Zachary F. Burton
Research Interests
Multi-subunit RNA polymerases are among the most complex and dynamic enzymes found in living systems. Human RNA polymerase II is comprised of 12 peptide subunits, each the product of a separate gene. The large enzyme is highly flexible and dynamic, as indicated by x-ray crystal structures of the homologous yeast RNA polymerase II, which is found in multiple conformations. Regulation of RNA polymerase II is important because messenger RNA synthesis is subverted during cancer and viral infection. Normal development requires constant modulation and re-direction of gene regulation programs. Interest in multi-subunit RNA polymerases within the scientific community was recently underscored by the awarding of the Nobel Prize for Chemistry to Dr. Roger Kornberg of Stanford University. Dr. Kornberg was the first to report x-ray crystal structures of yeast RNA polymerase II. The characteristic "crab claw" structure of multi-subunit RNA polymerases is evolved to support: 1) high fidelity and efficiency through the NTP-driven translocation mechanism; 2) high processivity by tight binding to DNA and the RNA-DNA hybrid; and 3) translocation stepped in single base increments.
NTP-driven translocation
Human RNA polymerase II catalyzes RNA synthesis by an NTP-driven translocation mechanism. NTPs base-pair to the DNA template at downstream sites prior to being translocated stepwise into the active site for incorporation into the RNA chain as an NMP unit, releasing pyrophosphate. Because NTPs are matched to their DNA complements prior to transfer to the active site, mis-loading of NTPs is suppressed, reducing transcription errors. NTP-dNMP base pairs act as allosteric effectors for translocation, and NTP-driven translocation is coupled to pyrophosphate release. Coupling NTP-driven translocation to pyrophosphate release links the beginning of the next bond addition to the final stage of the previous bond addition. In this manner, accurate NTP loading is coupled to the previous bond completion. Accurate NTP-driven translocation coupled to pyrophosphate release is a fidelity checkpoint in each bond addition. MORE
Recent Publications
Feig M, Burton ZF. RNA polymerase II flexibility during translocation from normal mode analysis. Proteins. 2009 Aug 5. [Epub ahead of print]
Domecq C, Kireeva M, Archambault J, Kashlev M, Coulombe B, Burton ZF. 2009. Site-directed mutagenesis, purification and assay of Saccharomyces cerevisiae RNA polymerase II. Protein Expr Purif. 69(2010)83–90. Link to article
Thompson NE, Glaser BT, Foley KM, Burton ZF, Burgess RR. 2009. Minimal promoter systems reveal the importance of conserved residues in the B-finger of human transcription factor IIB. J Biol Chem. 284(37):24754-66. Link to article
Kireeva M, Nedialkov YA, Gong XQ, Zhang C, Xiong Y, Moon W, Burton ZF, Kashlev M. (2009) Millisecond phase kinetic analysis of elongation catalyzed by human, yeast, and Escherichia coli RNA polymerase. Methods. Aug;48(4):333-45. Link to article
Kireeva ML, Nedialkov YA, Cremona GH, Purtov YA, Lubkowska L, Malagon F, Burton ZF, Strathern JN, Kashlev M. (2008) Transient reversal of RNA polymerase II active site closing controls fidelity of transcription elongation. Mol Cell. Jun 6;30(5):557-66. Link to reprint
Xiong Y, Burton ZF. (2007) A tunable ratchet driving human RNA polymerase II translocation adjusted by accurately templated nucleoside triphosphates loaded at downstream sites and by elongation factors. J Biol Chem. 14;282(50):36582-92. Link to reprint
Burton ZF, Feig M, Gong XQ, Zhang C, Nedialkov YA, Xiong Y. (2005) NTP-driven translocation and regulation of downstream template opening by multi-subunit RNA polymerases. Biochem Cell Biol 83(4):486-96. Review. Link to reprint.
Gong, XQ, Zhang, C, Feig, M, and Burton, Z.F. (2005) Dynamic error correction and regulation of downstream bubble opening by human RNA polymerase II. Mol Cell 18:461-470. Link to reprint.
Zhang,C., Zobeck, K.L., and Burton, Z.F.(2005) Human RNA polymerase II elongation in slow motion: role of the TFIIF RAP74 alpha 1 helix in nucleoside triphosphate-driven translocation. Mol Cell Bio 25:3583-3595.Link to reprint.
Ren, D., Nedialkov, Y. A, Li, F., Xu, D, Reimers, S., Finkelstein, A. and Burton, Z. F.(2005) Spacing requirements for simultaneous recognition of the adenovirus major late promoter TATAAAAG box and initiator element Arch Biochem Biophys 435:347-362A.Link to reprint. MORE