Structural Proteomics: annotating the genome using 3D structure
EMSL Project ID
3990
Abstract
We are applying for NMR spectrometer time at EMSL as a continuation of our structural proteomics project. Structural proteomics is based on the premise that a protein's biochemical function is often dictated by its 3 dimensional shape. Genome sequence of several organisms have shown that a large percentage of the genome encode for proteins which has no sequence homology to proteins of known function (currently refered to as hypothetical proteins). We hope the structures of these hypothetical proteins would provide some clues as to their function which can then be verified by other biochemical means. To date, our collaboration with Dr. Kennedy's laboratory had successfully solved 13 structures, 6 of which we were able to deduce the protein??s function.
Project Details
Project type
Capability Research
Start Date
2003-10-26
End Date
2004-10-29
Status
Closed
Released Data Link
Team
Principal Investigator
Related Publications
Haag JR, and CS Pikaard. 2011. "Multisubunit RNA Polymerases IV and V: Purveyors of Non-Coding RNA for Plant Gene Silencing ." Nature Reviews. Molecular Cell Biology 12:483-492. doi:10.1038/nrm3152
Haag JR, TS Ream, M Marasco, CD Nicora, AD Norbeck, L Pasa-Tolic, and CS Pikaard. 2012. "In vitro transcription activities of Pol IV, Pol V and RDR2 reveal coupling of Pol IV and RDR2 for dsRNA synthesis in plant RNA silencing." Molecular Cell 48(5):811-8. doi:10.1016/j.molcel.2012.09.027
He XJ, YF Hsu, O Pontes, J Zhu, J Lu, RA Bressan, CS Pikaard, C Wang, and JK Zhu. 2009. "NRPD4, a Protein Related to the RPB4 Subunit of RNA Polymerase II, is a Component of RNA Polymerases IV and V and is Required for RNA-directed DNA methylation ." Genes & Development 23:318-330. doi:10.1101/gad.1765209
Jeremy R. Haag, Thomas S. Ream, Michelle Marasco, Carrie D. Nicora, Angela D. Norbeck, Ljiljana Pasa-Tolic and Craig S. Pikaard. In vitro transcription activities of Pol IV, Pol V and RDR2 reveal coupling of Pol IV and RDR2 for dsRNA synthesis in plant RNA silencing. (submitted)
Moran JJ, HW Kreuzer, AJ Carman, JH Wahl, and DC Duckworth. 2012. "Multiple stable isotope characterization as a forensic tool to distinguish acid scavenger samples." Journal of Forensic Sciences 57(1):60-63. doi:10.1111/j.1556-4029.2011.01959.x
Pikaard, Craig S., Jeremy R. Haag, Olga M.F. Pontes, Todd Blevins and Ross Cocklin (2013). A transcription fork model for Pol IV and Pol V-dependent RNA-directed DNA methylation. Cold Spring Harb Symp Quant Biol (in press).
Tan EH, T Blevins, TS Ream, and CS Pikaard. 2012. "Functional Consequences of Subunit Diversity in RNA Polymerases II and V." Cell Reports 1(3):208-214. doi:10.1016/j.celrep.2012.01.004
Thomas Ream, Jeremy Haag and Craig S. Pikaard (2013). Plant multisubunit RNA polymerases IV and V. In: Nucleic Acid Polymerases, edited by Katsuhiko Murakami and Michael Trakselis. Springer (in press).
Tucker, Sarah L., Joshua Reece, Thomas S. Ream, and Craig S. Pikaard (2010). Evolutionary history of plant multisubunit RNA Polymerases IV and V: subunit origins via genome-wide and segmental gene duplications, retrotransposition and lineage-specific sub-functionalization. Cold Spring Harb Symp Quant Biol. 75:285-97.
Wierzbicki AT, R Cocklin, A Mayampurath, R Lister, MJ Rowley, BD Gregory, JR Ecker, H Tang, and CS Pikaard. 2012. "Spatial and Functional Relationships Among Pol V-Associated loci, Pol IV-Dependent siRNAs, and Cytosine Methylation in the Arabidopsis Epigenome." Genes & Development 26(16):1825-1836. doi:10.1101/gad.197772.112