Alice Barkan,is currently working in Institute of Molecular Biologyand doing Research in the Barkan lab is directed at understanding how the genetic machineries in the chloroplast and nucleus communicate to produce a chloroplast that is responsive to environmental and developmental cues. We study mechanisms by which nuclear genes influence the synthesis of chloroplast proteins, with a focus on RNA metabolism and translation. We also use the chloroplast as a system in which to explore fundamental aspects of RNA/protein interactions, including protein-facilitated group II intron splicing and the mechanisms employed by the pentatricopeptide repeat (PPR) family, a remarkable family of RNA binding proteins that plays a multitude of roles in mitochondrial and chloroplast gene expression. Our research combines genetic and biochemical approaches to identify relevant genes, define their in vivo functions, and elucidate the underlying mechanisms. Tools we have developed for this work include: (i) the Photosynthetic Mutant Library, a saturated collection of transposon-induced non-photosynthetic maize mutants; (ii) Mu-Illumina, a method that allows us to rapidly identify the Mu transposon insertion underlying phenotypes-of-interest in Mu-active maize lines; (iii) a RIP-chip assay that allows us to identify the native RNA ligands of chloroplast RNA binding proteins; (iv) a rapid ribosome profiling method that provides a genome-wide, quantitative, and high resolution readout of chloroplast translation in vivo; and (v) the POGs2 Database, which facilitates cross-species functional inferences in plants by displaying key functional attributes of orthologous proteins in maize, Arabidopsis, rice, and poplar. 

Chloroplast gene expression; RNA-protein interactions; nuclear-chloroplast crosstalk