Barkan Lab

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Selected Publications

• 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.
• Williams-Carrier R, Stiffler N, Belcher S, Kroeger T, Stern DB, Monde RA, Coalter R, and Barkan A. (2010) Use of Illumina-HTS to identify transposon insertions underlying mutant phenotypes in high-copy Mutator lines of maize. Plant J, 63:167-177.
• 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.
• Barkan A (2008) Genome-wide analysis of RNA-protein interactions in plants. In “Plant Systems Biology”, D. Belostotsky editor. Methods in Molecular Biology, 553: 13-37.
• Asakura Y, Bayraktar OA, and Barkan A (2008) Two CRM protein subfamilies cooperate in the splicing of group IIB introns in chloroplasts. RNA, 14:2319-32.
• Prikryl J, Watkins KP. Watkins, Friso G, van Wijk K, and Barkan A (2008) A member of the Whirly family is a multifunctional RNA and DNA binding protein that is essential for chloroplast biogenesis. Nucl. Acids Res., 36: 5152-65.
• 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.
• Schmitz-Linneweber C and Barkan A (2008) RNA splicing and RNA editing in chloroplasts. In “Cell and Molecular Biology of Plastids” , R Bock editor. Topics in Current Genetics, Vol. 19. pp. 213-248.
• Walker NS, Stiffler N, and Barkan A. (2007) POGS/PlantRBP: A database resource for comparative genomics in plants. Nucl. Acids Res., 35:D852-856.
• 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.
• 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.
• 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.
• Ostheimer GJ, Rojas M, Hadjivassiliou H, and Barkan A. (2006) Formation of the CRS2-CAF2 group II intron splicing complex is mediated by a 22 amino acid motif located in the C-terminal region of CAF2. J. Biol. Chem., 281: 4732-8
• 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.
• Asakura Y and Barkan A. (2006) Arabidopsis orthologs of maize chloroplast splicing factors promote splicing of orthologous and species-specific group II introns. Plant Phys., 142: 1656-1663.
• Ostheimer GJ, Hadjivassiliou H, Kloer DP, Barkan A, and Matthews BW. (2005) Structural analysis of the group II intron splicing factor CRS2 yields insights into its protein and RNA interaction surfaces. J. Mol Biol, 345: 51-68.
• Ostersetzer O, Cooke AM, Watkins KP and Barkan A . (2005) CRS1, a chloroplast group II intron splicing factor, promotes intron folding through specific interactions with two intron domains. Plant Cell, 17: 241-255.
• Schmitz-Linneweber C, Williams-Carrier R, and Barkan A (2005) RNA immunoprecipitation and microarray analysis show a chloroplast PPR protein to be associated with the 5’- region of mRNAs whose translation it activates. Plant Cell, 17: 2791-2804
• Asakura Y, Hirohashi T, Kikuchi S, Belcher S, Osborne E, Yano S, Terashima, Barkan A, and Nakai M . (2004) Maize Mutants Lacking Chloroplast FtsY Exhibit Pleiotropic Defects in the Biogenesis of Thylakoid Membranes. The Plant Cell, 16: 201-214.
• Stern DB, Hanson MR, and Barkan A. (2004) Genetics and genomics of chloroplast biogenesis: maize as a model system. Trends Plant Sci. 2004 Jun;9(6):293-301.
• Barkan A (2004) Intron splicing in plant organelles. In “Molecular Biology and Biotechnology of Plant Organelles”, C. Chase and H. Daniell, editors. Kluwer Academic Publishers. pp 281-308.
• Ostheimer GJ, Williams-Carrier R, Belcher S, Osborne E, Gierke J, and Barkan A. (2003) Group II Intron Splicing Factors Derived by Diversification of an Ancient RNA Binding Domain EMBO J. 22: 3919-3929.
• Williams PM and Barkan A. (2003) A chloroplast-localized PPR protein required for plastid ribosome accumulation. Plant J., 36:675-686.
• Ostheimer GJ, Barkan A, and Matthews BW. (2002) Crystal Structure of E. coli YhbY. A representative of a novel class of RNA-binding proteins. Structure. 10: 1593-1601.
• Jenkins BD and Barkan A. (2001) Recruitment of a peptidyl-tRNA hydrolase as a facilitator of group II intron splicing in chloroplasts. EMBO J., 20: 872-879.
• Till B, Schmitz-Linneweber C, Williams-Carrier R, and Barkan A. (2001) CRS1 is a novel group II intron splicing factor that was derived from a domain of ancient origin. RNA. 7: 1227-1238.
• Barkan A and Goldschmidt-Clermont M. (2000) Participation of nuclear genes in chloroplast gene expression. Biochimie, 82:559-72.
• Fisk DG, Walker MB and Barkan A. (1999) Molecular cloning of the maize gene crp1 reveals similarity between regulators of mitochondrial and chloroplast gene expression. EMBO J., 18: 2621-2630.
• McCormac D.J. and Barkan A. (1999) A nuclear gene in maize required for the translation of the chloroplast atpB/E mRNA. Plant Cell, 11: 1709-1716..
• Walker MB, Roy LM, Coleman E, Voelker R, and Barkan A. (1999) The maize tha4 gene functions in sec-independent protein transport in chloroplasts and is related to hcf106, tatA, and tatB. J. Cell Biology, 147: 267-275.
• Barkan A (1998) Approaches to investigating nuclear genes that function in chloroplast biogenesis in land plants. Methods in Enzymology, 297: 38-57.
• Roy L and Barkan A. (1998) A secY homolog is required for the elaboration of the chloroplast thylakoid membrane and for normal chloroplast gene expression. J. Cell Biology, 141:385-395.
• Voelker, R., Mendel-Hartvig, J., and Barkan A. (1997) Transposon-disruption of a maize nuclear gene, tha1, encoding a chloroplast secA homolog: in vivo role of secA in thylakoid protein targeting. Genetics, 145: 467-478
• Jenkins, B., Kulhanek, D., and Barkan, A. (1997) Nuclear mutations that block group II RNA splicing in maize chloroplasts reveal several intron classes with distinct requirements for splicing factors. Plant Cell, 9: 283-296.
• Voelker R and Barkan A. (1995) Two nuclear mutations disrupt distinct pathways for targeting proteins to the chloroplast thylakoid. EMBO J., 14: 3905-3914.
• Voelker R and Barkan A (1995) Nuclear genes required for post-translational steps in the biogenesis of the chloroplast cytochrome b6/f complex. Mol. Gen. Genet., 249: 507-514.
• Barkan A., Walker M, Nolasco M and Johnson D (1994) A nuclear mutation in maize blocks the processing and translation of several chloroplast mRNAs and provides evidence for the differential translation of alternative mRNA forms. EMBO J., 13: 3170-3181.
• Barkan A. (1993) Nuclear mutants of maize with defects in chloroplast polysome assembly have altered chloroplast RNA metabolism. Plant Cell, 5: 389-402.
• Barkan A and Martienssen RA (1991) Inactivation of maize transposon Mu suppresses a mutant phenotype by activating an outward-reading promoter near the end of Mu1. Proc. Natl. Acad. Sci. 88: 3502-3506.
• Barkan A (1989) Tissue-dependent plastid RNA splicing in maize: transcripts from four plastid genes are predominantly unspliced in leaf meristems and roots. The Plant Cell 1: 437-445.
• Martienssen RA, Barkan A, Freeling M, and Taylor WC. (1989) Molecular cloning of a nuclear gene involved in photosynthetic membrane organization in maize, and its regulation by Robertson's Mutator. EMBO J. 8: 1633-1640.
• Barkan A (1988) Proteins encoded by a complex chloroplast transcription unit are each translated from both monocistronic and polycistronic mRNAs. EMBO J. 7: 2637-2644.

Barkan Lab - 255 Klamath Hall - abarkan@uoregon.edu