Gene expression is fundamental to all organisms and studying how the genetic code is expressed in molecular terms is critical to cell development and understanding diseases. Our research interests are centered on understanding the mechanism of gene expression, particularly how information stored in genomic DNA is transcribed into RNA by the enzyme RNA polymerase – the first step and the key control point in the gene expression and one of the most fundamental processes required for life. We apply X-ray crystallography techniques to reveal three-dimensional structures of bacterial, archaeal and bacteriophage RNA polymerases for elucidating the mechanism of RNA transcription
Bacterial RNA polymerase
Escherichia coli RNA polymerase (RNAP) is the most studied bacterial RNAP and has been used as the model RNAP for screening and evaluating potential RNAP-targeting antibiotics. However, the X-ray crystal structure of E. coli RNAP has been limited to individual domains. We reported the X-ray structure of the E. coli RNAP σ70 holoenzyme, which shows the σ region 1.1 and α subunit C-terminal domain (αCTD) for the first time in the context of an intact RNAP. E. coli RNAP crystals can be prepared from a convenient overexpression system allowing further structural studies of bacterial RNAP mutants including functionally-deficient and antibiotic resistant RNAPs (Murakami, J Biol Chem 2013). We have also determined the crystal structures of E. coli RNAP in complex with global regulator, ppGpp and pppGpp, to identify their binding site on RNAP and to provide structure basis of the (p)ppGpp-dependent transcription regulation (Mechold et al., Nucleic Acid Res 2013).
The bacterial RNA polymerase inhibitor rifampicin is the cornerstone of current tuberculosis treatment. In collaboration with research groups in academia and the pharmaceutical companies AstraZeneca and Cubist Pharmaceuticals, we expanded our research program in new directions in which we are developing superior rifampicin-derivatives for effective tuberculosis treatment (Molodtsov et al., J Med Chem 2013) and developing a new RNA polymerase inhibitor as a broad spectrum antibiotic for therapeutic treatment of serious human pathogens.
In addition to E. coli RNAP structural studies, we determined the structures of the de novo initiation complex and the early stage transcription complex containing 6-mer RNA using Thermus thermophilus RNAP, a model bacterial RNAP for high-resolution crystallographic study. These structures highlight the interplay among RNAP, template DNA, and initiating NTP during transcription initiation, as well as the interaction between the σ factor region 3.2 and the 5’-end of RNA for releasing the σ factor from the RNAP core enzyme (Basu et al., J Biol Chem 2014). Since the structure around the active site is highly conserved in cellular RNAPs, mechanistic insights from the T. thermophilus RNAP could be applied to all cellular RNAPs.
- Basu, R.S., B.S. Warner, V. Molodtsov, D. Pupov, D. Esyunina, C. Fernandez-Tornero, A. Kulbachinskiy and K.S. Murakami (2014). Structural basis of transcription initiation by bacterial RNA polymerase holoenzyme. J Biol Chem 289, 24549-24559.
- Molodtsov, V., I.N. Nawarathne, N.T. Scharf, P.D. Kirchhoff, H.D.H. Showalter, G.A. Garcia and K.S. Murakami (2013). X-ray crystal structures of the Escherichia coli RNA polymerase in complex with Benzoxazinorifamycins. J Med Chem 56, 4758-4763.
- Mechold, U., K. Potrykus, H. Murphy, K.S. Murakami and M. Cashel (2013). Differential regulation by ppGpp versus pppGpp in Escherichia coli. Nucleic Acids Research 41, 6175-6189.
- Murakami, K.S. (2013). The X-ray crystal structure of Escherichia coli RNA polymerase Sigma70 Holoenzyme. J Biol Chem 288, 9126-9134.
- Basu, R.S., and K.S. Murakami (2013). Watching the bacteriophage N4 RNA polymerase transcription by time-dependent soak-trigger-freeze X-ray crystallography. J Biol Chem 288, 3305-3311.
- Chen, Y., R. Basu, M.L. Gleghorn, K.S. Murakami, and P.R. Carey (2011). Time-resolved events on the reaction pathway of transcript initiation by a single-subunit RNA polymerase: Raman crystallographic evidence. J Am Chem Soc 133, 12544-12555.
- Gleghorn, M.L., E.K. Davydova, R. Basu, L.B. Rothman-Denes, and K.S. Murakami (2011). X-ray crystallography structures elucidate the nucleotidyl transfer reaction of transcript initiation using two nucleotides. Proc Natl Acad Sci U S A 108, 3566-3571.
- Gleghorn, M.L., E.K. Davydova, L.B. Rothman-Denes, and K.S. Murakami (2008). Structural basis for DNA-hairpin promoter recognition by the bacteriophage N4 virion RNA polymerase. Mol Cell 37, 707-717.
- Murakami, K.S., E.K. Davydova, and L.B. Rothman-Denes (2008). X-ray crystal structure of the polymerase domain of the bacteriophage N4 virion RNA polymerase. Proc Natl Acad Sci U S A 105, 5046-5051.
Archaeal RNA polymerase
Structural studies of the archaeal transcription apparatus are just beginning to emerge. Interestingly, archaeal transcription appears to involve a mix of a eukaryotic-like transcription apparatus together with bacteria-like regulatory mechanisms. We reported the first crystal structure of an archaeal RNAP from the phyla creachaeota (Hirata et al., Nature 2008). Recently, we reported a second archaeal RNA polymerase structure from euryarchaeota, another major phyla in Archaea that has retained many features from the last common ancestor of Archaea and Eukaryote (June et al., Nature communications in press). We also reported the molecular view of the RNAP in complex with transcription elongation factor Spt4/5 (Klein et al., Proc Natl Acad Sci U S A 2011). We also investigated physiological roles of RNAP subunit (Hirata et al., Mol. Microbiol 2008), general transcription factor TBP (Reichlen et al., J Bacteriol 2010) and transcription factor MreA (Reichlen et al., MBio 2012).
- Jun, S-H., A. Hirata, T. Kanai, T.J. Santangelo, T. Imanaka, and K.S. Murakami (2014). The X-ray crystal structure of the euryarchaeal RNA polymerase in an open clamp configuration. Nature Communications in press.
- Reichlen, M.J., V.R. Vepachedu, K.S. Murakami, and J.G. Ferry (2012). MreA Functions in the Global Regulation of Methanogenic Pathways in Methanosarcina acetivorans. MBio 3 e00189-12.
- Klein, B.J., D. Bose, K.J. Baker, Z.M. Yusoff, X. Zhang and K.S. Murakami (2011). RNA polymerase and transcription elongation factor Spt4/5 complex structure. Proc Natl Acad Sci U S A 108, 546-550.
- Reichlen, M.J., K.S. Murakami, and J.G. Ferry (2010). Functional Analysis of the Three TBP Homologs in Methanosarcina acetivorans. J Bacteriol 192, 1511-1517.
- Hirata, A., B.J. Klein, and K.S. Murakami (2008). The X-ray crystal structure of RNA polymerase from Archaea. Nature 451, 851-854.
- Hirata, A., T. Kanai, T.J. Santangelo, M. Tajiri, K. Manabe, J.N. Reeve, T. Imanaka, and K.S. Murakami (2008). Archaeal RNA polymerase subunits E and F are not required for transcription in vitro, but a Thermococcus kodakarensis mutant lacking subunit F is temperature-sensitive. Mol. Microbiol 70, 623-633.
• Vadim Molodtsov (Postdoctoral scholar)
• Ritwika Basu (Postdoctoral scholar)
• Mohammad Almishwat (BMMB graduate student)