Single-cell assays shed light on decisive factors of development
Plenary Symposium I: Defining the Phenotype: Robustness, Resilience, and Stochastic Processes in Cellular Behavior at ASPB Worldwide Summit
After months of anticipation, the Plant Biology Worldwide Summit is finally kicking off. The current ASPB president Judy Callis welcomed participants from over 40 countries around the globe and asked the questions: why do genetically identical individuals have different phenotypic outcomes and how do plants (or plant cells) ensure the robustness of the desired outcomes?
These questions were addressed by four speakers.
Kent Bradford – Noises are patterns in reality
As a seed biologist, Kent Bradford laid out the history of seed research, which often used percentage to describe phenotypes (e.g., germination percentage). Although seeds are often seen as populations, the question of how small sub-populations influence research outcome always lingers. Using single-seed assays, Kent showed that responses of individual seeds span across various ranges, indicating that sensitivity variation exists among cells and the individuality is important to address the complexity in biological phenomena.
During the live Q&A, Kent elaborated that noises in experimental outcome should be seen as patterns, not outliers. These patterns represent the variation in biological processes and nature, and they contribute to the sensitivity and threshold to respond.
– The balance between defense and regeneration
After plants establish, allocation of resources become even more critical. Plants serve as an amazing model for studying regeneration, because of their fast and robust regeneration processes. Ken Birnbaum uses single cell RNA-seq and live imaging of fluorophore-labeled markers to study root meristem regeneration. The Arabidopsis root meristem can be completely regenerated within three days, but the initial regeneration process can be observed as quickly as two hours. Phases of regeneration include the initiation of developmental genes (e.g., WOX5), rapid cell division, loss of cell identities, and reestablishment of cell specificity. Cell division and chromatin opening are crucial in the regeneration process. However, the regulation of the early response gene WOX5 is not blocked by cell cycle inhibition or shutdown of chromatin opening, suggesting additional regulatory mechanism(s), especially in early response.
Plants, with limited resources, need to consider the balance between defense and regeneration. Ken described a recent discovery that blocking the glutamate receptors (GLRs) shifts plant’s efforts towards regeneration and decreases defenses. This provides an interesting lead to study the regeneration process.
Adrienne Roeder – Stochasticity and robustness in development
Sizes of organisms, organs, or cells are critical to maintain functions. Adrienne Roeder uses Arabidopsis sepals to ask the question of how cells in different sizes are created during development. On the back (abaxial) side of Arabidopsis sepals, giant cell numbers are correlated with levels of the transcription factor ATML1. Mapping ATML1 dosage with cellular development in the single-cell level revealed that the dosage doesn’t exactly predict whether the cell becomes a giant cell. Instead, the ATML1 dosage in the cell cycle G2 phase positively correlates with giant cell development.
Robustness is another important aspect in development. Just like both of our arms have the same lengths, sepals on the same flowers have the same lengths and sizes to ensure an intact flower structure. A mutant (vos2) with irregular sepals became a powerful tool to study the robustness in Arabidopsis flowers. During sepal development, vos2 mutant has slightly stiffer cell walls than wild type and altered hormone responses (low auxin transport and enhanced cytokinin signaling). Therefore, VOS2 is crucial in initiating sepal development via regulations of hormone signaling.
James Locke – Plant circadian clock
Plants determine cellular behaviors based on environmental cues, which are often noisy. James Locke uses plant circadian clock as a model system to understand the robustness of gene regulation. About 30% of Arabidopsis genes are oscillating based on light-dark cycles. When switched from having light-dark cycles to constant light, the magnitudes of oscillation decreases, which could be due to overall magnitude damping or desynchronization of individual cells. Single cell RNA-seq shows that the responses are tissue specific and computational modeling suggests waves of signaling reflect the combination of period difference across the plant and local cell-to-cell coupling.
Stochastic gene regulation may prepare plants for responding to stresses, but the question is how variable are plants. Single seedling RNA-seq reveals that highly variable genes are often stress response genes whereas low variable genes are genes involved in development. Lastly, the combination of modeling coupled with single cell techniques (RNA-seq and microscopy) can further our knowledge in plant circadian clock.
The Plenary Symposium I was a success
There were over one thousand participants during the first broadcast of the Plenary Symposium I and the live Q&A was vibrant. Additionally, the speakers were able to answer nearly all questions through the chat window, which provided great personal connections.
There are many networking opportunities (hallway hangout, networking, or requesting a zoom chat room) in the conference. Make sure to take advantage of the virtual format to connecting with amazing plant scientists around the world!