Proteomic and interactomic insights
Next-generation interactome maps of the four plant species of interest facilitate a systems understanding, as well as a pathway to manipulation, of important biological processes involved in biofuel and bioproduct production. Spatially relevant interactomes that underlie the successful growth and development of bioenergy relevant crop species, include those involved in cell wall biosynthesis and modification, floral and seed development, and oil biosynthesis.
Interactome maps are constructed by:
- Identifying protein targets from transcriptome atlases
- Exploring protein-protein and protein-carbohydrate interactions critical to bioenergy production in vivo
Moving from transcriptome to proteins
While transcriptomes provide a wealth of data, they can only give us information at the RNA level. Several recent studies in plants have indicated that RNA levels do not necessarily correlate with protein levels. In order to build robust networks underlying the growth and development of bioenergy relevant crops, the analyses use bulk proteomic data generated for organs or interest.
Inside the cell.
The components of the plant gene expression machinery function in the context of large multimeric complexes. The composition of these complexes, their dynamic regulation (e.g., through phase separation), and their developmental dynamics are largely unknown. Describing functional complexes, dynamics, and the protein ‘neighborhoods’ of key developmental regulators controlling cell decisions in vivo will reveal regulation scenarios for cell types involved in plant growth and development. The interactions between cell wall biosynthesis machinery inside the secretory system of the cell is also of interest; understanding which proteins interact with which will be key in mapping out wall biosynthesis pathways in a single-cell specific manner.
Within the cell wall
The dynamic modification of cell wall polysaccharides is an essential component of plant growth and development; however, we know little about how this remodeling occurs through protein activity and what protein-protein interactions might be involved within the cell wall space. For example, it is not clear whether most modifying proteins act in concert or independently and for others where interactions are regulatory (e.g., pectin modification) the details are virtually non-existent. Describing functional complexes and the protein ‘neighborhoods’ of wall modifying proteins is an essential component of understanding plant growth as it relates to biomass production.