Location: Molecular Plant Pathology Laboratory
2022 Annual Report
Objectives
Objective 1: Develop novel plant virus-based expression vectors through the characterization of plant virus and viroid genomes. [NP 303, C2, PS2A]
• Sub-objective 1.A. Characterize the genome expression strategies of plant viruses for vector development.
• Sub-objective 1.B. Develop novel plant virus-based expression vectors utilizing modules derived from plant viruses, viroids, and plant genes.
Objective 2: Identify changes in host gene expression and small RNA-mediated regulation associated with viroid and virus infection and spread as targets for disease management. [NP 303, C2, PS2A, PS2B]
• Sub-objective 2.A. Perform a functional analysis of genes and proteins involved in protein phosphorylation pathways in virus and viroid infection to identify targets for disease control.
• Sub-objective 2.B Identify the roles of viroid-specific small RNAs in plant disease.
Objective 3: Develop strategies using plant viruses for the production of antimicrobials for the prevention, treatment, and control of plant and animal diseases. [NP 303, C2, PS2A]
• Sub-objective 3.A. Evaluate novel functional proteins for control of plant diseases.
• Sub-objective 3.B. Develop functionally active proteins in plants for treatment and control of animal diseases.
Approach
This project has two goals: reducing crop losses due to plant pathogens and developing novel compounds to promote growth, improve feed efficiency, and control diseases in farm animals without the use of antibiotics. Fundamental new knowledge of plant pathogen genomes and complex host-pathogen molecular interactions are required to develop novel strategies for disease control. In animals, there are increased challenges to controlling pathogens impacting food safety and infecting livestock and poultry, yet there is a conflicting need to reduce overused antibiotics. Therefore, there is a demand for antibiotic alternatives and novel vaccines, antimicrobials, diagnostic reagents, and therapeutic compounds with reduced cost and low risk to humans, animals and the environment. The unifying concept of this project is the development and use of plant viral-based vectors as tools for the expression of nucleic acids and proteins in plants as a means of studying plant/pathogen interactions, and to develop methodologies useful to control plant pathogens and animal pathogens. In Objective 1, we will study plant virus and viroid genomes (and genome expression strategies) and develop and modify novel plant virus-based vectors based on marafi- tobamo- and potexviruses, viroid genomes, and plant genes. The plant virus-based vectors will be utilized to gain fundamental knowledge of plant virus and viroid host interactions and as tools for expression of heterologous nucleic acids and proteins in plants for plant and animal disease control. In Objective 2, we will perform experiments to evaluate changes in plant host gene expression, and the role of small RNA-mediated regulation, in virus and viroid infection and to determine if phosphorylation signaling pathways play a role in virus and viroid pathogenesis by using protein interaction and gene editing tools. In Objective 3, we will design and express novel antimicrobial proteins in plants to protect against phytopathogenic bacteria and we will design and produce novel recombinant proteins and modified plant virus-like particles which retain functional activity and immunogenicity for control of animal pathogens.
Progress Report
This is the final report for project 8042-22000-295-00D which ended March 15, 2022. New NP303 OSQR approved project 8042-22000-318-00D, entitled Development of Novel Disease Control Strategies Based on Virus and Viroid Biology" has been established. During the five year period, we made significant progress on all three Objectives of the project. In Objective 1, we developed full-length, infectious clones of Maize rayado fino virus and Pepino mosaic virus (PepMV) which were tested for infectivity in their respective hosts and their ability to serve as plant virus-based vectors for expression of heterologous proteins in plants. Modified vectors were created to enhance infectivity and protein expression. Tobacco rattle virus-based vector constructs were engineered to express the antisense RNAs for two tomato genes that are involved in viroid pathogenesis for use in gene silencing assays in tomato. Several virus-based vectors based on full-length clones of pepino mosaic virus were generated and were shown to replicate in inoculated leaves and express the GFP protein systemically in Nicotiana benthamiana; the TGB3 movement protein was mutated to generate virus that can systemically infected inoculated plants, including tomato. In Objective 2, we analyzed changes in gene expression of key genes, including basic helix loop helix transcription factors, involved in fertility and fruit development in tomato plants infected with pospiviroids. The fruits of viroid infected plants are small and have no commercial value and identification of interactions between viroid RNAs and their plant host contribute to our fundamental knowledge of viroid pathogenesis. We have identified three genes that are key for viroid infectivity and pathogenesis and designed and constructed guide RNAs to edit the genes using CRISPR technology to verify their role in disease and plant development. As no naturally occurring resistance is available for plant breeding, gene editing approaches offer more promise. We developed of a rapid diagnostic assay for the detection of tomato apical stunt viroid (TASVd) based on isothermal reverse-transcription-recombinase polymerase amplification. TASVd is not present in the US and is seed-transmitted, therefore the need for a rapid and sensitive assay to test for the viroid in seeds and propagation materials pre- and post-entry. We also developed real-time RT-PCR-specific assays for detection of coconut cadang-cadang, tomato apical stunt, pear blister canker, and coconut tinangaja viroids for the APHIS CAPS program and used these assays to test plant materials to verify presence/absence of the viroids for collaborators in the CAPS program. In Objective 3, we constructed a plant codon-optimized triple-acting fusion gene (TFnt) encoding the enzymatically-active domains of two bacteriophage endolysins and the mature version of lysostaphin for control of Staphylococcus aureus. The modified gene, when transiently expressed in Nicotiana benthamiana plants using the non-replicating Cowpea mosaic virus (CPMV)-based vector pEAQ-HT vector, produced 0.12 g/g fresh weight tissue of TFnt; purified TFnt was preferentially active against the gram-positive S. aureus. Therefore, the combination of codon optimization and transient expression facilitated production of a chimeric phage endolysin in plants. Experiments initiated with ARS Researchers in the Animal Biosciences and Biotechnology Laboratory, Beltsville, Maryland, resulted in the production of biologically active phage endolysins specific for Clostridium spp. In plants. Several endolysins were evaluated using a plant virus-based expression system, with resulting varying levels of protein expression. Further experimentation revealed that one endolysin, CP41, retained high levels of biological activity in plant sap and we have formulated plant tissues containing CP41 for feeding studies in chicks in a NIFA-funded study in collaboration with the University of Maryland Eastern Shore. These studies will continue in the new project. Isometric and bacilliform plant virus-like particles, based on prunus necrotic ringspot virus and maize rayado fino virus, respectively, were engineered to display cationic antimicrobial peptides on their surface. Our results reveal that the antimicrobial peptides can be incorporated into the particle without compromising particle integrity, as revealed by electron microscopy, and experiments to determine the antimicrobial activities of the displayed peptides revealed moderate biological activity against gram-negative bacteria. Predictive bioinformatics and network analyses were employed to gain insights into the pathways of ranscriptional programming in tomato plants infected with Potato spindle tuber viroid.
Accomplishments
1. Development of a rapid diagnostic test for tomato apical stunt viroid. Tomato apical stunt viroid (TASVd), a small nucleic acid plant pathogen, is a serious threat to tomato production worldwide as infection leads to reduced plant vigor, small and deformed fruit, and yield loss. TASVd is seed-transmitted and is easily transmitted mechanically from plant to plant once introduced. Seed treatments do not control transmission of the disease. Tomato seed imports into the U.S. require a phytosanitary certificate stating the seed are free from quarantine pospiviroids, including TASVd. Current methods for detection require costly equipment and specific training. For this reason, ARS scientists in Beltsville, Maryland, developed rapid, specific, sensitive, and easy to perform tests for TASVd detection in leaf and seed tissues that can be employed both in the laboratory and in the field for on-site diagnosis. These tests will be of use to scientists, growers, the industry, and regulatory agencies, who are developing methods and protocols to control viroid diseases.
2. Discovery of specific master transcription regulators of gene expression in tomato. Yield losses caused by viroids can reach from seventeen to sixty-four percent depending on the viroid strain and plant crop species. Viroid systemic infection in tomato is commonly associated with stunting, leaf distortion, veinal chlorosis, reduction of flower size, flower abortion, and reduced size and numbers of fruits. Despite significant achievements in the understanding of tomato fruit development and viroid RNA biology, the mechanisms by which viroid RNAs regulate gene expression of the complex regulatory pathways involved in plant development are not fully understood. Using an omics approach, ARS scientists in Beltsville, Maryland, and collaborators in Mexico identified specific master transcription regulators that regulate genes involved in critical signaling pathways affecting biological processes linked to metabolism and plant defense in viroid-infected plants. These discoveries will inform future strategies for controlling viroid disease and provide a foundation for understanding plant development and reproductive gene expression.
Review Publications
Hammond, R. 2021. Extraction and purification of viroids from Herbaceous hosts. Methods in Molecular Biology. 2316:65-70. https://doi.org/10.1007/978-1-0716-1464-8_6.
Hammond, R. 2021. Cloning and sequencing of viroids. Methods in Molecular Biology. 2316:237-242. https://doi.org/10.1007/978-1-0716-1464-8_20.
Hammond, R. 2021. Detection and characterization of viroids via biological assays on herbaceous hosts. Methods in Molecular Biology. 2316:23-28. https://doi.org/10.1007/978-1-0716-1464-8_2.
Kovalskaya, N., Hammond, R. 2021. Rapid diagnostic detection of tomato apical stunt viroid based on isothermal reverse transcription-recombinase polymerase amplification. Journal of Virological Methods. 300:114353. https://doi.org/10.1016/j.jviromet.2021.114353.
Avina-Padilla, K., Zambada-Moreno, O., Herrera-Oropeza, G., Jimenez-Limas, M., Abrahamian, P., Hammond, R., Hernandez-Rosales, M. 2022. Insights into the transcriptional reprogramming in tomato response to PSTVd variants using network approaches. International Journal of Molecular Sciences. 23:5983. https://doi.org/10.3390/ijms23115983.
