Katsuhiko Murakami
Professor of Biochemistry and Molecular Biology
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006 Althouse Lab
University Park, PA 16802 - kum14@psu.edu
- 814-865-2758
Research Summary
Structural and Mechanistic Enzymology of Prokaryotic RNA Polymerases
Huck Affiliations
- Center for RNA Molecular Biology
- Center for Structural Biology
- Molecular, Cellular, and Integrative Biosciences
Links
Publication Tags
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Dna Directed Rna Polymerases Bacterial Rna Rna Dna Holoenzymes Escherichia Coli Mycobacterium Tuberculosis Cleavage X Rays Crystal Structure Tuberculosis Sugars Deoxyribonucleic Acid Krm 1648 Transcription Rifampin Bacteria Proteins Mutation Nuclease Communication Ribosomal Rna Catalytic Domain Lycorine In Vitro TechniquesMost Recent Publications
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)
Lidiya Lisitskaya, Yeonoh Shin, Aleksei Agapov, Anna Olina, Ekaterina Kropocheva, Sergei Ryazansky, Alexei A. Aravin, Daria Esyunina, Katsuhiko S. Murakami, Andrey Kulbachinskiy, 2022, Nature Communications
Identification of SARS-CoV-2 inhibitors targeting Mpro and PLpro using in-cell-protease assay
Anoop Narayanan, Manju Narwal, Sydney A. Majowicz, Carmine Varricchio, Shay A. Toner, Carlo Ballatore, Andrea Brancale, Katsuhiko S. Murakami, Joyce Jose, 2022, Communications Biology
Programmable RNA targeting by bacterial Argonaute nucleases with unconventional guide binding and cleavage specificity
Lidiya Lisitskaya, Yeonoh Shin, Aleksei Agapov, Anna Olina, Ekaterina Kropocheva, Sergei Ryazansky, Alexei A. Aravin, Daria Esyunina, Katsuhiko S. Murakami, Andrey Kulbachinskiy, 2022, Nature Communications
Comprehensive transcription terminator atlas for Bacillus subtilis
Zachary F. Mandell, Rishi K. Vishwakarma, Helen Yakhnin, Katsuhiko S. Murakami, Mikhail Kashlev, Paul Babitzke, 2022, Nature Microbiology on p. 1918-1931
Optimization of Benzoxazinorifamycins to Improve Mycobacterium tuberculosis RNA Polymerase Inhibition and Treatment of Tuberculosis
Walajapet Rajeswaran, Shireen R. Ashkar, Pil H. Lee, Larisa Yeomans, Yeonoh Shin, Scott G. Franzblau, Katsuhiko S. Murakami, Hollis D. Showalter, George A. Garcia, 2022, ACS Infectious Diseases on p. 1422-1438
Optimization of Benzoxazinorifamycins to Minimize hPXR Activation for the Treatment of Tuberculosis and HIV Coinfection
Shireen R. Ashkar, Walajapet Rajeswaran, Pil H. Lee, Larisa Yeomans, Claire M. Thrasher, Scott G. Franzblau, Katsuhiko S. Murakami, Hollis D. Showalter, George A. Garcia, 2022, ACS Infectious Diseases on p. 1408-1421
The structure and activities of the archaeal transcription termination factor Eta detail vulnerabilities of the transcription elongation complex
Craig J. Marshall, M. Zuhaib Qayyum, Julie E. Walker, Katsuhiko S. Murakami, Thomas J. Santangelo, 2022, Proceedings of the National Academy of Sciences of the United States of America
On the stability of stalled RNA polymerase and its removal by RapA
James R. Portman, M. Zuhaib Qayyum, Katsuhiko S. Murakami, Terence R. Strick, 2022, Nucleic Acids Research on p. 7396-7405
Structural basis of ribosomal RNA transcription regulation
Yeonoh Shin, M. Zuhaib Qayyum, Danil Pupov, Daria Esyunina, Andrey Kulbachinskiy, Katsuhiko S. Murakami, 2021, Nature Communications
The mechanism of the nucleo-sugar selection by multi-subunit RNA polymerases
Janne J. Mäkinen, Yeonoh Shin, Eeva Vieras, Pasi Virta, Mikko Metsä-Ketelä, Katsuhiko S. Murakami, Georgiy A. Belogurov, 2021, Nature Communications
Most-Cited Papers
Recent functional insights into the role of (p)ppGpp in bacterial physiology
Vasili Hauryliuk, Gemma C. Atkinson, Katsuhiko S. Murakami, Tanel Tenson, Kenn Gerdes, 2015, Nature Reviews Microbiology on p. 298-309
Differential regulation by ppGpp versus pppGpp in Escherichia coli
Undine Mechold, Katarzyna Potrykus, Helen Murphy, Katsuhiko S. Murakami, Michael Cashel, 2013, Nucleic Acids Research on p. 6175-6189
X-ray crystal structure of escherichia coli RNA polymerase σ<sup>70</sup> holoenzyme
Katsuhiko S. Murakami, 2013, Journal of Biological Chemistry on p. 9126-9134
Structural basis of transcription initiation by bacterial RNA polymerase holoenzyme
Ritwika S. Basu, Brittany A. Warner, Vadim Molodtsov, Danil Pupov, Daria Esyunina, Carlos Fernández-Tornero, Andrey Kulbachinskiy, Katsuhiko S. Murakami, 2014, Journal of Biological Chemistry on p. 24549-24559
Structural biology of bacterial RNA polymerase
Katsuhiko S. Murakami, 2015, Biomolecules on p. 848-864
Structural basis for rifamycin resistance of bacterial RNA polymerase by the three most clinically important RpoB mutations found in Mycobacterium tuberculosis
Vadim Molodtsov, Nathan T. Scharf, Maxwell A. Stefan, George A. Garcia, Katsuhiko S. Murakami, 2017, Molecular Microbiology on p. 1034-1045
Fitness costs of rifampicin resistance in Mycobacterium tuberculosis are amplified under conditions of nutrient starvation and compensated by mutation in the β′ subunit of RNA polymerase
Taeksun Song, Yumi Park, Isdore Chola Shamputa, Sunghwa Seo, Sun Young Lee, Han Seung Jeon, Hongjo Choi, Myungsun Lee, Richard J. Glynne, S. Whitney Barnes, John R. Walker, Serge Batalov, Karina Yusim, Shihai Feng, Chang Shung Tung, James Theiler, Laura E. Via, Helena I.M. Boshoff, Katsuhiko S. Murakami, Bette Korber, Clifton E. Barry, Sang Nae Cho, 2014, Molecular Microbiology on p. 1106-1119
Allosteric Effector ppGpp Potentiates the Inhibition of Transcript Initiation by DksA
Vadim Molodtsov, Elena Sineva, Lu Zhang, Xuhui Huang, Michael Cashel, Sarah E. Ades, Katsuhiko S. Murakami, 2018, Molecular Cell on p. 828-839.e5
Structures of the RNA polymerase-σ<sup>54</sup> reveal new and conserved regulatory strategies
Yun Yang, Vidya C. Darbari, Nan Zhang, Duo Lu, Robert Glyde, Yi Ping Wang, Jared T. Winkelman, Richard L. Gourse, Katsuhiko S. Murakami, Martin Buck, Xiaodong Zhang, 2015, Science on p. 882-885
X-ray crystal structures of the Escherichia coli RNA polymerase in complex with benzoxazinorifamycins
Vadim Molodtsov, Irosha N. Nawarathne, Nathan T. Scharf, Paul D. Kirchhoff, H. D.Hollis Showalter, George A. Garcia, Katsuhiko S. Murakami, 2013, Journal of Medicinal Chemistry on p. 4758-4763
News Articles Featuring Katsuhiko Murakami
Feb 09, 2023
DNA stuck in the gears of the RNA production machine
Precise control of gene expression — ensuring that cells make the correct components in the right amount and at the right time — is vital for all organisms to function properly. Cells must regulate how genes encoded in the sequence of DNA are made into RNA molecules that can carry out cellular functions on their own or be further processed into proteins.
Full Article
Jan 22, 2021
Regulating the ribosomal RNA production line
Cryo-electron microscopy study allows researchers to visualize structural changes in an E. coli enzyme synthesizing ribosomal RNA that shift it between turbo- and slow-modes depending on the bacteria’s growth rate
Full Article
Oct 09, 2018
Discovery helps fight against drug-resistant Tuberculosis
Each year, approximately 10 million people fall ill with Tuberculosis (TB) and around 1.7 million die from the devastating disease worldwide. One of the main antibiotics for TB is rifampicin, however, many strains of the Tuberculosis-causing bacteria – Mycobacterium tuberculosis – have developed resistance to it. Approximately 600,000 people every year are diagnosed with rifampicin-resistant tuberculosis.
Full Article