A VQ-motif-containing protein fine-tunes rice immunity and growth by a hierarchical regulatory mechanism

Genome-wide identification of HbVQ proteins and their interaction with HbWRKY14 to regulate the expression of HbSRPP in Hevea brasiliensis

BACKGROUND

Valine-glutamine motif-containing proteins (VQ proteins) play important roles in plant growth, development and response to stress. However, information on the VQ gene family in rubber tree (Hevea brasiliensis Muell. Arg.) is limited.

RESULTS

In this study, a total of 21 VQ protein genes (named HbVQ1 ~ HbVQ21) were identified in rubber trees and divided into six subfamilies. Gene structure analysis revealed that most of HbVQs had no introns except for HbVQ5 and HbVQ20. Gene expression analysis revealed that HbVQ4, 5, and 21 were expressed at relatively high levels in latex. In addition, HbVQ4, 5, and 21 interact with the WRKY transcription factor HbWRKY14. Transient co-expression of HbVQ4 or HbVQ5 and HbWRKY14 resulted in relieved HbWRKY14-mediated transcription inhibition of the gene encoding small rubber particle protein (HbSRPP), whereas transient co-expression of HbVQ21 and HbWRKY14 resulted in increased HbWRKY14-mediated HbSRPP transcription inhibition.

CONCLUSIONS

In summary, HbVQ4, 5, and 21 interact with HbWRKY14 to regulate the expression of HbSRPP. This study provides insight into the functions of VQ proteins in regulating natural rubber biosynthesis.

Ubiquitination of OsCSN5 by OsPUB45 activates immunity by modulating the OsCUL3a-OsNPR1 module

The COP9 signalosome (CSN) is a highly conserved protein complex in eukaryotes, with CSN5 serving as its critical catalytic subunit. However, the role of CSN5 in plant immunity is largely unexplored. Here, we found that suppression of OsCSN5 in rice enhances resistance against the fungal pathogen Magnaporthe oryzae and the bacterial pathogen Xanthomonas oryzae pv. oryzae (Xoo) without affecting growth. OsCSN5 is ubiquitinated and degraded by the E3 ligase OsPUB45. Overexpression of OsPUB45 increased resistance against M. oryzae and Xoo, while dysfunction of OsPUB45 decreased resistance. In addition, OsCSN5 stabilized OsCUL3a to promote the degradation of a positive regulator OsNPR1. Overexpression of OsPUB45 compromised accumulation of OsCUL3a, leading to stabilization of OsNPR1, whereas mutations in OsPUB45 destabilized OsNPR1. These findings suggest that OsCSN5 stabilizes OsCUL3a to facilitate the degradation of OsNPR1, preventing its constitutive activation without infection. Conversely, OsPUB45 promotes the degradation of OsCSN5, contributing to immunity activation upon pathogen infection.

Multiple functions and regulatory networks of WRKY33 and its orthologs

Arabidopsis thaliana WRKY33 is currently one of the most studied members of the Group I WRKY transcription factor family. Research has confirmed that WRKY33 is involved in the regulation of various biological and abiotic stresses and occupies a central position in the regulatory network. The functional studies of orthologous genes of WRKY33 from other species are also receiving increasing attention. In this article, we summarized thirty-eight orthologous genes of AtWKRY33 from twenty-five different species. Their phylogenetic relationship and conserved WRKY domain were analyzed and compared. Similar to AtWKRY33, the well-studied orthologous gene members from rice and tomato also have multiple functions. In addition to playing important regulatory roles in responding to their specific pathogens, they are also involved in regulating various abiotic stresses and development. AtWKRY33 exerts its multiple functions through a complex regulatory network. Upstream transcription factors or other regulatory factors activate or inhibit the expression of AtWKRY33 at the chromatin and transcriptional levels. Interacting proteins affect the transcriptional activity of AtWKRY33 through phosphorylation, ubiquitination, SUMOylation, competition, or cooperation. The downstream genes are diverse and include three major categories: transcription factors, synthesis, metabolism, and signal transduction of various hormones, and disease resistance genes. In the regulatory network of AtWRKY33 orthologs, many conserved regulatory characteristics have been discovered, such as self-activation and phosphorylation by MAP kinases. This can provide a comparative reference for further studying the functions of other orthologous genes of AtWKRY33.

Rice E3 ubiquitin ligases: From key modulators of host immunity to potential breeding applications

To combat pathogen attacks, plants have developed a highly advanced immune system, which requires tight regulation to initiate robust defense responses while simultaneously preventing autoimmunity. The ubiquitin-proteasome system (UPS), which is responsible for degrading excess or misfolded proteins, has vital roles in ensuring strong and effective immune responses. E3 ligases, as key UPS components, play extensively documented roles in rice immunity by modulating the ubiquitination and degradation of downstream substrates involved in various immune signaling pathways. Here, we summarize the crucial roles of rice E3 ligases in both pathogen/microbe/damage-associated molecular pattern-triggered immunity and effector-triggered immunity, highlight the molecular mechanisms by which E3 ligases function in rice immune signaling, and emphasize the functions of E3 ligases as targets of pathogen effectors for pathogenesis. We also discuss potential strategies for application of immunity-associated E3 ligases in breeding of disease-resistant rice varieties without growth penalty. This review provides a comprehensive and updated understanding of the sophisticated and interconnected regulatory functions of E3 ligases in rice immunity and in balancing immunity with growth and development.

Engineering a conserved immune coreceptor into a primed state enhances fungal resistance in crops without growth penalty

Plants must tactically balance immunity and growth when combating lethal pathogens like fungi. CHITIN ELICITOR RECEPTOR KINASE 1 (CERK1), a conserved cell-surface co-receptor for the fungal elicitor chitin, enables plants to induce chitin-triggered immunity to counteract fungal invasion. Previously, we reported that bacterial infection can prime CERK1 through juxtamembrane (JM) phosphorylation to enhance fungal resistance, which only occurs in Arabidopsis (Arabidopsis thaliana) and its close relatives in Brassicaceae. Here, we aim to transfer the priming mechanism of Arabidopsis CERK1 (AtCERK1) to crop CERK1 via JM substitution. We revealed in protoplasts that the entire AtCERK1 JM variable region (AtJM) is essential for imparting the bacterial elicitor flg22-induced primed state to the Nicotiana benthamiana CERK1 (NbCERK1). The NbCERK1 chimera containing AtJM (NbCERK1AtJM) and similarly constructed rice (Oryza sativa) OsCERK1AtJM could undergo flg22-induced JM phosphorylation and confer enhanced antifungal immunity upon bacterial coinfection. Moreover, the NbCERK1AtJM+3D derivative with AtJM phosphomimetic mutations to mimic a constant primed state and similarly constructed OsCERK1AtJM+3D were sufficient to mediate strengthened chitin responses and fungal resistance in transgenic plants independent of bacterial infection. Importantly, no growth and reproduction defects were observed in these plants. Taken together, this study demonstrates that manipulating the primed state of a cell-surface immune receptor offers an effective approach to improve disease resistance in crops without compromising growth and yield and showcases how fundamental insights in plant biology can be translated into crop breeding applications.

Phytochrome B promotes blast disease resistance and enhances yield in rice

Phytochromes are red/far-red light receptors that regulate various aspects of plant growth, development, and stress responses. The precise mechanism by which phytochrome B (PhyB)-mediated light signaling influences plant defense and development remains unclear. In this study, we showed that PhyB enhances rice (Oryza sativa) blast disease resistance, tillering, and grain size compared to wild-type plants. Notably, PhyB interacted with and degraded grassy tiller 1 (GT1), a negative regulator of tiller development. Knockdown of GT1 in a phyB background partially rescued the diminished tillering of phyB. However, GT1 negatively regulates rice resistance to blast, suggesting that PhyB degradation of GT1 promotes tillering but not blast resistance. Previously, PhyB was found to interact with and degrade phytochrome-interacting factor 15 (PIL15), a key regulator of seed development that reduces rice resistance to blast and seed size. pil15 mutation in phyB mutants rescued phyB seed size and blast resistance, suggesting that PhyB might interact with and degrade PIL15 to negatively regulate blast resistance and seed size. PIL15 directly activated sugar will be eventually exported transporter 2a (SWEET2a). sweet2a mutants were less susceptible to blast disease compared to wild type. Collectively, these data demonstrate that PhyB promotes rice yield and blast resistance by inhibiting the transcription factors GT1 and PIL15 and downstream signaling.

Haplotype-resolved genome of a heterozygous wild peach reveals the PdaWRKY4-PdaCYP716A1 module mediates resistance to aphids by regulating betulin biosynthesis

Wild species of domesticated crops provide valuable genetic resources for resistance breeding. Prunus davidiana, a wild relative of peach with high heterozygosity and diverse stress tolerance, exhibits high resistance against aphids. However, the highly heterozygous genome of P. davidiana makes determining the underlying factors influencing resistance traits challenging. Here, we present the 501.7 Mb haplotype-resolved genome assembly of P. davidiana. Genomic comparisons of the two haplotypes revealed 18,152 structural variations, 2,699 Pda_hap1-specific and 2,702 Pda_hap2-specific genes, and 1,118 allele-specific expressed genes. Genome composition indicated 4.1% of the P. davidiana genome was non-peach origin, out of which 94.5% was derived from almond. Based on the haplotype genome, the aphid resistance quantitative trait locus (QTL) was mapped at the end of Pda03. From the aphid resistance QTL, PdaWRKY4 was identified as the major dominant gene, with a 9-bp deletion in its promoter of the resistant phenotype. Specifically, PdaWRKY4 regulates aphid resistance by promoting PdaCYP716A1-mediated anti-aphid metabolite betulin biosynthesis. Moreover, we employed a genome design to develop a breeding workflow for rapidly and precisely producing aphid-resistant peaches. In conclusion, this study identifies a novel aphid resistance gene and provides insights into genome design for the development of resistant fruit cultivars.

Jasmonic acid mediates Ca2+ dependent signal transduction and plant immunity

Pathogen attacks can cause significant damage to plants, posing a threaten to global food production. Plants have developed exquisite methods to rapidly store a key defensive hormone jasmonate (JA), which stimulates their entire evolutionary adaptive response to pathogen attack. However, understanding how plants initiate JA biosynthesis in response to pathogen attacks has remained elusive. In this review, we discuss the newly discovered JAV1-JAZ8-WRKY51 (JJW) complex, which plays a crucial role in regulating JA production to deter insect attacks. The JJW complex inhibits JA production in plants, maintaining a low baseline level of JA that promotes optimal plant development. However, when plants are attacked by insects, a rapid influx of calcium stimulates the JAV1 calcium-dependent protein phosphate, leading to the breakdown of the JJW complex and the activation of JA production. This surge in JA levels, initiates plant defense mechanisms against the invading insects. These findings shed light on the intricate defense system that plants have evolved to combat diseases.

Effectors and environment modulating rice blast disease: from understanding to effective control

Rice blast is a highly destructive crop disease that requires the interplay of three essential factors: the virulent blast fungus, the susceptible rice plant, and favorable environmental conditions. Although previous studies have focused mainly on the pathogen and rice, recent research has shed light on the molecular mechanisms by which the blast fungus and environmental conditions regulate host resistance and contribute to blast disease outbreaks. This review summarizes significant achievements in understanding the sophisticated modulation of blast resistance by Magnaporthe oryzae effectors and the dual regulatory mechanisms by which environmental conditions influence rice resistance and virulence of the blast fungus. Furthermore, it emphasizes potential strategies for developing blast-resistant rice varieties to effectively control blast disease.

Genome wide association study reveals new genes for resistance to striped stem borer in rice (Oryza sativa L.)

Rice is one of the most important food crops in the world and is important for global food security. However, damage caused by striped stem borer (SSB) seriously threatens rice production and can cause significant yield losses. The development and use of resistant rice varieties or genes is currently the most effective strategy for controlling SSB. We genotyped 201 rice samples using 2849855 high-confidence single nucleotide polymorphisms (SNPs). We conducted a genome-wide association study (GWAS) based on observed variation data of 201 rice cultivars resistant to SSB. We obtained a quantitative trait locus (QTL)-qRSSB4 that confers resistance to SSB. Through annotation and analysis of genes within the qRSSB4 locus, as well as qRT-PCR detection in resistant rice cultivars, we ultimately selected the candidate gene LOC_Os04g34140 (named OsRSSB4) for further analysis. Next, we overexpressed the candidate gene OsRSSB4 in Nipponbare through transgenic methods, resulting in OsRSSB4 overexpressing lines (OsRSSB4OE). In addition, we evaluated the insect resistance of OsRSSB4OE lines using wild type (Nipponbare) as a control. The bioassay experiment results of live plants showed that after 20 days of inoculation with SSB, the withering heart rate of OsRSSB4OE-34 and OsRSSB4OE-39 lines was only 8.3% and 0%, with resistance levels of 1 and 0, respectively; however, the withering heart rate of the wild-type reached 100%, with a resistance level of 9. The results of the in vitro stem bioassay showed that, compared with the wild-type, the average corrected mortality rate of the SSB fed on the OsRSSB4OE line reached 94.3%, and the resistance reached a high level. In summary, we preliminarily confirmed that OsRSSB4 positively regulates the defense of rice against SSB. This research findings reveal new SSB resistance gene resources, providing an important genetic basis for SSB resistance breeding in rice crops.

A distinct protein posttranslational modifications-linked OsATL32-OsPPKL2-OsGSK2 loop modulates rice immunity against blast disease

Protein posttranslational modifications play crucial roles in plant immunity through modulating a complicated signaling network mediated by different hormones. We previously demonstrated that OsATL32, an ATL-type E3 ligase, negatively contributes to rice immunity against Magnaporthe oryzae. Here, we show that OsATL32 forms a loop with OsPPKL2 and OsGSK2 through distinct protein posttranslational modifications to modulate rice immunity. OsATL32 ubiquitinates OsPPKL2, a protein phosphatase with Kelch-like repeat domains that exerts positive roles in regulating rice immunity against M. oryzae and chitin-triggered immune responses, for degradation. The glycogen synthase kinase 2 (OsGSK2), which acts as a negative regulator of rice immunity against M. oryzae and chitin-triggered immune responses, phosphorylates OsATL32 to elevate its protein stability and E3 ligase activity on OsPPKL2. Moreover, OsPPKL2 directly dephosphorylates OsGSK2, affecting its kinase activity on substrates including OsATL32 for phosphorylation. Like OsGSK2 as a BR signaling repressor, OsATL32 negatively regulates BR signaling; conversely, OsPPKL2 plays a positive role in BR signaling. These findings provide a molecular mechanism in which OsATL32 serves as a node connecting BR signaling and immunity by associating with OsPPKL2 and OsGSK2, assembling into a distinct protein posttranslational modifications-linked loop that functions in rice BR signaling and immunity.

The rice E3 ubiquitin ligase-transcription factor module targets two trypsin inhibitors to enhance broad-spectrum disease resistance

Broad-spectrum disease resistance (BSR) is crucial for controlling plant diseases and relies on immune signals that are subject to transcriptional and post-translational regulation. How plants integrate and coordinate these signals remains unclear. We show here that the rice really interesting new gene (RING)-type E3 ubiquitin ligase OsRING113 targets APIP5, a negative regulator of plant immunity and programmed cell death (PCD), for 26S proteasomal degradation. The osring113 mutants in Nipponbare exhibited decreased BSR, while the overexpressing OsRING113 plants showed enhanced BSR against Magnaporthe oryzae (M. oryzae) and Xanthomonas oryzae pv. oryzae (Xoo). Furthermore, APIP5 directly suppressed the transcription of the Bowman-Birk trypsin inhibitor genes OsBBTI5 and AvrPiz-t-interacting protein 4 (APIP4). Overexpression of these two genes, which are partially required for APIP5-mediated PCD and disease resistance, conferred BSR. OsBBTI5 and APIP4 associated with and stabilized the pathogenesis-related protein OsPR1aL, which promotes M. oryzae resistance. Our results identify an immune module with integrated and coordinated hierarchical regulations that confer BSR in plants.

OsATL32 ubiquitinates the reactive oxygen species-producing OsRac5-OsRbohB module to suppress rice immunity

Ubiquitination-mediated protein degradation is integral to plant immunity, with E3 ubiquitin ligases acting as key factors in this process. Here, we report the functions of OsATL32, a plasma membrane-localized Arabidopsis Tóxicos En Levadura (ATL)-type E3 ubiquitin ligase, in rice (Oryza sativa) immunity and its associated regulatory network. We found that the expression of OsATL32 is downregulated in both compatible and incompatible interactions between rice and the rice blast fungus Magnaporthe oryzae. The OsATL32 protein level declines in response to infection by a compatible M. oryzae strain or to chitin treatment. OsATL32 negatively regulates rice resistance to blast and bacterial leaf blight diseases, as well as chitin-triggered immunity. Biochemical and genetic studies revealed that OsATL32 suppresses pathogen-induced reactive oxygen species (ROS) accumulation by mediating ubiquitination and degradation of the ROS-producing OsRac5-OsRbohB module, which enhances rice immunity against M. oryzae. The protein phosphatase PHOSPHATASE AND TENSIN HOMOLOG enhances rice blast resistance by dephosphorylating OsATL32 and promoting its degradation, preventing its negative effect on rice immunity. This study provides insights into the molecular mechanism by which the E3 ligase OsATL32 targets a ROS-producing module to undermine rice immunity.

JrPHL8-JrWRKY4-JrSTH2L module regulates resistance to Colletotrichum gloeosporioides in walnut

Walnut anthracnose (Colletotrichum gloeosporioides) reduces walnut yield and quality and seriously threatens the healthy development of the walnut industry. WRKY transcription factors (TFs) are crucial regulatory factors involved in plant-pathogen interactions. Our previous transcriptome analysis results indicate that JrWRKY4 responds to infection by C. gloeosporioides, but its specific regulatory network and disease resistance mechanism are still unclear. Herein, the characteristics of JrWRKY4 as a transcription activator located in the nucleus were first identified. Gain-of-function and loss-of-function analyses showed that JrWRKY4 could enhance walnut resistance against C. gloeosporioides. A series of molecular experiments showed that JrWRKY4 directly interacted with the promoter region of JrSTH2L and positively regulated its expression. In addition, JrWRKY4 interacted with JrVQ4 to form the protein complex, which inhibited JrWRKY4 for the activation of JrSTH2L. Notably, a MYB TF JrPHL8 interacting with the JrWRKY4 promoter has also been identified, which directly bound to the MBS element in the promoter of JrWRKY4 and induced its activity. Our study elucidated a novel mechanism of the JrPHL8-JrWRKY4-JrSTH2L in regulating walnut resistance to anthracnose. This mechanism improves our understanding of the molecular mechanism of WRKY TF mediated resistance to anthracnose in walnut, which provides new insights for molecular breeding of disease-resistant walnuts in the future.

Lipid transfer protein StLTPa enhances potato disease resistance against different pathogens by binding and disturbing the integrity of pathogens plasma membrane

Potato is the third most important food crop worldwide. Potato production suffers from severe diseases caused by multiple detrimental plant pathogens, and broad-spectrum disease resistance genes are rarely identified in potato. Here we identified the potato non-specific lipid transfer protein StLTPa, which enhances species none-specific disease resistance against various pathogens, such as the oomycete pathogen Phytophthora infestans, the fungal pathogens Botrytis cinerea and Verticillium dahliae, and the bacterial pathogens Pectobacterium carotovorum and Ralstonia solanacearum. The StLTPa overexpression potato lines do not show growth penalty. Furthermore, we provide evidence that StLTPa binds to lipids present in the plasma membrane (PM) of the hyphal cells of P. infestans, leading to an increased permeability of the PM. Adding of PI(3,5)P2 and PI(3)P could compete the binding of StLTPa to pathogen PM and reduce the inhibition effect of StLTPa. The lipid-binding activity of StLTPa is essential for its role in pathogen inhibition and promotion of potato disease resistance. We propose that StLTPa enhances potato broad-spectrum disease resistance by binding to, and thereby promoting the permeability of the PM of the cells of various pathogens. Overall, our discovery illustrates that increasing the expression of a single gene in potato enhances potato disease resistance against different pathogens without growth penalty.

Transcription factor WRKY75 maintains auxin homeostasis to promote tomato defense against Pseudomonas syringae

The hemibiotrophic bacterial pathogen Pseudomonas syringae infects a range of plant species and causes enormous economic losses. Auxin and WRKY transcription factors play crucial roles in plant responses to P. syringae, but their functional relationship in plant immunity remains unclear. Here, we characterized tomato (Solanum lycopersicum) SlWRKY75, which promotes defenses against P. syringae pv. tomato (Pst) DC3000 by regulating plant auxin homeostasis. Overexpressing SlWRKY75 resulted in low free indole-3-acetic acid (IAA) levels, leading to attenuated auxin signaling, decreased expansin transcript levels, upregulated expression of PATHOGENESIS-RELATED GENES (PRs) and NONEXPRESSOR OF PATHOGENESIS-RELATED GENE 1 (NPR1), and enhanced tomato defenses against Pst DC3000. RNA interference-mediated repression of SlWRKY75 increased tomato susceptibility to Pst DC3000. Yeast one-hybrid, electrophoretic mobility shift assays, and luciferase activity assays suggested that SlWRKY75 directly activates the expression of GRETCHEN HAGEN 3.3 (SlGH3.3), which encodes an IAA-amido synthetase. SlGH3.3 enhanced tomato defense against Pst DC3000 by converting free IAA to the aspartic acid (Asp)-conjugated form IAA-Asp. In addition, SlWRKY75 interacted with a tomato valine-glutamine (VQ) motif-containing protein 16 (SlVQ16) in vivo and in vitro. SlVQ16 enhanced SlWRKY75-mediated transcriptional activation of SlGH3.3 and promoted tomato defense responses to Pst DC3000. Our findings illuminate a mechanism in which the SlVQ16-SlWRKY75 complex participates in tomato pathogen defense by positively regulating SlGH3.3-mediated auxin homeostasis.

Overexpression of Calcineurin B-like Interacting Protein Kinase 31 Promotes Lodging and Sheath Blight Resistance in Rice

A breakthrough "Green Revolution" in rice enhanced lodging resistance by using gibberellin-deficient semi-dwarf varieties. However, the gibberellic acid (GA) signaling regulation on rice disease resistance remains unclear. The resistance test showed that a positive GA signaling regulator DWARF1 mutant d1 was more susceptible while a negative GA signaling regulator Slender rice 1 (SLR1) mutant was less susceptible to sheath blight (ShB), one of the major rice diseases, suggesting that GA signaling positively regulates ShB resistance. To isolate the regulator, which simultaneously regulates rice lodging and ShB resistance, SLR1 interactors were isolated. Yeast two-hybrid (Y2H), bimolecular fluorescence complementation (BiFC), and Co-IP assay results indicate that SLR1 interacts with Calcineurin B-like-interacting protein kinase 31 (CIPK31). cipk31 mutants exhibited normal plant height, but CIPK31 OXs showed semi-dwarfism. In addition, the SLR1 level was much higher in CIPK31 OXs than in the wild-type, suggesting that CIPK31 OX might accumulate SLR1 to inhibit GA signaling and thus regulate its semi-dwarfism. Recently, we demonstrated that CIPK31 interacts and inhibits Catalase C (CatC) to accumulate ROS, which promotes rice disease resistance. Interestingly, CIPK31 interacts with Vascular Plant One Zinc Finger 2 (VOZ2) in the nucleus, and expression of CIPK31 accumulated VOZ2. Inoculation of Rhizoctonia solani AG1-IA revealed that the voz2 mutant was more susceptible to ShB. Thus, these data prove that CIPK31 promotes lodging and ShB resistance by regulating GA signaling and VOZ2 in rice. This study provides a valuable reference for rice ShB-resistant breeding.

Revisiting growth-defence trade-offs and breeding strategies in crops

Plants have evolved a multi-layered immune system to fight off pathogens. However, immune activation is costly and is often associated with growth and development penalty. In crops, yield is the main breeding target and is usually affected by high disease resistance. Therefore, proper balance between growth and defence is critical for achieving efficient crop improvement. This review highlights recent advances in attempts designed to alleviate the trade-offs between growth and disease resistance in crops mediated by resistance (R) genes, susceptibility (S) genes and pleiotropic genes. We also provide an update on strategies for optimizing the growth-defence trade-offs to breed future crops with desirable disease resistance and high yield.

Valsa mali PR1-like protein modulates an apple valine-glutamine protein to suppress JA signaling-mediated immunity

Apple Valsa canker (AVC) is a devastating disease of apple (Malus × domestica), caused by Valsa mali (Vm). The Cysteine-rich secretory protein, Antigen 5, and Pathogenesis-related protein 1 (CAP) superfamily protein PATHOGENESIS-RELATED PROTEIN 1-LIKE PROTEIN c (VmPR1c) plays an important role in the pathogenicity of Vm. However, the mechanisms through which it exerts its virulence function in Vm-apple interactions remain unclear. In this study, we identified an apple valine-glutamine (VQ)-motif-containing protein, MdVQ29, as a VmPR1c target protein. MdVQ29-overexpressing transgenic apple plants showed substantially enhanced AVC resistance as compared with the wild type. MdVQ29 interacted with the transcription factor MdWRKY23, which was further shown to bind to the promoter of the jasmonic acid (JA) signaling-related gene CORONATINE INSENSITIVE 1 (MdCOI1) and activate its expression to activate the JA signaling pathway. Disease evaluation in lesion areas on infected leaves showed that MdVQ29 positively modulated apple resistance in a MdWRKY23-dependent manner. Furthermore, MdVQ29 promoted the transcriptional activity of MdWRKY23 toward MdCOI1. In addition, VmPR1c suppressed the MdVQ29-enhanced transcriptional activation activity of MdWRKY23 by promoting the degradation of MdVQ29 and inhibiting MdVQ29 expression and the MdVQ29-MdWRKY23 interaction, thereby interfering with the JA signaling pathway and facilitating Vm infection. Overall, our results demonstrate that VmPR1c targets MdVQ29 to manipulate the JA signaling pathway to regulate immunity. Thus, this study provides an important theoretical basis and guidance for mining and utilizing disease-resistance genetic resources for genetically improving apples.

The GRAS protein OsDLA involves in brassinosteroid signalling and positively regulates blast resistance by forming a module with GSK2 and OsWRKY53 in rice

Brassinosteroids (BRs) play a crucial role in shaping the architecture of rice (Oryza sativa) plants. However, the regulatory mechanism of BR signalling in rice immunity remains largely unexplored. Here we identify a rice mutant dla, which exhibits decreased leaf angles and is insensitive to 24-epiBL (a highly active synthetic BR), resembling the BR-deficient phenotype. The dla mutation caused by a T-DNA insertion in the OsDLA gene leads to downregulation of the causative gene. The OsDLA knockout plants display reduced leaf angles and less sensitivity to 24-epiBL. In addition, both dla mutant and OsDLA knockout plants are more susceptible to rice blast compared to the wild type. OsDLA is a GRAS transcription factor and interacts with the BR signalling core negative regulator, GSK2. GSK2 phosphorylates OsDLA for degradation via the 26S proteasome. The GSK2 RNAi line exhibits enhanced rice blast resistance, while the overexpression lines thereof show susceptibility to rice blast. Furthermore, we show that OsDLA interacts with and stabilizes the WRKY transcription factor OsWRKY53, which has been demonstrated to positively regulate BR signalling and blast resistance. OsWRKY53 directly binds the promoter of PBZ1 and activates its expression, and this activation can be enhanced by OsDLA. Together, our findings unravel a novel mechanism whereby the GSK2-OsDLA-OsWRKY53 module coordinates blast resistance and plant architecture via BR signalling in rice.

The role and pathway of VQ family in plant growth, immunity, and stress response

MAIN CONCLUSION

This review provides a detailed description of the function and mechanism of VQ family gene, which is helpful for further research and application of VQ gene resources to improve crops. Valine-glutamine (VQ) motif-containing proteins are a large class of transcriptional regulatory cofactors. VQ proteins have their own unique molecular characteristics. Amino acids are highly conserved only in the VQ domain, while other positions vary greatly. Most VQ genes do not contain introns and the length of their proteins is less than 300 amino acids. A majority of VQ proteins are predicted to be localized in the nucleus. The promoter of many VQ genes contains stress or growth related elements. Segment duplication and tandem duplication are the main amplification mechanisms of the VQ gene family in angiosperms and gymnosperms, respectively. Purification selection plays a crucial role in the evolution of many VQ genes. By interacting with WRKY, MAPK, and other proteins, VQ proteins participate in the multiple signaling pathways to regulate plant growth and development, as well as defense responses to biotic and abiotic stresses. Although there have been some reports on the VQ gene family in plants, most of them only identify family members, with little functional verification, and there is also a lack of complete, detailed, and up-to-date review of research progress. Here, we comprehensively summarized the research progress of VQ genes that have been published so far, mainly including their molecular characteristics, biological functions, importance of VQ motif, and working mechanisms. Finally, the regulatory network and model of VQ genes were drawn, a precise molecular breeding strategy based on VQ genes was proposed, and the current problems and future prospects were pointed out, providing a powerful reference for further research and utilization of VQ genes in plant improvement.

Pijx confers broad-spectrum seedling and panicle blast resistance by promoting the degradation of ATP β subunit and OsRbohC-mediated ROS burst in rice

Rice blast, caused by the fungal pathogen Magnaporthe oryzae, is one of the most important diseases of rice. Utilization of blast-resistance genes is the most economical, effective, and environmentally friendly way to control the disease. However, genetic resources with broad-spectrum resistance (BSR) that is effective throughout the rice growth period are rare. In this work, using a genome-wide association study, we identify a new blast-resistance gene, Pijx, which encodes a typical CC-NBS-LRR protein. Pijx is derived from a wild rice species and confers BSR to M. oryzae at both the seedling and panicle stages. The functions of the resistant haplotypes of Pijx are confirmed by gene knockout and overexpression experiments. Mechanistically, the LRR domain in Pijx interacts with and promotes the degradation of the ATP synthase β subunit (ATPb) via the 26S proteasome pathway. ATPb acts as a negative regulator of Pijx-mediated panicle blast resistance, and interacts with OsRbohC to promote its degradation. Consistently, loss of ATPb function causes an increase in NAPDH content and ROS burst. Remarkably, when Pijx is introgressed into two japonica rice varieties, the introgression lines show BSR and increased yields that are approximately 51.59% and 79.31% higher compared with those of their parents in a natural blast disease nursery. In addition, we generate PPLPijx Pigm and PPLPijx Piz-t pyramided lines and these lines also have higher BSR to panicle blast compared with Pigm- or Piz-t-containing rice plants. Collectively, this study demonstrates that Pijx not only confers BSR to M. oryzae but also maintains high and stable rice yield, providing new genetic resources and molecular targets for breeding rice varieties with broad-spectrum blast resistance.

Large-Scale Identification and Characterization Analysis of VQ Family Genes in Plants, Especially Gymnosperms

VQ motif-containing (VQ) proteins are a class of transcription regulatory cofactors widely present in plants, playing crucial roles in growth and development, stress response, and defense. Although there have been some reports on the member identification and functional research of VQ genes in some plants, there is still a lack of large-scale identification and clear graphical presentation of their basic characterization information to help us to better understand this family. Especially in gymnosperms, the VQ family genes and their evolutionary relationships have not yet been reported. In this study, we systematically identified 2469 VQ genes from 56 plant species, including bryophytes, gymnosperms, and angiosperms, and analyzed their molecular and evolutionary features. We found that amino acids are only highly conserved in the VQ domain, while other positions are relatively variable; most VQ genes encode relatively small proteins and do not have introns. The GC content in Poaceae plants is the highest (up to 70%); these VQ proteins can be divided into nine subgroups. In particular, we analyzed the molecular characteristics, chromosome distribution, duplication events, and expression levels of VQ genes in three gymnosperms: Ginkgo biloba, Taxus chinensis, and Pinus tabuliformis. In gymnosperms, VQ genes are classified into 11 groups, with highly similar motifs in each group; most VQ proteins have less than 300 amino acids and are predicted to be located in nucleus. Tandem duplication is an important driving force for the expansion of the VQ gene family, and the evolutionary processes of most VQ genes and duplication events are relatively independent; some candidate VQ genes are preliminarily screened, and they are likely to be involved in plant growth and stress and defense responses. These results provide detailed information and powerful references for further understanding and utilizing the VQ family genes in various plants.

MdVQ10 promotes wound-triggered leaf senescence in association with MdWRKY75 and undergoes antagonistic modulation of MdCML15 and MdJAZs in apple

Wounding stress leads to leaf senescence. However, the underlying molecular mechanism has not been elucidated. In this study, we investigated the role of the MdVQ10-MdWRKY75 module in wound-induced leaf senescence. MdWRKY75 was identified as a key positive modulator of wound-induced leaf senescence by activating the expression of the senescence-associated genes MdSAG12 and MdSAG18. MdVQ10 interacted with MdWRKY75 to enhance MdWRKY75-activated transcription of MdSAG12 and MdSAG18, thereby promoting leaf senescence triggered by wounding. In addition, the calmodulin-like protein MdCML15 promoted MdVQ10-mediated leaf senescence by stimulating the interaction between MdVQ10 and MdWRKY75. Moreover, the jasmonic acid signaling repressors MdJAZ12 and MdJAZ14 antagonized MdVQ10-mediated leaf senescence by weakening the MdVQ10-MdWRKY75 interaction. Our results demonstrate that the MdVQ10-MdWRKY75 module is a key modulator of wound-induced leaf senescence and provides insights into the mechanism of leaf senescence caused by wounding.

Genome-wide identification and expression analysis of VQ gene family under abiotic stress in Coix lacryma-jobi L

BACKGROUND

Valine-glutamine (VQ) proteins are non-specific plant proteins that have a highly conserved motif: FxxhVQxhTG. These proteins are involved in the development of various plant organs such as seeds, hypocotyls, flowers, leaves and also play a role in response to salt, drought and cold stresses. Despite their importance, there is limited information available on the evolutionary and structural characteristics of VQ family genes in Coix lacryma-jobi.

RESULTS

In this study, a total of 31 VQ genes were identified from the coix genome and classified into seven subgroups (I-VII) based on phylogenetic analysis. These genes were found to be unevenly distributed on 10 chromosomes. Gene structure analysis revealed that these genes had a similar type of structure within each subfamily. Moreover, 27 of ClVQ genes were found to have no introns. Conserved domain and multiple sequence alignment analysis revealed the presence of a highly conserved sequences in the ClVQ protein. This research utilized quantitative real-time PCR (qRT-PCR) and promoter analysis to investigate the expression of ClVQ genes under different stress conditions. Results showed that most ClVQ genes responded to polyethylene glycol, heat treatment, salt, abscisic acid and methyl jasmonate treatment with varying degrees of expression. Furthermore, some ClVQ genes exhibited significant correlation in expression changes under abiotic stress, indicating that these genes may act synergistically in response to adversarial stress. Additionally, yeast dihybrid verification revealed an interaction between ClVQ4, ClVQ12, and ClVQ26.

CONCLUSIONS

This study conducted a genome-wide analysis of the VQ gene family in coix, including an examination of phylogenetic relationships, conserved domains, cis-elements and expression patterns. The goal of the study was to identify potential drought resistance candidate genes, providing a theoretical foundation for molecular resistance breeding.

Genome-wide characterization of the VQ genes in Triticeae and their functionalization driven by polyploidization and gene duplication events in wheat

Valine-glutamine motif-containing (VQ) proteins are transcriptional cofactors widely involved in plant growth, development, and response to various stresses. Although the VQ family has been genome-wide identified in some species, but the knowledge regarding duplication-driven functionalization of VQ genes among evolutionarily related species is still lacking. Here, 952 VQ genes have been identified from 16 species, emphasizing seven Triticeae species including the bread wheat. Comprehensive phylogenetic and syntenic analyses allow us to establish the orthologous relationship of VQ genes from rice (Oryza sativa) to bread wheat (Triticum aestivum). The evolutionary analysis revealed that whole-genome duplication (WGD) drives the expansion of OsVQs, while TaVQs expansion is associated with a recent burst of gene duplication (RBGD). We also analyzed the motif composition and molecular properties of TaVQ proteins, enriched biological functions, and expression patterns of TaVQs. We demonstrate that WGD-derived TaVQs have become divergent in both protein motif composition and expression pattern, while RBGD-derived TaVQs tend to adopt specific expression patterns, suggesting their functionalization in certain biological processes or in response to specific stresses. Furthermore, some RBGD-derived TaVQs are found to be associated with salt tolerance. Several of the identified salt-related TaVQ proteins were located in the cytoplasm and nucleus and their salt-responsive expression patterns were validated by qPCR analysis. Yeast-based functional experiments confirmed that TaVQ27 may be a new regulator to salt response and regulation. Overall, this study lays the foundation for further functional validation of VQ family members within the Triticeae species.

Genome-Wide Identification and Characterization of the VQ Motif-Containing Gene Family Based on Their Evolution and Expression Analysis under Abiotic Stress and Hormone Treatments in Foxtail Millet (Setaria italica L.)

Valine-glutamine (VQ) motif-containing proteins are transcriptional regulatory cofactors that play critical roles in plant growth and response to biotic and abiotic stresses. However, information on the VQ gene family in foxtail millet (Setaria italica L.) is currently limited. In this study, a total of 32 SiVQ genes were identified in foxtail millet and classified into seven groups (I-VII), based on the constructed phylogenetic relationships; the protein-conserved motif showed high similarity within each group. Gene structure analysis showed that most SiVQs had no introns. Whole-genome duplication analysis revealed that segmental duplications contributed to the expansion of the SiVQ gene family. The cis-element analysis demonstrated that growth and development, stress response, and hormone-response-related cis-elements were all widely distributed in the promoters of the SiVQs. Gene expression analysis demonstrated that the expression of most SiVQ genes was induced by abiotic stress and phytohormone treatments, and seven SiVQ genes showed significant upregulation under both abiotic stress and phytohormone treatments. A potential interaction network between SiVQs and SiWRKYs was predicted. This research provides a basis to further investigate the molecular function of VQs in plant growth and abiotic stress responses.

Genome-wide comparative analysis of the valine glutamine motif containing genes in four Ipomoea species

BACKGROUND

Genes with valine glutamine (VQ) motifs play an essential role in plant growth, development, and resistance to biotic and abiotic stresses. However, little information on the VQ genes in sweetpotato and other Ipomoea species is available.

RESULTS

This study identified 55, 58, 50 and 47 VQ genes from sweetpotato (I. batatas), I.triflida, I. triloba and I. nil, respectively. The phylogenetic analysis revealed that the VQ genes formed eight clades (I-VII), and the members in the same group exhibited similar exon-intron structure and conserved motifs distribution. The distribution of the VQ genes among the chromosomes of Ipomoea species was disproportional, with no VQ genes mapped on a few of each species' chromosomes. Duplication analysis suggested that segmental duplication significantly contributes to their expansion in sweetpotato, I.trifida, and I.triloba, while the segmental and tandem duplication contributions were comparable in I.nil. Cis-regulatory elements involved in stress responses, such as W-box, TGACG-motif, CGTCA-motif, ABRE, ARE, MBS, TCA-elements, LTR, and WUN-motif, were detected in the promoter regions of the VQ genes. A total of 30 orthologous groups were detected by syntenic analysis of the VQ genes. Based on the analysis of RNA-seq datasets, it was found that the VQ genes are expressed distinctly among different tissues and hormone or stress treatments. A total of 40 sweetpotato differentially expressed genes (DEGs) refer to biotic (sweetpotato stem nematodes and Ceratocystis fimbriata pathogen infection) or abiotic (cold, salt and drought) stress treatments were detected. Moreover, IbVQ8, IbVQ25 and IbVQ44 responded to the five stress treatments and were selected for quantitative reverse-transcription polymerase chain reaction (qRT-PCR) analysis, and the results were consistent with the transcriptome analysis.

CONCLUSIONS

Our study may provide new insights into the evolution of VQ genes in the four Ipomoea genomes and contribute to the future molecular breeding of sweetpotatoes.

Combined genome-wide association study and epistasis analysis reveal multifaceted genetic architectures of plant height in Asian cultivated rice

Plant height (PH) in rice (Oryza sativa) is an important trait for its adaptation and agricultural performance. Discovery of the semi-dwarf1 (SD1) mutation initiated the Green Revolution, boosting rice yield and fitness, but the underlying genetic regulation of PH in rice remains largely unknown. Here, we performed genome-wide association study (GWAS) and identified 12 non-repetitive QTL/genes regulating PH variation in 619 Asian cultivated rice accessions. One of these was an SD1 structural variant, not normally detected in standard GWAS analyses. Given the strong effect of SD1 on PH, we also divided 619 accessions into subgroups harbouring distinct SD1 haplotypes, and found a further 85 QTL/genes for PH, revealing genetic heterogeneity that may be missed by analysing a broad, diverse population. Moreover, we uncovered two epistatic interaction networks of PH-associated QTL/genes in the japonica (Geng)-dominant SD1^NIP subgroup. In one of them, the hub QTL/gene qphSN1.4/GAMYB interacted with qphSN3.1/OsINO80, qphSN3.4/HD16/EL1, qphSN6.2/LOC_Os06g11130, and qphSN10.2/MADS56. Sequence variations in GAMYB and MADS56 were associated with their expression levels and PH variations, and MADS56 was shown to physically interact with MADS57 to coregulate expression of gibberellin (GA) metabolic genes OsGA2ox3 and Elongated Uppermost Internode1 (EUI1). Our study uncovered the multifaceted genetic architectures of rice PH, and provided novel and abundant genetic resources for breeding semi-dwarf rice and new candidates for further mechanistic studies on regulation of PH in rice.

Platinum Nanocrystals Embedded in Three-Dimensional Graphene for High-Performance Li-O2 Batteries

Graphene is considered as a promising cathode candidate for Li-O₂ batteries because of its excellent electronic conductivity and oxygen adsorption capacity. However, for Li-O₂ batteries, the self-stacking effect caused by two-dimensional (2D) structural properties of graphene is not conducive to the rapid oxygen transport and mass transfer process, thereby affecting the electrode kinetics. Here, we successfully prepared three-dimensional (3D) graphene with different scales by plasma-enhanced chemical vapor deposition and physical pulverization strategies, in which CH₄ is the carbon source and H₂/Ar mixed gas is the etching gas. Meanwhile, we fabricated 3D graphene-based Pt nanocatalysts by an ultraviolet-assisted construction strategy and then applied them in Li-O₂ batteries. Systematic studies reveal a special relevance between electrochemical performance and graphene particle size, and the smaller-sized 3D graphene can better maintain the microstructure distribution in both the Pt embedding process and electrochemical applications, which is beneficial to the transport of oxygen and Li ions, lowering the decomposition energy barrier of Li₂O₂, and further obtaining reduced charge overpotential (0.22 V) and prolonged cycle life for Li-O₂ batteries. Finally, we anticipate that this work could promote the practical application of 2D materials and larger-sized 3D materials in Li-O₂ batteries.