Rose Lab Research Projects


Link directly to specific projects:

Overview



Epidermis micrograph
Transmission electron micrograph of a tomato fruit epidermis.

The outer surfaces of plant cells are comprised of diverse sets of polymers, including cell wall polysaccharides and proteins, as well as phenylpropanoid and lipid polymers in the case of more specialized cell types. These polymers are synthesized, secreted and assembled into elaborate matrices with architectures that vary, down to the level of heterogeneity within the specific cell wall faces of individual cells.


cell wall and cuticle model
A simplified diagram of structural layers at the outer surface of aerial plant organs.

Cell wall composition and organization are often dynamic and can change substantially during cell growth and differentiation, or in response to environmental conditions. Research in the Rose lab addresses questions related to how this heterogeneity is established, and examines a range of biological processes at the cell surface, in the interface between plants and their environments. The cell wall and cuticle play critical roles in providing biomechanical support, and protecting plants against pathogens and abiotic stresses. However, the relative contributions of specific compounds that are important for these different functions, and the mechanisms by which they are distributed and interact with each other within the wall framework, are not well understood.


Similarly, the biochemical environments of the apoplast (extracellular region), from the hydrophilic polysaccharide cell wall, to the hydrophobic cuticle, are likely to be highly varied in their composition with respect to the populations of resident proteins, peptide, secondary compounds and other molecules. However, this has yet to be resolved.


Here are examples of some ongoing projects in the Rose lab:


Plant Cuticle Composition, Architecture and Function



Stained cuticle
Tomato fruit cuticle stained with Oil Red O.

The plant cuticle is an extracellular hydrophobic layer that covers the aerial epidermis of all land plants, providing protection against desiccation and external environmental stresses. Considerable progress has been made in understanding the biosynthesis of two major cuticle components, the polymer cutin and cuticular waxes. However, the mechanisms of cuticle assembly, modification and the various functions of different cuticle components are still mostly mysterious.


Protein model
Three-dimensional model of a cell wall protein structure.

As an example, while the cuticle provides the primary barrier to water loss, remarkably little is known about the specific constituents that determine cuticle permeability, or how their synthesis is regulated. In a USDA funded project we are using tomato fruit as a model to identify the specific cuticular wax compounds that limiting desiccation.


This involves developing a detailed understanding of wax diversity, compositional dynamics and functional significance during development in response to drought stress in domesticated tomato (Solanum lycopersicum) and two wild relatives.


Specific objectives of the project include: (A) Identifying temporal and qualitative patterns of wax accumulation in cultivated tomato and wild tomato relatives (B) Characterizing the epidermal specific transcriptomes of these fruits to identify structural and regulatory gene networks that mediate cuticular wax production and deposition; (C) Using introgression lines (ILs) and backcrossed inbred lines (BILs) derived from wild tomato species to identify key genes that underlie qualitative and quantitative differences in fruit cuticular waxes; and (D) Evaluating the roles of putative wax associated structural and/or regulatory genes on wax production and their effects on cuticle properties and fruit traits.


In addition to waxes, the lab is interested in understanding the mechanisms by which the polyester cutin is assembled and modified. Specifically, we have been studying a family of proteins called cutin synthases, examining their mode of action, substrate specificity and the functions of different isoforms.


High Resolution Functional Genomics of Tomato Fruit Development and Environmental Responses



Fruit development Series
A tomato fruit developmental series.

Fruit represent unique plant developmental systems and are important components of human and animal diets. Tomato, an economically important crop, has emerged as the principal model for studies of fleshy fruit development, ripening, shelf life and nutritional quality.


Tomato Expression Atlas
The Tomato Expression Atlas (TEA) website.

However, many fundamental questions related to key aspects of the development, physiology, quality traits and environmental responses of fleshy fruit remain unanswered. The Rose lab, together with Catala, Giovannoni, Fei and Mueller groups at Cornell and the Boyce Thompson Institute, are collaborating on an NSF Plant Genome Research Program project to functionally evaluate, at an unprecedented level of temporal and spatial resolution, the hierarchy of regulatory, hormonal and structural systems that influence tomato fruit ontogeny.


CT Tomato
Computed Tomographic (CT) image of a tomato fruit.

Another goal is to characterize poorly understood responses of fruit to drought, an increasing problem in crop production. These studies will also include two phenotypically diverse wild relatives of tomato that show a high tolerance of water stress, and so may represent opportunities for crop improvement.


We are using laser capture microdissection (LCM) coupled with RNA-Seq based transcriptome profiling to interrogate the full range of tomato fruit pericarp cell types, as well as other tomato fruit tissues. The data are incorporated into a public ‘Tomato Expression Atlas’ (TEA) database, which is designed to display gene expression and co-expression data at the cell/tissue-type scale of resolution in multiple dimensions. The database also houses 2D, 3D and 4D images of the fruit that we are studying


Evolution of Plant Cell Structural Polymers in the Charophycean Green Algae: the Immediate Ancestors of Land Plants



Penium
Penium margaritaceum cell labeled with an anti-pectin monoclonal antibody (green).
The nucleus fluoresces red.

In addition to studying the macromolecular architecture of land plant cell walls, we are also interested in their evolutionary origins. The closest living relatives of land plants are the charophycean green algae (CGA), which diverged from the first terrestrial plants about 450 million years ago.


Penium
Light micrograph of Penium margaritaceum.

However, given their pivotal position in plant evolution, remarkably little is known about the specific molecular mechanisms underlying evolutionary adaptations that originally favored the CGA over other algae/aquatic organisms that would have enabled them to ‘climb onto land’ and survive the new harsh terrestrial conditions. How could the first land plants withstand the unprecedented abiotic stresses, such as desiccation and high levels of UV-radiation, and how did they adapt to the need for mechanical support in the absence of a buoyant aquatic environment?


Key adaptations would have included the development of a protective and structurally complex cell wall and protective barriers to resist desiccation. Together with David Domozych at Skidmore College we are using a range of CG A species to investigate the evolutionary origins of land plant cuticles and specific cell wall polysaccharides. In addition, we are developing the CGA desmid Pemium margaritaceum as a model experimental system, which involves establishing a toolbox of functional genomic tools, including a genetic transformation protocol. We hope to use Penium to better understand how plants can tolerate periodic desiccation and ultimately to improve water stress tolerance in crops.