Louise Prakash, Ph.D.

Professor, Dept. of Biochemistry and Molecular Biology, Senior Scientist, Sealy Center for Molecular Medicine

6.104 Blocker Medical Research Building
Galveston, TX 77555-1061 USA
Telephone: 409-747-8601
Fax: 409-747-8608
e-mail: l.prakash@utmb.edu

Our goals are to delineate the mechanisms of DNA repair processes in eukaryotes, and to determine how damage bypass occurs during DNA replication. We have identified key proteins responsible for post-replicative bypass of damaged DNA. One is Rad6-Rad18, in which an ubiquitin-conjugating enzyme (Rad6) exists in tight association with a DNA binding protein (Rad18), providing a mechanism for the targeting of ubiquitin-conjugating activity to damage sites in DNA. DNA polymerase η , which has the unusual ability to replicate through cyclobutane pyrimidine dimers (CPDs), was identified in our group; we showed that its mutational inactivation is the cause of the cancer-prone syndrome, the variant form of xeroderma pigmentosum in humans. Interestingly, Pol? replicates through a CPD with the same accuracy and efficiency as it replicates through undamaged DNAs.

Biochemical studies carried out in our group and structural studies done in collaboration with Aneel Aggarwal at Mt. Sinai School of Medicine, NY have revealed a high degree of specificity in the manner by which the various yeast and human translesion synthesis DNA polymerases accomplish lesion bypass. For example, Polη , which is specialized for replicating through CPDs, has the unique ability to hold two templating residues in its active site. DNA polymerases κ and ζ, on the other hand, are uniquely adapted for extending mispaired primer termini and for carrying out the extension step of lesion bypass, in which they extend from the nucleotide inserted opposite the lesion site by a DNA polymerase such as ι or Rev1. Pols κ and ζ differ in the types of lesions from which they can extend in very distinct and remarkable ways, and biochemical studies are revealing some highly unusual features that these polymerases adopt in performing their tasks.

Our combined genetic, biochemical, and structural approaches have yielded insights into the novel mechanisms of DNA synthesis adopted by the various yeast and human translesion synthesis DNA polymerases. We are now determining the in vivo contributions of these polymerases to error-free vs. mutagenic lesion bypass, and we are examining the mechanisms by which translesion synthesis DNA polymerases gain access to the replication fork and mediate lesion bypass.

Selected Publications

  1. Nair, D. T., R. E. Johnson, S. Prakash, L. Prakash, and A. K. Aggarwal (2004) Replication by human DNA polymerase-ι occurs by Hoogsteen base-pairing. Nature 430: 377-380.
  2. Prakash, S., R. E. Johnson, and L. Prakash (2005) Eukaryotic translesion synthesis DNA polymerases: specificity of structure and function. Annu. Rev. Biochem. 74:317-353.
  3. Johnson, R. E., L. Prakash, and S. Prakash (2005) Biochemical evidence for the requirement of Hoogsteen base pairing for replication by human DNA polymerase ι. Proc. Natl. Acad. Sci. 102: 10466-10471.
  4. Johnson, R. E., L. Prakash, and S. Prakash (2005) Distinct mechanisms of cis-syn thymine dimer bypass by Dpo4 and DNA polymerase η. Proc. Natl. Acad. Sci. 102: 12359-12364.
  5. Wolfle, W.T., R.E. Johnson, I.G. Minko, R.S. Lloyd, S. Prakash and L. Prakash (2005) Human DNA polymerase ι promotes replication through a ring-closed minor-groove adduct that adopts a syn conformation in DNA. Mol. Cell. Biol. 25:8748-8754.
  6. Nair, D. T., R. E. Johnson, L. Prakash, S. Prakash, and A. K. Aggarwal (2005) Rev1 employs a novel mechanism of DNA synthesis using a protein template. Science 309: 2219-2222.
  7. Acharya, N., L. Haracska, R. E. Johnson, I. Unk, S. Prakash, and L. Prakash (2005) Complex formation of yeast Rev1 and Rev7 proteins: a novel role for the polymerase-associated domain. Mol. Cell. Biol. 25: 9734-9740.
  8. Wolfle, W. T., R. E. Johnson, I. G. Minko, R. S. Lloyd, S. Prakash, and L. Prakash (2006) Replication past a trans-4-hydroxynonenal minor-groove adduct by the sequential action of human DNA polymerases ι and κ. Mol. Cell. Biol. 26: 381-386.
  9. Haracska, L., I. Unk, L. Prakash, and S. Prakash (2006) Ubiquitylation of yeast proliferating cell nuclear antigen and its implications for translesion DNA synthesis. Proc. Natl. Acad. Sci. 103: 64778-6482.
  10. Gangavarapu, V., L. Haracska, I. Unk, R. E. Johnson, S. Prakash and L. Prakash (2006) Mms2-Ubc13 dependent and independent roles of Rad5 ubiquitin ligase in postreplication repair and translesion DNA synthesis in Saccharomyces cerevisiae. Mol. Cell Biol. 26:7783-3390.