Paul Babitzke

Co-Director of the Center for RNA Molecular Biology; Stanley R. Person Professor of Molecular Biology


Paul Babitzke

Research Summary

Regulation of gene expression by RNA structure and RNA-binding proteins

Huck Affiliations

Links

Most Recent Publications

Characterization of bacterial intrinsic transcription terminators identified with TERMITe - a novel method for comprehensive analysis of Term-seq data

Jan Grzegorz Kosiński, Sandeepani Ranaweera, Agnieszka Chełkowska-Pauszek, Mikhail Kashlev, Paul Babitzke, Marek Zywicki, 2025, Nucleic Acids Research

NusG-dependent RNA polymerase pausing is a common feature of riboswitch regulatory mechanisms

Oshadhi T. Jayasinghe, Laura E. Ritchey, Thomas Breil, Paxton Newman, Helen Yakhnin, Paul Babitzke, 2024, Nucleic Acids Research on p. 12945-12960

A new reagent for in vivo structure probing of RNA G and U residues that improves RNA structure prediction alone and combined with DMS

Catherine A. Douds, Paul Babitzke, Philip C. Bevilacqua, 2024, RNA on p. 901-919

Multitier regulation of the E. coli extreme acid stress response by CsrA

Mark G. Gorelik, Helen Yakhnin, Archana Pannuri, Alyssa C. Walker, Christine Pourciau, Daniel Czyz, Tony Romeo, Paul Babitzke, 2024, Journal of Bacteriology

In vivo-like nearest neighbor parameters improve prediction of fractional RNA base-pairing in cells

Jacob P. Sieg, Elizabeth A. Jolley, Melanie J. Huot, Paul Babitzke, Philip C. Bevilacqua, 2023, Nucleic Acids Research on p. 11298-11317

CsrA positively and directly regulates the expression of the pdu, pocr, and eut genes required for the luminal replication of salmonella typhimurium

Jessica Nava-Galeana, Helen Yakhnin, Paul Babitzke, Víctor H. Bustamante, 2023, Microbiology spectrum

CsrA-Mediated Translational Activation of the hmsE mRNA Enhances HmsD-Dependent C-di-GMP-Enabled Biofilm Production in Yersinia pestis

Amelia R. Silva-Rohwer, Kiara Held, Helen Yakhnin, Paul Babitzke, Viveka Vadyvaloo, 2023, Journal of Bacteriology

Transcriptome-wide probing reveals RNA thermometers that regulate translation of glycerol permease genes in Bacillus subtilis

Elizabeth Jolley, Helen Yakhnin, E Yakhnin, David Tack, Paul Babitzke, Philip C. Bevilacqua, 2023, RNA on p. 1365-1378

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

Robust regulation of transcription pausing in Escherichia coli by the ubiquitous elongation factor NusG

Alexander V. Yakhnin, Mikhail Bubunenko, Zachary F. Mandell, Lucyna Lubkowska, Sara Husher, Paul Babitzke, Mikhail Kashlev, 2023, Proceedings of the National Academy of Sciences of the United States of America

Most-Cited Papers

Regulation of bacterial virulence by Csr (Rsm) systems

Christopher A. Vakulskas, Anastasia H. Potts, Babitzke Paul, Brian M.M. Ahmer, Romeo Tony, 2015, Microbiology and Molecular Biology Reviews on p. 193-224

Global role of the bacterial post-transcriptional regulator CsrA revealed by integrated transcriptomics

Anastasia H. Potts, Christopher A. Vakulskas, Archana Pannuri, Helen Yakhnin, Paul Babitzke, Tony Romeo, 2017, Nature Communications on p. 1596

Global regulation by CsrA and its RNA antagonists

T Romeo, P Babitzke, 2018, Microbiology spectrum on p. 341-354

NusA-dependent transcription termination prevents misregulation of global gene expression

Smarajit Mondal, Alexander V. Yakhnin, Aswathy Sebastian, Istvan Albert, Paul Babitzke, 2016, Nature Microbiology

Diverse Mechanisms and Circuitry for Global Regulation by the RNA-Binding Protein CsrA

Christine Pourciau, Ying Jung Lai, Mark Gorelik, Paul Babitzke, Tony Romeo, 2020, Frontiers in Microbiology

NusG is a sequence-specific RNA polymerase pause factor that binds to the non-template DNA within the paused transcription bubble

Alexander V. Yakhnin, Katsuhiko S. Murakami, Paul Babitzke, 2016, Journal of Biological Chemistry on p. 5299-5308

Regulation of CsrB/C sRNA decay by EIIA<sup>Glc</sup> of the phosphoenolpyruvate: Carbohydrate phosphotransferase system

Yuanyuan Leng, Christopher A. Vakulskas, Tesfalem R. Zere, Bradley S. Pickering, Paula I. Watnick, Paul Babitzke, Tony Romeo, 2016, Molecular Microbiology on p. 627-639

Antagonistic control of the turnover pathway for the global regulatory sRNA CsrB by the CsrA and CsrD proteins

Christopher A. Vakulskas, Yuanyuan Leng, Hazuki Abe, Takumi Amaki, Akihiro Okayama, Paul Babitzke, Kazushi Suzuki, Tony Romeo, 2016, Nucleic Acids Research on p. 7896-7910

Circuitry linking the catabolite repression and Csr global regulatory systems of Escherichia coli

Archana Pannuri, Christopher A. Vakulskas, Tesfalem Zere, Louise C. McGibbon, Adrianne N. Edwards, Dimitris Georgellis, Paul Babitzke, Tony Romeo, 2016, Journal of Bacteriology on p. 3000-3015

NusG controls transcription pausing and RNA polymerase translocation throughout the Bacillus subtilis genome

Alexander V. Yakhnin, Peter C. FitzGerald, Carl McIntosh, Helen Yakhnin, Maria Kireeva, Joshua Turek-Herman, Zachary F. Mandell, Mikhail Kashlev, Paul Babitzke, 2020, Proceedings of the National Academy of Sciences of the United States of America on p. 21628-21636

News Articles Featuring Paul Babitzke

May 29, 2026

Third Center for RNA Molecular Biology Symposium brings together researchers

Since 2009, the Center for RNA Molecular Biology has provided a space for researchers across Penn State to gather to share ideas, develop skills and foster collaboration. What started as a joint lab meeting in 1998 has since grown into a center that is composed of a diverse group of faculty, graduate students and postdocs from departments including biochemistry and molecular biology, chemistry, biology and chemical engineering.

Full Article

Nov 14, 2025

Penn State molecular biologist named Don Bryant Chair in Microbial Physiology

Paul Babitzke, Stanley R. Person Professor of Molecular Biology and director of the Center for RNA Molecular Biology at Penn State, has been named the Don Bryant Chair in Microbial Physiology in the Department of Biochemistry and Molecular Biology.

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Feb 23, 2023

Nobel Prize-winning Penn State alumnus Paul Berg dies

Penn State alumnus Paul Berg, who received the 1980 Nobel Prize in chemistry, died Feb. 15 at his home in Stanford, California, surrounded by loved ones. He was 96.

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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.

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