1. Auxin Signaling

Auxin regulates a vast array of growth and developmental processes throughout the life cycle of plants. Auxin responses are highly context-dependent, concentration-dependent, and can involve changes in cell division, cell expansion, and cell fate. Auxin regulation of transcription involves a core pathway consisting of the TIR1/AFB F-box proteins, the Aux/IAA transcriptional repressors, and the ARF transcription factors. Auxin is perceived by a transient coreceptor complex consisting of a TIR1/AFB protein and an Aux/IAA protein. Auxin binding to the coreceptor results in the degradation of the Aux/IAA and the derepression of ARF-based transcription. Although the basic outlines of this pathway are now well established, it remains unclear how the specificity of the pathway is conferred. We are interested in dissecting the auxin signaling specificity using genomics, molecular biology, and biochemistry. The Aux/IAA proteins mediate diverse physiological and developmental processes in plants. We demonstrated that transcriptional control of Aux/IAA genes plays a central role in the establishment of the auxin-signaling pathways that regulate organogenesis, growth, and environmental response. We proposed Aux/IAAs are hubs for integrating hormone and environmental signals. We are interested in deciphering the Aux/IAA-mediated regulation of plant growth in response to changing environmental conditions.

Auxin Signaling Pathway and its role in Plant Growth, Development, and Stresses

Plants face numerous biotic and abiotic stresses throughout their life. They use hormones to cope with environmental signals. Auxin is well known for its role in plant growth and development. However, in the recent literature, there is enough evidence for the important roles of auxin in many abiotic stresses.

2. Drought Tolerance Mechanisms

Due to the adverse effects of climate change, prolonged periods of drought are happening regularly. This leads to reduced crop yield. So, there is a pressing need for drought-tolerant plants. However, it is complex to generate drought-tolerant crops due to the overlap in signaling mechanisms. So, we are interested in understanding the molecular details of this process by genetically manipulating the auxin signaling pathway. These findings may lead to generate drought-tolerant plants.

Recently, we discovered that auxin can close stomata using aliphatic glucosinolate 4-MSO in Arabidopsis. Auxin antagonizes ABA signaling in guard cells. Auxin acts as a negative regulator of drought stress, and AUX/IAA proteins act as a positive regulator of drought stress (Salehin et al., Nature Communications, 2019). Our group is further interested in researching this glucosinolate-auxin-mediated stomata signaling pathway in molecular detail using genetics, molecular genomics, and cell biology.

We use Arabidopsis thaliana and Brassica oleracea as model plants in these experiments. Ultimately, we are interested in translating these findings into Brassica Vegetables, Soybeans, and Rice.

Repression of Auxin Signaling in Root Tips by Abiotic Stress

Aliphatic Glucosinolate Biosynthesis is Disrupted in few aux/iaa Mutants

Regulation of guard cell expansion and shrinkage by glucosinolates and auxin.

3. CRISPR-Mediated Trait Improvement

We are interested in using genome editing technologies to improve economically important traits such as yield improvement in Brassica vegetables and Soybeans. Plant hormones are an excellent target for doing this. Plant growth hormone auxin is emerging as a critical regulator of drought stress. Following the lead from our published research in Arabidopsis, our lab developed Brassica oleracea MYB28 overexpressing lines. We also have myb28 CRISPR mutant lines. These plants have higher and no aliphatic glucosinolates, respectively. Aliphatic glucosinolates play a role in plant defense, stress tolerance, and have anti-cancer properties. So, these available plants in our lab are excellent genetic tools to dissect drought signaling and improve drought tolerance in Brassica vegetables. We also plan to test them in a murine model of lung cancer.

Recently, we developed a polyvalent guide RNA (pgRNA)-based antiviral to kill plant viruses. We are interested in expanding this pgRNA CRISPR technology to control viral infection in economically important North Carolina crops. We also use a pooled CRISPR library in collaboration with Eilon Shani, Tel Aviv University, to identify new plant growth, development, and abiotic stress genes. We are combining CRISPR mutant libraries with forward genetic screens to knock out closely related multiple-family genes to unravel novel phenotypes and pathways that are hidden due to genetic redundancy. We are searching for novel abiotic stress (drought, salinity, heat), yield, and growth regulators.

Design Principle of pgRNA Guides

Multi-knock in vivo CRISPR and forward genomics in Arabidopsis thaliana for UNKNOWN and PKR genes

Depletion of Viral RNA by pgRNA guides in N. Benthi Leaves

4. Role of SCF E3 Ligases in Abiotic Stress Tolerance

There are almost 700 F-BOX E3 ligases in Arabidopsis thalaina compared to around ~70 in Humans. The molecular function of only a handful of them is known in Arabidopsis. So, why is it difficult to study their role, and why is there such an expansion of these genes in Arabidopsis? To address these issues and functionally characterize novel F-box proteins in abiotic stress signaling, we are interested in identifying and characterizing novel F-box E3 ligase proteins involved in drought and salinity tolerance. If they interact with auxin signaling pathways, then it will be further interesting, as we are trying to leverage auxin signaling pathways in providing drought tolerance. We have collaborated with the Gendron Lab at Yale University to use a decoy (dominant negative) library against a subset of abiotic stress-responsive F-box genes to explore in detail. Unraveling the molecular mechanisms of regulated proteolysis is important for plants and may inform us about novel drug discovery strategies.

5. Machine Learning and AI-based Early Detection of Drought in Soybean Fields

We are exploring the Natural Variation of Global Soybean Accessions from USDA.