Alice Barkan - Publications

Affiliations: 
University of Oregon, Eugene, OR, United States 
Area:
Biochemistry, Molecular Biology, Botany Biology

65 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2016 Hammani K, Takenaka M, Miranda R, Barkan A. A PPR protein in the PLS subfamily stabilizes the 5'-end of processed rpl16 mRNAs in maize chloroplasts. Nucleic Acids Research. PMID 27095196 DOI: 10.1093/Nar/Gkw270  0.36
2016 Pfalz J, Holtzegel U, Barkan A, Weisheit W, Mittag M, Pfannschmidt T. Corrigendum. ZmpTAC12 binds single-stranded nucleic acids and is essential for accumulation of the plastid-encoded polymerase complex in maize. The New Phytologist. 209: 886. PMID 26763682 DOI: 10.1111/nph.13803  0.36
2015 Zoschke R, Watkins KP, Miranda RG, Barkan A. The PPR-SMR protein PPR53 enhances the stability and translation of specific chloroplast RNAs in maize. The Plant Journal : For Cell and Molecular Biology. PMID 26643268 DOI: 10.1111/Tpj.13093  0.36
2015 Ort DR, Merchant SS, Alric J, Barkan A, Blankenship RE, Bock R, Croce R, Hanson MR, Hibberd JM, Long SP, Moore TA, Moroney J, Niyogi KK, Parry MA, Peralta-Yahya PP, et al. Redesigning photosynthesis to sustainably meet global food and bioenergy demand. Proceedings of the National Academy of Sciences of the United States of America. PMID 26124102 DOI: 10.1073/Pnas.1424031112  0.36
2015 Belcher S, Williams-Carrier R, Stiffler N, Barkan A. Large-scale genetic analysis of chloroplast biogenesis in maize. Biochimica Et Biophysica Acta. 1847: 1004-16. PMID 25725436 DOI: 10.1016/J.Bbabio.2015.02.014  0.36
2015 Gully BS, Cowieson N, Stanley WA, Shearston K, Small ID, Barkan A, Bond CS. The solution structure of the pentatricopeptide repeat protein PPR10 upon binding atpH RNA. Nucleic Acids Research. 43: 1918-26. PMID 25609698 DOI: 10.1093/Nar/Gkv027  0.36
2015 Pfalz J, Holtzegel U, Barkan A, Weisheit W, Mittag M, Pfannschmidt T. ZmpTAC12 binds single-stranded nucleic acids and is essential for accumulation of the plastid-encoded polymerase complex in maize. The New Phytologist. 206: 1024-37. PMID 25599833 DOI: 10.1111/Nph.13248  0.36
2014 Fristedt R, Williams-Carrier R, Merchant SS, Barkan A. A thylakoid membrane protein harboring a DnaJ-type zinc finger domain is required for photosystem I accumulation in plants. The Journal of Biological Chemistry. 289: 30657-67. PMID 25228689 DOI: 10.1074/Jbc.M114.587758  0.36
2014 Hammani K, Barkan A. An mTERF domain protein functions in group II intron splicing in maize chloroplasts. Nucleic Acids Research. 42: 5033-42. PMID 24500208 DOI: 10.1093/Nar/Gku112  0.36
2014 Barkan A, Small I. Pentatricopeptide repeat proteins in plants. Annual Review of Plant Biology. 65: 415-42. PMID 24471833 DOI: 10.1146/Annurev-Arplant-050213-040159  0.36
2014 Williams-Carrier R, Zoschke R, Belcher S, Pfalz J, Barkan A. A major role for the plastid-encoded RNA polymerase complex in the expression of plastid transfer RNAs. Plant Physiology. 164: 239-48. PMID 24246379 DOI: 10.1104/Pp.113.228726  0.36
2013 Tomcal M, Stiffler N, Barkan A. POGs2: a web portal to facilitate cross-species inferences about protein architecture and function in plants. Plos One. 8: e82569. PMID 24340041 DOI: 10.1371/Journal.Pone.0082569  0.36
2013 Zoschke R, Watkins KP, Barkan A. A rapid ribosome profiling method elucidates chloroplast ribosome behavior in vivo. The Plant Cell. 25: 2265-75. PMID 23735295 DOI: 10.1105/Tpc.113.111567  0.36
2013 Germain A, Hotto AM, Barkan A, Stern DB. RNA processing and decay in plastids. Wiley Interdisciplinary Reviews. Rna. 4: 295-316. PMID 23536311 DOI: 10.1002/Wrna.1161  0.36
2012 Sosso D, Canut M, Gendrot G, Dedieu A, Chambrier P, Barkan A, Consonni G, Rogowsky PM. PPR8522 encodes a chloroplast-targeted pentatricopeptide repeat protein necessary for maize embryogenesis and vegetative development Journal of Experimental Botany. 63: 5843-5857. PMID 22945943 DOI: 10.1093/Jxb/Ers232  0.36
2012 Barkan A, Rojas M, Fujii S, Yap A, Chong YS, Bond CS, Small I. A combinatorial amino acid code for RNA recognition by pentatricopeptide repeat proteins. Plos Genetics. 8: e1002910. PMID 22916040 DOI: 10.1371/Journal.Pgen.1002910  0.36
2012 Asakura Y, Galarneau E, Watkins KP, Barkan A, van Wijk KJ. Chloroplast RH3 DEAD box RNA helicases in maize and Arabidopsis function in splicing of specific group II introns and affect chloroplast ribosome biogenesis. Plant Physiology. 159: 961-74. PMID 22576849 DOI: 10.1104/Pp.112.197525  0.36
2012 Barbour JE, Liao IT, Stonaker JL, Lim JP, Lee CC, Parkinson SE, Kermicle J, Simon SA, Meyers BC, Williams-Carrier R, Barkan A, Hollick JB. required to maintain repression2 is a novel protein that facilitates locus-specific paramutation in maize. The Plant Cell. 24: 1761-75. PMID 22562610 DOI: 10.1105/Tpc.112.097618  0.36
2012 Khrouchtchova A, Monde RA, Barkan A. A short PPR protein required for the splicing of specific group II introns in angiosperm chloroplasts. Rna (New York, N.Y.). 18: 1197-209. PMID 22495966 DOI: 10.1261/Rna.032623.112  0.36
2012 Hammani K, Cook WB, Barkan A. RNA binding and RNA remodeling activities of the half-a-tetratricopeptide (HAT) protein HCF107 underlie its effects on gene expression. Proceedings of the National Academy of Sciences of the United States of America. 109: 5651-6. PMID 22451905 DOI: 10.1073/Pnas.1200318109  0.36
2012 Majeran W, Friso G, Asakura Y, Qu X, Huang M, Ponnala L, Watkins KP, Barkan A, van Wijk KJ. Nucleoid-enriched proteomes in developing plastids and chloroplasts from maize leaves: a new conceptual framework for nucleoid functions. Plant Physiology. 158: 156-89. PMID 22065420 DOI: 10.1104/Pp.111.188474  0.36
2012 Francs-Small CC, Kroeger T, Zmudjak M, Ostersetzer-Biran O, Rahimi N, Small I, Barkan A. A PORR domain protein required for rpl2 and ccmF(C) intron splicing and for the biogenesis of c-type cytochromes in Arabidopsis mitochondria. The Plant Journal : For Cell and Molecular Biology. 69: 996-1005. PMID 22060106 DOI: 10.1111/J.1365-313X.2011.04849.X  0.36
2011 Barkan A. Studying the structure and processing of chloroplast transcripts. Methods in Molecular Biology (Clifton, N.J.). 774: 183-97. PMID 21822840 DOI: 10.1007/978-1-61779-234-2_12  0.36
2011 Barkan A. Expression of plastid genes: organelle-specific elaborations on a prokaryotic scaffold. Plant Physiology. 155: 1520-32. PMID 21346173 DOI: 10.1104/Pp.110.171231  0.36
2011 Prikryl J, Rojas M, Schuster G, Barkan A. Mechanism of RNA stabilization and translational activation by a pentatricopeptide repeat protein. Proceedings of the National Academy of Sciences of the United States of America. 108: 415-20. PMID 21173259 DOI: 10.1073/Pnas.1012076108  0.36
2009 Barkan A. Genome-wide analysis of RNA-protein interactions in plants. Methods in Molecular Biology (Clifton, N.J.). 553: 13-37. PMID 19588099 DOI: 10.1007/978-1-60327-563-7_2  0.36
2009 Pfalz J, Bayraktar OA, Prikryl J, Barkan A. Site-specific binding of a PPR protein defines and stabilizes 5' and 3' mRNA termini in chloroplasts. The Embo Journal. 28: 2042-52. PMID 19424177 DOI: 10.1038/Emboj.2009.121  0.36
2008 Asakura Y, Bayraktar OA, Barkan A. Two CRM protein subfamilies cooperate in the splicing of group IIB introns in chloroplasts. Rna (New York, N.Y.). 14: 2319-32. PMID 18799595 DOI: 10.1261/Rna.1223708  0.36
2008 Prikryl J, Watkins KP, Friso G, van Wijk KJ, Barkan A. A member of the Whirly family is a multifunctional RNA- and DNA-binding protein that is essential for chloroplast biogenesis. Nucleic Acids Research. 36: 5152-65. PMID 18676978 DOI: 10.1093/Nar/Gkn492  0.36
2008 Williams-Carrier R, Kroeger T, Barkan A. Sequence-specific binding of a chloroplast pentatricopeptide repeat protein to its native group II intron ligand. Rna (New York, N.Y.). 14: 1930-41. PMID 18669444 DOI: 10.1261/Rna.1077708  0.36
2007 Asakura Y, Barkan A. A CRM domain protein functions dually in group I and group II intron splicing in land plant chloroplasts. The Plant Cell. 19: 3864-75. PMID 18065687 DOI: 10.1105/Tpc.107.055160  0.36
2007 Watkins KP, Kroeger TS, Cooke AM, Williams-Carrier RE, Friso G, Belcher SE, van Wijk KJ, Barkan A. A ribonuclease III domain protein functions in group II intron splicing in maize chloroplasts. The Plant Cell. 19: 2606-23. PMID 17693527 DOI: 10.1105/Tpc.107.053736  0.36
2007 Walker NS, Stiffler N, Barkan A. POGs/PlantRBP: a resource for comparative genomics in plants. Nucleic Acids Research. 35: D852-6. PMID 17142226 DOI: 10.1093/Nar/Gkl795  0.36
2007 Barkan A, Klipcan L, Ostersetzer O, Kawamura T, Asakura Y, Watkins KP. The CRM domain: an RNA binding module derived from an ancient ribosome-associated protein. Rna (New York, N.Y.). 13: 55-64. PMID 17105995 DOI: 10.1261/Rna.139607  0.36
2007 Schmitz-linneweber C, Barkan A. RNA splicing and RNA editing in chloroplasts Topics in Current Genetics. 19: 213-248. DOI: 10.1007/4735_2007_0233  0.36
2006 Asakura Y, Barkan A. Arabidopsis orthologs of maize chloroplast splicing factors promote splicing of orthologous and species-specific group II introns. Plant Physiology. 142: 1656-63. PMID 17071648 DOI: 10.1104/Pp.106.088096  0.36
2006 Ostheimer GJ, Rojas M, Hadjivassiliou H, Barkan A. Formation of the CRS2-CAF2 group II intron splicing complex is mediated by a 22-amino acid motif in the COOH-terminal region of CAF2. The Journal of Biological Chemistry. 281: 4732-8. PMID 16379013 DOI: 10.1074/Jbc.M508921200  0.36
2005 Schmitz-Linneweber C, Williams-Carrier R, Barkan A. 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: 2791-804. PMID 16141451 DOI: 10.1105/Tpc.105.034454  0.36
2005 Ostersetzer O, Cooke AM, Watkins KP, Barkan A. CRS1, a chloroplast group II intron splicing factor, promotes intron folding through specific interactions with two intron domains. The Plant Cell. 17: 241-55. PMID 15598799 DOI: 10.1105/Tpc.104.027516  0.36
2005 Ostheimer GJ, Hadjivassiliou H, Hadjivasiliou H, Kloer DP, Barkan A, Matthews BW. Structural analysis of the group II intron splicing factor CRS2 yields insights into its protein and RNA interaction surfaces. Journal of Molecular Biology. 345: 51-68. PMID 15567410 DOI: 10.1016/J.Jmb.2004.10.032  0.36
2004 Stern DB, Hanson MR, Barkan A. Genetics and genomics of chloroplast biogenesis: maize as a model system. Trends in Plant Science. 9: 293-301. PMID 15165561 DOI: 10.1016/J.Tplants.2004.04.001  0.36
2003 Williams PM, Barkan A. A chloroplast-localized PPR protein required for plastid ribosome accumulation. The Plant Journal : For Cell and Molecular Biology. 36: 675-86. PMID 14617068 DOI: 10.1046/J.1365-313X.2003.01915.X  0.36
2003 Ostheimer GJ, Williams-Carrier R, Belcher S, Osborne E, Gierke J, Barkan A. Group II intron splicing factors derived by diversification of an ancient RNA-binding domain. The Embo Journal. 22: 3919-29. PMID 12881426 DOI: 10.1093/Emboj/Cdg372  0.36
2002 Ostheimer GJ, Barkan A, Matthews BW. Crystal structure of E. coli YhbY: a representative of a novel class of RNA binding proteins. Structure (London, England : 1993). 10: 1593-601. PMID 12429100 DOI: 10.1016/S0969-2126(02)00886-9  0.36
2001 Jenkins BD, Barkan A. Recruitment of a peptidyl-tRNA hydrolase as a facilitator of group II intron splicing in chloroplasts Embo Journal. 20: 872-879. PMID 11179231 DOI: 10.1093/Emboj/20.4.872  0.36
2000 Barkan A, Goldschmidt-Clermont M. Participation of nuclear genes in chloroplast gene expression Biochimie. 82: 559-572. PMID 10946107 DOI: 10.1016/S0300-9084(00)00602-7  0.36
1999 Walker MB, Roy LM, Coleman E, Voelker R, Barkan A. The maize tha4 gene functions in sec-independent protein transport in chloroplasts and is related to hcf106, tatA, and tatB. The Journal of Cell Biology. 147: 267-76. PMID 10525534 DOI: 10.1083/Jcb.147.2.267  0.36
1999 McCormac DJ, Barkan A. A nuclear gene in maize required for the translation of the chloroplast atpB/E mRNA Plant Cell. 11: 1709-1716. PMID 10488237 DOI: 10.1105/Tpc.11.9.1709  0.36
1999 Fisk DG, Walker MB, Barkan A. Molecular cloning of the maize gene crp1 reveals similarity between regulators of mitochondrial and chloroplast gene expression. The Embo Journal. 18: 2621-30. PMID 10228173 DOI: 10.1093/Emboj/18.9.2621  0.36
1998 Roy LM, Barkan A. A SecY homologue is required for the elaboration of the chloroplast thylakoid membrane and for normal chloroplast gene expression Journal of Cell Biology. 141: 385-395. PMID 9548717 DOI: 10.1083/Jcb.141.2.385  0.36
1998 Barkan A. Approaches to investigating nuclear genes that function in chloroplast biogenesis in land plants Methods in Enzymology. 297: 38-57. DOI: 10.1016/S0076-6879(98)97006-9  0.36
1997 Jenkins BD, Kulhanek DJ, Barkan A. 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. PMID 9090875 DOI: 10.1105/Tpc.9.3.283  0.36
1995 Voelker R, Barkan A. Nuclear genes required for post-translational steps in the biogenesis of the chloroplast cytochrome b6f complex in maize Mgg Molecular &Amp; General Genetics. 249: 507-514. PMID 8544816 DOI: 10.1007/Bf00290576  0.36
1991 Barkan A, Martienssen RA. Inactivation of maize transposon Mu suppresses a mutant phenotype by activating an outward-reading promoter near the end of Mu1 Proceedings of the National Academy of Sciences of the United States of America. 88: 3502-3506. PMID 1849660 DOI: 10.1073/Pnas.88.8.3502  0.36
1990 Martienssen R, Barkan A, Taylor WC, Freeling M. Somatically heritable switches in the DNA modification of Mu transposable elements monitored with a suppressible mutant in maize Genes and Development. 4: 331-343. PMID 2159936 DOI: 10.1101/Gad.4.3.331  0.36
1989 Barkan A. 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. PMID 2562564 DOI: 10.1105/Tpc.1.4.437  0.36
1988 Gruissem W, Barkan A, Deng XW, Stern D. Transcriptional and post-transcriptional control of plastid mRNA levels in higher plants. Trends in Genetics : Tig. 4: 258-63. PMID 3070872 DOI: 10.1016/0168-9525(88)90033-9  0.36
1988 Good PJ, Welch RC, Barkan A, Somasekhar MB, Mertz JE. Both VP2 and VP3 are synthesized from each of the alternative spliced late 19S RNA species of simian virus 40. Journal of Virology. 62: 944-53. PMID 2828689 DOI: 10.1128/Jvi.62.3.944-953.1988  0.36
1987 Barkan A, Welch RC, Mertz JE. Missense mutations in the VP1 gene of simian virus 40 that compensate for defects caused by deletions in the viral agnogene. Journal of Virology. 61: 3190-8. PMID 3041040 DOI: 10.1128/Jvi.61.10.3190-3198.1987  0.36
1987 Rock CD, Barkan A, Taylor WC. The maize plastid psbB-psbF-petB-petD gene cluster: spliced and unspliced petB and petD RNAs encode alternative products Current Genetics. 12: 69-77. PMID 2835175 DOI: 10.1007/Bf00420729  0.36
1984 Barkan A, Mertz JE. The number of ribosomes on simian virus 40 late 16S mRNA is determined in part by the nucleotide sequence of its leader. Molecular and Cellular Biology. 4: 813-6. PMID 6325897 DOI: 10.1128/MCB.4.4.813  0.36
1983 Mertz JE, Murphy A, Barkan A. Mutants deleted in the agnogene of simian virus 40 define a new complementation group. Journal of Virology. 45: 36-46. PMID 6296443 DOI: 10.1128/jvi.45.1.36-46.1983  0.36
1982 Johnson AD, Barkan A, Mertz JE. Nucleotide sequence analysis of the recombinant joints in 16 naturally arising deletion mutants of simian virus 40. Virology. 123: 464-9. PMID 6294985 DOI: 10.1016/0042-6822(82)90281-1  0.36
1981 Ghosh PK, Roy P, Barkan A, Mertz JE, Weissman SM, Lebowitz P. Unspliced functional late 19S mRNAs containing intervening sequences are produced by a late leader mutant of simian virus 40. Proceedings of the National Academy of Sciences of the United States of America. 78: 1386-90. PMID 6262793 DOI: 10.1073/Pnas.78.3.1386  0.36
1981 Barkan A, Mertz JE. DNA sequence analysis of simian virus 40 mutants with deletions mapping in the leader region of the late viral mRNA's: mutants with deletions similar in size and position exhibit varied phenotypes. Journal of Virology. 37: 730-7. PMID 6261017 DOI: 10.1128/jvi.37.2.730-737.1981  0.36
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