Author: slquinlan

J Vis Exp. 2026 Mar 20;(229). doi: 10.3791/69753.

ABSTRACT

Phytophthora is an oomycete genus that contains numerous destructive plant pathogens, among which is the broad-host-range species P. palmivora. Functional genomics of Phytophthora has been constrained by the limited availability of robust, easy-to-implement transformation methods. Among the available approaches, Agrobacterium-mediated transformation (AMT) is particularly attractive because it requires minimal specialized equipment and often produces stable transformants with single-copy gene insertions. Most AMT protocols for fungal and oomycete transformation use minimal medium (MM) salts in Agrobacterium induction and co-cultivation media. Preparing these media typically involves making and mixing multiple stock solutions, with some containing numerous components at different concentrations. The process is time-consuming and error-prone, therefore leading to inconsistent transformation success. Here, we present a streamlined, simple, and reproducible AMT protocol for P. palmivora that uses commercially available Murashige and Skoog (MS) basal medium to prepare the Agrobacterium induction and co-cultivation media. This protocol has also been successfully applied to transform P. capsici and may be applied to other Phytophthora spp. as well.

PMID:41941429 | DOI:10.3791/69753

FEBS J. 2026 Mar 31. doi: 10.1111/febs.70528. Online ahead of print.

ABSTRACT

Serine hydroxymethyltransferase (SHMT) is a conserved enzyme in folate-mediated one-carbon metabolism, where it contributes to nucleotide biosynthesis, methylation capacity, and cellular stress responses. Amino acid polymorphisms of soybean SHMT8 are known to affect the resistance of soybean to its primary pathogen, the soybean cyst nematode (SCN). A set of SHMT8 variants from ethyl methanesulfonate (EMS)-mutagenized soybean populations has been identified with varying resistance phenotypes, but their biochemical consequences remain poorly understood. Here, we use biochemical and structural studies to assess the impacts of the A149T variant on soybean SHMT8. Despite the conservative nature of the substitution, A149T reduces folate binding, pyridoxal-5′-phosphate-dependent catalysis, and thermal stability. High-resolution crystal structures (1.9-2.3 Å resolution) reveal only very minor structural changes. However, while the usual tetrameric assembly of the enzyme is retained at the high protein concentration in crystals, multiple other methods including a 2.9 Å cryo-electron microscopy (cryo-EM) structure show that the A149T variant is predominantly a dimer. Significant structural changes in the dimer are consistent with the observed biochemical impacts of the variant and help explain the well-known reduction in activity associated with dimerization of SHMT in other systems. We also find destabilization of the tetrameric assembly in other SHMT8 variants associated with changes in SCN resistance, suggesting that weakened oligomerization may be a common consequence of such mutations. Together, these results highlight quaternary structure as a critical determinant of SHMT8 activity and stability and suggest a potential mechanistic link between enzyme biochemistry and soybean defense.

PMID:41914311 | DOI:10.1111/febs.70528

Antimicrob Agents Chemother. 2026 Mar 30:e0168925. doi: 10.1128/aac.01689-25. Online ahead of print.

ABSTRACT

Annually, aspergillosis, candidiasis, cryptococcosis, and mucormycosis result in approximately 1,500,000, 650,000, 120,000, and 59,000 deaths, respectively. Mortality rates among patients receiving antifungal drug treatment range from 30% to 90%. Therefore, there is an urgent need to improve the efficacy of antifungal drug therapies against infections by these high-priority fungal diseases. Aspergillus fumigatus, Candida albicans, Cryptococcus neoformans, and Rhizopus delemar are the most common causative pathogens. We have previously developed DectiSomes, which are liposomes loaded with antifungal drugs and coated with the carbohydrate recognition domains of mouse Dectin-1 and/or Dectin-2. We demonstrated that the murine DectiSomes efficiently bound and killed these pathogens growing in vitro and/or in mouse disease models. With the plan to move DectiSomes into the clinic with the human Dectin orthologs, we were concerned that the significant sequence divergence between mouse and human Dectin-1 and Dectin-2 carbohydrate recognition domains could have altered pathogen specificity. Herein, we compared the functionality of the human and mouse Dectin-1 and Dectin-2 orthologs in targeting DectiSomes to these pathogens. Binding and growth inhibition data on A. fumigatus and C. neoformans supported their functional similarity, while results with C. albicans and R. delemar indicated some functional divergence. Despite these differences, our results demonstrate that both human and mouse DectiSomes are effective at binding and killing all four diverse fungal pathogens.

PMID:41910313 | DOI:10.1128/aac.01689-25

Front Plant Sci. 2026 Mar 13;17:1733525. doi: 10.3389/fpls.2026.1733525. eCollection 2026.

ABSTRACT

Drought is the most damaging abiotic stress affecting soybean production, with variable rainfall contributing significantly to year-to-year yield variability. Breeding efforts aim to develop cultivars with stable and competitive yields under both drought and non-drought stressed conditions. However, drought tolerance in soybean is a highly complex trait, influenced by diverse physiological, morphological, genetic factors and environments. Identifying genotypes with improved drought tolerance is challenging because traditional phenotyping methods for drought tolerance are subjective and time-consuming. Furthermore, quantitative trait loci (QTLs) associated with drought tolerance typically exhibit small effects and limited consistency across environments and populations. These challenges highlight the need for improved methodologies to identify and evaluate promising sources of genetic variation. This review summarizes the current state of drought tolerance breeding in soybean and discusses recent advances in remote sensing, transcriptomics, proteomics, and metabolomics aimed at enhancing drought tolerance research and cultivar development in soybean.

PMID:41907757 | PMC:PMC13021458 | DOI:10.3389/fpls.2026.1733525

J Am Soc Mass Spectrom. 2026 Mar 29. doi: 10.1021/jasms.5c00440. Online ahead of print.

ABSTRACT

O-acetylation, a common modification in rhamnogalacturonan I (RG-I), is critical for various biological processes, including plant growth, stress responses, and pathogen defense. Precise determination of the degree and specific positions of acetylation is therefore essential. To date, nuclear magnetic resonance (NMR) and tandem mass spectrometry have been employed to identify O-acetyl positions in pectin oligosaccharides. Although NMR is effective, it requires pure, high-concentration samples. Tandem mass spectrometry (MS), which uses smaller sample amounts, faces challenges due to O-acetyl migration between monosaccharide positions. The multiple steps in pectin sample analysis can further promote O-acetyl migration, especially near free hydroxyl groups. Moreover, during tandem MS, O-acetyl groups may detach, complicating the accurate tracking. This study presents an approach to lock O-acetyl groups by introducing trideuteroacetyl and propionyl substituents onto free hydroxyls of RG-I or partially acetylated RG-I. By combining matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS and electrospray ionization (ESI) MS with MS/MS or tandem mass spectrometry (MSⁿ), we devised a way to determine the monosaccharide sequence in the oligomer and the precise positions of O-acetyl groups in partially acetylated RG-I. This method enables the study of the regiospecificity of recombinant pectin O-acetyltransferases and can be applied to other oligosaccharides to determine acyl positions.

PMID:41906310 | DOI:10.1021/jasms.5c00440

Physiol Plant. 2026 Mar-Apr;178(2):e70840. doi: 10.1111/ppl.70840.

ABSTRACT

Viral suppressors of RNA silencing (VSRs) are proteins that interfere with antiviral defense mechanisms and enhance infection. For plant viruses, VSRs can be encoded in viral genomes and satellite molecules and play an important role in the virus’s life cycle and in overcoming host defenses. However, a comprehensive review on the multifunctionality of VSRs and their role in the worldwide spread of plant viral diseases has not been performed. Here, we aim to synthesize the current understanding of the role of VSRs in the pathogenesis of Solanaceous plants, a family that includes many crops and medicinal plants. We focus on three key areas: (1) the diversity of VSRs and the mechanisms used to suppress antiviral defense, (2) the role of VSRs in viral pathogenesis beyond interfering with host RNA-silencing, and (3) the coevolution between VSRs and plant host proteins. Additionally, we describe how VSRs promote the development of diseases by altering various steps in viral pathogenicity via induction of counter-defense mechanisms. Specifically, a substantial body of evidence suggests that VSRs induce the suppression of antiviral silencing, abrogation of phytohormone signaling, and downregulation of R-gene-mediated host defense. Furthermore, we discuss how identifying and characterizing novel interactions between VSRs and Solanaceous host factors may be leveraged for developing sustainable pathogen and pest management strategies.

PMID:41881836 | DOI:10.1111/ppl.70840

ACS ES T Eng. 2026 Feb 24;6(3):1089-1105. doi: 10.1021/acsestengg.5c00635. eCollection 2026 Mar 13.

ABSTRACT

Efficient nutrient management is critical for crop growth and sustainable resource consumption (e.g., nitrogen and energy). Current approaches require lengthy analyses, preventing real-time optimization; similarly, imaging facilitates rapid phenotyping but can be computationally intensive, preventing deployment under resource constraints. This study proposes a flexible, tiered pipeline for anomaly detection and status estimation (fresh weight, dry mass, and tissue nutrients), including a comprehensive energy analysis of approaches that span the efficiency-accuracy spectrum. Using a nutrient depletion experiment with three treatments (T1-100%, T2-50%, and T3-25% fertilizer strength) and multispectral imaging, we developed a hierarchical pipeline using an autoencoder for early warning. Further, we compared two status estimation modules of different complexity for more detailed analysis: vegetation index features with machine learning (random forest, RF) and raw whole-image deep learning (vision transformer, ViT). Results demonstrated high-efficiency anomaly detection (73% net detection of T3 samples 9 days after transplanting) at substantially lower energy than embodied energy in wasted nitrogen. The state estimation modules show trade-offs, with ViT outperforming RF on phosphorus and calcium estimation (R ² 0.61 vs 0.58, 0.48 vs 0.35) at higher energy cost. With our modular pipeline, this work opens up opportunities for edge diagnostics and practical opportunities for agricultural sustainability.

PMID:41853757 | PMC:PMC12993859 | DOI:10.1021/acsestengg.5c00635

Nature. 2026 Mar 18. doi: 10.1038/s41586-026-10227-x. Online ahead of print.

ABSTRACT

Cinchona alkaloids, which have been studied for more than 250 years, are plant-derived natural products that have collectively had a substantial impact in medicine and basic science^1-5. Examples of cinchona alkaloids include quinine, a historically important antimalarial drug, and cinchonidine, a chiral catalyst widely used in process chemistry. However, it is still largely unknown how plants synthesize these well-known compounds. Here we report the discovery of genes responsible for the biosynthesis of the distinctive quinoline-quinuclidine scaffold of cinchona alkaloids. A combination of isotopic labelling, gene silencing, single-nucleus RNA sequencing and comparative transcriptomics revealed the involvement of several unexpected biosynthetic transformations. We also describe a previously unreported quaternary amine intermediate that is generated through an unusual enzymatic cyclization. We show that dihydroquini(di)none, dihydrocinchoni(di)none and cinchoni(di)none can be produced when these genes are heterologously expressed in Nicotiana benthamiana. Furthermore, we demonstrate that this N. benthamiana expression platform can convert non-native fluorinated and chlorinated tryptamine substrates into dihydrocinchoni(di)none analogues, which suggests that these biosynthetic enzymes can be leveraged to produce halogenated cinchona alkaloid derivatives. These discoveries uncover the long-standing mystery of how the cinchona alkaloid scaffold is biosynthesized and highlight prospects for access to these compounds through metabolic engineering approaches.

PMID:41851462 | DOI:10.1038/s41586-026-10227-x

Phytopathology. 2026 Mar 17. doi: 10.1094/PHYTO-01-26-0021-SA. Online ahead of print.

ABSTRACT

The cosmopolitan bacterium Pantoea agglomerans is renowned for its dual nature, with some strains promoting plant growth and aiding in the suppression of pests and phytopathogens, while others have been linked to plant disease and opportunistic human infections. This duality hampers the biotechnological application of this bacterium and underpins the necessity for taxonomic refinement. The genomes of 295 P. agglomerans strains were subjected to phylogenomic analyses (core genome phylogeny, ANI and dDDH), with strains consistently resolving as two coherent clades supported by proteome content analysis. Average interclade dDDH values (79.1%) fall near the proposed subspecies threshold. Comparative genomic analysis identified clade-specific orthologues and phenotypic assays demonstrate that citrate utilisation distinguishes the two clades. Based on these genotypic and phenotypic markers, we propose delineation of two subspecies of P. agglomerans, subspecies agglomerans (which includes the P. agglomerans type strain) and subsp. jekyllhydei, to reflect the dual nature of this versatile bacterial species.

PMID:41842656 | DOI:10.1094/PHYTO-01-26-0021-SA

Plant J. 2026 Mar;125(6):e70777. doi: 10.1111/tpj.70777.

ABSTRACT

Vigna unguiculata (L.) Walp. is a dryland legume crop, providing essential food and nutritional security for millions of people across the semi-arid tropics, in Africa, Asia and Latin America. However, as a typical ‘orphan crop’, cowpea has long remained underrepresented in global genomic research to support crop improvement. Here, we conducted the largest genetic diversity analysis of cowpea to date, comprising 10 617 accessions sourced from seven international collections. Using genotyping-by-sequencing, we characterised the global patterns of genetic diversity, assessed redundancy within and across collections, and examined the geographic structure of the cowpea global allele pool. Our results revealed nine distinct genetic groups with clear geographic associations and fine-scale population differentiation, reflecting dispersal history, regional adaptation and the influence of modern breeding. Duplication across collections was detected, highlighting the need for improved curation and integration of germplasm resources. Landraces from sub-Saharan Africa do not fully capture the genetic diversity present in several other geographic regions, indicating the existence of abundant and untapped genetic resources worldwide. These findings not only provide insights into the genetic structure and evolutionary history of cowpea but also offer a valuable foundation for harnessing global germplasm diversity to enhance breeding potential and accelerate crop improvement.

PMID:41830563 | DOI:10.1111/tpj.70777