regulate immunity by non-proteolytically ubiquitinating their substrates, influencing protein activity without leading to degradation. Plants employ complex regulatory mechanisms that balance growth, development, and immunity (Wang et al., 2021). It is worth noting that ubiquitination and phosphorylation are two key mechanisms that regulate the activity of immune-associated proteins, diminishing the fitness cost associated with immune response activation (Wang et al., 2021). A growing body of evidence highlights significant crosstalk between these two PTMs in balancing the plant growth–immunity trade-off. The recent findings by Wang et al. (2024) illustrate how under normal conditions, OsCIE1 prevents OsCERK1-mediated autoimmunity through its ubiquitination, thus promoting growth. Conversely, in the presence of the microbe-associated molecular pattern chitin, OsCERK1 is activated and phosphorylates OsCIE1, inhibiting its E3 ligase activity, which in turn enhances the kinase activity of OsCERK1 in promoting immune responses (Wang et al., 2024). These findings illuminate the crucial functions of OsCIE1 in managing the immunity–yield trade-off by minimizing excessive OsCERK1-triggered immune signaling. Therefore, OsCIE1, as a brake, and OsCERK1, as a switch, establish a dual-state brake–switch relationship through the interplay of ubiquitination and phosphorylation, allowing for rapid and resilient immune responses while avoiding autoimmunity (Figure 1). Regulation of the growth–immunity trade-off by non-proteolytic polyubiquitination of rice OsCERK1 and IPA1 by the E3 ligases OsCIE1 and IPI7 in rice Under normal conditions, the rice E3 ligase OsCIE1 targets the active phosphorylated form of the receptor kinase OsCERK1 for polyubiquitination to repress its kinase activity, potentially preventing OsCERK1-mediated signaling from activating the expression of immunity-related genes (IRGs) and autoimmunity while minimizing fitness costs, thus promoting growth. The transcription factor IPA1 activates the expression of yield-related genes (YRGs), promoting rice growth and productivity. Under pressure from pathogen attacks, Magnaporthe oryzae and the microbe-associated molecular pattern chitin activate OsCERK1 to phosphorylate OsCIE1, attenuating its E3 ligase activity to “release the brake” and initiating OsCERK1-triggered immune responses. M. oryzae infection also accelerates the phosphorylation of IPA1 and promotes the activity of the E3 ligase IPI7 to polyubiquitinate phosphorylated IPA1 at K29. The resulting K29-polyubiquitinated and phosphorylated IPA1 gains enhanced transactivation activity and preferentially transactivates the expression of IRGs, thereby activating immune responses. By contrast, the K29-polyubiquitinated but unphosphorylated form of IPA1 maintains its DNA-binding specificity toward YRGs, potentially compensating for the penalty caused by pathogen-activated IPA1 (K29-polyubiquitinated and phosphorylated). The figure was created with Biorender.com. IPA1 has been extensively studied for its dual roles in promoting rice immunity and yield by transactivating the expression of growth- and immunity-related genes. M. oryzae infection triggers the phosphorylation of IPA1 at serine 163 (S163), altering its DNA-binding specificity from targeting panicle development-related genes to immunity-related genes (Wang et al., 2018). Shi et al. (2024) showed that M. oryzae infection also induces IPI7-mediated non-proteolytic polyubiquitination of IPA1, which serves as a prerequisite for the transactivation of defense genes driven by phosphorylated IPA1 (Shi et al., 2024). Notably, IPI7 does not affect the transcriptional transactivation of growth-related genes by unphosphorylated IPA1 (Shi et al., 2024). Therefore, ubiquitinated but unphosphorylated IPA1 can target growth-related genes, potentially offsetting yield penalties caused by ubiquitinated and phosphorylated pathogen-activated IPA1, confirming the dual roles of IPI7 in facilitating rice immunity while sustaining growth. This idea is supported by the observation that knocking out IPI7 blocks immunity initiated by phosphorylated IPA1 and dramatically mitigates the yield penalty (Shi et al., 2024). These findings suggest an additional regulatory layer orchestrated by PTMs that ensures effective immune responses while minimizing the fitness cost associated with IPA1 activation (Figure 1). Generally, ubiquitinated proteins undergo distinct fates depending on the types of ubiquitination mark they carry. For instance, K48-linked polyubiquitination is particularly well studied and leads to the proteolytic turnover of substrate proteins involved in rice immune responses (Yan et al., 2024). By contrast, non-K48-linked polyubiquitination often contributes to protein stability, internalization, and sorting. However, the current understanding of the biological function and molecular mechanism by which non-K48-linked polyubiquitination balances the plant immunity–growth trade-off remains relatively limited. The studies by Wang et al. (2024) and Shi et al. (2024) provide insight into the intricate molecular mechanisms by which OsCIE1-mediated and IPI7-mediated non-proteolytic polyubiquitination coordinates with phosphorylation to regulate rice immunity and yield (Figure 1), broadening our knowledge of how E3 ligases fine-tune growth and immune responses. Notably, several questions remain. It is well understood that OsCERK1, ubiquitinated by the E3 ligases OsCIE1 and SPOTTED LEAF 11 (SPL11), recruits OsCIE1 and PLANT U-BOX 44 UBIQUITIN LIGASE (OsPUB44) for phosphorylation upon recognition of PAMPs (Ichimaru et al., 2022; Wang et al., 2024). How do these E3 ligases interact during OsCERK1-activated immune responses? Given that IPI7 targets diverse substrates for proteolytic and non-proteolytic polyubiquitination (Shi et al., 2024; Yan et al., 2024), resulting in distinct fates for these substrates and affecting their functions in immunity and growth, how are these regulatory mechanisms synchronized to influence IPI7-based rice immune responses? Additionally, during ubiquitination, E3 ligases pair with specific E2 conjugating enzymes to control the fates of ubiquitinated substrates. For instance, OsCIE1 interacts with E2 enzyme UBIQUITIN CONJUGATING ENZYME 8 (OsUBC8), forming an OsCIE1–OsUBC8 complex, which can be blocked by the OsCERK1-mediated phosphorylation of OsCIE1 at S237 (Wang et al., 2024). Notably, the S237 residue is conserved in E3 ligases across kingdoms, thus serving as a phosphorylation switch that dynamically regulates the function of E3 ligases (Wang et al., 2024). Given the fact that the E2 enzyme OsUBC26 works with IPI7 as a partner (Liu et al., 2021), how are their interactions regulated for differential functions in immunity and growth? How are the substrates ubiquitinated by OsCIE1 and IPA1 deubiquitinated to put a stop to immune responses and promote growth? Which deubiquitinating enzymes are involved in this step? Moreover, IPI1 targets IPA1 for degradation by polyubiquitination at K48 in panicles and at K63 in the shoot apex, thus modulating rice architecture (Wang et al., 2017), while IPI7 polyubiquitinates IPA1 at K27, enhancing its transactivation of immunity-related genes (Shi et al., 2024). What are the molecular mechanisms that enable IPI1 and IPI7 to ubiquitinate IPA1 at different sites for immunity and growth? Addressing these questions will provide fresh perspectives on the regulatory networks comprising E3 ligases in rice immunity and yield, and help develop new strategies to balance growth and immunity for healthier, high-yielding crops. We sincerely thank the National Natural Science Foundation of China (No. 32072403 and No. 31871945) for financial support. The authors declare no conflict of interest. F.S. and Y.Y. conceptualized the manuscript. Y.Y., H.W., Y.B., and L.T. drafted the manuscript and prepared the figure. F.S. revised the manuscript. All authors read and approved the final manuscript.