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Research Summary:
We study the molecular mechanisms by which extrachromosomal DNA elements maintain themselves stably and at relatively high copy numbers without endangering their host organisms. The model system we employ is the 2 micron plasmid of Saccharomyces cerevisiae. The plasmid has a copy number of approximately 60 per cell, and is rarely lost during cell division. The high plasmid stability is ensured by a partitioning system that includes two plasmid proteins and a cis-acting DNA locus. The plasmid also utilizes an amplification mechanism to compensate for rare stochastic downward fluctuations in copy number. A site-specific DNA recombination system encoded by the plasmid is responsible for this copy number control.
The research projects in the laboratory explore recombination mechanisms, test models for recombination mediated DNA amplification and examine plasmid segregation using tools of molecular genetics and cell biology.
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Publications:
2010 Kachroo, A. H., Ma, C. H., Rowley, P. A., Maciaszek, A. D., Guga, P. and Jayaram, M., Restoration of catalytic functions in Cre recombinase mutants by electrostatic compensation between active site and DNA substrate, Nucleic Acids Res. in press
2010 Rowley, P. A., Kachroo, A. H., Ma, C. H., Maciaszek, A. D., Guga, P. and Jayaram, M., Electrostatic suppression allows tyrosine site-specific recombination in the absence of a conserved catalytic arginine, J. Biol. Chem in press
2010 Ghosh, S. K., Huang, C. H., Hajra, S., and Jayaram, M., Cohesin embraces 2 micron plasmid sisters in a tri-linked catenane complex, Nucleic Acids Res. 38: 570-584
2009 Kachroo, A., Jayaram, M. and Rowley, P. A., Metabolic Engineering without plasmids, Nat Biotech 8: 729-731
2009 Ma, C. H., Kachroo, A. H., Maciaszek, A., Guga, P. and Jayaram, M., Reactions of Cre with methylphosphonate DNA: similarities and contrasts with Flp and vaccinia topoisomerase, PLoS One 4: e7248
2009 Ma, C. H., Rowley, P. A., Maciaszek, A., Guga, P. and Jayaram, M., Active site electrostatics protect genome integrity by blocking abortive hydrolysis during DNA recombination, Embo J. 28: 1745-1756
2009 Cui, H., Ghosh, S. K., and Jayaram, M., The selfish 2 micron plasmid of Saccharomyces cerevisiae utilizes the nuclear motor Kip1p but not Cin8p for its localization and equal segregation, J. Cell Biol. 185: 251-264
2007 Jayaram, M., Split target specificity of ResT: a design for protein delivery, site selectivity and regulation of enzyme activity , Mol. Microbiol. 64: 574-579
2007 Du, Q., Livshits, A., Kwiatek, A., Jayaram, M., and Vologodskii, A. , Protein induced local DNA bends regulate global topology of recombination products, J. Mol. Biol. 368: 170-182
2007 Ma, C. H., Kwiatek, A., Bolusani, S., Voziyanov, Y., and Jayaram, M., Unveiling hidden catalytic activities of the conserved His-trp-III in tyrosine recombinases, J. Mol. Biol. 368: 183-196
2006 Hajra, S. Ghosh, S. K., and Jayaram, M., The centromere-specific histone variant Cse4p (CENP-A) is essential for chromatin architecture at the yeast 2 micron circle partitioning locus., J. Cell Biol. 174: 779-790
2006 Bolusani, S, Ma, C. H., Paek, A., Konieczka, J., Jayaram, M., and Voziyanov, Y. , Evolution of a site-specific variant that utilizes native genomic sequences as recombination target sites., Nucleic Acids Res. i34: 5259-5269
2005 Yin, Z., Jayaram, M., Pathania, S., and Harshey, R. M., The Mu transposase wraps distant DNA sites within a functional transpososome in the absence of DNA supercoiling, J. Biol. Chem. 280: 6149-6156
2005 Dobson, M. J., Pickett, A. J., Velmurugan, S., Pinder, J. B., Barrett, L. A., Jayaram, M. and Chew, J. S., The 2 micron plasmid causes cell death in Saccharomyces with a mutation in Ulp1 protease , Mol. Cell. Biol. 25: 4299-4310
2005 Mehta, S., Yang, X. M., Jayaram, M,, and Velmurugan, S., A novel role for the mitotic spindle in promoting DNA segregation in yeast: promoting 2 micron plasmid-cohesin association, Mol. Cell. Biol. 25: 4283-4298
2004 Jayaram, M. Mehta, S. Uzri, D. and Velmurugan, S., Site-specific recombination and partitioning systems in the stable high-copy propagation of the 2 micron yeast plasmid, Prog. Nucleic Acids Res Mol. Biol. 77: 127-172
2004 Yang, X.M., Mehta, S. Uzri, D., Jayaram, M. and Velmurugan, S., Mutations in a partitioning protein and altered chromatin structure at the partitioning locus prevent cohesin recruitment by the Saccharomyces cerevisiae plasmid and cause plasmid missegregation, Mol. Cell. Biol. 24: 5290-5303
2004 Konieczka, J., Paek, A., Jayaram, M. and Voziyanov, Y., Recombination of hybrid target sites by binary combinations of Flp variants: Mutations that foster interprotomer collaboration and enlarge substrate tolerance, J. Mol. Biol. 339: 365-378
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