Comparative leaf development and cell specific differentiation in C3 and C4 leaves of maize, sorghum and rice; a systems analysis
Plants are classified as C3 or C4 species based on the primary product of carbon fixation in photosynthesis. C4 plants account for 20-30% of terrestrial biomass production, even if they represent only few percent of all plant species. C4-type plants, such as maize, have traits that greatly increase their efficiency of carbon-fixation especially when water or nitrogen are limiting.
Therefore C4 species are attractive for biofuel production while introducing C4 traits into rice may help to raise productivity and alleviate food shortages. The key C4 traits are (1) specialization and cooperation of two leaf photosynthetic cell types (mesophyll and bundle sheath) for photosynthesis, (2) enhanced movement of metabolites between cooperating cells, and (3) high density of leaf venation. For a recent review on C4 differentiation– see Majeran and van Wijk (2009) Trends in Plant Biology.
 

We are studying C3 and C4 leaf development and cellular differentiation through large scale comparative proteome analysis (Majeran et al (2005) Plant Cell; Majeran et al 2008 MCP). Discoveries and putative key regulators and functions are then pursued using various functional essays and research strategies. Complementary analyses are carried out by various collaborating groups. Funding is currently provided by the National Science Foundation (#0701736).

Chloroplast biogenesis and protein homeostasis in Arabidopsis and maize
Plastids are a defining feature of plants whose diverse metabolic functions fundamentally impact plant yield and adaptation to environmental stress. Plastids are essential organelles of prokaryotic origin present in virtually every plant cell; about 12% of all plant nuclear genes encode for plastid-localized proteins, underscoring the importance of plastids. In addition, plastids also have their own genome with some 100 genes. Plastid size, shape, and function depend on the cell type. Chloroplasts are green plastids, found in leaves, stems, flower and green fruits, and carry out photosynthesis and synthesize many essential secondary metabolites. To understand chloroplast function and protein homeostasis, we systematically identified proteins and their oligomeric complexes in chloroplasts of maize and Arabidopsis thaliana. We also developed and implemented different quantitative and comparative proteomics tools to study the response of Arabidopsis chloroplasts to light stress and to analyze chloroplast biogenesis mutants.

Currently we focus on the function of the chloroplast Clp protease system, which is essential for plant growth and development. Using reverse genetics, we are characterizing structures, functions and substrates of this proteolytic Clp system and we take a ‘systems’ view of the chloroplast and surrounding cell to understand functional and regulatory networks (currently supported by the National Science Foundation). (#0718897)

In a separate, but related project, we aim to advance understanding of the DNA/RNA/protein networks underlying chloroplast biogenesis through concerted genetic, proteomic, and DNA-RNA analyses. This involves characterization of: i) new chloroplast biogenesis genes through a forward-genetic strategy that combines IIlumina sequencing with a deep collection of non-photosynthetic maize mutants, ii) Identifying protein components of immunopurified macromolecular assemblies involved in plastid biogenesis through high sensitivity mass spectrometry and iii) Use of genome-wide RNA/DNA coimmunoprecipitation assays to identify the RNA or DNA sequences associated with nucleic-acid binding proteins. (#0922560)


PLANT PROTEOMICS AND MASS SPECTROMETRY
Most cellular functions are carried out by proteins. Therefore knowing the complete set of expressed proteins, their subcellular localization and interactions is important. Proteomics is the systematic analysis of large sets of proteins and relies on the modern mass spectrometers, combined with the availability of sequenced genomes and bioinformatics tools. We develop and implement proteomics tools to solve question in plant biology. Together with our Cornell colleague Dr Qi Sun, we also developed the Plant Proteomics Database (PPDB) to provide an integrated resource for experimentally identified proteins in the key species Arabidopsis, maize (Zea mays) and rice (see Sun et al. 2009. NAR).