We are pursuing basic research activities to understand the molecular mechanisms by which plants mediate innate immunity. This includes determining how plant immune receptors recognize invading pathogens, initiate immune signaling, and execute defense responses. Towards reaching this goal, we are taking multiple complementary approaches including forward and reverse genetic screens, biochemical and live cell imaging approaches along with innovative genomics and proteomics approaches.
Innate Immune Signaling
Both plants and animals rely on cell-surface and intracellular immune receptors to defend against pathogens. The front line of innate immunity in plants involves recognition of highly conserved microbe/pathogen associated molecular patterns (MAMPs/PAMPs) such as bacterial flagellin or fungal chitin by cell surface pattern recognition receptors (PRRs) leading to PAMP-triggered immunity (PTI) to limit pathogen growth. Highly evolved pathogens deliver effector proteins to interfere with the PTI. Plants have evolved with intracellular nucleotide-binding domain leucine-rich repeat (NLR) class of receptors that recognize pathogen effectors and activate effector-triggered immunity (ETI). The PTI and ETI pathways share many components; the increase in the amplitude of the signals during ETI that often culminates in hypersensitive response programmed cell death (HR-PCD) that physically isolates the infection. Our long-term goal is to understand the molecular mechanisms by which immune receptors recognize pathogens and initiate immune signaling.
Subcellular dynamics of NLR Immune Receptors
We study N immune receptor-mediated defense against Tobacco Mosaic Virus (TMV) as one of the model to understand immune signaling. N is the first plant Toll-Interleukin-1 receptor homology Region (TIR) domain containing NLR class of immune receptor (TIR-NLR) cloned in Barbara Baker’s Laboratory. N is a nucleocytoplasmic receptor and recognizes the helicase domain (referred to as p50) within the TMV replicase. Upon p50 recognition in the cytoplasm, N associates with the Squamosa Promoter-binding-protein-Like 6 (SPL6) transcription factor (TF) in the nucleus. Interestingly, N associates with SPL6 in the nucleus only in the presence of defense eliciting p50. SPL6 is also required for Arabidopsis TIR-NLR RPS4-mediated resistance to Pseudomonas syringae bacteria expressing the AvrRps4 effector. These findings point to SPL6 as one of the conserved nuclear components of TIR-NLR signaling. Similar to plants, the mammalian nuclear NLR proteins CIITA and NLRC5 interact with TFs to promote the transcription of MHC class II and class I genes. We are dissecting subcellular sites and dynamics of NLR function during immune signaling (funded by NSF).
Inter-organellar Communication During Innate Immunity
We discovered that chloroplasts play an important role during TIR-NLR N-mediated recognition of TMV and immune signaling. The chloroplast-localized NRIP1 function in recognition of the TMV p50 effector. NRIP1 is recruited to the cytosol and nucleus upon infection with TMV. Interestingly during immune response, chloroplasts dynamically change their morphology by sending out stroma-filled tubular projections known as stromules. Although stromules were first described over 50 years ago, their biological function remains elusive. In a recently published paper, we show that stromules are strongly induced during ETI and PTI and they function during the progression of PCD during immune responses. Stromules make connections to nuclei during immunity and these connections are involved in the transport of signaling molecules and defense proteins from chloroplasts to nucleus. These novel discoveries are providing evidence for stromules as signal conduits in inter-organellar communication during immune response. In a collaborative project with Jeffrey Caplan’s group at University of Delaware, we are investigating function of chloroplasts and stromules in innate immunity and PCD and their communication with other organelles (funded by NIH).
Macroautophagy, hereafter referred to as autophagy, is a dynamic process that is conserved across eukaryotes and entails the engulfment of cellular components or cargoes in double membrane vesicles called autophagosomes. Autophagosomes are then targeted to the vacuole/lysosome for degradation or recycling. Autophagosome formation and cargo delivery is regulated by a series of Autophagy (Atg) core proteins that are conserved form yeast to higher eukaryotes including plants. It has been well established that recycling of long-lived cellular proteins and organelles by autophagy is an important adaptive response to nutrient deprivation. However, recent studies have revealed that autophagy participates in other diverse biological processes including cellular differentiation and development, tissue homoeostasis, aging, senescence, cancer, innate and adaptive immunity, and programmed cell death (PCD). Our long-term goal is to understand the molecular mechanisms by which autophagy regulate different biological processes in plants especially innate immunity and HR-PCD.
Atg8 is a widely used marker to monitor autophagy in vivo. We have developed novel Atg8 sensor system to monitor autophagy in plants and also to identify modulators of autophagy. In collaboration with Stacey Harmer’s group at UC Davis, we are investigating mechanistic link between autophagy and metabolism (funded by NSF-EAGER).
Virulence and resistance determinants of vector-transmitted viruses
Tomato spotted wilt virus (TSWV) and Tomato yellow leaf curl virus (TYLCV) are two most economically important viruses that infect tomato worldwide including the US. These viruses are transmitted plant-to-plant by insect vectors and management of these viruses is difficult and often relies heavily on the use of insecticides to control the vectors. In a collaborative project with Robert Gilbertson, Diane Ullman and Ilias Tagkopoulos groups at UC Davis, we are using genomic approaches to gain insights into the interplay between the host plant’s resistance mechanisms and the viruses’ virulence mechanisms during TSWV and TYLCV infection (funded by NSF-PGRP).
We are using clustered regularly interspaced short palindromic repeat (CRISPR)-associated protein 9 (Cas9) based approach to engineer resistance to cassava infecting viruses in collaboration with Vincent Fondong's group at Delaware State University. In addition, we are optimizing viral vectors to deliver Cas9 and gRNA into plants for genome editing.