Welcome to Chloroplast Phenomics

As the site of photosynthesis, the chloroplast is the defining organelle of green plants and may be thought of as the world’s life-support system. We have chosen it for functional genomics studies because it produces many molecules important to agriculture and human health yet is similar in complexity to a bacterial cell.

Project Objectives

Our long term goal as plant biochemists is to understand the metabolic functioning of the plastid. In this proposal we focus on the task of assigning function to the nuclear genes encoding plastid-targeted products.

Our specific objectives are to:

  1. Use informatic and phenotypic approaches to significantly enrich the annotation of all nuclear-encoded genes whose products are known or predicted to be imported into the plastid.
  2. Identify those genes whose inactivation leads to a specific observable metabolic or morphological phenotype and experimentally assign functional attributes to these genes. The value of this phenotype-driven approach is well documented, and despite decades of forward genetic screens in Arabidopsis, the function of the vast majority of genes remain experimentally undefined.
  3. Use flux analysis to map primary metabolism in the developing seed and determine patterns of plasticity and rigidity in this network. Metabolic flux mapping can both illuminate individual gene function in the context of the network of central metabolism and answer general, fundamental questions about seed metabolism.
  4. Generate hypotheses about gene function using statistical tools to reveal connections among metabolic phenotypes and correlations with gene and other expression measurements. The quantitative results of the primary and secondary analyses will be subjected to statistical analysis and whenever possible will be related to existing transcriptional datasets (e.g. AtGenExpress) and proteomic and/or metabolomic data sets as these become available. This will reveal correlations that suggest mechanisms and regulation of integrated biochemical functions that single functional analyses or one level of expression cannot be expected to show.
  5. Build an easy-to-use, publicly accessible database integrated into a website to disseminate the information openly and without IP restrictions.
  6. Educate current and future plant scientists in studying gene function at the genome-wide level. Because of the range of experimental and theoretical expertise that the PIs bring to the project, their close proximity on a single campus, and the integrated management plan of this project, the PIs, students, postdoctoral associates, and technical support staff will learn multiple approaches and their integration. By introducing faculty from primarily-undergraduate institutions and from local high schools as well as undergraduates to this collaborative, integrative approach to biological enquiry, we will impact a broad range of students and citizens in systems-wide approaches and cutting-edge tools for plant genomics and biochemistry.