Paul Babitzke

Co-Director of the Center for RNA Molecular Biology; Professor of Biochemistry and Molecular Biology

Paul Babitzke

Research Summary

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

Huck Affiliations

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Rna Gene Expression Proteins Messenger Rna Dna Directed Rna Polymerases Bacillus Subtilis Escherichia Coli Dna Protein Carbon Bacteria Rna Binding Proteins Rna Stability Transcription Factors In Vitro Techniques Protein Biosynthesis Ribosomes Ribonuclease E Peptide Elongation Factors Genes Operon Iron Transcription Homeostasis Genome

Most Recent Publications

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

CsrA coordinates the expression of ribosome hibernation and anti-σ factor proteins

Christine Pourciau, Helen Yakhnin, Elena Borisovna Yakhnina, Archanna Pannuri, Mark G. Gorelik, Ying-Jung Lai, Tony Romeo, Paul Babitzke, 2023, mBio on p. e0258523

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

Expression of Bacillus subtilis ABCF antibiotic resistance factor VmlR is regulated by RNA polymerase pausing, transcription attenuation, translation attenuation and (p)ppGpp

Hiraku Takada, Zachary Mandell, Helen Yakhnin, Anastasiya Glazyrina, Shinobu Chiba, Tatsuaki Kurata, Kelvin Wu, Ben Tresco, Andrew Myers, Gemma Aktinson, Paul Babitzke, Vasili Hauryliuk, 2022, Nucleic Acids Research on p. 6174-6189

Analysis of mRNA Decay Intermediates in Bacillus subtilis 3' Exoribonuclease and RNA Helicase Mutant Strains

Shivani Chhabra, Zachary F. Mandell, Bo Liu, Paul Babitzke, David H. Bechhofer, 2022, mBio

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

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

Global effects of the DEAD-box RNA helicase DeaD (CsdA) on gene expression over a broad range of temperatures

Christopher A. Vakulskas, Archana Pannuri, Diana Cortés-Selva, Tesfalem R. Zere, Brian M. Ahmer, Paul Babitzke, Tony Romeo, 2014, Molecular Microbiology on p. 945-958

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/Spt5: Are there common functions of this ubiquitous transcription elongation factor?

Alexander V. Yakhnin, Paul Babitzke, 2014, Current Opinion in Microbiology on p. 68-71