个人简介

Ph.D., University of Wisconsin B.S., Massachusetts Institute of Technology

研究领域

Biochemistry/Molecular Biology/

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.

近期论文

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Barkan A, Small I (2014) Pentatricopeptide Repeat Proteins in Plants. Annu. Rev. Plant Biol 65: 415-442. Hammani K, Barkan A. (2014) An mTERF Domain Protein Functions in Group II Intron Splicing in Maize Chloroplasts. Nucl Acids Res 42:5033-42. Willians-Carrier R., Zoschke R, Belcher S, Pfalz J, Barkan A. (2014) A major role for the plastid-encoded RNA polymerase complex in the expression of plastid tRNAs. Plant Physiol. 164: 239-48. Tomcal M, Stiffler N, Barkan A. (2013) POGs2: A Web Portal to Facilitate Cross-Species Inferences About Protein Architecture and Function in Plants. PLoS ONE, 8(12):e82569 Germain A, Hotto A, Barkan A, and Stern D (2013) RNA processing and decay in plastids. WIRES RNA, 4: 295-316. Zoschke R, Watkins K, Barkan A. (2013) A rapid ribosome profiling method elucidates chloroplast ribosome behavior in vivo. Plant Cell, 25:2265-75. Sun T, Germain A, Hammani K, Barkan A, Hanson MR, and Bentolila S. (2013) An RNA recognition motif-containing protein is required for plastid RNA editing in Arabidopsis and maize. PNAS, 110:E1169-78. Udy DB, Belcher S, Williams-Carrier R, Gualberto JM, Barkan A. (2012) Effects of reduced chloroplast gene copy number on chloroplast gene expression in maize. Plant Phys, 160:1420-31. Feiz L, Williams-Carrier R, Wostrikoff K, Belcher S, Barkan A, and Stern DB. (2012) Ribulose-1,5-Bis-Phosphate Carboxylase/Oxygenase Accumulation Factor1 Is Required for Holoenzyme Assembly in Maize. Plant Cell, 24:3435-46. Barkan A, Rojas M, Fujii S, Yap A, Chong YS, Bond CS and Small I. (2012) A Combinatorial Amino Acid Code for RNA Recognition by Pentatricopeptide Repeat Proteins. PLOS Genetics, 8: e1002910. Zoschke R, Kroeger T, Belcher S, Schöttler M, Barkan A, and Schmitz-Linneweber C. (2012) The Pentatricopeptide Repeat-SMR Protein ATP4 promotes translation of the chloroplast atpB/E mRNA. Plant J, 72:547-58. Asakura Y, Galarneau E, Watkins K, Barkan A, and van Wijk K. (2012) Chloroplast RH3 DEAD-box RNA helicases in Zea mays and Arabidopsis thaliana function in splicing of specific group II introns and affect chloroplast ribosome biogenesis. Plant Phys. 159: 961-74. Khrouchtchova A, Monde R, and Barkan A. (2012) A short PPR protein required for the splicing of specific group II introns in angiosperm chloroplasts. RNA, 18: 1197-1209. Hammani K, Cook W, and Barkan A. (2012) RNA binding and RNA remodeling activities of the Half-a-Tetratricopeptide (HAT) protein HCF107 underlie its effects on gene expression. PNAS, 109(15):5651-6. Barkan A (2011) Studying the structure and processing of chloroplast transcripts. In "Chloroplast Research In Arabidopsis: Methods and Protocols", P. Jarvis editor. Methods in Molecular Biology. Colas des Francs-Small C, Kroeger T, Zmudjak M, Ostersetzer O, Rahimi N, Small I, and A Barkan. (2011) A PORR domain protein required for rpl2 and ccmFC intron splicing and for the biogenesis of c-type cytochromes in Arabidopsis mitochondria. Plant J, Epub Nov 7, 2011. Zhelyazkova P, Rojas M, Hammani K, Voelker R, Vargas-Suarez M, Börner T and A Barkan. (2011) Protein-mediated protection as the predominant mechanism for defining processed mRNA termini in land plant chloroplasts. Nucl. Acids Res. Epub Dec 8, 2011. Watkins KP, Rojas M, Friso G, van Wijk KJ, Meurer J, Barkan A. (2011) APO1 Promotes the Splicing of Chloroplast Group II Introns and Harbors a Plant-Specific Zinc-Dependent RNA Binding Domain. Plant Cell. 23(3):1082-92. Barkan A. (2011) Expression of plastid genes: organelle-specific elaborations on a prokaryotic scaffold. Plant Physiol. 155(4):1520-32. Prikryl J, Rojas M, Schuster G, and Barkan A. (2011) Mechanism of RNA stabilization and translational activation by a pentatricopeptide repeat protein. Proc. Natl. Acad. Sci. USA, 108:415-420.