PUBLICATIONS 2017-12-05T23:15:00+00:00

Publications

2017
Molodtsov, V., Sineva, E., Zhang, L., Huang, X., Cashel, M., Ades, S.E., and Murakami, K.S. (2017). Allosteric effector ppGpp potentiates the inhibition of transcript initiation by DksA. BioRxiv.

Murakami, K.S., Shin, Y., Turnbough, C.L., Jr., and Molodtsov, V. (2017). X-ray crystal structure of a reiterative transcription complex reveals an atypical RNA extension pathway. Proc Natl Acad Sci U S A 114, 8211-8216. DOI: 10.1073/pnas.1702741114

Molodtsov, V., Scharf, N.T., Stefan, M.A., Garcia, G.A., and Murakami, K.S. (2017). Structural basis for rifamycin resistance of bacterial RNA polymerase by the three most clinically important RpoB mutations found in Mycobacterium tuberculosis. Mol Microbiol 103, 1034-1045. DOI: 10.1111/mmi.13606

Scharf, N.T., Molodtsov, V., Kontos, A., Murakami, K.S., and Garcia, G.A. (2017). Novel chemical scaffolds for inhibition of Rifamycin-resistant RNA polymerase discovered from high-throughput screening. SLAS Discov 22, 287-297. DOI: 10.1177/2472555216679994

2016
Yakhnin, A.V., Murakami, K.S., and Babitzke, P. (2016). NusG Is a sequence-specific RNA polymerase pause factor that binds to the non-template DNA within the paused transcription bubble. J Biol Chem 291, 5299-5308. DOI: 10.1074/jbc.M115.704189

Gu, H., Yoshinari, S., Ghosh, R., Ignatochkina, A.V., Gollnick, P.D., Murakami, K.S., and Ho, C.K. (2016). Structural and mutational analysis of archaeal ATP-dependent RNA ligase identifies amino acids required for RNA binding and catalysis. Nucleic Acids Res 44, 2337-2347. DOI: 10.1093/nar/gkw094

2015
Molodtsov, V., Fleming, P.R., Eyermann, C.J., Ferguson, A.D., Foulk, M.A., McKinney, D.C., Masse, C.E., Buurman, E.T., and Murakami, K.S. (2015). X-ray crystal structures of Escherichia coli RNA polymerase with switch region binding inhibitors enable rational design of squaramides with an improved fraction unbound to human plasma protein. J Med Chem 58, 3156-3171. DOI: 10.1021/acs.jmedchem.5b00050

Yang, Y., Darbari, V.C., Zhang, N., Lu, D., Glyde, R., Wang, Y.P., Winkelman, J.T., Gourse, R.L., Murakami, K.S., Buck, M., et al. (2015). TRANSCRIPTION. Structures of the RNA polymerase-sigma54 reveal new and conserved regulatory strategies. Science 349, 882-885. DOI: 10.1126/science.aab1478

2014
Basu, R.S., Warner, B.A., Molodtsov, V., Pupov, D., Esyunina, D., Fernandez-Tornero, C., Kulbachinskiy, A., and Murakami, K.S. (2014). Structural basis of transcription initiation by bacterial RNA polymerase holoenzyme. J Biol Chem 289, 24549-24559. DOI: 10.1074/jbc.M114.584037

Jun, S.H., Hirata, A., Kanai, T., Santangelo, T.J., Imanaka, T., and Murakami, K.S. (2014). The X-ray crystal structure of the euryarchaeal RNA polymerase in an open-clamp configuration. Nat Commun 5, 5132. DOI: 10.1038/ncomms6132

Song, T., Park, Y., Shamputa, I.C., Seo, S., Lee, S.Y., Jeon, H.S., Choi, H., Lee, M., Glynne, R.J., Barnes, S.W., et al. (2014). Fitness costs of rifampicin resistance in Mycobacterium tuberculosis are amplified under conditions of nutrient starvation and compensated by mutation in the beta’ subunit of RNA polymerase. Mol Microbiol 91, 1106-1119. DOI: 10.1111/mmi.12520

2013
Mechold, U., Potrykus, K., Murphy, H., Murakami, K.S., and Cashel, M. (2013). Differential regulation by ppGpp versus pppGpp in Escherichia coli. Nucleic Acids Res 41, 6175-6189. DOI: 10.1093/nar/gkt302

Molodtsov, V., Nawarathne, I.N., Scharf, N.T., Kirchhoff, P.D., Showalter, H.D., Garcia, G.A., and Murakami, K.S. (2013). X-ray crystal structures of the Escherichia coli RNA polymerase in complex with benzoxazinorifamycins. J Med Chem 56, 4758-4763. DOI: 10.1021/jm4004889

Murakami, K.S. (2013). X-ray crystal structure of Escherichia coli RNA polymerase s70 holoenzyme. J Biol Chem 288, 9126-9134. DOI: 10.1074/jbc.M112.430900

Basu, R.S., and Murakami, K.S. (2013). Watching the bacteriophage N4 RNA polymerase transcription by time-dependent soak-trigger-freeze X-ray crystallography. J Biol Chem 288, 3305-3311. DOI: 10.1074/jbc.M112.387712

Sarkar, P., Sardesai, A.A., Murakami, K.S., and Chatterji, D. (2013). Inactivation of the bacterial RNA polymerase due to acquisition of secondary structure by the omega subunit. J Biol Chem 288, 25076-25087. DOI: 10.1074/jbc.M113.468520

2012
Reichlen, M.J., Vepachedu, V.R., Murakami, K.S., and Ferry, J.G. (2012). MreA functions in the global regulation of methanogenic pathways in Methanosarcina acetivorans. MBio 3, e00189-00112. DOI: 10.1128/mBio.00189-12

2011
Chen, Y., Basu, R., Gleghorn, M.L., Murakami, K.S., and Carey, P.R. (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. DOI: 10.1021/ja201557w

Gleghorn, M.L., Davydova, E.K., Basu, R., Rothman-Denes, L.B., and Murakami, K.S. (2011). X-ray crystal structures elucidate the nucleotidyl transfer reaction of transcript initiation using two nucleotides. Proc Natl Acad Sci U S A 108, 3566-3571. DOI: 10.1073/pnas.1016691108

Klein, B.J., Bose, D., Baker, K.J., Yusoff, Z.M., Zhang, X., and Murakami, K.S. (2011). RNA polymerase and transcription elongation factor Spt4/5 complex structure. Proc Natl Acad Sci U S A 108, 546-550. DOI: 10.1073/pnas.1013828108

2010
Reichlen, M.J., Murakami, K.S., and Ferry, J.G. (2010). Functional analysis of the three TATA binding protein homologs in Methanosarcina acetivorans. J Bacteriol 192, 1511-1517. DOI: 10.1128/JB.01165-09

2008
Gleghorn, M.L., Davydova, E.K., Rothman-Denes, L.B., and Murakami, K.S. (2008). Structural basis for DNA-hairpin promoter recognition by the bacteriophage N4 virion RNA polymerase. Mol Cell 32, 707-717. DOI: 10.1016/j.molcel.2008.11.010

Hirata, A., Kanai, T., Santangelo, T.J., Tajiri, M., Manabe, K., Reeve, J.N., Imanaka, T., and Murakami, K.S. (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. DOI: 10.1111/j.1365-2958.2008.06430.x

Hirata, A., Klein, B.J., and Murakami, K.S. (2008). The X-ray crystal structure of RNA polymerase from Archaea. Nature 451, 851-854. DOI: 10.1038/nature06530

Murakami, K.S., Davydova, E.K., and Rothman-Denes, L.B. (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. DOI: 10.1073/pnas.0712325105

Suharti, S., Murakami, K.S., de Vries, S., and Ferry, J.G. (2008). Structural and biochemical characterization of flavoredoxin from the archaeon Methanosarcina acetivorans. Biochemistry 47, 11528-11535. DOI: 10.1021/bi801012p

2006
Imashimizu, M., Hanaoka, M., Seki, A., Murakami, K.S., and Tanaka, K. (2006). The cyanobacterial principal sigma factor region 1.1 is involved in DNA-binding in the free form and in transcription activity as holoenzyme. FEBS Lett 580, 3439-3444. DOI: 10.1016/j.febslet.2006.05.017


Publications before joining Penn State University (Postdoc and Ph. D. training)

Chlenova, M., S. Masuda, K.S. Murakami, V. Nikiforov, S.A. Darst, and A. Mustaev (2005). Structure and function of lineage-specific sequence insertions in the bacterial RNA polymerase beta’ subunit. J Mol Biol 353, 138-154.

Masuda, S., K.S. Murakami, S. Wang, C. Anders Olson, J. Donigian, F. Leon, S.A. Darst, and E.A. Campbell (2004). Crystal structures of the ADP and ATP bound forms of the Bacillus anti-sigma factor SpoIIAB in complex with the anti-anti-sigma SpoIIAA. J Mol Biol 340, 941-956.

Artsimovitch, I., V. Svetlov, K.S. Murakami, and R. Landick (2003). Co-overexpression of E. coli RNA polymerase subunits allows isolation and analysis of mutant enzymes lacking lineage-specific sequence insertions. J Biol Chem 278, 12344-12355.

Nickels, B.E., S.L. Dove, K.S. Murakami, S.A. Darst, and A. Hochschild (2002). Protein-protein and protein-DNA interactions of sigma70 region 4 involved in transcription activation by lambdacI. J Mol Biol 324, 17-34.

Murakami, K.S., S. Masuda, and S.A. Darst (2002). Structural basis of transcription initiation: T. aquaticus RNA polymerase holoenzyme at 4 Å resolution. Science 296, 1280–1284.

Murakami, K.S., S. Masuda, E.A. Campbell, O. Muzzin, and S.A. Darst (2002). Structural basis of transcription initiation: an RNA polymerase holoenzyme-DNA complex. Science 296, 1285-1290.

Finney, A.H., R.J. Blick, K. Murakami, A. Ishihama, and A.M. Stevens (2002). Role of the C-terminal domain of the alpha subunit of RNA polymerase in LuxR-dependent transcriptional activation of the lux operon during quorum sensing. J Bacteriol 184, 4520-4528.

Campbell, E.A., N. Korzheva, A. Mustaev, K. Murakami, S. Nair, A. Goldfarb, and S.A. Darst (2000). Structural mechanism for rifampicin inhibition of bacterial RNA polymerase. Cell 104, 901–912.

Otomo, T., T. Yamazaki, K. Murakami, A. Ishihama, and Y. Kyogoku (2000). Structural study of the N-terminal domain of the alpha subunit of Escherichia coli RNA polymerase solubilized with non-denaturing detergents. J Biochem (Tokyo) 128, 337-344.

Harada, Y., T. Funatsu, K. Murakami, Y. Nonoyama, A. Ishihama, and T. Yanagida (1999). Single-molecule imaging of RNA polymerase-DNA interactions in real time. Biophys J 76, 709-15.

Prost, J.F., D. Negre, C. Oudot, K. Murakami, A. Ishihama, A.J. Cozzone, and J.C. Cortay (1999). Cra-dependent transcriptional activation of the icd gene of Escherichia coli. J Bacteriol 181, 893-898.

Miyake, R., K. Murakami, J.T. Owens, D.P. Greiner, O.N. Ozoline, A. Ishihama, and C.F. Meares (1998). Dimeric association of Escherichia coli RNA polymerase alpha subunits, studied by cleavage of single-cysteine alpha subunits conjugated to iron-(S)-1-[p-(bromoacetamido)benzyl]ethylenediaminetetraacetate. Biochemistry 37, 1344-1349.

Negre, D., C. Oudot, J.F. Prost, K. Murakami, A. Ishihama, A.J. Cozzone, and J.C. Cortay (1998). FruR-mediated transcriptional activation at the ppsA promoter of Escherichia coli. J Mol Biol 276, 355-365.

Owens, J.T., A.J. Chmura, K. Murakami, N. Fujita, A. Ishihama, and C.F. Meares (1998). Mapping the promoter DNA sites proximal to conserved regions of sigma70 in an Escherichia coli RNA polymerase-lacUV5 open promoter complex. Biochemistry 37, 7670-7675.

Owens, J.T., R. Miyake, K. Murakami, A.J. Chmura, N. Fujita, A. Ishihama, and C.F. Meares (1998). Mapping the sigma70 subunit contact sites on Escherichia coli RNA polymerase with a sigma70-conjugated chemical protease. Proc Natl Acad Sci U S A 95, 6021-6026.

Ozoline, O.N., N. Fujita, K. Murakami, and A. Ishihama (1998). Monitoring of RNA polymerase-DNA UP element interaction by a fluorescent probe conjugated to alpha subunit. Eur J Biochem 253, 371-381.

Ozoline, O.N., K. Murakami, T. Negishi, N. Fujita, and A. Ishihama (1998). Specific fluorescent labeling of two functional domains in RNA polymerase alpha subunit. Proteins 30, 183-192.

Boucher, P.E., K. Murakami, A. Ishihama, and S. Stibitz (1997). Nature of DNA binding and RNA polymerase interaction of the Bordetella pertussis BvgA transcriptional activator at the fha promoter. J Bacteriol 179, 1755-1763.

Choy, H.E., R.R. Hanger, T. Aki, M. Mahoney, K. Murakami, A. Ishihama, and S. Adhya (1997). Repression and activation of promoter-bound RNA polymerase activity by Gal repressor. J Mol Biol 272, 293-300.

Chugani, S.A., M.R. Parsek, C.D. Hershberger, K. Murakami, A. Ishihama, and A.M. Chakrabarty (1997). Activation of the catBCA promoter: probing the interaction of CatR and RNA polymerase through in vitro transcription. J Bacteriol 179, 2221-2227.

Murakami, K., M. Kimura, J.T. Owens, C.F. Meares, and A. Ishihama (1997). The two alpha subunits of Escherichia coli RNA polymerase are asymmetrically arranged and contact different halves of the DNA upstream element. Proc Natl Acad Sci U S A  94, 1709-1714.

Murakami, K., J.T. Owens, T.A. Belyaeva, C.F. Meares, S.J. Busby, and A. Ishihama (1997). Positioning of two alpha subunit carboxy-terminal domains of RNA polymerase at promoters by two transcription factors. Proc Natl Acad Sci U S A 94, 11274-11278.

Yang, J., K. Murakami, H. Camakaris, N. Fujita, A. Ishihama, and A.J. Pittard (1997). Amino acid residues in the alpha-subunit C-terminal domain of Escherichia coli RNA polymerase involved in activation of transcription from the mtr promoter. J Bacteriol 179, 6187-6191.

Artsimovitch, I., K. Murakami, A. Ishihama, and M.M. Howe (1996). Transcription activation by the bacteriophage Mu Mor protein requires the C-terminal regions of both alpha and sigma70 subunits of Escherichia coli RNA polymerase. J Biol Chem 271, 32343-32348.

Giladi, H., K. Murakami, A. Ishihama, and A.B. Oppenheim (1996). Identification of an UP element within the IHF binding site at the PL1- PL2 tandem promoter of bacteriophage lambda. J Mol Biol 260, 484-491.

Murakami, K., N. Fujita, and A. Ishihama (1996). Transcription factor recognition surface on the RNA polymerase alpha subunit is involved in contact with the DNA enhancer element. EMBO J 15, 4358-4367.

Tang, Y., K. Murakami, A. Ishihama, and P.L. deHaseth (1996). Upstream interactions at the lambda pRM promoter are sequence nonspecific and activate the promoter to a lesser extent than an introduced UP element of an rRNA promoter. J Bacteriol 178, 6945-6951.

Hauryliuk, V., Atkinson, G.C., Murakami, K.S., Tenson, T., and Gerdes, K. (2015). Recent functional insights into the role of (p)ppGpp in bacterial physiology. Nat Rev Microbiol 13, 298-309. DOI: 10.1038/nrmicro3448

Murakami, K.S. (2015). Structural biology of bacterial RNA polymerase. Biomolecules 5, 848-864. DOI: 10.3390/biom5020848

Jun, S.H., Reichlen, M.J., Tajiri, M., and Murakami, K.S. (2011). Archaeal RNA polymerase and transcription regulation. Crit Rev Biochem Mol Biol 46, 27-40. DOI: 10.3109/10409238.2010.538662

Hirata, A., and Murakami, K.S. (2009). Archaeal RNA polymerase. Curr Opin Struct Biol 19, 724-731. DOI: 10.1016/j.sbi.2009.10.006 DOI: 10.1016/j.sbi.2009.10.006

Murakami, K.S., and Trakselis, M.A. (eds.) Nucleic Acid Polymerases in Nucleic Acids and Molecular Biology series. vol 30, Springer. 2013. ISBN 978-3-642-39796-7. Link

Out through the window: Crystal structure reveals details of nonstandard RNA transcription. Link 1 | Link 2

Murakami, K.S. (2013). Targeting multidrug resistance in tuberculosis treatment. International Innovation, November, 88-90. Research Media, United Kingdom. View PDF

Ritwika Basu (2014). MECHANISTIC INVESTIGATIONS OF NUCLEOTIDYL-TRANSFER REACTION AND DE NOVO INITIATION IN RNA POLYMERASES BY X-RAY CRYSTALLOGRAPHY. LINK

Brittany Warner (2012). A STRUCTURAL STUDY OF BACTERIAL RNA POLYMERASE CONFORMATIONAL CHANGES DURING TRANSCRIPTION ELONGATION. LINK

Brianna J. Klein (2010). CRYSTAL STRUCTURE AND BIOCHEMICAL ANALYSIS OF ARCHAEAL RNA POLYMERASE TRANSCRIPTION ELONGATION FACTORS. LINK

Matthew J. Reichlen (2010). FUNCTIONAL ASSESSMENT OF TRANSCRIPTIONAL REGULATION IN THE METHANOGEN, METHANOSARCINA ACETIVORANS. LINK

Momoko Tajiri (2008). ROLES OF ARCHAEAL GENERAL TRANSCRIPTION FACTORS TFB1 AND TFB2 IN THERMOCOCCUS KODAKARENSIS DURING HEAT STRESS RESPONSE. LINK

Michael L. Gleghorn (2008). X-RAY CRYSTAL STRUCTURES EXPLAIN DNA-HAIRPIN PROMOTER BINDING AND DE NOVO TRANSCRIPTION INITIATION FOR THE N4 VIRION RNA POLYMERASE. LINK