Katsuhiko Murakami - Penn State Cancer Institute
Researcher Profile
Katsuhiko Murakami
Professor, Biochemistry & Molecular Biology
Scientific Program:Mechanisms of Carcinogenesis
Research Interests
- DNA-Directed RNA Polymerases
- DNA
- Escherichia coli
- Bacterial RNA
- X-Rays
- RNA
- In Vitro Techniques
- Enzymes
- Holoenzymes
- Transcription Factors
- Transcriptional Activation
- Mycobacterium tuberculosis
Recent Publications
2024
Qayyum, MZ, Imashimizu, M, Leanca, M, Vishwakarma, RK, Riaz-Bradley, A, Yuzenkova, Y & Murakami, KS 2024, 'Structure and function of the Si3 insertion integrated into the trigger loop/helix of cyanobacterial RNA polymerase', Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 8, pp. e2311480121. https://doi.org/10.1073/pnas.2311480121
2023
Vishwakarma, RK, Qayyum, MZ, Babitzke, P & Murakami, KS 2023, 'Allosteric mechanism of transcription inhibition by NusG-dependent pausing of RNA polymerase', Proceedings of the National Academy of Sciences of the United States of America, vol. 120, no. 7, e2218516120. https://doi.org/10.1073/pnas.2218516120
Narwal, M, Armache, JP, Edwards, TJ & Murakami, KS 2023, 'SARS-CoV-2 polyprotein substrate regulates the stepwise Mpro cleavage reaction', Journal of Biological Chemistry, vol. 299, no. 5, 104697. https://doi.org/10.1016/j.jbc.2023.104697
Colman, DR, Veach, A, Stefánsson, A, Wurch, L, Belisle, BS, Podar, PT, Yang, Z, Klingeman, D, Senba, K, Murakami, KS, Kristjánsson, JK, Björnsdóttir, SH, Boyd, ES & Podar, M 2023, 'Tectonic and geological setting influence hot spring microbiology', Environmental microbiology, vol. 25, no. 11, pp. 2481-2497. https://doi.org/10.1111/1462-2920.16472
2022
Lisitskaya, L, Shin, Y, Agapov, A, Olina, A, Kropocheva, E, Ryazansky, S, Aravin, AA, Esyunina, D, Murakami, KS & Kulbachinskiy, A 2022, 'Author Correction: Programmable RNA targeting by bacterial Argonaute nucleases with unconventional guide binding and cleavage specificity (Nature Communications, (2022), 13, 1, (4624), 10.1038/s41467-022-32079-5)', Nature communications, vol. 13, no. 1, 4839. https://doi.org/10.1038/s41467-022-32616-2
Mandell, ZF, Vishwakarma, RK, Yakhnin, H, Murakami, KS, Kashlev, M & Babitzke, P 2022, 'Comprehensive transcription terminator atlas for Bacillus subtilis', Nature Microbiology, vol. 7, no. 11, pp. 1918-1931. https://doi.org/10.1038/s41564-022-01240-7
Narayanan, A, Narwal, M, Majowicz, SA, Varricchio, C, Toner, SA, Ballatore, C, Brancale, A, Murakami, KS & Jose, J 2022, 'Identification of SARS-CoV-2 inhibitors targeting Mpro and PLpro using in-cell-protease assay', Communications Biology, vol. 5, no. 1, 169. https://doi.org/10.1038/s42003-022-03090-9
Portman, JR, Zuhaib Qayyum, M, Murakami, KS & Strick, TR 2022, 'On the stability of stalled RNA polymerase and its removal by RapA', Nucleic acids research, vol. 50, no. 13, pp. 7396-7405. https://doi.org/10.1093/nar/gkac558
Rajeswaran, W, Ashkar, SR, Lee, PH, Yeomans, L, Shin, Y, Franzblau, SG, Murakami, KS, Showalter, HD & Garcia, GA 2022, 'Optimization of Benzoxazinorifamycins to Improve Mycobacterium tuberculosis RNA Polymerase Inhibition and Treatment of Tuberculosis', ACS Infectious Diseases, vol. 8, no. 8, pp. 1422-1438. https://doi.org/10.1021/acsinfecdis.1c00636
Ashkar, SR, Rajeswaran, W, Lee, PH, Yeomans, L, Thrasher, CM, Franzblau, SG, Murakami, KS, Showalter, HD & Garcia, GA 2022, 'Optimization of Benzoxazinorifamycins to Minimize hPXR Activation for the Treatment of Tuberculosis and HIV Coinfection', ACS Infectious Diseases, vol. 8, no. 8, pp. 1408-1421. https://doi.org/10.1021/acsinfecdis.1c00635
Lisitskaya, L, Shin, Y, Agapov, A, Olina, A, Kropocheva, E, Ryazansky, S, Aravin, AA, Esyunina, D, Murakami, KS & Kulbachinskiy, A 2022, 'Programmable RNA targeting by bacterial Argonaute nucleases with unconventional guide binding and cleavage specificity', Nature communications, vol. 13, no. 1, 4624. https://doi.org/10.1038/s41467-022-32079-5
Marshall, CJ, Qayyum, MZ, Walker, JE, Murakami, KS & Santangelo, TJ 2022, 'The structure and activities of the archaeal transcription termination factor Eta detail vulnerabilities of the transcription elongation complex', Proceedings of the National Academy of Sciences of the United States of America, vol. 119, no. 32, e2207581119. https://doi.org/10.1073/pnas.2207581119
2021
Qayyum, MZ, Molodtsov, V, Renda, A & Murakami, KS 2021, 'Structural basis of RNA polymerase recycling by the Swi2/Snf2 family of ATPase RapA in Escherichia coli', Journal of Biological Chemistry, vol. 297, no. 6, 101404. https://doi.org/10.1016/j.jbc.2021.101404
Shin, Y, Qayyum, MZ, Pupov, D, Esyunina, D, Kulbachinskiy, A & Murakami, KS 2021, 'Structural basis of ribosomal RNA transcription regulation', Nature communications, vol. 12, no. 1, 528. https://doi.org/10.1038/s41467-020-20776-y
Mäkinen, JJ, Shin, Y, Vieras, E, Virta, P, Metsä-Ketelä, M, Murakami, KS & Belogurov, GA 2021, 'The mechanism of the nucleo-sugar selection by multi-subunit RNA polymerases', Nature communications, vol. 12, no. 1, 796. https://doi.org/10.1038/s41467-021-21005-w
Qayyum, MZ, Shin, Y & Murakami, KS 2021, Transcription | RNA polymerase reaction in bacteria. in Encyclopedia of Biological Chemistry: Third Edition. vol. 4, Elsevier, pp. 358-364. https://doi.org/10.1016/B978-0-12-819460-7.00252-8
Shin, Y & Murakami, KS 2021, Watching the bacterial RNA polymerase transcription reaction by time-dependent soak-trigger-freeze X-ray crystallography. in CE Cameron, JJ Arnold & LS Kaguni (eds), Viral Replication Enzymes and their Inhibitors Part A. Enzymes, vol. 49, Academic Press, pp. 305-314. https://doi.org/10.1016/bs.enz.2021.06.009
2020
Jun, SH, Hyun, J, Cha, JS, Kim, H, Bartlett, MS, Cho, HS & Murakami, KS 2020, 'Direct binding of TFEα opens DNA binding cleft of RNA polymerase', Nature communications, vol. 11, no. 1, 6123. https://doi.org/10.1038/s41467-020-19998-x
Haupenthal, J, Kautz, Y, Elgaher, WAM, Pätzold, L, Röhrig, T, Laschke, MW, Tschernig, T, Hirsch, AKH, Molodtsov, V, Murakami, KS, Hartmann, RW & Bischoff, M 2020, 'Evaluation of Bacterial RNA Polymerase Inhibitors in a Staphylococcus aureus-Based Wound Infection Model in SKH1 Mice', ACS Infectious Diseases, vol. 6, no. 10, pp. 2573-2581. https://doi.org/10.1021/acsinfecdis.0c00034
Kouba, T, Koval’, T, Sudzinová, P, Pospíšil, J, Brezovská, B, Hnilicová, J, Šanderová, H, Janoušková, M, Šiková, M, Halada, P, Sýkora, M, Barvík, I, Nováček, J, Trundová, M, Dušková, J, Skálová, T, Chon, URR, Murakami, KS, Dohnálek, J & Krásný, L 2020, 'Mycobacterial HelD is a nucleic acids-clearing factor for RNA polymerase', Nature communications, vol. 11, no. 1, 6419. https://doi.org/10.1038/s41467-020-20158-4
Black, SJ, Ozdemir, AY, Kashkina, E, Kent, T, Rusanov, T, Ristic, D, Shin, Y, Suma, A, Hoang, T, Chandramouly, G, Siddique, LA, Borisonnik, N, Sullivan-Reed, K, Mallon, JS, Skorski, T, Carnevale, V, Murakami, KS, Wyman, C & Pomerantz, RT 2020, 'Publisher Correction: Molecular basis of microhomology-mediated end-joining by purified full-length Polθ (Nature Communications, (2019), 10, 1, (4423), 10.1038/s41467-019-12272-9)', Nature communications, vol. 11, no. 1, 1831. https://doi.org/10.1038/s41467-020-15551-y
Shin, Y, Hedglin, M & Murakami, KS 2020, 'Structural basis of reiterative transcription from the pyrG and pyrBI promoters by bacterial RNA polymerase', Nucleic acids research, vol. 48, no. 4, pp. 2144-2155. https://doi.org/10.1093/nar/gkz1221