PAUL L BABITZKE

Summary

Affiliation: Pennsylvania State University
Country: USA

Publications

  1. ncbi request reprint Regulation of tryptophan biosynthesis: Trp-ing the TRAP or how Bacillus subtilis reinvented the wheel
    P Babitzke
    Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park 16802, USA
    Mol Microbiol 26:1-9. 1997
  2. ncbi request reprint Regulation of transcription attenuation and translation initiation by allosteric control of an RNA-binding protein: the Bacillus subtilis TRAP protein
    Paul Babitzke
    Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
    Curr Opin Microbiol 7:132-9. 2004
  3. ncbi request reprint CsrB sRNA family: sequestration of RNA-binding regulatory proteins
    Paul Babitzke
    Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
    Curr Opin Microbiol 10:156-63. 2007
  4. doi request reprint Regulation of translation initiation by RNA binding proteins
    Paul Babitzke
    Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
    Annu Rev Microbiol 63:27-44. 2009
  5. ncbi request reprint A Mg2+-dependent RNA tertiary structure forms in the Bacillus subtilis trp operon leader transcript and appears to interfere with trpE translation control by inhibiting TRAP binding
    Janell E Schaak
    Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
    J Mol Biol 332:555-74. 2003
  6. ncbi request reprint The trp RNA-binding attenuation protein (TRAP) of Bacillus subtilis regulates translation initiation of ycbK, a gene encoding a putative efflux protein, by blocking ribosome binding
    Helen Yakhnin
    Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
    Mol Microbiol 61:1252-66. 2006
  7. pmc CsrA regulates translation of the Escherichia coli carbon starvation gene, cstA, by blocking ribosome access to the cstA transcript
    Ashok K Dubey
    Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
    J Bacteriol 185:4450-60. 2003
  8. pmc The trp RNA-binding attenuation protein of Bacillus subtilis regulates translation of the tryptophan transport gene trpP (yhaG) by blocking ribosome binding
    Helen Yakhnin
    Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
    J Bacteriol 186:278-86. 2004
  9. pmc Molecular basis of TRAP-5'SL RNA interaction in the Bacillus subtilis trp operon transcription attenuation mechanism
    Adam P McGraw
    Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
    RNA 15:55-66. 2009
  10. pmc RNA sequence and secondary structure participate in high-affinity CsrA-RNA interaction
    Ashok K Dubey
    Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
    RNA 11:1579-87. 2005

Collaborators

Detail Information

Publications22

  1. ncbi request reprint Regulation of tryptophan biosynthesis: Trp-ing the TRAP or how Bacillus subtilis reinvented the wheel
    P Babitzke
    Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park 16802, USA
    Mol Microbiol 26:1-9. 1997
    ..In the case of trpG, TRAP binds to nine repeats that overlap the ribosome-binding site, thereby blocking translation...
  2. ncbi request reprint Regulation of transcription attenuation and translation initiation by allosteric control of an RNA-binding protein: the Bacillus subtilis TRAP protein
    Paul Babitzke
    Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
    Curr Opin Microbiol 7:132-9. 2004
    ..In addition, bound TRAP regulates translation initiation of pabA, trpP and ycbK by directly blocking ribosome binding. The anti-TRAP protein inhibits TRAP activity by competing with RNA for the RNA binding surface of TRAP...
  3. ncbi request reprint CsrB sRNA family: sequestration of RNA-binding regulatory proteins
    Paul Babitzke
    Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
    Curr Opin Microbiol 10:156-63. 2007
    ....
  4. doi request reprint Regulation of translation initiation by RNA binding proteins
    Paul Babitzke
    Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
    Annu Rev Microbiol 63:27-44. 2009
    ..Examples also exist in which the bound protein traps the ribosome in a complex that is incapable of initiating translation...
  5. ncbi request reprint A Mg2+-dependent RNA tertiary structure forms in the Bacillus subtilis trp operon leader transcript and appears to interfere with trpE translation control by inhibiting TRAP binding
    Janell E Schaak
    Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
    J Mol Biol 332:555-74. 2003
    ..Results from expression studies using trpE'-'lacZ translational fusions and RNA-directed cell-free translation experiments suggest that the Mg(2+)-dependent tertiary structure inhibits TRAP's ability to regulate translation of trpE...
  6. ncbi request reprint The trp RNA-binding attenuation protein (TRAP) of Bacillus subtilis regulates translation initiation of ycbK, a gene encoding a putative efflux protein, by blocking ribosome binding
    Helen Yakhnin
    Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
    Mol Microbiol 61:1252-66. 2006
    ..We also identified two dipeptide coding minigenes between the Shine-Dalgarno sequence and start codon of ycbK. Expression of one of the minigenes modestly interfered with translation of ycbK...
  7. pmc CsrA regulates translation of the Escherichia coli carbon starvation gene, cstA, by blocking ribosome access to the cstA transcript
    Ashok K Dubey
    Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
    J Bacteriol 185:4450-60. 2003
    ..These results establish that CsrA regulates translation of cstA by sterically interfering with ribosome binding...
  8. pmc The trp RNA-binding attenuation protein of Bacillus subtilis regulates translation of the tryptophan transport gene trpP (yhaG) by blocking ribosome binding
    Helen Yakhnin
    Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
    J Bacteriol 186:278-86. 2004
    ....
  9. pmc Molecular basis of TRAP-5'SL RNA interaction in the Bacillus subtilis trp operon transcription attenuation mechanism
    Adam P McGraw
    Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
    RNA 15:55-66. 2009
    ....
  10. pmc RNA sequence and secondary structure participate in high-affinity CsrA-RNA interaction
    Ashok K Dubey
    Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
    RNA 11:1579-87. 2005
    ..A mutational analysis of one selected ligand confirmed that the conserved ACA, GGA, and GU residues were critical for CsrA binding and that RNA secondary structure participates in CsrA-RNA recognition...
  11. pmc TRAP-5' stem loop interaction increases the efficiency of transcription termination in the Bacillus subtilis trpEDCFBA operon leader region
    Adam P McGraw
    Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
    RNA 13:2020-33. 2007
    ....
  12. pmc Translation control of trpG from transcripts originating from the folate operon promoter of Bacillus subtilis is influenced by translation-mediated displacement of bound TRAP, while translation control of transcripts originating from a newly identified tr
    Helen Yakhnin
    Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
    J Bacteriol 189:872-9. 2007
    ..We found that TRAP-dependent regulation of trpG expression is more extensive for a transcript originating from P(trpG) and that transcripts originating from P(trpG) are not subject to translation-mediated displacement of bound TRAP...
  13. ncbi request reprint CsrA of Bacillus subtilis regulates translation initiation of the gene encoding the flagellin protein (hag) by blocking ribosome binding
    Helen Yakhnin
    Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
    Mol Microbiol 64:1605-20. 2007
    ..Toeprint and cell-free translation studies demonstrate that bound CsrA prevents ribosome binding to the hag transcript, thereby inhibiting translation initiation and Hag synthesis...
  14. pmc CsrA inhibits translation initiation of Escherichia coli hfq by binding to a single site overlapping the Shine-Dalgarno sequence
    Carol S Baker
    Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
    J Bacteriol 189:5472-81. 2007
    ..The interaction of CsrA with hfq mRNA is the first example of a CsrA-regulated gene that contains only one CsrA binding site...
  15. ncbi request reprint RNA polymerase pausing regulates translation initiation by providing additional time for TRAP-RNA interaction
    Alexander V Yakhnin
    Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
    Mol Cell 24:547-57. 2006
    ..These results establish that pausing is capable of playing a role in regulating translation in bacteria...
  16. pmc NusA-stimulated RNA polymerase pausing and termination participates in the Bacillus subtilis trp operon attenuation mechanism invitro
    Alexander V Yakhnin
    Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
    Proc Natl Acad Sci U S A 99:11067-72. 2002
    ..Finally, NusA-stimulated termination is cooperative, suggesting that binding of multiple NusA molecules influences termination...
  17. ncbi request reprint CsrA regulates glycogen biosynthesis by preventing translation of glgC in Escherichia coli
    Carol S Baker
    Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
    Mol Microbiol 44:1599-610. 2002
    ..This inhibition of translation probably contributes to destabilization of the glgC transcript that was observed previously...
  18. pmc Mechanism of NusG-stimulated pausing, hairpin-dependent pause site selection and intrinsic termination at overlapping pause and termination sites in the Bacillus subtilis trp leader
    Alexander V Yakhnin
    Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
    Mol Microbiol 76:690-705. 2010
    ..NusA was found to increase both pausing and termination by reducing the rate of transcription. We also found that NusG-stimulated pausing is sequence specific and that NusG does not affect termination...
  19. ncbi request reprint Role of RNA structure in transcription attenuation in Bacillus subtilis: the trpEDCFBA operon as a model system
    Paul Babitzke
    Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
    Methods Enzymol 371:392-404. 2003
  20. pmc Function of the Bacillus subtilis transcription elongation factor NusG in hairpin-dependent RNA polymerase pausing in the trp leader
    Alexander V Yakhnin
    Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
    Proc Natl Acad Sci U S A 105:16131-6. 2008
    ..Overexpression of nusG reduces trp operon expression to a larger extent than overexpression of nusA...
  21. pmc Phylogenetic conservation of RNA secondary and tertiary structure in the trpEDCFBA operon leader transcript in Bacillus
    Janell E Schaak
    Department of Biochemistry and Molecular Biology, The Huck Institute for Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
    RNA 9:1502-15. 2003
    ..These data indicate that RNA secondary and tertiary structures involved in TRAP-mediated translation control are conserved in at least four Bacillus species...
  22. pmc CsrA represses translation of sdiA, which encodes the N-acylhomoserine-L-lactone receptor of Escherichia coli, by binding exclusively within the coding region of sdiA mRNA
    Helen Yakhnin
    Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
    J Bacteriol 193:6162-70. 2011
    ..Thus, this represents the first example of CsrA preventing translation by interacting solely within the coding region of an mRNA target...

Research Grants14

  1. MECHANISM OF TRP GENE REGULATION BY TRAP-RNA RECOGNITION
    Paul Babitzke; Fiscal Year: 2007
    ..Genetic and biochemical experiments will be carried out to understand how the relative placement of the triplet repeats influences TRAP-mediated translation control of these three genes. ..
  2. MECHANISM OF TRP GENE REGULATION BY TRAP-RNA RECOGNITION
    Paul Babitzke; Fiscal Year: 2004
    ..Finally, the possible role of an RNA pseudoknot in regulating translation and/or mRNA stability of the trp operon will be determined by several genetic and biochemical approaches. ..
  3. MECHANISM OF TRP GENE REGULATION BY TRAP-RNA RECOGNITION
    Paul Babitzke; Fiscal Year: 1999
    ..The defects associated with various mutant TRAP proteins will be determined using available techniques. A collaboration with William Royer will continue to determine the crystal structure of the TRAP-RNA complex. ..
  4. MECHANISM OF TRP GENE REGULATION BY TRAP-RNA RECOGNITION
    Paul Babitzke; Fiscal Year: 2009
    ..Genetic and biochemical experiments will be carried out to understand how the relative placement of the triplet repeats influences TRAP-mediated translation control of these three genes. ..