Hailing Jin

Distinguished Professor & Cy Mouradick Chair

Member of the National Academy of Sciences

Member of the National Academy of Inventors

Highly Cited Researcher by Charivate

Research Interests:

Cross-kingdom RNA communication
Extracellular vesicle–mediated RNA trafficking
Regulatory mechanisms of plant RNAi machinery
Nanotechnology-mediated Spray-induced gene silencing for disease control
Antimicrobial peptides for crop protection

Research Projects

My lab studies the roles of RNAs and peptides in plant microbial interaction, aiming to elucidate the molecular mechanisms of plant immunity and pathogen virulence. Our overall goal is to develop effective and environmentally friendly strategies to control plant diseases and to ensure sufficient food production.

Our main research projects are listed below.

Cross-Kingdom RNAi and Extracellular Vesicle-Mediated RNA Trafficking Between Plants and Pathogens

Eukaryotic small RNAs (sRNAs) are short non-coding regulatory molecules that induce RNA interference (RNAi) by guiding mRNA cleavage, translational inhibition or chromatin modifications. sRNAs play an important role in regulating gene expression during plant-pathogen interactions. While most sRNAs function endogenously, we discovered that some sRNAs travel across organismal boundaries between hosts and microbes to silence genes in trans in the interacting organisms (Weiberg et al., Science, 2013; Cai et al., Science, 2018), a mechanism called “Cross-kingdom RNAi.” We further demonstrated that plants utilize extracellular vesicles, mainly exosomes, to protect and transport RNAs into their fungal pathogens and silence fungal virulence-related genes (Cai et al., Science, 2018; He et al., Nature Plants 2021). Complimenting these findings, we also discovered that fungi also utilize extracellular vesicles to send RNAs into their plant hosts, where they are then internalized through clathrin-mediated endocytosis (He et al., Nature Communications 2023). Since our initial studies in plant-fungal interactions, Cross-kingdom RNAi has been observed in many interaction systems, including animal-pathogen and parasite interactions. Recently, we show that plant mRNAs can also be transported by extracellular vesicles to fungal cells and get translated by fungal ribosomes. The protein products of the tranferred plant mRNAs can inhibit fungal virulence (S. Wang et al., Cell Host & Microbe 2024).

Uncovering the mechanisms that govern the cross-kingdom RNA communication will help in the development of novel eco-friendly disease management strategies.

Fungal RNA Uptake and Spray Induced Gene Silencing

The ultimate goal of fundamental research is to translate new discoveries into real-world applications. In order to do this, our lab is working on developing innovative RNA-based fungicides for crop protection using the mechanism of Environmental RNAi. Environmental RNAi was initially discovered in the nematode, Caenorhabditis elegans. Our lab discovered that some fungal pathogens, including B. cinerea, can also efficiently take up RNAs from the environment. Uncovering the currently unknown precise mechanisms of fungal RNA uptake is a key aspect of our lab’s current research goals.

The discovery that environmental RNAi is present in fungi inspired us to develop spray-induced gene silencing (SIGS) to control fungal pathogens. In SIGS techniques, fungal gene targeting RNAs are externally applied to both pre- and post-harvest crops in order to inhibit fungal disease formation. This technique can successfully reduce B. cinerea symptoms in postharvest plant materials including, flowers, leaves, and fruits. It has also successfully reduced disease in plants infected by S. sclerotiorum, F. graminearum and Verticillium. We are actively working towards plant protection against other aggressive fungal pathogens.

RNA is an attractive eco-friendly fungicide because it is already present in most of our food and can be easily digested by animals, whereas traditional pesticides often leave toxic residues in the environment and can be harmful to humans and animals. However, a major hurdle of RNA-based fungicide is its relative instability in the environment. To combat these limitations, we developed lipid and nanoparticle-based strategies to protect RNAs from environmental decay to ensure effective SIGS. Ultimately, we hope to develop an RNA-based next generation of antifungals for crop protection, which could also be adapted for human health applications.

Regulatory Mechanisms of RNAi Machinery in Plant-Pathogen Interactions

My lab also studies the function and regulation of RNAi pathway components, mostly Argonaute (AGO) proteins in plant immunity. AGO proteins are the core components of RNAi complexes, which selectively bind with small RNAs and silence target genes with complementary sequences. We discovered that Arabidopsis AGO positively regulates antibacterial immunity by associating with miR393*, which targets a Golgi-localized SNARE gene MEMB12 and leads to increased secretion of antimicrobial peptide and confers resistance. Since miR393 also contributes to antibacterial immunity by suppressing auxin receptors, miR393*/miR393 represent a novel example of a miRNA*/miRNA pair that functions in the same cellular pathway (host immunity) through two distinct AGOs. We further demonstrated that small RNA duplex structures and AGO PIWI domain contribute to the selective loading of small RNAs in different AGO proteins, AGO1 and AGO2. Most recently, we revealed that Arabidopsis AGO2-mediated gene silencing is dual regulated by arginine methylation. Methylated arginine residues promote AGO2 degradation and are also bound by Tudor-domain proteins which degrade AGO2-associated small RNAs. The methyltransferase responsible for AGO2 arginine methylation is down-regulated during infection, which results in accumulation of AGO2 and AGO2 related small RNAs and leads to the activation of plant defense response. Currently, we are still focusing on the regulation and post-translational modification of AGO proteins in responses to pathogen attacks.

Plant-Derived Antimicrobial Peptides and Peptide-Based Disease Control Solutions

Huanglongbing (HLB), also called Citrus Greening disease, is the most devastating citrus disease caused by the unculturable bacterium, Canidatus Liberbacter asiaticus (CLas), which is transmitted by the Asian Citrus Psyllid. Almost all commercial citrus varieties are susceptible to this disease and there are currently no effective management strategies to combat HLB. Through comparative analysis of small RNA profiles and target gene expression between HLB-tolerant citrus relatives and hybrids and susceptible citrus varieties, we identified a panel of candidate defense regulators for HLB-tolerance. we developed a novel rapid functional screening method, using a C. Liberibacter solanacearum (CLso)/potato psyllid/Nicotiana benthamiana interaction system to mimic the natural transmission and infection circuit of the HLB complex. When combined with efficient virus-induced gene silencing in N. benthamiana, this innovative cost-effective method allows for rapid functional characterization of plant defense regulators against CLas. Using this approach, we identified several promising key regulators and proteins that contribute to defense responses against HLB, including novel antimicrobial peptides, receptor like kinases and signaling proteins, which have the potential to be used in HLB disease management strategies.