Alice Barkan
Alice Barkan
Professor of Biology
B.S., Massachusetts Institute of Technology
Ph.D., University of Wisconsin
Member of: Institute of Molecular Biology
Office: Onyx Bridge Room 280
Telephone: 541-346-5145
Lab: Onyx Bridge Room 270
Telephone: 541-346-2546

Barkan Lab Website

Research Interests

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 post-transcriptional control and RNA/protein interactions. Our research is grounded in a genetic approach, in which we identify nuclear genes that function in chloroplast biogenesis through the analysis of mutations in the nuclear genome that disrupt photosynthesis. We have generated a collection of >2000 non-photosynthetic maize mutants caused by the insertion of Mu transposons. We use the collection as both a forward- and reverse-genetic resource, to guide us to nuclear genes that participate in specific aspects of chloroplast biogenesis and to determine the functions of genes of known sequence but unknown function.

Current projects focus on protein-facilitated group II intron splicing, and on two recently recognized protein families, the CRM and PPR families, that are largely plant-specific and that play essential roles in chloroplast and mitochondrial gene expression. Tools we have developed for this work include the Photosynthetic Mutant Library (PML), a RIP-chip assay that allows us to identify the RNA ligands of organellar RNA binding proteins, and POGs/PlantRBP, a database that groups predicted Arabidopsis, rice, and maize proteins into Putative Orthologous Groups (POGs), with an annotation emphasis on predicted RNA Binding Proteins (RBPs).

Selected Publications

Zoschke R, Watkins K, Barkan A. (2013) A rapid ribosome profiling method elucidates chloroplast ribosome behavior in vivo. Plant Cell, 25:2265-75.

Barkan A, Rojas M, Fujii S, Yap A, Chong YS, Bond CS, Small I. (2012) A combinatorial amino acid code for RNA recognition by pentatricopeptide repeat proteins. PLOS Genet 8: e1002910

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

Hammani K, Cook W, and Barkan A. RNA binding and RNA remodeling activities of the Half-a-Tetratricopeptide (HAT) protein HCF107 underlie its effects on gene expression. PNAS, in press.

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.

Prikryl J, Rojas M, Schuster G, Barkan A. (2011) Mechanism of RNA stabilization and translational activation by a pentatricopeptide repeat protein. Proc Natl Acad Sci U S A. 108(1):415-20.

Williams-Carrier R, Stiffler N, Belcher S, Kroeger T, Stern DB, Monde RA, Coalter R, Barkan A. (2010) Use of Illumina sequencing to identify transposon insertions underlying mutant phenotypes in high-copy Mutator lines of maize. Plant J. 63(1):167-77.

Pfalz J, Bayraktar OA, Prikryl J, and Barkan A. (2009) Site-specific binding of a PPR protein defines and stabilizes 5’ and 3’ mRNA termini in chloroplasts. EMBO J. 28: 2042-2052.

Kroeger TS, Watkins KP, Friso G, van Wijk K, and Barkan A. (2009) A plant-specific RNA binding domain revealed through analysis of chloroplast group II intron splicing. Proc. Natl. Acad. Sci., 106: 4537-42

Beick S, Schmitz-Linneweber, Williams-Carrier R, Jensen B, and Barkan A. (2008) The pentatricopeptide repeat protein PPR5 stabilizes a specific tRNA precursor in maize chloroplasts. Molec. Cell. Biol. 28:5337-47.

Williams-Carrier RE, Kroeger T, and Barkan A. (2008) Sequence-specific binding of a chloroplast pentatricopeptide repeat protein to its native group II intron ligand. RNA, 14: 1930-41.

Asakura Y and Barkan A. (2007) A CRM domain protein functions dually in group I and group II intron splicing in land plant chloroplasts. Plant Cell, 19: 3864-75.

Watkins KP, Kroeger TS, Cooke AM, Williams-Carrier RE, Friso G, Belcher SE, van Wijk KJ, and Barkan A. (2007) A Ribonuclease III Domain Protein Functions in Group II Intron Splicing in Maize Chloroplasts. Plant Cell, 19: 2606-2623

Barkan A, Klipcan L, Ostersetzer O, Kawamura T, Asakura Y, and Watkins K. (2007) The CRM domain: an RNA binding module derived from an ancient ribosome-associated protein. RNA, 13:55-64.

Walker NS, Stiffler N, and Barkan A. (2007) POGS/PlantRBP: A database resource for comparative genomics in plants.Nucl. Acids Res., Jan; 35

Schmitz-Linneweber C, Williams-Carrier R, Williams-Voelker PM, Kroeger TS, Vichas A, and Barkan A. (2006) A pentatricopeptide repeat protein facilitates the trans-splicing of the maize chloroplast rps12 pre-mRNA. Plant Cell, 18:2650-63.

Schmitz-Linneweber C, Williams-Carrier R, Barkan A. (2005) RNA Immunoprecipitation and Microarray Analysis Show a Chloroplast Pentatricopeptide Repeat Protein to Be Associated with the 5' Region of mRNAs Whose Translation It Activates The Plant Cell 17:2791-2804

Ostersetzer O., A.M. Cooke, K.P. Watkins, and A. Barkan. (2005) CRS1, a Chloroplast Group II Intron Splicing Factor, Promotes Intron Folding through Specific Interactions with Two Intron Domains. Plant Cell 17:241-55.

Ostheimer G.J., R. Williams-Carrier, S. Belcher, E. Osborne, J. Gierke, and A. Barkan (2003) Group II intron splicing factors derived by duplication and diversification of an ancient RNA binding domain. EMBO J 22:3919-29.

Department of Physics | Department of Chemistry | Department of Biology | UO Life Sciences | University of Oregon