Molecular Plant-microbe Interactions最新文献

Zymoseptoria tritici causes Septoria tritici blotch, which significantly reduces yields of wheat. To investigate infection phase-specific gene expression in the pathogen, we analyzed gene expression during infection of susceptible and resistant wheat cultivars, as well as the nonhost species barley, at 1, 3, 6, 10, 17, and 23 days postinoculation (DPI). There were dramatic differences in pathogen gene expression at 10 DPI in the susceptible compared with both resistant interactions. The most pronounced differences in pathogen gene expression were observed at 3 DPI in both the susceptible and resistant host interactions compared with the nonhost. Thirty-one putative effectors showed early expression during the susceptible compared with the nonhost interaction; six were selected for subcellular localization studies. Using Agrobacterium-mediated transient expression in Nicotiana benthamiana, subcellular localization assays revealed that two candidate effectors localized to putative mobile cytosolic bodies when expressed without their signal peptides, suggesting potential roles in intracellular signaling or host gene regulation. When expressed with their signal peptides, four candidate effectors localized to the cytosol, whereas one did not accumulate to detectable levels. Comparison of pathogen gene expression in the susceptible host with expression in the resistant hosts identified genes expressed during the transition from biotrophic to necrotrophic growth at 10 DPI. Comparison of pathogen gene expression in resistant and susceptible hosts, versus in the nonhost barley, identified genes involved in initial colonization and host recognition. These results contribute to understanding candidate effectors that are activated early during infection and may play a role in the suppression of plant immunity. [Formula: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Fusarium wilt of strawberry, caused by the soilborne fungal pathogen Fusarium oxysporum f. sp. fragariae (Fof), is one of the greatest threats to cultivated strawberry. The pathogen penetrates strawberry plants through roots, severely affecting roots and crowns and resulting in rapid wilting and death. Research into the genetic basis of resistance to Fof has identified five loci, FW1 to FW5, that confer resistance to Fusarium wilt of strawberry and one Fof effector, SIX6. Although it is hypothesized that FW1 recognizes the SIX6 effector, the underlying resistance gene is unknown. A new isolate of Fof that breaks FW1-mediated resistance recently emerged and poses a significant threat to the California strawberry industry, the source of 88 to 91% of the strawberries produced in the United States. There are still significant gaps surrounding the molecular and physiological interaction between Fof and strawberry and the evolution of pathogenicity of Fof isolates unaffected by FW1. This review summarizes our current knowledge, identifies knowledge gaps, and provides a summary of genomic and molecular tools currently available to study the Fof-strawberry interaction. [Formula: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Despite large omics datasets, the prediction of eukaryotic genes is still challenging. We have developed a new method to improve the prediction of eukaryotic genes and demonstrate its utility using the genome of the fungal wheat pathogen Zymoseptoria tritici. From 10,933 to 13,260 genes were predicted by four previous annotations, but only one third were identical. A novel bioinformatics suite, InGenAnnot, was developed to improve Z. tritici gene annotation using Iso-Seq full-length transcript sequences. The best gene models were selected among different ab initio gene predictions, according to transcript and protein evidence. Overall, 13,414 reannotated gene models (RGMs) were predicted, improving previous annotations. Iso-Seq transcripts outlined 5' and 3' untranslated regions for 73% of the RGMs and alternative transcripts mainly due to intron retention. Our results showed that the combination of different ab initio gene predictions and evidence-driven curation improved gene annotation of a eukaryotic genome. It also provided new insights into the transcriptional landscape of this fungus. [Formula: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Cercospora janseana is the causal agent of narrow brown leaf spot (NBLS) on rice, an increasingly problematic disease in the southern United States. Historically, this disease was considered sporadic and a minor nuisance; however, recent NBLS epidemics and the resulting detrimental impacts on yield underscore the need for a deeper understanding of the pathogen's population biology. In this study, we used whole-genome sequencing of 136 C. janseana isolates collected from Louisiana and Texas to investigate genetic diversity, population structure, and possible reproductive strategies. Our results revealed a high level of genetic diversity across sampling years and locations. Population structure and phylogenetic analyses identified two distinct lineages, with most isolates belonging to a dominant lineage found in both states. Despite the disparity in observed lineage frequencies, overall population differentiation was minimal, indicating ongoing gene flow across regional boundaries. Linkage disequilibrium decay and index of association analyses revealed evidence for a population that predominantly reproduces clonally with infrequent sexual reproduction. However, nearly equal frequencies of mating type idiomorphs in most sampled populations indicate ongoing or past sexual reproduction to some extent. Taken together, these results suggest that C. janseana populations are diverse, migrate between production regions, and exhibit a mixed mode of reproduction. These findings have important implications for the development of integrated disease management and pathogen monitoring practices to ultimately mitigate the impacts of this resurgent disease. [Formula: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Plants recognize pathogen-associated molecular patterns via pattern recognition receptors, leading to the activation of pattern-triggered immunity in response to pathogen attack. Phytophthora infestans ceramide D (Pi-Cer D) is a sphingolipid from the oomycete pathogen P. infestans. Pi-Cer D is cleaved by the plant extracellular ceramidase NEUTRAL CERAMIDASE 2 (NCER2), and the resulting 9-methyl-branched sphingoid base is recognized by the plant receptor RESISTANT TO DFPM-INHIBITION OF ABSCISIC ACID SIGNALING 2 (RDA2) at the plasma membrane to transduce a defense signal. However, additional components are likely involved in sphingolipid recognition, which remain to be identified. Here, we employed a screen based on Lumi-Map technology to look for Arabidopsis (Arabidopsis thaliana) mutants with altered defense responses to Pi-Cer D. We identified three mutants showing diminished responses to Pi-Cer D and elf18, each carrying mutations in STAUROSPORIN AND TEMPERATURE SENSITIVE 3-LIKE A (STT3A), which encodes an oligosaccharyltransferase. The stt3a mutants exhibited higher susceptibility to the pathogen Colletotrichum higginsianum than the wild type. In stt3a mutants, the molecular mass of NCER2 and RDA2 proteins appeared smaller, indicating that STT3A is involved in posttranslational modification of the proteins. An enzymatic deglycosylation assay revealed that NCER2 and RDA2 are N-glycosylated. These findings suggest that STT3A contributes to plant immunity via posttranslational modification of proteins including NCER2 and RDA2. [Formula: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

The soil bacterium Sinorhizobium meliloti can proliferate by leveraging its nitrogen-fixing symbiosis with legumes that form indeterminate root nodules, such as Medicago sativa (alfalfa) and M. truncatula. In contrast to determinate-nodulating legumes, such as Glycine max (soybean) and Lotus japonicus, indeterminate-nodulating legumes impose terminal differentiation on nitrogen-fixing (N₂-fixing) rhizobia. Thus, the bacterial population is split between those that benefit the plant by N₂ fixation, but are a reproductive dead end, and those that are undifferentiated, capable of resuming free-living growth but not fixing nitrogen. We show that in mixed nodules colonized by nearly isogenic strains, with one N₂-fixing and one unable to fix N₂ (Fix-), alfalfa do not preferentially penalize the Fix- strain, allowing "cheating" at the expense of the plant and the N₂ fixer. Thus, a Fix- strain that successfully conodulates with an N₂-fixing strain can benefit from resources the host provides to the nodule in response to N₂ fixed by the conodulating strain. Coinvasion of alfalfa nodules with an N₂-fixing strain may be a successful strategy for a Fix- strain to cheat both the plant that provides fixed carbon and the N₂-fixing strain. [Formula: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

The soybean-Bradyrhizobium symbiosis enables symbiotic nitrogen fixation (SNF) within root nodules, reducing reliance on synthetic N fertilizers. However, nitrogen fixation is transient, peaking several weeks after Bradyrhizobium colonization and declining as nodules senesce in coordination with host development. To investigate the regulatory mechanisms governing SNF and senescence, we conducted a temporal transcriptomic analysis of soybean nodules colonized with Bradyrhizobium diazoefficiens USDA110. Weekly nodule samples (2 to 10 weeks postinoculation, wpi) were analyzed using RNA and small RNA sequencing, and acetylene reduction assays assessed nitrogenase activity from 4 to 7 wpi. We identified three major nodule developmental phases: early development (2 to 3 wpi), nitrogen fixation (3 to 8 wpi), and senescence (8 to 10 wpi). Soybean showed extensive transcriptional reprogramming during senescence, whereas Bradyrhizobium underwent major transcriptional shifts early in development before stabilizing during nitrogen fixation. We identified seven soybean genes and several microRNAs as candidate biomarkers of nitrogen fixation, including lipoxygenases (Lox), suggesting roles for oxylipin metabolism. Soy hemoglobin-2 (Hb2), previously classified as nonsymbiotic, was upregulated during senescence, implicating oxidative stress responses within aging nodules. Upregulation of the Bradyrhizobium paa operon and rpoH during senescence suggesting metabolic adaptation for survival beyond symbiosis. Additionally, Bradyrhizobium nif gene expression showed stage-specific regulation, with nifK peaking at 2 wpi, nifD and nifA at 2 and 10 wpi, and nifH, nifW, and nifS at 10 wpi. These findings provide insights into SNF regulation and nodule aging, revealing temporal gene expression patterns that could inform breeding or genetic engineering strategies to enhance nitrogen fixation in soybeans and other legume crops. [Formula: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

A major challenge in plant-microbe interaction research is understanding how plants distinguish between commensal and pathogenic microorganisms. We compared Arabidopsis responses to two contrasting bacterial strains, the plant growth-promoting (PGP) Pseudomonas sp. CH267 and the pathogen Burkholderia glumae PG1, using integrated multi-omics analyses. The pathogen triggered stronger transcriptional reprogramming and proteomic changes in roots than the PGP strain, and both strains also affected numerous leaf proteins, indicating systemic responses. Interaction with both strains increased the abundance of sulfur-containing metabolites camalexin, glutathione, and cysteine, in particular under pathogen treatment, which corresponded with elevated total sulfur in the leaves. Root and root exudate metabolomes significantly changed, with amino acids and tricarboxylic acid cycle intermediates accumulating in roots but being diminished in the exudates. Integrative analysis across the omics datasets revealed strong correlations between metabolite levels, protein abundance, and transcript levels, highlighting new links between sulfur metabolism, defense pathways, and mineral nutrition, including iron. Together, these findings uncover the complex multilayered nature of Arabidopsis responses to commensal and pathogenic bacteria and identify new connections across different regulatory levels. [Formula: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.