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Abstract Regulatory networks coordinate metabolism to control how plants adapt to biotic and abiotic stresses. This coordination can align transcriptional shifts across metabolic pathways using cis-regulatory elements shared across the enzyme genes within these pathways. While the role of transcription factors (TFs) in controlling this process across pathways is well known, less is known regarding the role of shared cis-regulatory elements across the genes in a pathway. Sharing cis-regulatory elements across the genes in an enzyme complex or pathway, can create coordinated regulation of the pathway by a TF. However, it is unclear if all the genes in a pathway or enzyme complex need to be fully coordinated for maximal function. For example, if one gene in an enzyme complex loses a cis-regulatory element, it may not alter the function of the enzyme complexes function if post-transcriptional or compensatory transcriptional changes are sufficient to balance the complex. To test how cis-modular membership shapes the function of an enzyme complex, we used CRISPR/Cas9 to abolish a common cis-regulatory element across the promoters of nine genes required for the mitochondrial pyruvate dehydrogenase complex (mtPDC). This complex is composed of three apoenzymes and is a central hub coordinating carbon flow between glycolysis and the tricarboxylic acid (TCA) cycle. Different combinations of these cis-element mutations were tested across the genes in the complex inArabidopsis thalianaand the created genotypes were phenotyped for altered enzyme function using digital growth analysis, disease assays, metabolomics, and transcriptomics. This analysis revealed that mutating cis-element motifs of genes in this enzyme complex produced distinct phenotypes, displaying promoter-specific buffering and modularity. 

Abstract Data reduction methods are frequently employed in large genomics and phenomics studies to extract core patterns, reduce dimensionality, and alleviate multiple testing effects. Principal component analysis (PCA), in particular, identifies the components that capture the most variance within omics datasets. While data reduction can simplify complex datasets, it remains unclear how the use of PCA impacts downstream analyses such as quantitative trait loci (QTL) or genome-wide association (GWA) approaches and their biological interpretation. In QTL studies, an alternative to data reduction is the use of post-hoc data summarization approaches, such as hotspot analysis, which involves mapping individual traits and consolidating results based on shared genomic locations. To evaluate how different analytical approaches may alter the biological insights derived from multi-dimensional QTL datasets, we compared individual trait hotspots with PCA-based QTL mapping using transcriptomic and metabolomic data from a structured recombinant inbred line population. Interestingly, these two approaches identified different genomic regions and genetic architectures. These findings suggest that mapping PCA-reduced data does not merely streamline analyses but may generate a fundamentally different view of the underlying genetic architecture compared to individual trait mapping and hotspot analysis. Thus, the use of PCA and other data reduction techniques prior to QTL or GWAS mapping should be carefully considered to ensure alignment with the specific biological question being addressed. 

Abstract Bidirectional flow of information shapes the outcome of the host–pathogen interactions and depends on the genetics of each organism. Recent work has begun to use co-transcriptomic studies to shed light on this bidirectional flow, but it is unclear how plastic the co-transcriptome is in response to genetic variation in both the host and pathogen. To study co-transcriptome plasticity, we conducted transcriptomics using natural genetic variation in the pathogen, Botrytis cinerea, and large-effect genetic variation abolishing defense signaling pathways within the host, Arabidopsis thaliana. We show that genetic variation in the pathogen has a greater influence on the co-transcriptome than mutations that abolish defense signaling pathways in the host. Genome-wide association mapping using the pathogens’ genetic variation and both organisms’ transcriptomes allowed an assessment of how the pathogen modulates plasticity in response to the host. This showed that the differences in both organism's responses were linked to trans-expression quantitative trait loci (eQTL) hotspots within the pathogen's genome. These hotspots control gene sets in either the host or pathogen and show differential allele sensitivity to the host’s genetic variation rather than qualitative host specificity. Interestingly, nearly all the trans-eQTL hotspots were unique to the host or pathogen transcriptomes. In this system of differential plasticity, the pathogen mediates the shift in the co-transcriptome more than the host. 

Abstract Botrytis cinereaPers. Fr. (teleomorph:Botryotinia fuckeliana) is a necrotrophic fungal pathogen that attacks a wide range of plants. This updated pathogen profile explores the extensive genetic diversity ofB. cinerea, highlights the progress in genome sequencing, and provides current knowledge of genetic and molecular mechanisms employed by the fungus to attack its hosts. In addition, we also discuss recent innovative strategies to combatB. cinerea. TaxonomyKingdom: Fungi, phylum: Ascomycota, subphylum: Pezizomycotina, class: Leotiomycetes, order: Helotiales, family: Sclerotiniaceae, genus:Botrytis, species:cinerea. Host rangeB. cinereainfects almost all of the plant groups (angiosperms, gymnosperms, pteridophytes, and bryophytes). To date, 1606 plant species have been identified as hosts ofB. cinerea. Genetic diversityThis polyphagous necrotroph has extensive genetic diversity at all population levels shaped by climate, geography, and plant host variation. PathogenicityGenetic architecture of virulence and host specificity is polygenic using multiple weapons to target hosts, including secretory proteins, complex signal transduction pathways, metabolites, and mobile small RNA. Disease control strategiesEfforts to controlB. cinerea, being a high‐diversity generalist pathogen, are complicated. However, integrated disease management strategies that combine cultural practices, chemical and biological controls, and the use of appropriate crop varieties will lessen yield losses. Recently, studies conducted worldwide have explored the potential of small RNA as an efficient and environmentally friendly approach for combating grey mould. However, additional research is necessary, especially on risk assessment and regulatory frameworks, to fully harness the potential of this technology. 

Abstract Autophagy in eukaryotes functions to maintain homeostasis by degradation and recycling of long-lived and unwanted cellular materials. Autophagy plays important roles in pathogenicity of various fungal pathogens, suggesting that autophagy is a novel target for development of antifungal compounds. Here, we describe bioluminescence resonance energy transfer (BRET)-based high-throughput screening (HTS) strategy to identify compounds that inhibit fungal ATG4 cysteine protease-mediated cleavage of ATG8 that is critical for autophagosome formation. We identified ebselen (EB) and its analogs ebselen oxide (EO) and 2-(4-methylphenyl)−1,2-benzisothiazol-3(2H)-one (PT) as inhibitors of fungal pathogensBotrytis cinereaandMagnaporthe oryzaeATG4-mediated ATG8 processing. The EB and its analogs inhibit spore germination, hyphal development, and appressorium formation inAscomycotapathogens,B. cinerea, M. oryzae,Sclerotinia sclerotiorumandMonilinia fructicola. Treatment with EB and its analogs significantly reduced fungal pathogenicity. Our findings provide molecular insights to develop the next generation of antifungal compounds by targeting autophagy in important fungal pathogens. 

Abstract Botrytis cinerea is a fungal pathogen that causes necrotic disease on more than a thousand known hosts widely spread across the plant kingdom. How B. cinerea interacts with such extensive host diversity remains largely unknown. To address this question, we generated an infectivity matrix of 98 strains of B. cinerea on 90 genotypes representing eight host plants. This experimental infectivity matrix revealed that the disease outcome is largely explained by variations in either the host resistance or pathogen virulence. However, the specific interactions between host and pathogen account for 16% of the disease outcome. Furthermore, the disease outcomes cluster among genotypes of a species but are independent of the relatedness between hosts. When analyzing the host specificity and virulence of B. cinerea, generalist strains are predominant. In this fungal necrotroph, specialization may happen by a loss in virulence on most hosts rather than an increase of virulence on a specific host. To uncover the genetic architecture of Botrytis host specificity and virulence, a genome-wide association study (GWAS) was performed and revealed up to 1492 genes of interest. The genetic architecture of these traits is widespread across the B. cinerea genome. The complexity of the disease outcome might be explained by hundreds of functionally diverse genes putatively involved in adjusting the infection to diverse hosts. 

SUMMARY Eudicot plant species have leaves with two surfaces: the lower abaxial and the upper adaxial surface. Each surface varies in a diversity of components and molecular signals, resulting in potentially different degrees of resistance to pathogens. We tested howBotrytis cinerea, a necrotroph fungal pathogen, interacts with the two different leaf surfaces across 16 crop species and 20 Arabidopsis genotypes. This showed that the abaxial surface is generally more susceptible to the pathogen than the adaxial surface. In Arabidopsis, the differential lesion area between leaf surfaces was associated with jasmonic acid (JA) and salicylic acid (SA) signaling and differential induction of defense chemistry across the two surfaces. When infecting the adaxial surface, leaves mounted stronger defenses by producing more glucosinolates and camalexin defense compounds, partially explaining the differential susceptibility across surfaces. Testing a collection of 96B. cinereastrains showed the genetic heterogeneity of growth patterns, with a few strains preferring the adaxial surface while most are more virulent on the abaxial surface. Overall, we show that leaf–Botrytis interactions are complex with host‐specific, surface‐specific, and strain‐specific patterns.