Colorado State University

Link to Recent Publications

We are actively seeking highly motivated and passionate researchers (Graduate Students and Postdoctoral Scholars) with a strong interest in plant biology. We are looking for candidates with expertise in genomics and bioinformatics to investigate plant processes at the molecular, cellular, and organismal levels. If you have experience in these areas and are interested in joining our team, please send your CV to reddy@colostate.edu.

Members of our research group will have the opportunity to collaborate with Professor Asa Ben-Hur’s lab in the Department of Computer Science at Colorado State University. His lab applies machine learning tools to analyze next-generation sequencing data, addressing complex biological questions in gene regulation.

Research Focus:

One of the fundamental questions in plant biology is understanding how plants sense and respond to both environmental (abiotic and biotic) and hormonal signals that regulate cellular processes, growth, and development. Our group is studying several key areas:

1. Calcium-Mediated Signal Transduction: We focus on calcium sensors and their target proteins, which play essential roles in various plant processes.
2. RNA Splicing: Our research investigates splicing regulatory proteins and how plants regulate basic and alternative splicing of pre-messenger RNAs in response to stresses.
3. Plant Disease Resistance: Understanding the calcium/calmodulin-mediated molecular mechanisms that underlie plant immunity.
4. Production of commercially important chemicals in plants: Moving bacterial pathways into plants to produce desired chemicals.
5. Synthetic Signal Transduction Circuits in Plants: Engineering synthetic pathways to understand and manipulate plant signaling.

To achieve our research objectives, we employ a variety of molecular, cellular, genetic, biochemical, bioinformatics, and computational tools. Our studies utilize Arabidopsis, maize, sorghum, rice, potato, and Miscanthus. In addition, computational analyses of alternative splicing and protein-protein interactions are carried out in collaboration with Professor Asa Ben-Hur’s lab.

Calcium Signaling and Plant Responses:

Calcium and calmodulin are crucial players in plant signal transduction, involved in processes such as growth, development, and responses to pathogens and abiotic stresses. We have extensively characterized several gene families associated with calcium signaling. Notably, our comprehensive screen for calcium sensors and calmodulin-interacting proteins has identified several hundred calcium signaling proteins, including transcription factors and molecular motors.

Over the past two decades, we have focused on the roles of calmodulin-binding proteins in plant growth, stress responses, and disease resistance. For instance, we identified a novel calcium/calmodulin-regulated microtubule motor protein involved in cell morphogenesis and division. Furthermore, we have elucidated signaling pathways involving calmodulin target proteins critical for disease resistance and abiotic stress responses. Additionally, we have shown that a pollen-specific calmodulin-binding protein plays a pivotal role in pollen germination. Our group is also engaged in developing chimeric motors and receptors by combining modular domains from plant and animal proteins for potential applications in synthetic biology and nanobiotechnology.

Gene Regulation and Alternative Splicing:

Alternative splicing of pre-mRNAs is a key process in regulating the complexity of the transcriptome and the diversity of the proteome. Our studies have identified several splicing regulators, such as serine/arginine-rich (SR) proteins, and have analyzed their functions through genetic, biochemical, and cell biological approaches. Through our work on Arabidopsis SR genes, we have uncovered extensive alternative splicing, generating over 90 splice variants from just 15 genes. Stress conditions have been found to induce rapid changes in alternative splicing, enabling plants to quickly reprogram gene expression at the splicing level. This highlights the dynamic nature of the plant transcriptome in response to stress. We have recently developed a genetically encoded splicing reporter that allows easy monitoring of splicing.

Current Research Focus:

Our current research is centered on genome-scale analyses of calmodulin-regulated transcription factors and stress-regulated alternative splicing in various plant mutants. We are utilizing high-throughput sequencing technologies, including Illumina, PacBio, and Nanopore, to characterize plant transcriptomes, alternative splicing, and the epitranscriptome.

A comprehensive understanding of how plants respond to stress will enable us to engineer plants that thrive under challenging environmental conditions. Additionally, we are exploring the possibility of introducing bacterial biochemical pathways into plants to produce novel chemicals with potential applications in agriculture and biotechnology.