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Correction to "A novel MAP kinase-interacting protein MoSmi1 regulates development and pathogenicity in Magnaporthe oryzae". 对 "一种新的与 MAP 激酶相互作用的蛋白 MoSmi1 可调控木格鲁氏杆菌的发育和致病性 "的更正。
IF 4.8 1区 农林科学 Q1 PLANT SCIENCES Pub Date : 2024-08-01 DOI: 10.1111/mpp.13503

Wang, Y., Cui, X., Xiao, J., Kang, X., Hu, J., Huang, Z. et al. A novel MAP kinase-interacting protein MoSmi1 regulates development and pathogenicity in Magnaporthe oryzae. Molecular Plant Pathology. 2024; 25, e13493. In section 2.1 (Results), first sentence, the reference citation to Zhang, Chen, et al. (2022) should be deleted. The correct sentence is "Through RNA sequencing (RNA-seq) analysis, we previously found that the gene MGG_03970 was upregulated in the ΔMonap1 mutant (Zhang, Wang, et al., 2022)." In section 4.2 (Experimental Procedures), paragraph 2, seventh sentence, β-tubulin-pYF11 should be deleted. The correct sentence is "The same method was used to obtain the wild-type strain Guy11 expressing Sep3-pYF11 or Sep5-pYF11, and ΔMosmi1 expressing Sep3-pYF11 or Sep5-pYF11." We apologize for these errors.

Wang, Y., Cui, X., Xiao, J., Kang, X., Hu, J., Huang, Z. et al. A novel MAP kinase-interacting protein MoSmi1 regulates development and pathogenicity in Magnaporthe oryzae.分子植物病理学》。2024; 25, e13493.在第 2.1 节(结果)第一句中,引用 Zhang, Chen, et al. (2022) 的参考文献应删除。正确的句子是:"通过 RNA 测序(RNA-seq)分析,我们之前发现 MGG_03970 基因在 ΔMonap1 突变体中上调(Zhang, Wang, et al.,2022)"。第 4.2 节(实验步骤),第 2 段,第七句,β-tubulin-pYF11 应删除。正确的句子是 "用同样的方法获得表达 Sep3-pYF11 或 Sep5-pYF11 的野生型菌株 Guy11,以及表达 Sep3-pYF11 或 Sep5-pYF11 的 ΔMosmi1"。我们对这些错误表示歉意。
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引用次数: 0
Evasion of wheat resistance gene Lr15 recognition by the leaf rust fungus is attributed to the coincidence of natural mutations and deletion in AvrLr15 gene. 叶锈病真菌之所以能识别小麦抗性基因 Lr15,是因为 AvrLr15 基因发生了自然突变和缺失。
IF 4.8 1区 农林科学 Q1 PLANT SCIENCES Pub Date : 2024-07-01 DOI: 10.1111/mpp.13490
Zhongchi Cui, Songsong Shen, Linshuo Meng, Xizhe Sun, Yuqing Jin, Yuanxia Liu, Daqun Liu, Lisong Ma, Haiyan Wang

Employing race-specific resistance genes remains an effective strategy to protect wheat from leaf rust caused by Puccinia triticina (Pt) worldwide, while the newly emerged Pt races, owing to rapid genetic evolution, frequently overcome the immune response delivered by race-specific resistance genes. The molecular mechanisms underlying the newly evolved virulence Pt pathogen remain unknown. Here, we identified an avirulence protein AvrLr15 from Pt that induced Lr15-dependent immune responses. Heterologously produced AvrLr15 triggered pronounced cell death in Lr15-isogenic wheat leaves. AvrLr15 contains a functional signal peptide, localized to the plant nucleus and cytosol and can suppress BAX-induced cell death. Evasion of Lr15-mediated resistance in wheat was associated with a deletion and point mutations of amino acids in AvrLr15 rather than AvrLr15 gene loss in the Lr15-breaking Pt races, implying that AvrLr15 is required for the virulence function of Pt. Our findings identified the first molecular determinant of wheat race-specific immunity and facilitated the identification of the first AVR/R gene pair in the Pt-wheat pathosystem, which will provide a molecular marker to monitor natural Pt populations and guide the deployment of Lr15-resistant wheat cultivars in the field.

在全球范围内,使用种族特异性抗性基因仍然是保护小麦免受由三尖杉核菌(Pt)引起的叶锈病侵袭的有效策略,而新出现的 Pt 种族由于基因进化迅速,往往能克服种族特异性抗性基因所产生的免疫反应。新进化的具有毒力的 Pt 病原的分子机制仍然未知。在这里,我们从铂中发现了一种诱导 Lr15 依赖性免疫反应的无毒蛋白 AvrLr15。异源生产的 AvrLr15 会引发 Lr15 异源小麦叶片细胞的明显死亡。AvrLr15含有一个功能性信号肽,定位于植物细胞核和细胞质,可抑制BAX诱导的细胞死亡。在小麦中,Lr15介导的抗性的逃避与AvrLr15中氨基酸的缺失和点突变有关,而不是Lr15-breaking Pt株系中AvrLr15基因的缺失,这意味着AvrLr15是Pt毒力功能所必需的。我们的发现确定了小麦种族特异性免疫的第一个分子决定因素,并促进了铂-小麦病原系统中第一个 AVR/R 基因对的鉴定,这将为监测天然铂种群和指导抗 Lr15 小麦栽培品种的田间部署提供分子标记。
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引用次数: 0
Inhibition of Monilinia fructicola sporulation and pathogenicity through eucalyptol-mediated targeting of MfCat2 by Streptomyces lincolnensis strain JCP1-7. 林肯链霉菌 JCP1-7 株通过桉叶油醇介导的 MfCat2 靶向作用抑制果核莫尼菌孢子和致病性。
IF 4.8 1区 农林科学 Q1 PLANT SCIENCES Pub Date : 2024-07-01 DOI: 10.1111/mpp.13484
Shan Chen, Haorong Yang, Meijun Chen, Weina Liu, Shaorui Tian, Rong Mu, Fan Jia, Changyun Liu, Guanhua Ma, Xianchao Sun, Guokang Chen

Peach brown rot, attributed to Monilinia fructicola, presents a significant threat to postharvest peach cultivation, causing losses of up to 80%. With an increasing number of countries, spearheaded by the European Union, imposing bans on chemical agents in fruit production, there is a growing interest in mining highly active antibacterial compounds from biological control strains for postharvest disease management. In this study, we highlight the unique ability of Streptomyces lincolnensis strain JCP1-7 to inhibit M. fructicola sporulation, despite its limited antimicrobial efficacy. Through GC-MS analysis, eucalyptol was identified as the key compound. Fumigation of diseased fruits with eucalyptol at a concentration of 0.0335 μg cm-3 demonstrated an in vivo inhibition rate against M. fructicola of 93.13%, completely suppressing spore formation. Transcriptome analysis revealed the impact of eucalyptol on multiple pathogenesis-related pathways, particularly through the inhibition of catalase 2 (Cat2) expression. Experiments with a MfCat2 knockout strain (ΔMfCat2) showed reduced pathogenicity and sensitivity to JCP1-7 and eucalyptol, suggesting MfCat2 as a potential target of JCP1-7 and eucalyptol against M. fructicola. Our findings elucidate that eucalyptol produced by S. lincolnensis JCP1-7 inhibits M. fructicola sporulation by regulating MfCat2, thereby effectively reducing postharvest peach brown rot occurrence. The use of fumigation of eucalyptol offers insights into peach brown rot management on a large scale, thus making a significant contribution to agricultural research.

桃褐腐病是由果核菌(Monilinia fructicola)引起的,对桃采后栽培构成了严重威胁,造成的损失高达 80%。随着以欧盟为首的越来越多的国家禁止在水果生产中使用化学制剂,人们对从生物防治菌株中挖掘高活性抗菌化合物用于采后病害管理的兴趣与日俱增。在本研究中,我们强调了林肯链霉菌(Streptomyces lincolnensis)菌株 JCP1-7 抑制果蝇孢子的独特能力,尽管其抗菌效果有限。通过气相色谱-质谱分析,桉叶油醇被确定为关键化合物。用 0.0335 μg cm-3 浓度的桉叶油醇熏蒸病果,对果蝇孢子菌的体内抑制率为 93.13%,完全抑制了孢子的形成。转录组分析表明,桉叶油醇对多种致病相关途径都有影响,尤其是通过抑制过氧化氢酶 2(Cat2)的表达。用MfCat2基因敲除菌株(ΔMfCat2)进行的实验表明,该菌株的致病性降低,对JCP1-7和桉叶油醇的敏感性也降低,这表明MfCat2是JCP1-7和桉叶油醇防治果蝇的潜在靶标。我们的研究结果阐明,林肯菌 JCP1-7 产生的桉叶油醇可通过调节 MfCat2 抑制果腐菌孢子的生长,从而有效减少采后桃褐腐病的发生。使用桉叶油醇熏蒸为大规模管理桃褐腐病提供了启示,从而为农业研究做出了重大贡献。
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引用次数: 0
A fatty acid elongase complex regulates cell membrane integrity and septin-dependent host infection by the rice blast fungus. 脂肪酸伸长酶复合物调控细胞膜的完整性以及稻瘟病真菌对隔膜依赖性宿主的感染。
IF 4.8 1区 农林科学 Q1 PLANT SCIENCES Pub Date : 2024-07-01 DOI: 10.1111/mpp.13494
Jia Su, Youpin Xu, Mingliang Lei, Yingying Meng, Siqi Zhang, Hongrui Liu, Caicun Zhu, Jinhua Chen, Tianxin Zhang, Jiawei Liu, Yunxiang Lin, Zhaorui Yan, Weitao Li, Jing Wang, Xuewei Chen, Min He

Very-long-chain fatty acids (VLCFAs) regulate biophysical properties of cell membranes to determine growth and development of eukaryotes, such as the pathogenesis of the rice blast fungus Magnaporthe oryzae. The fatty acid elongase Elo1 regulates pathogenesis of M. oryzae by modulating VLCFA biosynthesis. However, it remains unknown whether and how Elo1 associates with other factors to regulate VLCFA biosynthesis in fungal pathogens. Here, we identified Ifa38, Phs1 and Tsc13 as interacting proteins of Elo1 by proximity labelling in M. oryzae. Elo1 associated with Ifa38, Phs1 and Tsc13 on the endoplasmic reticulum (ER) membrane to control VLCFA biosynthesis. Targeted gene deletion mutants Δifa38, Δphs1 and Δtsc13 were all similarly impaired as Δelo1 in vegetative growth, conidial morphology, stress responses in ER, cell wall and membrane. These deletion mutants also displayed severe damage in cell membrane integrity and failed to organize the septin ring that is essential for penetration peg formation and pathogenicity. Our study demonstrates that M. oryzae employs a fatty acid elongase complex to regulate VLCFAs for maintaining or remodelling cell membrane structure, which is important for septin-mediated host penetration.

超长链脂肪酸(VLCFA)调节细胞膜的生物物理特性,从而决定真核生物的生长和发育,例如稻瘟病真菌Magnaporthe oryzae的致病机理。脂肪酸伸长酶 Elo1 通过调节 VLCFA 的生物合成来调控 M. oryzae 的致病机理。然而,Elo1 是否以及如何与其他因子结合以调控真菌病原体中的 VLCFA 生物合成仍然未知。在这里,我们通过近距离标记法在 M. oryzae 中鉴定出了 Ifa38、Phs1 和 Tsc13 作为 Elo1 的互作蛋白。Elo1 与内质网(ER)膜上的 Ifa38、Phs1 和 Tsc13 相互作用,控制 VLCFA 的生物合成。靶向基因缺失突变体Δifa38、Δphs1和Δtsc13在无性生殖、分生孢子形态、ER、细胞壁和细胞膜的应激反应方面都与Δelo1有类似的缺陷。这些缺失突变体的细胞膜完整性也受到了严重破坏,无法组织对穿刺钉的形成和致病性至关重要的隔膜环。我们的研究表明,M. oryzae 利用脂肪酸伸长酶复合物来调节 VLCFAs,以维持或重塑细胞膜结构,这对于肽键介导的宿主穿透非常重要。
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引用次数: 0
Histone (de)acetylation in epigenetic regulation of Phytophthora pathobiology. 组蛋白(去)乙酰化在植病菌病理生物学表观遗传学调控中的作用。
IF 4.8 1区 农林科学 Q1 PLANT SCIENCES Pub Date : 2024-07-01 DOI: 10.1111/mpp.13497
Yufeng Guan, Joanna Gajewska, Jolanta Floryszak-Wieczorek, Umesh Kumar Tanwar, Ewa Sobieszczuk-Nowicka, Magdalena Arasimowicz-Jelonek

Phytophthora species are oomycetes that have evolved a broad spectrum of biological processes and improved strategies to cope with host and environmental challenges. A growing body of evidence indicates that the high pathogen plasticity is based on epigenetic regulation of gene expression linked to Phytophthora's rapid adjustment to endogenous cues and various stresses. As 5mC DNA methylation has not yet been identified in Phytophthora, the reversible processes of acetylation/deacetylation of histone proteins seem to play a pivotal role in the epigenetic control of gene expression in oomycetes. To explore this issue, we review the structure, diversity, and phylogeny of histone acetyltransferases (HATs) and histone deacetylases (HDACs) in six plant-damaging Phytophthora species: P. capsici, P. cinnamomi, P. infestans, P. parasitica, P. ramorum, and P. sojae. To further integrate and improve our understanding of the phylogenetic classification, evolutionary relationship, and functional characteristics, we supplement this review with a comprehensive view of HATs and HDACs using recent genome- and proteome-level databases. Finally, the potential functional role of transcriptional reprogramming mediated by epigenetic changes during Phytophthora species saprophytic and parasitic phases under nitro-oxidative stress is also briefly discussed.

噬菌体是一种卵菌纲真菌,已进化出多种生物过程和改进策略,以应对宿主和环境的挑战。越来越多的证据表明,病原体的高度可塑性是基于基因表达的表观遗传调控,这与噬菌体快速适应内源线索和各种压力有关。由于尚未在噬菌体中发现 5mC DNA 甲基化,组蛋白乙酰化/去乙酰化的可逆过程似乎在卵菌基因表达的表观遗传调控中发挥着关键作用。为了探讨这个问题,我们综述了六种危害植物的疫霉菌中组蛋白乙酰转移酶(HATs)和组蛋白去乙酰化酶(HDACs)的结构、多样性和系统发育:P. capsici、P. cinnamomi、P. infestans、P. parasitica、P. ramorum 和 P. sojae。为了进一步整合和提高我们对系统发育分类、进化关系和功能特征的理解,我们利用最新的基因组和蛋白质组级数据库对 HATs 和 HDACs 进行了全面的分析,以补充本综述。最后,我们还简要讨论了在硝基氧化胁迫下,由表观遗传变化介导的转录重编程在噬菌体物种萎缩期和寄生期的潜在功能作用。
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引用次数: 0
Phosphatidylethanolamines link ferroptosis and autophagy during appressorium formation of rice blast fungus. 磷脂酰乙醇胺在稻瘟病真菌的附属体形成过程中连接了铁突变和自噬。
IF 4.8 1区 农林科学 Q1 PLANT SCIENCES Pub Date : 2024-07-01 DOI: 10.1111/mpp.13489
Qiao Liu, Ruhui Long, Chaoxiang Lin, Xinping Bi, Zhibin Liang, Yi Zhen Deng

A cell death pathway, ferroptosis, occurs in conidial cells and is critical for formation and function of the infection structure, the appressorium, in the rice blast fungus Magnaporthe oryzae. In this study, we identified an orthologous lysophosphatidic acid acyltransferase (Lpaat) acting at upstream of phosphatidylethanolamines (PEs) biosynthesis and which is required for such fungal ferroptosis and pathogenicity. Two PE species, DOPE and SLPE, that depend on Lpaat function for production were sufficient for induction of lipid peroxidation and the consequent ferroptosis, thus positively regulating fungal pathogenicity. On the other hand, both DOPE and SLPE positively regulated autophagy. Loss of the LPAAT gene led to a decrease in the lipidated form of the autophagy protein Atg8, which is probably responsible for the autophagy defect of the lpaatΔ mutant. GFP-Lpaat was mostly localized on the membrane of lipid droplets (LDs) that were stained by the fluorescent dye monodansylpentane (MDH), suggesting that LDs serve as a source of lipids for membrane PE biosynthesis and probably as a membrane source of autophagosome. Overall, our results reveal novel intracellular membrane-bound organelle dynamics based on Lpaat-mediated lipid metabolism, providing a temporal and spatial link of ferroptosis and autophagy.

在稻瘟病真菌 Magnaporthe oryzae 中,分生孢子细胞中存在一种细胞死亡途径--铁突变,这种途径对于感染结构--附着体--的形成和功能至关重要。在这项研究中,我们发现了一种同源的溶血磷脂酸酰基转移酶(Lpaat),它作用于磷脂酰乙醇胺(PEs)生物合成的上游,是这种真菌铁突变和致病性所必需的。依赖 Lpaat 功能产生的两种 PE(DOPE 和 SLPE)足以诱导脂质过氧化反应和随之而来的铁变态反应,从而对真菌的致病性起到积极的调节作用。另一方面,DOPE 和 SLPE 对自噬有积极的调节作用。LPAAT 基因缺失导致自噬蛋白 Atg8 的脂化形式减少,这可能是 lpaatΔ 突变体自噬缺陷的原因。GFP-Lpaat主要定位于被荧光染料单丹戊烷(MDH)染色的脂滴(LDs)膜上,这表明LDs是膜PE生物合成的脂质来源,也可能是自噬体的膜来源。总之,我们的研究结果揭示了基于 Lpaat 介导的脂质代谢的新型细胞内膜结合细胞器动力学,为铁突变和自噬提供了时空联系。
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引用次数: 0
A cyclic di-GMP-binding adaptor protein interacts with a N5-glutamine methyltransferase to regulate the pathogenesis in Xanthomonas citri subsp. citri. 环状双GMP结合适配蛋白与N5-谷氨酰胺甲基转移酶相互作用,调控柠檬黄单胞菌亚种的致病机理。
IF 4.8 1区 农林科学 Q1 PLANT SCIENCES Pub Date : 2024-07-01 DOI: 10.1111/mpp.13496
Yu Shi, Tianfang Cheng, Qing Wei Cheang, Xiaoyan Zhao, Zeling Xu, Zhao-Xun Liang, Linghui Xu, Junxia Wang

The second messenger cyclic diguanylate monophosphate (c-di-GMP) regulates a wide range of bacterial behaviours through diverse mechanisms and binding receptors. Single-domain PilZ proteins, the most widespread and abundant known c-di-GMP receptors in bacteria, act as trans-acting adaptor proteins that enable c-di-GMP to control signalling pathways with high specificity. This study identifies a single-domain PilZ protein, XAC3402 (renamed N5MapZ), from the phytopathogen Xanthomonas citri subsp. citri (Xcc), which modulates Xcc virulence by directly interacting with the methyltransferase HemK. Through yeast two-hybrid, co-immunoprecipitation and immunofluorescent staining, we demonstrated that N5MapZ and HemK interact directly under both in vitro and in vivo conditions, with the strength of the protein-protein interaction decreasing at high c-di-GMP concentrations. This finding distinguishes N5MapZ from other characterized single-domain PilZ proteins, as it was previously known that c-di-GMP enhances the interaction between those single-domain PilZs and their protein partners. This observation is further supported by the fact that the c-di-GMP binding-defective mutant N5MapZR10A can interact with HemK to inhibit the methylation of the class 1 translation termination release factor PrfA. Additionally, we found that HemK plays an important role in Xcc pathogenesis, as the deletion of hemK leads to extensive phenotypic changes, including reduced virulence in citrus plants, decreased motility, production of extracellular enzymes and stress tolerance. Gene expression analysis has revealed that c-di-GMP and the HemK-mediated pathway regulate the expression of multiple virulence effector proteins, uncovering a novel regulatory mechanism through which c-di-GMP regulates Xcc virulence by mediating PrfA methylation via the single-domain PilZ adaptor protein N5MapZ.

第二信使环二甘氨酸单磷酸酯(c-di-GMP)通过不同的机制和结合受体调节细菌的各种行为。单链 PilZ 蛋白是细菌中已知最广泛和最丰富的 c-di-GMP 受体,它作为反式作用适配蛋白,使 c-di-GMP 能够以高度特异性控制信号通路。本研究从植物病原黄单胞菌柠檬亚种(Xcc)中发现了一种单链 PilZ 蛋白 XAC3402(更名为 N5MapZ),它通过与甲基转移酶 HemK 直接相互作用来调节 Xcc 的毒力。通过酵母双杂交、共免疫沉淀和免疫荧光染色,我们证明了 N5MapZ 和 HemK 在体外和体内条件下都能直接相互作用,在高 c-di-GMP 浓度下,蛋白质间相互作用的强度降低。这一发现将 N5MapZ 与其他特征性单域 PilZ 蛋白区分开来,因为之前已知 c-di-GMP 会增强这些单域 PilZ 与其蛋白伙伴之间的相互作用。c-di-GMP 结合缺陷突变体 N5MapZR10A 能与 HemK 相互作用,抑制 1 类翻译终止释放因子 PrfA 的甲基化,这一事实进一步证实了这一观点。此外,我们还发现 HemK 在 Xcc 的致病过程中起着重要作用,因为缺失 hemK 会导致广泛的表型变化,包括柑橘植株的毒力降低、运动能力下降、胞外酶的产生和抗逆性降低。基因表达分析表明,c-di-GMP 和 HemK 介导的途径可调控多种毒力效应蛋白的表达,从而发现了一种新的调控机制,即 c-di-GMP 通过单链 PilZ 适配蛋白 N5MapZ 介导 PrfA 甲基化,从而调控 Xcc 的毒力。
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引用次数: 0
Correction to 'Identification of differentially expressed genes in a resistant versus a susceptible blueberry cultivar after infection by Colletotrichum acutatum'. 对 "抗性与易感性蓝莓栽培品种在受到Colletotrichum acutatum感染后差异表达基因的鉴定 "的更正。
IF 4.8 1区 农林科学 Q1 PLANT SCIENCES Pub Date : 2024-07-01 DOI: 10.1111/mpp.13495
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引用次数: 0
A novel MAP kinase-interacting protein MoSmi1 regulates development and pathogenicity in Magnaporthe oryzae. 一种新的与 MAP 激酶相互作用的蛋白 MoSmi1 可调控木格氏真菌的发育和致病性。
IF 4.8 1区 农林科学 Q1 PLANT SCIENCES Pub Date : 2024-07-01 DOI: 10.1111/mpp.13493
Yu Wang, Xinyue Cui, Junlian Xiao, Xiaoru Kang, Jinmei Hu, Zhicheng Huang, Na Li, Chuyu Yang, Yuemin Pan, Shulin Zhang

The cell wall is the first barrier against external adversity and plays roles in maintaining normal physiological functions of fungi. Previously, we reported a nucleosome assembly protein, MoNap1, in Magnaporthe oryzae that plays a role in cell wall integrity (CWI), stress response, and pathogenicity. Moreover, MoNap1 negatively regulates the expression of MoSMI1 encoded by MGG_03970. Here, we demonstrated that deletion of MoSMI1 resulted in a significant defect in appressorium function, CWI, cell morphology, and pathogenicity. Further investigation revealed that MoSmi1 interacted with MoOsm1 and MoMps1 and affected the phosphorylation levels of MoOsm1, MoMps1, and MoPmk1, suggesting that MoSmi1 regulates biological functions by mediating mitogen-activated protein kinase (MAPK) signalling pathway in M. oryzae. In addition, transcriptome data revealed that MoSmi1 regulates many infection-related processes in M. oryzae, such as membrane-related pathway and oxidation reduction process. In conclusion, our study demonstrated that MoSmi1 regulates CWI by mediating the MAPK pathway to affect development and pathogenicity of M. oryzae.

细胞壁是抵御外部逆境的第一道屏障,在维持真菌正常生理功能方面发挥作用。此前,我们报道了一种核糖体组装蛋白--MoNap1,它在木格氏真菌的细胞壁完整性(CWI)、应激反应和致病性中发挥作用。此外,MoNap1 负向调节由 MGG_03970 编码的 MoSMI1 的表达。在这里,我们证明了缺失 MoSMI1 会导致贴壁功能、CWI、细胞形态和致病性的显著缺陷。进一步研究发现,MoSmi1与MoOsm1和MoMps1相互作用,并影响MoOsm1、MoMps1和MoPmk1的磷酸化水平,表明MoSmi1通过介导有丝分裂原激活蛋白激酶(MAPK)信号通路调控M.此外,转录组数据显示,MoSmi1 还调控着许多与 M. oryzae 感染相关的过程,如膜相关途径和氧化还原过程。总之,我们的研究表明,MoSmi1 通过介导 MAPK 通路来调控 CWI,从而影响 M. oryzae 的发育和致病性。
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引用次数: 0
Predicting symptom severity in PSTVd-infected tomato plants using the PSTVd genome sequence. 利用 PSTVd 基因组序列预测受 PSTVd 感染的番茄植株的症状严重程度。
IF 4.8 1区 农林科学 Q1 PLANT SCIENCES Pub Date : 2024-07-01 DOI: 10.1111/mpp.13469
Jianqiang Sun, Yosuke Matsushita

Viroids, one of the smallest known infectious agents, induce symptoms of varying severity, ranging from latent to severe, based on the combination of viroid isolates and host plant species. Because viroids are transmissible between plant species, asymptomatic viroid-infected plants may serve as latent sources of infection for other species that could exhibit severe symptoms, occasionally leading to agricultural and economic losses. Therefore, predicting the symptoms induced by viroids in host plants without biological experiments could remarkably enhance control measures against viroid damage. Here, we developed an algorithm using unsupervised machine learning to predict the severity of disease symptoms caused by viroids (e.g., potato spindle tuber viroid; PSTVd) in host plants (e.g., tomato). This algorithm, mimicking the RNA silencing mechanism thought to be linked to viroid pathogenicity, requires only the genome sequences of the viroids and host plants. It involves three steps: alignment of synthetic short sequences of the viroids to the host plant genome, calculation of the alignment coverage, and clustering of the viroids based on coverage using UMAP and DBSCAN. Validation through inoculation experiments confirmed the effectiveness of the algorithm in predicting the severity of disease symptoms induced by viroids. As the algorithm only requires the genome sequence data, it may be applied to any viroid and plant combination. These findings underscore a correlation between viroid pathogenicity and the genome sequences of viroid isolates and host plants, potentially aiding in the prevention of viroid outbreaks and the breeding of viroid-resistant crops.

病毒病是已知的最小传染源之一,根据病毒病分离株和寄主植物种类的组合,可引起不同严重程度的症状,从潜伏到严重不等。由于病毒病可在植物物种间传播,无症状的病毒感染植物可能成为其他物种的潜伏传染源,从而表现出严重症状,有时会导致农业和经济损失。因此,在不进行生物实验的情况下预测病毒病在寄主植物中诱发的症状,可以大大加强病毒病危害的控制措施。在此,我们利用无监督机器学习开发了一种算法,用于预测寄主植物(如番茄)中由病毒病(如马铃薯纺锤形块茎病毒;PSTVd)引起的疾病症状的严重程度。该算法模仿被认为与病毒致病性有关的 RNA 沉默机制,只需要病毒和宿主植物的基因组序列。它包括三个步骤:将病毒体的合成短序列与宿主植物基因组进行比对、计算比对覆盖率,以及使用 UMAP 和 DBSCAN 根据覆盖率对病毒体进行聚类。通过接种实验验证了该算法在预测病毒引起的病害症状严重程度方面的有效性。由于该算法只需要基因组序列数据,因此可以应用于任何病毒和植物的组合。这些发现强调了拟病毒致病性与拟病毒分离株和寄主植物基因组序列之间的相关性,可能有助于预防拟病毒爆发和培育抗拟病毒作物。
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Molecular plant pathology
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