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Katsuhiko Murakami

Professor of Biochemistry and Molecular Biology
Murakami Photo

About Me

Katsuhiko Murakami started his research career as a graduate student in the National Institute of Genetics and the Graduate University of Advanced Studies in Japan, received Ph. D. in 1997. He engaged in postdoctoral study at the Rockefeller University (1998-2003) for determining the X-ray crystal structure of bacterial RNA polymerase. He joined the Department of Biochemistry and Molecular Biology at Pennsylvania State University in 2003 and became a full Professor in 2015.


Program or Departmental Affiliations

BMMB Graduate Program Molecular, Cellular, and Integrative Biosciences (MCIBS) The Penn State Cancer Institute


Editorial Boards and Professional Organizations

Editorial board member, Journal of Biological Chemistry



Center for Structural Biology
Center for RNA Molecular Biology


Research Summary

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 and cryo-electron microscopy techniques to reveal three-dimensional structures of bacterial, archaeal and bacteriophage RNA polymerases for elucidating the mechanisms of RNA transcription and its regulation. Since the COVID-19 pandemic started, my group has performed studies on proteins involved in SARS_CoV_2 replication to help end the pandemic by utilizing knowledge and skills gained from our main research.


Honors and Awards

1997 - 1998 Research Fellow of the Center of Excellence, Japan
1998 - 2000 Human Frontier Science Program Postdoctoral Fellow
2000 - 2001 Norman and Rosita Winston Postdoctoral Fellow
2005 - 2009 Pew Scholars Program in the Biomedical Sciences
2020 AAAS Fellow




Selected Publications

  1. Vishwakarma RK, Qayyum MZ, Babitzke P, Murakami KS. (2023). Allosteric mechanism of transcription inhibition by NusG-dependent pausing of RNA polymerase. Proc Natl Acad Sci U S A. 120(7):e2218516120.
  2. Narwal M, Armache J-P, Edwards TJ, Murakami KS. (2023). SARS-CoV-2 polyprotein substrate regulates the stepwise Mpro cleavage reaction. J Biol Chem. 299(5):104697.
  3. 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 Commun. 13(1):4624.
  4. Shin Y, Qayyum MZ, Pupov D, Esyunina D, Kulbachinskiy A, Murakami KS. (2021). Structural basis of ribosomal RNA transcription regulation. Nature Commun. 12, 528.
  5. 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 Commun. 11(1):6123.