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), and with display features that facilitate comparative analyses..
Projects
Protein-Facilitated Group II Intron Splicing
Pentatricopeptide Repeat Proteins: In vivo functions and biochemical mechanisms
CRM Domain Proteins: In vivo functions and biochemical mechanisms
NSF PGRP Project
 Selected Publications
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, in press.
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
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.
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., H. Hadjivasiliou, D.P. Kloer, A. Barkan, and B.W.
Matthews. (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.
Williams P.M. and A. Barkan (2003) A chloroplast-localized PPR protein
required for plastid ribosome accumulation. Plant
J 365:675-86.
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.
Ostheimer G.J., A. Barkan, and B.W. Matthews. (2002) Crystal Structure
of E. coli YhbY. A representative of a novel class of RNA-binding proteins. Structure 10:1593-1601.
Till B., C. Schmitz-Linneweber, R. Williams-Carrier, and A. Barkan
(2001) CRS1 is a novel group II intron splicing factor that was derived from
a domain of ancient origin. RNA 7:1227-38.
Jenkins, B.D. and A. Barkan (2001) Recruitment of a peptidyl-tRNA
hydrolase as a facilitator of group II intron splicing in chloroplasts. EMBO
J 20:872-9.
Walker, M.B., L.M. Roy, E. Coleman, R. Voelker, and A. Barkan (1999)
The maize tha4 gene functions in sec-independent protein transport in
chloroplasts and is related to hcf106, tatA, and tatB.
J Cell Biol 147:267-75.
Fisk, D.G., M.B. Walker, and A. Barkan (1999) Molecular cloning of
the maize gene crp1 reveals similarity between regulators of mitochondrial
and chloroplast gene expression. EMBO J 18:2621-30.
Roy, L. and A. Barkan (1998) A secY homolog is required for
the elaboration of the chloroplast thylakoid membrane and for normal chloroplast
gene expression. J Cell Biol 141:385-95.
Jenkins, B., D. Kulhanek, and A. Barkan (1997) Nuclear mutations
that block group II RNA splicing in maize chloroplasts reveal several intron
classes with distinct requirements for splicing factors. Plant Cell 9:283-96.
Voelker, R., J. Mendel-Hartvig, and A. Barkan (1997) Transposon-disruption
of a maize nuclear gene, tha1, encoding a chloroplast SecA homolog: in
vivo role of SecA in thylakoid protein targeting. Genetics 145:467-78.
Voelker, R., and A. Barkan (1995) Two nuclear mutations disrupt distinct
pathways for targeting proteins to the chloroplast thylakoid. EMBO J 14:3905-14.
Barkan, A., M. Walker, M. Nolasco, and D. Johnson (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 13:3170-81.
Barkan A. (1989) Tissue-dependent plastid RNA splicing in maize:
transcripts from four plastid genes are predominantly unspliced in leaf meristems
and roots. Plant Cell 1:437-45. |
