Katsuhiko Murakami

Faculty Director of the Cryo-Electron Microscopy Core Facility; Professor of Biochemistry and Molecular Biology

Katsuhiko Murakami

Research Summary

Structural and Mechanistic Enzymology of Prokaryotic RNA Polymerases

Huck Affiliations

Links

Most Recent Publications

Structure and function of the Si3 insertion integrated into the trigger loop/helix of cyanobacterial RNA polymerase

M. Zuhaib Qayyum, Masahiko Imashimizu, Miron Leanca, Rishi K. Vishwakarma, Amber Riaz-Bradley, Yulia Yuzenkova, Katsuhiko S. Murakami, 2024, Proceedings of the National Academy of Sciences of the United States of America

Tectonic and geological setting influence hot spring microbiology

Daniel R. Colman, Allison Veach, Andri Stefánsson, Louie Wurch, B. Shafer Belisle, Peter T. Podar, Zamin Yang, Dawn Klingeman, Kazuyo Senba, Katsuhiko S. Murakami, Jakob K. Kristjánsson, Snædís H. Björnsdóttir, Eric S. Boyd, Mircea Podar, 2023, Environmental Microbiology on p. 2481-2497

Murakami selected as Innovation Fund investigator by Pew Charitable Trusts

Katsuhiko Murakami, 2023,

Essential process for SARS-CoV-2 viral replication visualized

Katsuhiko Murakami, 2023,

SARS-CoV-2 polyprotein substrate regulates the stepwise M<sup>pro</sup> cleavage reaction

Manju Narwal, Jean Paul Armache, Thomas J. Edwards, Katsuhiko S. Murakami, 2023, Journal of Biological Chemistry

Allosteric mechanism of transcription inhibition by NusG-dependent pausing of RNA polymerase

Rishi K. Vishwakarma, M. Zuhaib Qayyum, Paul Babitzke, Katsuhiko S. Murakami, 2023, Proceedings of the National Academy of Sciences of the United States of America

DNA stuck in the gears of the RNA production machine

Katsuhiko Murakami, 2023,

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

Comprehensive transcription terminator atlas for Bacillus subtilis

Zachary Mandell, Rishi Vishwakarma, R Vishwakarma, Helen Yakhnina, H Yakhnin, K Murakami KS, Katsuhiko Murakami, Mikhail Kashlev, Paul Babitzke, 2022, Nature Microbiology on p. 1918-1931

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

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

Identification of SARS-CoV-2 inhibitors targeting Mpro and PLpro using in-cell-protease assay

Anoop Narayanan, Manju Narwal, Sydney Majowicz, Carmine Varricchio, Shay Toner, Carlo Ballotore, Carlo Ballatore, Andrea Brancale, Katsuhiko S. Murakami, Joyce Jose, 2022, Communications Biology on p. 169

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

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

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

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

Molecular basis of microhomology-mediated end-joining by purified full-length Polθ

Samuel J. Black, Ahmet Y. Ozdemir, Ekaterina Kashkina, Tatiana Kent, Timur Rusanov, Dejan Ristic, Yeonoh Shin, Antonio Suma, Trung Hoang, Gurushankar Chandramouly, Labiba A. Siddique, Nikita Borisonnik, Katherine Sullivan-Reed, Joseph S. Mallon, Tomasz Skorski, Vincenzo Carnevale, Katsuhiko S. Murakami, Claire Wyman, Richard T. Pomerantz, 2019, Nature Communications on p. 4423

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

Cryo-EM structure of Escherichia coli <sup>70</sup> RNA polymerase and promoter DNA complex revealed a role of non-conserved region during the open complex formation

Anoop Narayanan, Frank S. Vago, Kunpeng Li, M. Zuhaib Qayyum, Dinesh Yernool, Wen Jiang, Katsuhiko S. Murakami, 2018, Journal of Biological Chemistry on p. 7367-7375

News Articles Featuring Katsuhiko Murakami

Oct 31, 2024

Huck researchers reflect on the 2024 Nobel Prize in Chemistry

This month, the Nobel Prize in Chemistry was awarded to three scientists credited with historic breakthroughs surrounding proteins and their structures. Three Huck researchers working on similar challenges chime in with their thoughts.

Full Article

Oct 24, 2023

Biochemist selected as Innovation Fund investigator by Pew Charitable Trusts

Katsuhiko Murakami, professor of biochemistry and molecular biology at Penn State, has been selected as a member of the 2023 class of Innovation Fund investigators by the Pew Charitable Trusts.

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Jun 05, 2023

Essential process for SARS-CoV-2 viral replication visualized

During the replication of the SARS-CoV-2 virus, a long string of connected proteins is cleaved apart into individual proteins. This process is interrupted by an FDA-approved drug to treat COVID-19; however, the mechanistic details of this cleavage process are still unclear. Now, a team led by researchers at Penn State has produced the most detailed images to date of this process, revealing that these proteins are cleaved in a consistent order likely dictated by the structure of the protein string.

Full Article

May 30, 2023

Essential process for SARS-CoV-2 viral replication visualized

During the replication of the SARS-CoV-2 virus, a long string of connected proteins is cleaved apart into individual proteins.

Full Article

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