Director: Fatma Kaplan, Ph.D.
Environmental stress can be abiotic and biotic in nature. Abiotic stress factors include chemicals, light, mechanical, temperature, etc. Biotic stress factors can be bacteria, fungus, insects, nematodes, etc. To understand plant acclimation to environmental stress I use many approaches including biochemical, chemical, development, genomics, metabolomics, molecular genetics, and more…….
Effect of nematode pheromones on plant metabolism: This project examines how nematode pheromone affects plant transcriptome, metabolome and plant root volatiles.
This project is very dear to my heart because this is where I integrate my Ph.D. training in plant molecular biology with postdoctoral training in chemistry and interorganismal signaling.
This project has three parts:
- Pheromone effect on plant root metabolism internally
- Pheromone effect on plant root volatiles
- Pheromone’s role in root to shoot interaction
As soon as I identified and confirmed the presence of ascaroside in RKN dispersal larvae/ J2s in December 2011, I wrote and submitted a Fulbright Research award in August 2012 which passed the US peer-review. Based on the feedback from my mentors at the University of Florida, I improved the proposal and reapplied to Fulbright for research and teaching award in August 2013 for metabolite profiling in Dr. Joachim Kopka’s lab at the Max Planck Institute, Golm, Germany. This time the Fulbright proposal was selected as an alternative proposal for funding for 2014-2015. Title for research proposal: Nematode plant interaction through nematode quorum sensing signals Major goal: to determine plant metabolomic response to nematode quorum sensing signals (ascaroside pheromones) in plant roots and shoots (root-shoot interaction). Title for teaching proposal: Analysis of big data for biologists. Major goal: To develop a course curriculum and prepare lectures for analysis of big data such as transcriptomic and metabolomic data sets.
Developing a method to collect plant root volatile for plants in small pots
The goal is to discover whether plant roots release volatile compounds in response to ascaroside pheromones and whether plant released VOCs are attractive or repulsive to other nematodes.
Of course, the first step is to be able to collect plant root volatiles without stressing the plants. Collecting volatile compounds in the plant root zone without disturbing the plant roots is a challenging task, particularly when they are in small pots. As you can imagine, this project had lots of setbacks. Right about the time my appointment ended in May 2012 at the USDA, I developed a non-invasive probe to collect plant root volatiles. I finally succeeded in collecting volatiles from tomato roots in small pots. After May 2012, I started a company (Kaplan Schiller Research LLC), continued to collaborate with USDA scientists, developed a better probe (Kaplan and Schiller 2015 copyright the probe designs) and manufactured it.
Dr. Kaplan’s background on plant abiotic and biotic stress
Abiotic stress. During my Ph.D. training in Dr. Charles Guy’s lab at the University of Florida (UF), I studied abiotic stress; specifically, acclimation to temperature stress; cold, freezing and heat stress. I investigated the role of carbohydrate degradation in cold acclimation and thermotolerance during vegetative growth. I found that maltose, the product of beta-amylase and a disaccharide, acts as a compatible solute during cold and heat shock. I demonstrated that it can preserve the activity of the electron transport chain in vitro using isolated thylakoid membranes and in vivo using RNAi and T-DNA knock out lines. (Kaplan and Guy 2004 Plant Physiol. and 2005 Plant J.). I also showed that decreased beta-amylase transcript levels in RNAi lines were correlated with reduced maltose which is an intermediate in starch degradation in Arabidopsis leaves. Five years later, my dissertation work was cited by a Plant Physiology Text Book (Ed. Taiz and Zieger. 2010) in the carbohydrate degradation section. Furthermore, to understand how all the metabolic pathways acted in concert during temperature acclimation, I used high throughput technologies such as transcript and metabolite profiling. First, I integrated metabolomics data with physiological data using a theoretical framework that I developed based on temperature acclimation (cold acclimation and thermotolerance). Then, I discovered that most heat shock responses were shared with cold-shock responses at the metabolite level, a previously unknown relationship. Additionally, I discovered that salicylic acid (SA) was induced by both cold and heat shock suggesting that SA is involved in cold acclimation and thermotolerance (Kaplan et al. 2004 Plant Physiol. Cited by >500). SA is one of the signaling components of systemic acquired resistance (SAR) that represents plant immune response (Hopkins and Huner 2009). Later, it was shown by other groups that SA was necessary for plant basal thermotolerance, but not acquired (Plant J (2004) 38: 432–447). Furthermore, to understand how transcript profile and metabolite profile correlate, I integrated microarray data and metabolite profile data for 22 metabolic pathways at a time when there were no standard tools available to analyze time course data sets. I found that regulatory processes independent of transcript abundance represented a key part of the metabolic adjustments during cold acclimation (Kaplan et al. 2007 Plant J. cited by >150).
During postdoctoral training in 2005 in Dr. Lanfang Levine’s lab at NASA/ Kennedy Space Center with Dr. Charles Guy, I expanded this work to plant responses to elevated and super elevated (SE) [CO2]. I moved one step further and investigated two different developmental stages; vegetative stage and right before reproductive stage. I found that plant molecular response (transcript and metabolic) to elevated and SE [CO2] are developmentally controlled. I also discovered that there is a fundamental difference in the way plants respond to elevated and SE [CO2] at the molecular level for photosynthetic acclimation (Kaplan et al. 2012 PLoS ONE). Additionally, I found many similar responses at the molecular levels between abiotic and biotic stress from my own data sets on temperature stress (Kaplan et al. 2004 Plant Physiol.), elevated CO2 and from published data sets on biotic stresses. Again, there were many overlapping molecular responses in response to both abiotic stress and biotic stress (Kaplan et al. 2012 PLoS ONE).
In 2005, I got an opportunity for postdoctoral training in interorganismal signaling at the National High Magnetic Field Laboratory in the Edison Lab. The training included isolation of biologically active signaling compounds using activity guided purification and nuclear magnetic resonance (NMR) based structural elucidation. I isolated and elucidated the structure of the Caenorhabditis elegans mate finding pheromone (Srinivasan and Kaplan et al. 2008 Nature 454: 1115 – 1118). Then I expanded my pheromone work to parasitic nematodes; plant and insect parasitic nematodes in 2008 at the Center for Medical, Agricultural and Veterinary Entomology (CMAVE), USDA-ARS.
Biotic stress. At the same time, I applied my skills in NMR based structural elucidation of novel compounds to recruit collaborators and gain experience on how plants respond to parasites, pathogens, and pests, so I could work on plant response to plant parasitic nematodes. In the following collaborations, I led the NMR based structural elucidation of known and novel biologically active compounds from plants in response to biotic factors. The biotic factors included bacteria, fungus, insects, where plants defend themselves directly by producing defensive compounds and/or indirectly by recruiting natural enemies or by deterring the pests. Additionally, the defensive compounds can be regulated by development.
Plant direct defense during vegetative growth and germination. In this collaborative project, I learned how plants respond to insect feeding and fungal infection. I led NMR based structural elucidation of novel diterpenoid and sesquiterpenoid phytoalexins, which are induced in response to fungal infection and insect feeding from maize stems (Proc. Nat. Acad. Sci. (2011) 108: 5455 – 5460 and Plant Physiol. (2011) 156: 2082–2097). Not surprisingly, they inhibit fungal growth and deter insects from feeding. Also, they are regulated by plant hormones such as JA and ethylene together as well as developmentally where they are produced by germinating seedlings without pathogen attack. Very recently, I led structural elucidation of known and novel maize death acids (10-oxo-11-phytoenoate (10-OPEA) and derivatives), which are induced in response to fungal infection in maize leaves and suppresses fungal and insect growth (Proc. Nat. Acad. Sci. (2015).
Plant direct defense during postharvest by storage roots. In this collaborative project, I learned that during storage, sweetpotato storage roots produce toxins in response to fungal infection to defend themselves. I led the NMR based structural elucidation of ipomeamarone and dehydro-ipomeamarone, both of which are known compounds (J. Agric. Food Chem. (2015) 63: 335–342 ).
Plant indirect defense by roots. In response to insect feeding, citrus tree roots release a volatile organic compound (VOC), pregeijerene, to attract a natural enemy, entomopathogenic nematodes (EPNs), which infect insect pests. In this project, I led the NMR based structural elucidation of pregeijerene, a known compound (PLoS ONE (2012) 7: e38146).