Tal6b/AvrXa27A, a hidden TALE targeting the susceptibility gene OsSWEET11a and the resistance gene Xa27 in rice

Transcription activator-like effectors of Xanthomonas oryzae pv. oryzae hijack host transcriptional regulation through OsWRKYs

Transcription activator-like effectors (TALEs) mimic eukaryotic transcriptional activators and translocate into host plant cells via the bacterial type III secretion system (T3SS) during pathogenic interactions. They play a crucial role in disease development by regulating host genes. Despite this, the regulatory mechanisms by which TALEs control OsWRKY transcription factors (TFs) remain poorly understood. In this study, we show that two TALEs from Xanthomonas oryzae pv. oryzae (Xoo) individually modulate two OsWRKY TFs, resulting in increased susceptibility and reduced host defense. Specifically, Xoo1219 and Xoo2145 activate the expression of OsWRKY104 and OsWRKY55, respectively, through direct interactions. OsWRKY104 increases the susceptibility to Xoo by activating OsSWEET11 and OsSWEET14, while OsWRKY55 suppresses host defense against Xoo by directly regulating OsWRKY62. These findings suggest that TALEs hijack the host's OsWRKY TFs to create a favorable environment for bacterial survival.

The battle within: Discovering new insights into phytopathogen interactions and effector dynamics

Phytopathogen interactions are complicated and constantly evolving, driven by a never-ending war amongst the host's immune defenses and the pathogen's virulence strategies. This comprehensive review examines the intricate mechanisms of effector-triggered immunity (ETI) and how pathogen effectors use host cellular progressions to promote infection. This review article investigates the modification of Phytopathogen effectors and plant resistance proteins, highlighting the role of meta-population dynamics and rapid adaptation. Additionally, it highlights the influence of environmental impact and climate change on host-pathogen interactions, describing their significant impact on disease dynamics and pathogen evolution. Effector proteins are crucial in sabotaging plant immunity, with bacterial, fungal, oomycete, and nematode effectors targeting common host protein networks and phytohormone pathways. Additionally, the review discusses advanced approaches for classifying effector targets, such as bioinformatics and single-cell transcriptomics, highlighting their importance in developing effective disease management strategies. Further insights are described into how effectors control phytohormone pathways, shedding light on how pathogens exploit host signaling. This review covers structural studies and protein modeling that have advanced effector prediction and our understanding of their functions and evolution, while providing an overview of phytopathogen interactions and future directions for effector research.

Transcriptome Analysis Reveals That a Gti1/Pac2 Family Gene, CpSge1, Regulates Fungal Growth, Stress Response, and Virulence in Cryphonectria parasitica

The Gti1/Pac2 family comprises crucial transcription factors widely distributed in fungi with generally two members, Gti1 (also known as Wor1, Ryp1, or Sge1), and Pac2, where the Gti1 homologues play significant roles in the growth, spore production, and pathogenicity of various pathogenic fungi. Despite its recognized significance, the roles of this family in Cryphonectria parasitica, the pathogen responsible for chestnut blight (a globally significant forest disease), remain unexplored. In this study, CpSge1 was identified in C. parasitica and then knocked out to explore its functions. The results showed that CpSge1 significantly affected the vegetative growth, conidiation, hydrophobicity, and stress tolerance of C. parasitica. Notably, the CpSge1 deletion mutants were significantly less pathogenic compared with the wild type. Transcriptomic analysis of the wild type and the CpSge1 deletion mutant during the vegetative growth and infection stages revealed that CpSge1 regulated a number of pathogenicity-related genes in C. parasitica. A yeast one-hybrid assay verified the direct binding of CpSge1 to the promoter regions of genes encoding pectin lyase CpPL1 and major facilitator superfamily transporter CpMF1. In summary, these data suggest that CpSge1 is the core regulator of fungal growth, stress tolerance, gene expression, and virulence in C. parasitica, which may improve our understanding of the molecular pathogenesis of C. parasitica and help us to develop effective control strategies.

Sugar transporters: mediators of carbon flow between plants and microbes

Pathogens and symbiotic microorganisms significantly influence plant growth and crop productivity. Enhancing crop disease resistance and maximizing the beneficial role of symbiotic microorganisms in agriculture constitute critical areas of scientific investigation. A fundamental aspect of plant-microorganisms interactions revolves around nutritional dynamics, characterized by either "food shortage" or "food supply" scenarios. Notably, pathogenic and symbiotic microorganisms predominantly utilize photosynthetic sugars as their primary carbon source during host colonization. This phenomenon has generated substantial interest in the regulatory mechanisms governing sugar transport and redistribution at the plant-microorganism interface. Sugar transporters, which primarily mediate the allocation of sugars to various sink organs, have emerged as crucial players in plant-pathogen interactions and the establishment of beneficial symbiotic associations. This review systematically categorized plant sugar transporters and highlighted their functional significance in mediating plant interactions with pathogenic and beneficial microorganisms. Furthermore, we synthesized recent advancements in understanding the molecular regulatory mechanisms of these transporters and identified key scientific questions warranting further investigation. Elucidating the roles of sugar transporters offers novel strategies for enhancing crop health and productivity, thereby contributing to agricultural sustainability and global food security.

Xoo Effector TalAE73-Targeted OsLTPL23 Mediates Bacterial Blight Resistance in Rice

Transcription activator-like effectors (TALEs) secreted from Xanthomonas oryzae pv oryzae (Xoo) function as a pathogenicity factor to activate rice bacterial blight (BB) susceptibility, conforming to the gene-for-gene paradigm as well as resistance. Xoo pathotypes generally harbor one to three major TALEs targeting OsSWEET genes to determine pathogenicity; conversely, the immunity events mediated by minor TALEs have not been taken seriously. Here, we demonstrated that lipid transfer protein encoding gene OsLTPL23 positively regulates rice resistance to Xoo pathotype PXO61, and TalAE73PXO61, a representative member of the most widely distributed TALE family in 135 Xoo isolates, transcriptionally activates OsLTPL23 expression. Further, TalAE73PXO61 is an avirulence protein, causing effector-triggered immunity in compatible rice-Xoo interaction. In addition, reactive oxygen species accumulation, nitrate uptake, and salicylic acid homeostasis are transcriptionally and physiologically associated with OsLTPL23-dependent BB resistance.

Two TAL effectors of Xanthomonas citri promote pustule formation by directly repressing the expression of GRAS transcription factor in citrus

Citrus bacterial canker (CBC), caused by Xanthomonas citri subsp. citri (Xcc), poses a significant threat to the citrus industry. Xcc employs the transcription activator-like effector (TALE) PthA4 to target the major susceptibility (S) gene CsLOB1 in citrus, promoting host susceptibility to bacterial canker. However, the contribution of other Xcc TALEs, aside from PthA4, to virulence remains underexplored. In this study, we characterized two PthA1 variants, designated PthA5 and PthA6, which facilitate Xcc infection in susceptible citrus species by promoting the formation of hypertrophy and hyperplasia symptoms. Both PthA5 and PthA6 bind directly to effector-binding elements (EBEs) in the promoter of CsGRAS9, suppressing its expression. CsGRAS9 negatively regulates Xcc growth in citrus and contributes to CBC resistance. Notably, natural variations in the EBEs of the FhGRAS9 promoter, a homolog of CsGRAS9 in Hong Kong kumquat, prevent Xcc from affecting FhGRAS9 expression. Using the PTG/Cas9 system, we generated proCsGRAS9-edited sweet orange lines #18-2 and #23, which contain 86-bp and 62-bp deletions in the EBE regions of the CsGRAS9 promoter. These mutant lines showed enhanced CsGRAS9 expression and increased resistance to CBC during Xcc infection. Several GA-related genes and CsTAC1, regulated by CsGRAS9, were also identified. This is the first report that TALEs act as repressors of a resistance gene to confer host susceptibility.

WRKY36-PIL15 Transcription Factor Complex Negatively Regulates Sheath Blight Resistance and Seed Development in Rice

Sheath blight (ShB) causes severe yield loss in rice. Previously, we demonstrated that the sugar will eventually be exported and the transporter 11 (SWEET11) mutation significantly improved rice resistance to ShB, but it caused severe defects in seed development. The present study found that WRKY36 and PIL15 directly activate SWEET11 to negatively regulate ShB. Interestingly, WRKY36 interacted with PIL15, WRKY36 and PIL15 directly activates miR530 to negatively regulate seed development. WRKY36 interacted with a key BR signaling transcription factor WRKY53. AOS2 is an effector protein from Rhizoctonia solani (R. solani) that interacts with WRKY53. Interestingly, AOS2 also interacts with WRKY36 and PIL15 to activate SWEET11 for sugar nutrition for R. solani. These data collectively suggest that WRKY36-PIL15 negatively regulates ShB resistance and seed development via the activation of SWEET11 and miR530, respectively. In addition, WRKY36 and PIL15 are the partners of the effector protein AOS2 by which R. solani hijacks sugar nutrition from rice.

Two TAL Effectors of Xanthomonas citri pv. malvacearum Induce Water Soaking by Activating GhSWEET14 Genes in Cotton

Bacterial blight of cotton (BBC) caused by Xanthomonas citri pv. malvacearum (Xcm) is an important and destructive disease affecting cotton plants. Transcription activator-like effectors (TALEs) released by the pathogen regulate cotton resistance to the susceptibility. In this study, we sequenced the whole genome of Xcm Xss-V2-18 and identified eight tal genes: seven on the plasmids and one on the chromosome. Deletion and complementation experiments of Xss-V2-18 tal genes demonstrated that Tal1b is required for full virulence on cotton. Transcriptome profiling coupled with TALE-binding element prediction revealed that Tal1b targets GhSWEET14A04/D04 and GhSWEET14D02 simultaneously. Expression analysis confirmed the independent inducibility of GhSWEET14A04/D04 and GhSWEET14D02 by Tal1b, whereas GhSWEET14A04/D04 is additionally targeted by Tal1. Moreover, β-glucuronidase and Xa10-mediated hypersensitive response assays indicated that the effector-binding element (EBEs) are required for the direct and specific activation of the candidate targets by Tal1 and Ta1b. These insights enhance our understanding of the underlying mechanisms of bacterial blight in cotton and might lead to improved resistance through EBEs disruption or a TALE-trap strategy.

Whole Genome Sequencing and Comparative Genomic Analysis of Pseudomonas aeruginosa SF416, a Potential Broad-Spectrum Biocontrol Agent Against Xanthomonas oryzae pv. oryzae

Rice is one of the most important staple crops worldwide. However, the bacterial blight of rice caused by Xanthomonas oryzae pv. oryzae (Xoo) poses a major threat to the production of rice. In this study, we isolated and identified the strain Pseudomonas aeruginosa SF416, which exhibited significant antagonistic activity against Xoo, from a soil sample collected in a winter wheat field in Shannanzhalang County, Tibet, China. The bacterial solution (BS) and cell-free supernatant (CFS) of SF416 had significant prevention effects for the bacterial blight of rice, with an efficacy of 45.1% and 34.18%, respectively, while they exhibited a slightly lower therapeutic efficiency of 31.64% and 25.09%. The genomic analysis showed that P. aeruginosa SF416 contains genes involved in cell motility, colonization, cold and hot shock proteins, antibiotic resistance, and plant growth promotion. SF416 also harbors two sets of phenazine-1-carboxylic acid (PCA) synthesis gene clusters, phz1 (phzA1-G1) and phz2 (phzA2-G2), and other phenozine product-synthesis--related genes phzS, phzM, and phzH, as well as genes in the SF416 genome that share high similarity with the ones in the genomes of P. aeruginosa M18, suggesting that the two sets of PCA synthesis gene clusters are responsible for the antagonistic effect of SF416 against Xoo. A comparative antiSMASH analysis revealed that P. aeruginosa SF416 contains 17 gene clusters related to secondary metabolite synthesis, 7 of which, encoding for pyochelin, azetidomonamide A/B, L-2-amino-4-methoxy-trans-3-butenoic acid, hydrogen cyanide, pyocyanine, pseudopaline, and bicyclomycin, are conserved in strains of P. aeruginosa. Moreover, SF416 can produce protease and siderophores and display a broad-spectrum antagonistic activity against various major plant pathogenic bacteria and fungi. The results suggest that P. aeruginosa SF416 could be a potential candidate agent for the bacterial blight of rice.

Transcriptome Analysis of Rice Near-Isogenic Lines Inoculated with Two Strains of Xanthomonas oryzae pv. oryzae, AH28 and PXO99A

Rice bacterial blight (BB), caused by Xanthomonas oryzae pv. oryzae (Xoo), is a major threat to rice production and food security. Exploring new resistance genes and developing varieties with broad-spectrum and high resistance has been a key focus in rice disease resistance research. In a preliminary study, rice cultivar Fan3, exhibiting high resistance to PXO99A and susceptibility to AH28, was developed by enhancing the resistance of Yuehesimiao (YHSM) to BB. This study performed a transcriptome analysis on the leaves of Fan3 and YHSM following inoculation with Xoo strains AH28 and PXO99A. The analysis revealed significant differential expression of 14,084 genes. Among the transcription factor (TF) families identified, bHLH, WRKY, and ERF were prominent, with notable differences in the expression of OsWRKY62, OsWRKY76, and OsbHLH6 across samples. Over 100 genes were directly linked to disease resistance, including nearly 30 NBS-LRR family genes. Additionally, 11 SWEET family protein genes, over 750 protein kinase genes, 63 peroxidase genes, and eight phenylalanine aminolysase genes were detected. Gene ontology (GO) analysis showed significant enrichment in pathways related to defense response to bacteria and oxidative stress response. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis indicated that differentially expressed genes (DEGs) were enriched in phenylpropanoid biosynthesis and diterpenoid biosynthesis pathways. Gene expression results from qRT-PCR were consistent with those from RNA-Seq, underscoring the reliability of the findings. Candidate genes identified in this study that may be resistant to BB, such as NBS-LRR family genes LOC_Os11g11960 and LOC_Os11g12350, SWEET family genes LOC_Os01g50460 and LOC_Os01g12130, and protein kinase-expressing genes LOC_Os01g66860 and LOC_Os02g57700, will provide a theoretical basis for further experiments. These results suggest that the immune response of rice to the two strains may be more concentrated in the early stage, and there are more up-regulated genes in the immune response of the high-resistant to PXO99A and medium-resistant to AH28, respectively, compared with the highly susceptible rice. This study offers a foundation for further research on resistance genes and the molecular mechanisms in Fan3 and YHSM.

Xanthomonas oryzae pv. oryzicola effector Tal10a directly activates rice OsHXK5 expression to facilitate pathogenesis

Bacterial leaf streak (BLS), caused by Xanthomonas oryzae pv. oryzicola (Xoc), is a major bacterial disease in rice. Transcription activator-like effectors (TALEs) from Xanthomonas can induce host susceptibility (S) genes and facilitate infection. However, knowledge of the function of Xoc TALEs in promoting bacterial virulence is limited. In this study, we demonstrated the importance of Tal10a for the full virulence of Xoc. Through computational prediction and gene expression analysis, we identified the hexokinase gene OsHXK5 as a host target of Tal10a. Tal10a directly binds to the gene promoter region and activates the expression of OsHXK5. CRISPR/Cas9-mediated gene editing in the effector binding element (EBE) of OsHXK5 significantly increases rice resistance to Xoc, while OsHXK5 overexpression enhances the susceptibility of rice plants and impairs rice defense responses. Moreover, simultaneous editing of the promoters of OsSULTR3;6 and OsHXK5 confers robust resistance to Xoc in rice. Taken together, our findings highlight the role of Tal10a in targeting OsHXK5 to promote infection and suggest that OsHXK5 represents a potential target for engineering rice resistance to Xoc.

Rice Promoter Editing: An Efficient Genetic Improvement Strategy

Gene expression levels in rice (Oryza sativa L.) and other plant species are determined by the promoters, which directly control phenotypic characteristics. As essential components of genes, promoters regulate the intensity, location, and timing of gene expression. They contain numerous regulatory elements and serve as binding sites for proteins that modulate transcription, including transcription factors and RNA polymerases. Genome editing can alter promoter sequences, thereby precisely modifying the expression patterns of specific genes, and ultimately affecting the morphology, quality, and resistance of rice. This paper summarizes research on rice promoter editing conducted in recent years, focusing on improvements in yield, heading date, quality, and disease resistance. It is expected to inform the application of promoter editing and encourage further research and development in crop genetic improvement with promote.

Constructed Rice Tracers Identify the Major Virulent Transcription Activator-Like Effectors of the Bacterial Leaf Blight Pathogen

Xanthomonas oryzae pv. oryzae (Xoo) injects major transcription activator-like effectors (TALEs) into plant cells to activate susceptibility (S) genes for promoting bacterial leaf blight in rice. Numerous resistance (R) genes have been used to construct differential cultivars of rice to identify races of Xoo, but the S genes were rarely considered. Different edited lines of rice cv. Kitaake were constructed using CRISPR/Cas9 gene-editing, including single, double and triple edits in the effector-binding elements (EBEs) located in the promoters of rice S genes OsSWEET11a, OsSWEET13 and OsSWEET14. The near-isogenic lines (NILs) were used as tracers to detect major TALEs (PthXo1, PthXo2, PthXo3 and their variants) in 50 Xoo strains. The pathotypes produced on the tracers determined six major TALE types in the 50 Xoo strains. The presence of the major TALEs in Xoo strains was consistent with the expression of S genes in the tracers, and it was also by known genome sequences. The EBE editing had little effect on agronomic traits, which was conducive to balancing yield and resistance. The rice-tracers generated here provide a valuable tool to track major TALEs of Xoo in Asia which then shows what rice cultivars are needed to combat Xoo in the field.