In silico prediction of active site and in vitro DNase and RNase activities of Helicoverpa-inducible pathogenesis related-4 protein from Cicer arietinum

Metabolomics-driven investigation of plant defense response against pest and pathogen attack

The advancement of metabolomics has assisted in the identification of various bewildering characteristics of the biological system. Metabolomics is a standard approach, facilitating crucial aspects of system biology with absolute quantification of metabolites using minimum samples, based on liquid/gas chromatography, mass spectrometry and nuclear magnetic resonance. The metabolome profiling has narrowed the wide gaps of missing information and has enhanced the understanding of a wide spectrum of plant-environment interactions by highlighting the complex pathways regulating biochemical reactions and cellular physiology under a particular set of conditions. This high throughput technique also plays a prominent role in combined analyses of plant metabolomics and other omics datasets. Plant metabolomics has opened a wide paradigm of opportunities for developing stress-tolerant plants, ensuring better food quality and quantity. However, despite advantageous methods and databases, the technique has a few limitations, such as ineffective 3D capturing of metabolites, low comprehensiveness, and lack of cell-based sampling. In the future, an expansion of plant-pathogen and plant-pest response towards the metabolite architecture is necessary to understand the intricacies of plant defence against invaders, elucidation of metabolic pathway operational during defence and developing a direct correlation between metabolites and biotic stresses. Our aim is to provide an overview of metabolomics and its utilities for the identification of biomarkers or key metabolites associated with biotic stress, devising improved diagnostic methods to efficiently assess pest and pathogen attack and generating improved crop varieties with the help of combined application of analytical and molecular tools.

Phylogenetic Analysis of the PR-4 Gene Family in Euphorbiaceae and Its Expression Profiles in Tung Tree (Vernicia fordii)

Pathogenesis-related protein-4 (PR-4) is generally believed to be involved in physiological processes. However, a comprehensive investigation of this protein in tung tree (Vernicia fordii) has yet to be conducted. In this study, we identified 30 PR-4 genes in the genomes of Euphorbiaceae species and investigated their domain organization, evolution, promoter cis-elements, expression profiles, and expression profiles in the tung tree. Sequence and structural analyses indicated that VF16136 and VF16135 in the tung tree could be classified as belonging to Class II and I, respectively. Phylogenetic and Ka/Ks analyses revealed that Hevea brasiliensis exhibited a significantly expanded number of PR-4 genes. Additionally, the analysis of promoter cis-elements suggested that two VfPR-4 genes may play a role in the response to hormones and biotic and abiotic stress of tung trees. Furthermore, the expression patterns of VfPR-4 genes and their responses to 6-BA, salicylic acid, and silver nitrate in inflorescence buds of tung trees were evaluated using qRT-PCR. Notably, the expression of two VfPR-4 genes was found to be particularly high in leaves and early stages of tung seeds. These results suggest that VF16136 and VF16135 may have significant roles in the development of leaves and seeds in tung trees. Furthermore, these genes were found to be responsive to 6-BA, salicylic acid, and silver nitrate in the development of inflorescence buds. This research provides valuable insights for future investigation into the functions of PR-4 genes in tung trees.

A comprehensive investigation of lipid-transfer proteins from Cicer arietinum disentangles their role in plant defense against Helicoverpa armigera-infestation

Lipid Transfer Proteins (LTPs) play a crucial role in synthesizing lipid barrier polymers and are involved in defense signaling during pest and pathogen attacks. Although LTPs are conserved with multifaceted roles in plants, these are not yet identified and characterized in Cicer arietinum. In this study, a genome-wide analysis of LTPs was executed and their physiochemical properties, biochemical function, gene structure analysis, chromosomal localization, promoter analysis, gene duplication, and evolutionary analysis were performed using in silico tools. Furthermore, tissue-specific expression analysis and gene expression analysis during pest attack was also conducted for the LTPs. A total of 48 LTPs were identified and named as CaLTPs. They were predicted to be small unstable proteins with "Glycolipid transfer protein" and "Alpha-Amylase Inhibitors, Lipid Transfer and Seed Storage" domains, that are translocated to the extracellular region. CaLTPs were predicted to possess 3-4 introns and were located on all the eight chromosomes of chickpea with half of the CaLTPs being localized on chromosomes 4, 5, and 6, and found to be closely related to LTPs of Arabidopsis thaliana and Medicago trancatula. Gene duplication and synteny analysis revealed that most of the CaLTPs have evolved due to tandem or segmental gene duplication and were subjected to purifying selection during evolution. The promoters of CaLTPs had development-related, phytohormone-responsive, and abiotic and biotic stress-related cis-acting elements. A few CaLTP transcripts exhibited differential expression in diverse tissue types, while others showed no/very low expression. Out of 20 jasmonate-regulated CaLTPs, 14 exhibited differential expression patterns during Helicoverpa armigera-infestation, indicating their role in plant defense response. This study identified and characterized CaLTPs from an important legume, C. arietinum, and indicated their involvement in plant defense against H. armigera-infestation, which can be further utilized to explore lipid signaling during plant-pest interaction and pest management.

Full-Length Transcriptome Characterization and Functional Analysis of Pathogenesis-Related Proteins in Lilium Oriental Hybrid 'Sorbonne' Infected with Botrytis elliptica

Gray mold (Botrytis elliptica) causes a deleterious fungal disease that decreases the ornamental value and yield of lilies. Lilium oriental hybrid 'Sorbonne' is a variety that is resistant to gray mold. Understanding the mechanism of resistance against B. elliptica infection in 'Sorbonne' can provide a basis for the genetic improvement in lily plants. In this study, a PacBio Sequel II system was used to sequence the full-length transcriptome of Lilium 'Sorbonne' after inoculation with B. elliptica. A total of 46.64 Gb subreads and 19,102 isoforms with an average length of 1598 bp were obtained. A prediction analysis revealed 263 lncRNAs, and 805 transcription factors, 4478 simple sequence repeats, and 17,752 coding sequences were identified. Pathogenesis-related proteins (PR), which may play important roles in resistance against B. elliptica infection, were identified based on the full-length transcriptome data and previously obtained second-generation transcriptome data. Nine non-redundant potential LhSorPR proteins were identified and assigned to two groups that were composed of two LhSorPR4 and seven LhSorPR10 proteins based on their genetic relatedness. The real-time quantitative reverse transcription PCR (qRT-PCR) results showed that the patterns of expression of nine differentially expressed PR genes under B. elliptica stress were basically consistent with the results of transcriptome sequencing. The pattern of expression of LhSorPR4s and LhSorPR10s genes in different tissues was analyzed, and the expression of each gene varied. Furthermore, we verified the function of LhSorPR4-2 gene in Lilium. The expression of LhSorPR4-2 was induced by phytohormones such as methyl jasmonate, salicylic acid, and ethephon. Moreover, the promoter region of LhSorPR4-2 was characterized by several functional domains associated with phytohormones and stress response. The overexpression of LhSorPR4-2 gene in 'Sorbonne' increased the resistance of the lily plant to B. elliptica and correlated with high chitinase activity. This study provides a full-length transcript database and functionally analyzed the resistance of PR gene to B. elliptica in Lilium, thereby introducing the candidate gene LhSorPR4-2 to breed resistance in Lilium.

Pathogenesis-related protein-4 (PR-4) gene family in Qingke (Hordeum vulgare L. var. nudum): genome-wide identification, structural analysis and expression profile under stresses

BACKGROUND

Pathogenesis-related (PR) proteins are active participants of plant defense against biotic and abiotic stresses. The PR-4 family features a Barwin domain at the C-terminus, which endows the host plant with disease resistance. However, comprehensive analysis of PR-4 genes is still lacking in Qingke (Hordeum vulgare L. var. nudum).

METHODS AND RESULTS

Herein, a total of four PR-4 genes were identified from the genome of Qingke through HMM profiling. Devoid of the chitin-binding domain, these 4 proteins were grouped as class II PR-4s. Phylogenic analysis revealed that 127 PR-4s from 47 species were clustered into 3 major groups, among which the four Qingke PR-4s were claded into group I. Analysis of gene structure demonstrated that no intron was found in 3 out of the 4 Qingke PR-4s, and HOVUSG0928500 was the only gene contained one intron. An array of cis-acting motifs were detected in promoters of Qingke PR-4 genes, including elements associated with hormone response, light response, stress response, growth and development processes and binding sites of transcription factors, implying their diverse role. Expression profiling confirmed that Qingke PR-4s were involved in defense response against drought, cold and powdery mildews infection, and transcription of HOVUSG1974300 and HOVUSG5705400 was differentially regulated by MeJA and SA.

CONCLUSION

Findings of the study provided insights into the genetic basis of the PR-4 family genes, and would promote further investigation on protein function and utilization.

Dynamics of Zea mays transcriptome in response to a polyphagous herbivore, Spodoptera litura

Zea mays defense response is well-crafted according to the physical and chemical weapons utilized by their invaders during the coevolutionary period. Maize plants employ diversified defense strategies and alter the spatiotemporal distribution of several classes of defensive compounds to affect insect herbivore performance. However, only little knowledge is available about the defense orchestration of maize in response to Spodoptera litura, a voracious Noctuidae pest. In order to decipher the defense status of Zea mays (African tall variety) against S. litura, a comparative feeding bioassay was executed, which revealed reduced performance of the herbivore on maize. In order to understand the molecular mechanism behind maize tolerance against S. litura, a microarray-based genome-wide expression analysis was performed. The comparative analysis displayed 792 differentially expressed genes (DEGs), wherein 357 genes were upregulated and 435 genes were downregulated at fold change ≥ 2 and p value ≤ 0.05. The upregulated genes were identified and categorized as defense-related, oxidative stress-related, transcription regulatory genes, protein synthesis genes, phytohormone-related, and primary and secondary metabolism-related. In contrast, downregulated genes were mainly associated with plant growth and development, indicating a balance of growth and defense response and utilization of a highly evolved C-diversion response were noticed. Maize plants showed better tolerance against herbivory and maintained its fitness using a combinatorial strategy. This peculiar response of Zea mays against S. litura offers an excellent possibility of managing polyphagous pests by spicing up the plant's defensive response with tolerance mechanism.

Differential Transcription and Alternative Splicing in Cotton Underly Specialized Defense Responses Against Pests

The green mirid bug (Apolygus lucorum) and the cotton bollworm (Helicoverpa armigera) are both preferred to live on cotton but cause different symptoms, suggesting specialized responses of cotton to the two insects. In this study, we investigated differential molecular mechanisms underlying cotton plant defenses against A. lucorum and H. armigera via transcriptomic analyses. At the transcription level, jasmonate (JA) signaling was dominated in defense against H. armigera whereas salicylic acid (SA) signaling was more significant in defense against A. lucorum. A set of pathogenesis-related (PR) genes and protease inhibitor genes were differentially induced by the two insects. Insect infestations also had an impact on alternative splicing (AS), which was altered more significantly by the H. armigera than A. lucorum. Interestingly, most differential AS (DAS) genes had no obvious change at the transcription level. GO analysis revealed that biological process termed "RNA splicing" and "cellular response to abiotic stimulus" were enriched only in DAS genes from the H. armigera infested samples. Furthermore, insect infestations induced the retained intron of GhJAZs transcripts, which produced a truncated protein lacking the intact Jas motif. Taken together, our data demonstrate that the specialized cotton response to different insects is regulated by gene transcription and AS as well.

Changes in gene expression in potato meristems treated with the sprout suppressor 1,4-dimethylnaphthalene are dependent on tuber age and dormancy status

Commercial storage of potatoes often relies on the use of sprout inhibitors to prolong storage and reduce spoilage. The compound 1,4-dimethylnaphthalene (DMN) has seen increase application as a sprout inhibitor in the potato industry as older chemistries are being phased out. The mode of action of DMN is poorly understood as is the sensitivity of potato tissues to this new class of inhibitor. During storage potato tubers transition from a state of endo-dormant to eco-dormant and it is not known if the DMN response is consistent across this developmental transition. RNA-seq gene expression profiling was used to establish if stored potato tubers (Solanum tuberosum cv La Chipper) have differential sensitivity to DMN as tubers age. DMN was applied at three different times during storage; just after harvest when tubers are in endo-dormancy, midwinter at early eco-dormancy, and in spring during late eco-dormancy when sprouting was prevented via exposure to cold storage temperatures. Changes in gene expression were lowest during endo-dormancy while midwinter and spring treatments exhibited a greater and more diverse expression response. Functional analysis of differential gene expression demonstrated gene sets associated with DNA replication, cell division, and DNA methylation are suppressed after DMN treatment. However, gene sets associated with salicylic acid, jasmonic acid, abiotic and biotic stress responses are elevated by DMN only after endodormancy terminates. Gene clusters associated with pathogenesis related proteins PR-4 and PR-5 are also upregulated in response to DMN. These results indicate that DMN sensitivity changes as potato tubers age and transition from endo-dormant to eco-dormant in storage and the overall response is a shift in gene classes that regulate growth and response to stress.