Graduate student and undergraduate assistant positions are available in the Ronald Laboratory for the following projects:
Isolate and characterize receptors that bind sTyr peptides using high-throughput screens.
In 1995, the Ronald laboratory isolated and characterized the rice immune receptor XA21. XA21 binds a small sTyr peptide required for activation of XA21-mediated immunity (RaxX) produced by the model Gram-negative bacterial pathogen Xanthomonas oryzae pv. oryzae (Xoo). We have characterized the RaxX-XA21 pair, an excellent model for understanding sulfated peptide-receptor interaction and function. In addition to activating the immune response in XA21 plants, RaxX is critical for virulence in hosts that lack the XA21 immune receptor. We discovered that RaxX exerts its effects by mimicking the plant peptide PSY, an 18-aa sTyr peptide that promotes root growth by inducing cell elongation. We hypothesize that RaxX-induced host cell elongation provides a niche for bacterial multiplication. Although we have gained deep insight into the RaxX-XA21 interaction, we have not yet identified the PSY receptor(s). Isolation and characterization of these receptors will facilitate studies of the molecular requirements for sTyr-receptor mediated signaling and reveal how specific receptor-peptide interactions can lead to such dramatic and diverse phenotypes (immunity vs. root growth). For this purpose, we will exploit the tractable Arabidopsis, moss (Bezanilla lab), and rice systems to identify and characterize receptors that bind PSY peptides in high-throughput screens led by postdoctoral fellows Ellen Rim and Alyx Shigenaga and collaborator Prof Valley Stewart.
Together these experiments will lead to the identification of receptor and/or coreceptors that bind the sTyr peptides RaxX and PSY and elucidate the molecular basis of diverse biological functions of sTyr peptides.
Identify and analyze sTyr binding interfaces and screen for receptors with new sTyr ligand binding specificities.
We will carry out structural analysis of sTyr peptides in complex with their cognate receptors, validate the importance of identified interaction residues on both the receptor and ligand through in vivo mutagenesis studies, and build a high-throughput platform to screen for receptors with new ligand binding specificities. As needed, we will generate atomic resolution structural models using computational tools that produce protein-peptide predictions through machine learning and motif alignment strategies. The structural analysis will inform genetic approaches to determine the contribution of binding interface residues to immune and growth functions. We have already identified key residues in RaxX that are critical for its ability to activate XA21-mediated immunity but are not critical for root growth. To validate the receptor-peptide structures obtained by crystallography and/or prediction algorithms, we will disrupt interface residues in XA21 rice and/or Arabidopsis plants using CRISPR-Cas9 base editing. Alternatively, we will express the XA21 receptor mutated at putative interface residues in Kitaake lacking XA21, and the mutated Arabidopsis PSY receptors in Arabidopsis plants lacking the wild-type PSY receptor. We will assess the effects of these receptor mutations on RaxX and PSY binding using established disease resistance assays, root growth assays and molecular marker readouts. New insight into sTyr peptide-receptor binding interfaces will then inform high-throughput screens to engineer receptors with new sTyr ligand binding specificities.
Identify transcriptional regulators that interact with promoter regions of small, sulfated peptide families
The successful candidate will work with postdoctoral fellows and Dee Dee Luu to identify the gene networks that drive tissue specific expression of sulfated peptide-mediated root development using Y1H or other approaches. We will use CRISPR-based approaches to mutate corresponding promoters regions in target genes in collaboration with David Savage, UC Berkeley (David Savage lab) to uncover key regions that enhance root development and beneficial microbial associations in collaboration with Jennifer Pett-Ridge and Jill Banfield (Banfield lab).
Advance our mechanistic understanding of plant-microbe interactions and the soil carbon cycle.
New, scalable approaches to capture significant amounts of atmospheric carbon (on the scale of gigatons per year [Gt/yr]) are urgently needed to slow, and perhaps even reverse, global warming. Living organisms—plants, microbes, and fungi—are excellent targets for a scalable solution, having both an immense potential to capture carbon from the atmosphere and store it in stable biomass that covers the surfaces of continents.
Root system architecture (RSA)—the length, number, position, and angle of different root types—determines the soil volume explored by the root and plays a major role in flow of carbon into the soil. RSA and root exudates shape the identity and functional capacities of soil microbiota; roughly half of the carbon fixed through plant photosynthesis is deposited by roots into the soil. As part of this project, we will examine relationships among plant genes, root system architecture, root exudates (including organic acids, sugars, amino acids and other small molecules secreted from the root), and soil mineral surfaces.
To achieve these goals, the candidate will work with postdoctoral fellows Artur Junior and Flor Ercoli, and bioinformatician Rashmi Jain to screen our fully sequenced mutagenized rice population (KitBase) to identify rice plants with deep, robust root systems. Using stable isotope tracing, we will track the flow of carbon from roots into the soil microbial community and surrounding mineral matrix using genome-resolved isotope tracing tools that our IGI team members have pioneered. We will use high throughput CRISPR screens to optimize target genes to produce root system architecture traits and exudates that enhance beneficial microbial associations and lead to soil aggregation, a key mechanism of soil carbon sequestration.
Our collaborators on this project are Jill Banfield, Jennifer Pett-Ridge, David Savage and other team members at UC Davis and the Innovative Genomics Institute.
This project is funded by the Chan-Zuckerberg Initiative.
PENDING. Engineer sorghum for disease resistance and altered root system architecture. Engineer sorghum genes demonstrated to confer disease resistance in rice using CRISPR in sorghum and assess for alterations in genome structure and resistance. The successful candidate will isolate sorghum orthologs, carry out edits, engineer sorghum, carry out progeny analysis and genome sequencing, infect with a fungal and a bacterial pathogen. The candidate will also Engineer sorghum with PSY for altered root length and assess exudates: isolate sorghum orthologs, assess expression patterns engineer sorghum, assess exudates in collaboration with scientists at the Joint Bioenergy Institute and Innovative Genomics Institute.
Prospective Graduate Students
Prof. Ronald is interested in working with highly motivated, creative graduate students with good communication skills. She is committed to increasing the diversity of graduates in plant genetics and creating an inclusive laboratory environment. She maintains diversity, equity, and inclusion practices consistent with those developed by UC Davis. If you think that the Ronald lab would be a good fit for you, please apply to one of these UC Davis graduate groups, which Prof. Ronald is affiliated with:
- Biochemistry and Molecular Biology
- Integrative Genetics and Genomics
- Plant Pathology
- Plant Biology
Please see specific program for application instructions. Each program has advisors that would be glad to provide application tips.
If you are interested in conducting an honors thesis with one of our ongoing projects or would like to work as a research assistant with the group, please email Prof. Ronald to discuss available opportunities.