Paul Babitzke
About Me
Paul Babitzke obtained his B.A. in Biomedical Science at St. Cloud State University and his Ph.D. in Genetics from the University of Georgia. He worked as a postdoctoral scientist for 3 years at Stanford University prior to joining the faculty at Penn State University in 1994. He is currently the Stanley R. Person Professor of Molecular Biology and Director of the Center for RNA Molecular Biology.
Research Interest
Regulation of gene expression by RNA structure and RNA-binding proteins
Research Summary
Gene expression is regulated at the level of transcription, translation and mRNA stability. The transcription cycle consists of initiation, elongation and termination, each of which can be regulated. We are investigating fundamental mechanisms that affect transcription elongation and termination. We also investigate a variety of genes in which RNA binding proteins control gene expression by transcription attenuation (regulated termination), repression of translation initiation, and/or mRNA stability.
The Bacillus subtilis trp operon is regulated by TRAP-mediated transcription attenuation and translation repression mechanisms. The general transcription elongation factors NusA and NusG participate in the attenuation mechanism by stimulating RNA polymerase pausing at the nucleotide just preceding the critical overlap between the antiterminator and terminator structures. Thus, NusA- and NusG-dependent pausing provides additional time for TRAP to bind to the nascent transcript and promote termination. TRAP also regulates translation of the trp operon. TRAP binding to trp operon readthrough transcripts promotes formation of an RNA structure that prevents ribosome binding. NusA- and NusG-dependent pausing plays a vital role in this mechanism as well. NusA stimulates pausing by assisting with pause hairpin formation, whereas NusG makes sequence-specific contacts with T residues in the non-template DNA (ntDNA) strand within the paused transcription bubble. As RNAP and template DNA must move with respect to one another for elongation to resume, interaction of NusG with both components inhibits elongation.
Until recently the two trp pause sites were the only two known NusG-dependent pause sites in any organism. Using a genomic approach called RNET-seq, we identified >1000 NusG-dependent pause sites in the B. subtilis transcriptome. Pausing at one such site is required for inducing expression of tlrB, a gene encoding a 23S rRNA methyltransferase. TlrB-mediated methylation confers tylosin resistance by preventing binding of this antibiotic to the ribosome. Pausing is also required for regulating expression of the ribD riboswitch by providing additional time for FMN binding to the nascent ribD transcript. We are also exploring the mechanism by which NusA- and NusG-dependent pausing controls expression of other genes in B. subtilis.
Intrinsic (Rho-independent) and Rho-dependent termination are the two transcription termination mechanisms identified in bacteria. Canonical intrinsic terminators consist of a strong RNA hairpin followed by a U-tract. Term-seq studies identified a new class of intrinsic terminator that requires NusA. NusA-dependent terminators tend to have weak RNA hairpins and/or distal U-tract interruptions. Our unpublished studies indicate that NusG is another intrinsic termination factor. We are exploring the interrelationship between NusG-dependent pausing and NusG-dependent termination. Our hypothesis is that NusG stimulates pausing prior to transcript release at NusG-dependent termination sites. We are conducting biochemical studies to test this hypothesis. We are also exploring the effects of Rho on termination. Of particular interest, we found that Rho actually participates in intrinsic (Rho-independent) termination. We are exploring the mechanistic basis for this important discovery.
We are also using RNA structure-seq to identify new regulatory mechanisms (attenuation, antitermination, riboswitches, RNA thermometers) that control gene expression in response to various stresses. This work is being conducted in collaboration with Drs. Philip Bevilacqua and Sarah Assmann at Penn State.
Another major effort in the lab involves genetic and biochemical characterization of the Csr global regulatory system. Csr regulates several hundred E. coli genes, thereby mediating global changes in cellular physiology during the transition between exponential and stationary phase growth. Four major components of Csr include an RNA binding protein (CsrA), two small RNA (sRNA) antagonists of CsrA (CsrB and CsrC), and CsrD, a protein that targets degradation of CsrB and CsrC by RNase E.
CsrA represses translation initiation of numerous genes by binding to their translation initiation regions. Bound CsrA prevents ribosome binding, thereby repressing a variety of processes, including gluconeogenesis, glycogen biosynthesis, quorum sensing and biofilm formation. In contrast, CsrA activates glycolysis, acetate and iron metabolism, and motility. CsrA activates flagella biosynthesis by preventing degradation of the flhDC transcript by RNase E. We recently identified the first known CsrA-mediated translational activation mechanism. We are continuing to explore this global regulatory system in E. coli using omics, genetics and biochemistry approaches. For example, we are using structure-seq to footprint CsrA across the entire transcriptome in vivo. We have also initiated a metabolomics study to identify new pathways that are affected by the Csr system. All of the Csr work is being performed in collaboration with Dr. Tony Romeo at the University of Florida.
Honors and Awards
- Chair, NIGMS Microbial Physiology and Genetics-subcommittee 2 (MBC-2) (2004)
- Chair, Division H, American Society for Microbiology (ASM) (2006)
- Daniel R. Tershak Teaching Award (2009)
- Divisional Group IV Representative, American Society for Microbiology (ASM) (2011-2015)
- Charles E. Kaufman New Initiative Research Award (2016)
- Fellow, American Association for the Advancement of Science (AAAS) (2016)
- Fellow, American Academy of Microbiology (AAM) (2017)
- St. Cloud State University Biological Sciences Distinguished Alumni Award (2018)