Chemical Biology/Genetics, Molecular Biophysics, Nucleic Acids, Proteins & Enzymology
Our longest running program was directed toward understanding the enzymology of DNA replication with primary focus on a prototypical cellular replicase, the DNA polymerase III holoenzyme. Because of the conserved nature of replication mechanisms, many central principles were established using this system. Our contributions included identifying most of the replicase components, their organization and function. Our most recent focus was on the signaling networks that led to coordinated action of the leading and lagging strand replicase and the cycling of the lagging strand polymerase, during Okazaki fragment synthesis.
The low GC Gram-positive bacteria diverged from E. coli approximately two billion years ago. This model organism provided an opportunity to learn how the central themes of DNA replication varied in highly divergent organisms. We established a full in vitro system that requires 13 purified proteins. Among our contributions, we showed that lagging strand synthesis requires two DNA polymerase IIIs. DnaE elongates RNA primers and then hands off synthesis to Pol C. DnaE is slow, but highly processive. Thus, the exchange is by an active process whereby Pol C displaces DnaE.
This program was directed toward the discovery and development of small molecules that block each of the steps of the replication process. These were sought to provide tools for studying the mechanism of DNA replication. It was anticipated that a subset of the compounds discovered would provide leads for development of novel antibacterials.
We discovered a novel highly processive thermophilic replicase that, coupled with replication fork proteins, should be capable of rapidly replicating entire chromosomes and megabase segments of DNA.
For a more complete description of our key research contributions, please see the McHenry lab research page.
Dohrmann, P.R., Correa, R., Frisch R.L., Rosenberg, S.M., McHenry, C.S. (2016) “The DNA polymerase III holoenzyme contains gamma and is not a trimeric polymerase.” Nucl. Acids Res. 44, 1285-1297.
Yuan, Q. and McHenry, C. (2014) Cycling of the E. coli lagging strand polymerase is triggered exclusively by the availability of a new primer at the replication fork. Nucleic Acids Res. 42, 1747-1756.
McHenry, C. (2011) Breaking the Rules: Bacteria That Use Several DNA Polymerase IIIs. EMBO Rep. 12, 408-414.
McHenry, C. (2011) DNA Replicases from a Bacterial Perspective. Annu. Rev. Biochem., 80, 403-436.
Dallmann, H.G.,Fackelmayer, O.J., Tomer, G., Chen, J.Y., Wiktor-Becker, A., Ferrara, T., Pope, C., Oliveira, M.T., Burgers, P.M.J., Kaguni, L.K. and McHenry, C. (2010) Parallel Multiplicative Target Screening Against Divergent Bacterial Replicases: Identification of Specific Inhibitors with Broad Spectrum Potential. Biochemistry, 49, 2551-2562.
Downey, C.D. and McHenry, C. (2010) Chaperoning of a Replicative Polymerase onto a Newly-Assembled DNA Bound Sliding Clamp by the Clamp Loader. Mol. Cell, 37,481-491.
Sanders, G.M., Dallmann, H.G. and McHenry, C. (2010) Reconstitution of the B. subtilis Replisome with 13 Proteins including Two Distinct Replicases. Mol. Cell, 37, 273-281.
Stano, N., Chen, J. and McHenry, C. (2006) A Coproofreading Zn+2-dependent Exonuclease within a Bacterial Replicase. Nat. Struct. Mol. Biol.,13, 458-459.
Dohrmann, P.R. and McHenry, C., (2005) A Bipartite Polymerase–Processivity Factor Interaction: Only the Internal beta Binding Site of the alpha Subunit is Required for Processive Replication by the DNA Polymerase III Holoenzyme. J. Mol. Biol., 350, 228-239.
Bullard J.M., Williams J.C., Acker W.K., Jacobi C,. Janjic N. and McHenry C. (2002) DNA Polymerase III Holoenzyme from Thermus thermophilus: Identification, Expression, Purification of Components and Use to Reconstitute a Processive Replicase. J. Biol. Chem., 277, 13401-13408.
Pritchard, A.E. and McHenry, C. (2001) Assembly of DNA Polymerase III Holoenzyme: Co-assembly of gamma and tau is Inhibited by DnaX Complex Accessory Proteins but Stimulated by DNA polymerase III Core. J. Biol. Chem., 276, 35217-35222.
Glover, B. and McHenry, C. (2001) The DNA Polymerase III Holoenzyme: An Asymmetric Dimeric Replicative Complex with Leading and Lagging Strand Polymerases. Cell, 105, 925–934.
Pritchard, A., Dallmann, G., Glover, B. and McHenry, C. (2000) A Novel Assembly Mechanism for the DNA Polymerase III Holoenzyme DnaX Complex: Association of delta-delta' with DnaX4 Forms DnaX3delta-delta'. EMBO J., 19, 6536-6545.
Glover, B.P. and McHenry, C. (2000) The DnaX-binding Subunits delta' and psi Are Bound to gamma and Not tau in the DNA Polymerase III Holoenzyme. J. Biol. Chem., 275, 3017-3020.
Kim, D.R. and McHenry,C. (1996) Biotin Tagging Deletion Analysis of Domain Limits Involved in Protein-Macromolecular Interactions: Mapping the tau Binding Domain of the DNA Polymerase III alpha Subunit. J. Biol. Chem., 271, 20690-20698.
Kim, S., Dallmann, H.G., McHenry, C. and Marians, K.J. (1996) Coupling of a Replicative Polymerase and Helicase: A tau-DnaB Interaction Mediates Rapid Replication Fork Movement. Cell, 84, 643-650.
Reems, J., Wood, S. and McHenry, C. (1995) E. coli DNA Polymerase III Holoenzyme Subunits alpha, beta and gamma Directly Contact the Primer Template. J. Biol Chem., 270, 5606-5613.
You, J-C. and McHenry, C. (1994) HIV Nucleocapsid Protein Accelerates Strand Transfer of the Terminally Redundant Sequences Involved in Reverse Transcription. J. Biol. Chem., 269, 31491-31495.
Wu, C.A., Zechner, E.L., Reems, J., McHenry, C., and Marians, K.J. (1992) Coordinated Leading- and Lagging-strand Synthesis at the Escherichia coli DNA Replication Fork: V. Primase Action Regulates the Cycle of Okazaki Fragment Synthesis. J. Biol. Chem., 267, 4074-4083.
Flower, A. and McHenry, C. (1990) The gamma Subunit of DNA Polymerase III Holoenzyme of Escherichia coli is Produced by Ribosomal Frameshifting. Proc. Natl. Acad. Sci. U.S.A., 87, 3713-3717.
LaDuca, R., Crute, J., McHenry, C. and Bambara, R. (1986) The beta Subunit of the Escherichia coli DNA Polymerase III Holoenzyme Interacts Functionally with the Catalytic Core in the Absence of other Subunits. J. Biol. Chem., 261, 7550-7557.
McHenry, C. (1982) Purification and Characterization of Escherichia coli DNA Polymerase III': Identification of tau as a Subunit of the DNA Polymerase III Holoenzyme. J. Biol. Chem., 257, 2657-2663.
McHenry, C. and Crow, W. (1979) DNA Polymerase III Escherichia coli: Purification and Identification of Subunits. J. Biol. Chem., 254, 1748-1753.
McHenry, C. and Kornberg, A. (1977) DNA Polymerase III Holoenzyme of Escherichia coli: Purification and Resolution into Subunits. J. Biol. Chem., 252, 6478-6484 and correction of publishers inversion, left to right, of figure 3 253, 645.
Santi, D. and McHenry, C. (1972) 5-Fluorodeoxyuridylate: Covalent Complex with Thymidylate Synthetase. Proc. Nat. Acad. Sci., 69, 1855-1857.
For a complete listing of papers, see McHenry Lab Publications Page.