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Katsuhiko Murakami

Professor of Biochemistry and Molecular Biology
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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

The BMMB Graduate Program The Penn State Cancer Institute


Editorial Boards and Professional Organizations

A member of Faculty of 1000 Biology (Structural Biology, Transcription and Translation Section)

Editorial board member, Journal of Biological Chemistry



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.


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


Selected Publications

  1. Mosaei H, Molodtsov V, Kepplinger B, Harbottle J, Moon CW, Jeeves RE, Ceccaroni L, Shin Y, Morton-Laing S, Marrs ECL, Wills C, Clegg W, Yuzenkova Y, Perry JD, Bacon J, Errington J, Allenby NEE, Hall MJ, Murakami KS, Zenkin N. Mode of Action of Kanglemycin A, an Ansamycin Natural Product that Is Active against Rifampicin-Resistant Mycobacterium tuberculosis. Molecular Cell. 2018; 72(2):263-274.e5. PubMed [journal] PMID: 30244835, PMCID: PMC6202310
  2. Narayanan A, Vago FS, Li K, Qayyum MZ, Yernool D, Jiang W, Murakami KS. Cryo-EM structure of Escherichia coli 70 RNA polymerase and promoter DNA complex revealed a role of  non-conserved region during the open complex formation. The Journal of Biological Chemistry. 2018; 293(19):7367-7375. PubMed [journal] PMID: 29581236, PMCID: PMC5949986
  3. Molodtsov V, Sineva E, Zhang L, Huang X, Cashel M, Ades SE, Murakami KS. Allosteric Effector ppGpp Potentiates the Inhibition of Transcript Initiation by  DksA. Molecular Cell. 2018; 69(5):828-839.e5. NIHMSID: NIHMS938489 PubMed [journal] PMID: 29478808, PMCID: PMC5837818
  4. Murakami KS, Shin Y, Turnbough CL Jr, Molodtsov V. X-ray crystal structure of a reiterative transcription complex reveals an atypical RNA extension pathway. Proceedings of the National Academy of Sciences of the United States of America.  2017; 114(31):8211-8216. PubMed [journal] PMID: 28652344, PMCID: PMC5547606
  5. Molodtsov V, Scharf NT, Stefan MA, Garcia GA, Murakami KS. Structural basis for rifamycin resistance of bacterial RNA polymerase by the three most clinically important RpoB mutations found in Mycobacterium tuberculosis. Molecular Microbiology. 2017; 103(6):1034-1045. NIHMSID: NIHMS840349 PubMed [journal] PMID: 28009073, PMCID: PMC5344776
  6. Hauryliuk V, Atkinson GC, Murakami KS, Tenson T, Gerdes K. Recent functional insights into the role of (p)ppGpp in bacterial physiology. Nature Reviews. Microbiology. 2015; 13(5):298-309. NIHMSID: NIHMS738404 PubMed [journal] PMID: 25853779, PMCID: PMC4659695
  7. Hirata A, Klein BJ, Murakami KS. The X-ray crystal structure of RNA polymerase from Archaea. Nature. 2008; 451(7180):851-4. NIHMSID: NIHMS167984 PubMed [journal] PMID: 18235446, PMCID: PMC2805805