KP4 to control Ustilago tritici in wheat: Enhanced greenhouse resistance to loose smut and changes in transcript abundance of pathogen related genes in infected KP4 plants

Killer yeasts: expanding frontiers in the age of synthetic biology

Killer yeasts secrete protein toxins that are selectively lethal to other yeast and filamentous fungi. These exhibit exceptional genetic and functional diversity, and have several biotechnological applications. However, despite decades of research, several limitations hinder their widespread adoption. In this perspective we contend that technical advances in synthetic biology present an unprecedented opportunity to unlock the full potential of yeast killer systems across a spectrum of applications. By leveraging these new technologies, engineered killer toxins may emerge as a pivotal new tool to address antifungal resistance and food security. Finally, we speculate on the biotechnological potential of re-engineering host double-stranded (ds) RNA mycoviruses, from which many toxins derive, as a safe and noninfectious system to produce designer RNA.

Functional Clustering of Metabolically Related Genes Is Conserved across Dikarya

Transcriptional regulation is vital for organismal survival, with many layers and mechanisms collaborating to balance gene expression. One layer of this regulation is genome organization, specifically the clustering of functionally related, co-expressed genes along the chromosomes. Spatial organization allows for position effects to stabilize RNA expression and balance transcription, which can be advantageous for a number of reasons, including reductions in stochastic influences between the gene products. The organization of co-regulated gene families into functional clusters occurs extensively in Ascomycota fungi. However, this is less characterized within the related Basidiomycota fungi despite the many uses and applications for the species within this clade. This review will provide insight into the prevalence, purpose, and significance of the clustering of functionally related genes across Dikarya, including foundational studies from Ascomycetes and the current state of our understanding throughout representative Basidiomycete species.

Enantioselective Fungicidal Activity and Toxicity to Early Wheat Growth of the Chiral Pesticide Triticonazole

In this study, the enantioselective activity of the chiral fungicide triticonazole (TRZ) against target pathogens of seed-borne diseases and the effect on the early phenotypic indexes and physiological and biochemical indexes of wheat following the soaking of seeds were studied. S-TRZ had low fungicidal activity and significantly inhibited the germination of wheat seeds. Seedlings in the S-TRZ treatment group suffered severe oxidative damage; the contents of glutathione (GSH) and malondialdehyde (MDA) were significantly increased. S-TRZ significantly inhibited the synthesis of gibberellin (GA) and ethylene (ETH), while it significantly increased that of jasmonic acid (JA). R-TRZ showed the highest activity against two smut fungi; the treatment of seeds with 5 g (ai)/100 kg R-TRZ had little influence on early wheat growth. The plant hormones were synthesized normally; seedlings grew well, and the fresh weight increased significantly following this treatment. Based on these data, we propose to develop and apply R-TRZ using the national recommended doses to control seed-borne diseases of wheat.

Complete Chromosome-Scale Genome Sequence Resource for Sporisorium panici-leucophaei, the Causal Agent of Sourgrass Smut Disease

Here, we present the first complete chromosome-level genome assembly of the smut fungus strain Sporisorium panici-leucophaei SPL10A, the causal agent of the sourgrass (Digitaria insularis) smut disease. Combining Illumina paired-end and Nanopore long reads, we generated a final assembly composed of 23 chromosomes (22 nuclear and one mitochondrial) with 18,915,934 bp. Gene prediction accomplished using extrinsic evidence from the sugarcane smut fungus Sporisorium scitamineum originated a total of 6,402 protein-encoding genes. The secretome (388 proteins) and the effectorome repertoires (68 candidates) were also predicted, given their crucial roles in plant-pathogen interactions. The complete telomere-to-telomere chromosome sequences of this poorly studied fungus will provide a valuable resource for future comparative genomic studies among smuts to unravel their underlying pathogenicity mechanisms.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Metabolomics Intervention Towards Better Understanding of Plant Traits

The majority of the most economically important plant and crop species are enriched with the availability of high-quality reference genome sequences forming the basis of gene discovery which control the important biochemical pathways. The transcriptomics and proteomics resources have also been made available for many of these plant species that intensify the understanding at expression levels. However, still we lack integrated studies spanning genomics–transcriptomics–proteomics, connected to metabolomics, the most complicated phase in phenotype expression. Nevertheless, for the past few decades, emphasis has been more on metabolome which plays a crucial role in defining the phenotype (trait) during crop improvement. The emergence of modern high throughput metabolome analyzing platforms have accelerated the discovery of a wide variety of biochemical types of metabolites and new pathways, also helped in improving the understanding of known existing pathways. Pinpointing the causal gene(s) and elucidation of metabolic pathways are very important for development of improved lines with high precision in crop breeding. Along with other-omics sciences, metabolomics studies have helped in characterization and annotation of a new gene(s) function. Hereby, we summarize several areas in the field of crop development where metabolomics studies have made its remarkable impact. We also assess the recent research on metabolomics, together with other omics, contributing toward genetic engineering to target traits and key pathway(s).

Genetic modification to improve disease resistance in crops

Plant pathogens are a significant challenge in agriculture despite our best efforts to combat them. One of the most effective and sustainable ways to manage plant pathogens is to use genetic modification (GM) and genome editing, expanding the breeder's toolkit. For use in the field, these solutions must be efficacious, with no negative effect on plant agronomy, and deployed thoughtfully. They must also not introduce a potential allergen or toxin. Expensive regulation of biotech crops is prohibitive for local solutions. With 11-30% average global yield losses and greater local impacts, tackling plant pathogens is an ethical imperative. We need to increase world food production by at least 60% using the same amount of land, by 2050. The time to act is now and we cannot afford to ignore the new solutions that GM provides to manage plant pathogens.

qPCR and loop mediated isothermal amplification for rapid detection of Ustilago tritici

Loose smut of wheat caused by the basidiomycete fungus Ustilago tritici, a seed-borne disease, is difficult to control because of the expanse of wheat planting area and difficulty in pathogen detection. In this study, real-time fluorescence quantitative PCR (qPCR) and loop-mediated isothermal amplification (LAMP) assays are used to rapidly amplify the DNA of U. tritici. Five pairs of primers for qPCR and two series primers for LAMP were designed. Primarily, the specificity of the primer was assessed by using genomic DNA of U. tritici, Fusarium graminearum, Blumeria graminis, Rhizoctonia cerealis, Puccinia striiformis, Bipolaris sorokiniana, and Alternaria solani as templates. Further, the amplification systems were optimized. Finally, the sensitivity of qPCR and LAMP assays were evaluated. The results showed that the primer Y-430 F/R, Y-307 F/R, Y-755 F/R, and Y-139 F/R for qPCR and primers L-139 and L-988 for LAMP could be used for U. tritici detection. In the sensitivity test, the detection limit of qPCR assay was identified as 10 pg μL⁻¹ of genomic DNA, the detection limit for LAMP assay was 100 fg μL⁻¹. We successfully performed qPCR and LAMP assays on wheat loose smut wheat samples. This paper establishes two methods for U. tritici detection, which can be used for diagnosis of wheat loose smut in the laboratory and in the field.

Phylogeography and Population Structure Analysis Reveal Diversity by Gene Flow and Mutation in Ustilago segetum (Pers.) Roussel tritici Causing Loose Smut of Wheat

Ustilago segetum (Pers.) Roussel tritici (UST) causes loose smut of wheat account for considerable grain yield losses globally. For effective management, knowledge of its genetic variability and population structure is a prerequisite. In this study, UST isolates sampled from four different wheat growing zones of India were analyzed using the second largest subunit of the RNA polymerase II (RPB2) and a set of sixteen neutral simple sequence repeats (SSRs) markers. Among the 112 UST isolates genotyped, 98 haplotypes were identified. All the isolates were categorized into two groups (K = 2), each consisting of isolates from different sampling sites, on the basis of unweighted paired-grouping method with arithmetic averages (UPGMA) and the Bayesian analysis of population structure. The positive and significant index of association (I_A = 1.169) and standardized index of association (rBar_D = 0.075) indicate population is of non-random mating type. Analysis of molecular variance showed that the highest variance component is among isolates (91%), with significantly low genetic differentiation variation among regions (8%) (F_st = 0.012). Recombination (R_m = 0) was not detected. The results showed that UST isolates have a clonal genetic structure with limited genetic differentiation and human arbitrated gene flow and mutations are the prime evolutionary processes determining its genetic structure. These findings will be helpful in devising management strategy especially for selection and breeding of resistant wheat cultivars.

Fusarium graminearum KP4-like proteins possess root growth-inhibiting activity against wheat and potentially contribute to fungal virulence in seedling rot

The virally encoded KP4 killer toxin protein was first identified from Ustilago maydis (Um), and its homologues are present in diverse fungi and in one species of moss. No KP4-like (KP4L) proteins have been functionally characterized. Here, we report the identification and functional analysis of four KP4L proteins from Fusarium graminearum (Fg), the primary causal pathogen of Fusarium head blight (FHB), which is also known to associate with seedling rot of wheat. The four FgKP4L proteins (FgKP4L-1, -2, -3 and -4) are encoded by small open reading frames (378-825 bp) located on chromosome 1 with the FgKP4L-1, -2 and -3 genes clustering together. Sequence analysis indicated that FgKP4L proteins have conserved domains predicted to form a three-dimensional alpha/beta-sandwich structure as first reported for UmKP4, with FgKP4L-4 featuring double Kp4 domains. Further analyses revealed that the FgKP4L genes are expressed in vitro under certain stress conditions, and all up-regulated during FHB and/or seedling rot development, the recombinant FgKP4L-2 protein does not induce cell death in wheat leaves or spikelets, but inhibits root growth of young seedlings, and the elimination of the FgKP4L-1/-2/-3 gene cluster from the fungal genome results in reduced virulence in seedling rot but not in FHB. Database searches revealed KP4L proteins from ∼80 fungal species with more than half from human/animal pathogens. Phylogenetic analysis suggested that UmKP4 and the moss KP4L proteins are closely related to those from a zygromycete and Aspergillus, respectively, implying cross-kingdom horizontal gene transfer.