Publications by Paul Babitzke

2007

Yakhnin, H., A. V. Yakhnin, and P. Babitzke. 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 trpG promoter is not. J. Bacteriol. 189:872-879.

Babitzke, P. and T. Romeo. CsrB sRNA family: sequestration of RNA-binding regulatory proteins. Curr. Opin. Microbiol. 10:156-163.

Yakhnin, H., P. Pandit, T. J. Petty, C. S. Baker, T. Romeo, and P. Babitzke. CsrA of Bacillus subtilis regulates translation initiation of the gene encoding the flagellin protein (hag) by blocking ribosome binding. Mol. Microbiol. 64:1605-1620.

Baker, C. S., L. A. Eöry, H. Yakhnin, J. Mercante, T. Romeo, and P. Babitzke. CsrA inhibits translation initiation of Escherichia coli hfq by binding to a single site overlapping the Shine-Dalgarno sequence. J. Bacteriol. 189:5472-5481.

Lapouge, K., E. Sineva, M. Lindell, K. Starke, C. S. Baker, P. Babitzke, and D. Haas. Mechanism of hcnA mRNA recognition in the Gac/Rsm signal transduction pathway of Pseudomonas fluorescens. Mol. Microbiol. 66:341-356.

McGraw, A., P. C. Bevilacqua, and P. Babitzke. TRAP-5' stem-loop interaction increases the efficiency of transcription termination in the Bacillus subtilis trpEDCFBA operon leader region. RNA 13:2020-2033.

2006

Yakhnin, H., A. V. Yakhnin, and P. Babitzke. 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. Mol. Microbiol. 61:1252-1266.

Suzuki, K., P. Babitzke, S. R. Kushner, and T. Romeo. Identification of a novel regulatory protein (CsrD) that targets the global regulatory RNAs CsrB and CsrC for degradation by RNase E. Genes Dev. 20:2605-2617.

Mercante, J., K. Suzuki, X. Cheng, P. Babitzke, and T. Romeo. Comprehensive alanine-scanning mutagenesis of Escherichia coli CsrA defines two subdomains of critical functional importance. J. Biol. Chem. 281:31832-31842.

Yakhnin, A. V., H. Yakhnin, and P. Babitzke. RNA polymerase pausing participates in the Bacillus subtilis trpE translation control mechanism by providing additional time for TRAP to bind to the nascent trp leader transcript. Mol. Cell 24:547-557

2005

Wang, X., A. K. Dubey, K. Suzuki, C. S. Baker, P. Babitzke, and Tony Romeo. CsrA post-transcriptionally represses pgaABCD, responsible for the synthesis of a biofilm polysaccharide adhesion of Escherichia coli. Mol. Microbiol. 56:1648-1663.

 
Gollnick, P., P. Babitzke, A. Antson, and C. Yanofsky. Complexity in regulation of tryptophan biosynthesis in Bacillus subtilis. Ann. Rev. Genet. 39:47-68.
 
Dubey, A. K., C. S. Baker, T. Romeo, and P. Babitzke. RNA sequence and secondary structure participate in high-affinity CsrA-RNA interaction. RNA 11:1579-1587.

2004

Yakhnin, H., H. Zhang, A.V. Yakhnin, and P. Babitzke. The trp RNA-binding attenuation protein of Bacillus subtilis regulates translation of the tryptophan transport gene trpP (yhaG) by blocking ribosome binding. J. Bacteriol. 186:278-286.

Deikus, G., P. Babitzke, and D.H. Bechhofer. Recycling of a regulatory protein by degradation of the RNA to which it binds. Proc. Natl. Acad. Sci. USA 101:2747-2751.

Babitzke, P. Regulation of transcription attenuation and translation initiation by allosteric control of an RNA-binding protein: the Bacillus subtilis TRAP protein. Curr. Opin. Microbiol. 7:132-139.

Yakhnin, H. and P. Babitzke. Gene replacement method for determining conditions in which Bacillus subtilis genes are essential or dispensable for cell viability. Appl. Microbiol. Biotechnol. 64:382-386.

2003

Weilbacher, T., K. Suzuki, A.K. Dubey, X. Wang, S. Gudapaty, I. Morozov, C.S. Baker, D. Georgellis, P. Babitzke, and T. Romeo. A novel sRNMA component of the carbon storage regulatory system of Escherichia coli. Mol. Microbiol. 48:657-670.

Dubey, A.K., C.S. Baker, K. Suzuki, D. Jones, P. Pandit, T. Romeo, and P. Babitzke. CsrA regulates translation of the Escherichia coli carbon starvation gene, cstA, by blocking ribosome access to the cstA transcript. J. Bacteriol. 185:4450-4460.

Schaak, J.E., H. Yakhnin, P.C. Bevilacqua, and P. Babitzke. 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. J. Mol. Biol. 332:555-574.

Schaak, J.E., P. Babitzke, and P.C. Bevilacqua. Phylogenetic conservation of RNA secondary and tertiary structure in the trpEDCFBA operon leader transcript in Bacillus. RNA 9:1502-1515.

Babitzke, P., J. Schaak, A.V. Yakhnin, and P.C. Bevilacqua. Role of RNA structure in transcription attenuation in Bacillus subtilis: The trpEDCFBA operon as a model system. Methods Enzymol. 371:392-404.

2002

Valbuzzi, A., P. Gollnick, P. Babitzke, and C. Yanofsky. The anti-TRAP protein AT recognizes the tryptophan-activated RNA binding domain of the TRAP regulatory protein. J. Biol. Chem. 277:10608-10613.

Baker, C.S., I. Morozov, K. Suzuki, T. Romeo, and P. Babitzke. CsrA regulates glycogen biosynthesis by preventing translation of glgC in Escherichia coli. Mol. Microbiol. 44:1599-1610.

Yakhnin, A.V., and P. Babitzke. NusA-stimulated RNA polymerase pausing and termination participates in the Bacillus subtilis trp operon attenuation mechanism in vitro. Proc. Natl. Acad. Sci. USA 99:11067-11072.

Suzuki, K., X. Wang, T. Weilbacher, A.-K. Pernestig, Ö. Melefors, D. Georgellis, P. Babitzke, and T. Romeo. Regulatory circuitry of the CsrA/CsrB and BarA/UvrY systems of Escherichia coli. J. Bacteriol. 184:5130-5140.

Gollnick, P., and P. Babitzke. Transcription attenuation. Biochim. Biophys. Acta. 1577:240-250.

Gollnick, P., P. Babitzke, E. Merino, and C. Yanofsky. Aromatic amino acid metabolism in Bacillus subtilis. In: Bacillus subtilis and Its Close Relatives: From Genes to Cells. (A. Sonenshein, ed.), pp. 233-244, American Society for Microbiology, Washington, D.C.

2001

Wei, B.L., A.-M. Brun-Zinkernagel, J.W. Simecka, B.M. Prub, P. Babitzke, and T. Romeo. Positive regulation of motility and flhDC expression by the RNA-binding protein CsrA of Escherichia coli. Mol. Microbiol. 40:245-256.

Babitzke, P., and P. Gollnick. Posttranscription initiation control of tryptophan metabolism in Bacillus subtilis by the trp RNA-binding attenuation protein (TRAP), anti-TRAP, and RNA structure. J. Bacteriol. 183:5795-5802.

Yakhnin, H., J.E. Babiarz, A.V. Yakhnin, and P. Babitzke. Expression of the Bacillus subtilis trpEDCFBA operon is regulated by translational coupling and Rho termination factor. J. Bacteriol. 183:5918-5926.

Gudapaty, S., K. Suzuki, X. Wang, P. Babitzke, and T. Romeo. Regulatory interactions of Csr components: The RNA binding protein CsrA activates csrB transcription in Escherichia coli. J. Bacteriol. 183:6017-6027.

Gollnick, P., P. Babitzke, E. Merino, and C. Yanofsky. Aromatic amino acid metabolism in Bacillus subtilis. In: Bacillus subtilis and Its Closet Relatives: from Genes to Cells. (A. Sonenshein, ed.), pp. 233-244, American Society for Microbiology, Washington, D.C.

2000

Yakhnin, A.V., J.J. Trimble, C.R. Chiaro, and P. Babitzke. Effects of Mutations in the L-tryptophan Binding Pocket of the trp RNA-binding Attenuation Protein of Bacillus subtilis. J. Biol. Chem. 275:4519-4524.

Du, H., A.V. Yakhnin, S. Dharmaraj, and P. Babitzke. trp RNA-binding Attenuation Protein (TRAP)-5’ Stem-loop RNA Interaction is Required for Proper Transcription Attenuation Control of the Bacillus subtilis trpEDCFBA Operon. J. Bacteriol. 182:1819-1827.

1999

Babitzke, P. and P. Gollnick. Attenuation of Transcription. In: Encyclopedia of Molecular Biology, (T.E. Creighton, ed.), pp. 216-220, John Wiley & Sons, Inc., New York, NY.

Gollnick, P. and P. Babitzke. Antitermination Control of Gene Expression. In: Encyclopedia of Molecular Biology, (T.E. Creighton, ed.), pp. 173-177, John Wiley & Sons, Inc., New York, NY.

Sudershana, S., H. Du, M. Mahalanabis, and P. Babitzke. A 5' Stem Loop Participates in the Transcription Attenuation Mechanism that Controls Expression of the Bacillus subtilis trpEDCFBA Operon. J. Bacteriol. 181:5742-5749.

1998

Hansen, D. and P. Babitzke. trp RNA-binding Attenuation Protein-mediated Long Distance RNA Refolding Regulates Translation of trpE in Bacillus subtilis. J. Biol. Chem. 273:20494-20503.

Granger, L., E.B. O'Hara, R. Wang, F.V. Meffen, K. Armstrong, S.D. Yancey, P. Babitzke, and S.R. Kushner. The Escherichia coli mrsC Gene is Required for Cell Growth and mRNA Decay. J. Bacteriol. 180:1920-1928.

Zeljka, K., P. Babitzke, and E. Hoffman. Myotonic Dystrophy: Molecular Windows on a Complex Etiology. Nucleic Acids Res. 26:1363-1368.

1997

Babitzke, P. Regulation of Tryptophan Biosynthesis: Trp-ing the TRAP or How Bacillus subtilis Reinvented the Wheel. Mol. Microbiol. 26:1-9.

Hansen, D., R. Tarpey, and P. Babitzke. The trp RNA-binding Attenuation Protein Regulates TrpG Synthesis by Binding to the trpG Ribosome Binding Site of Bacillus subtilis. J. Bacteriol. 179:2582-2586.

1996

Babitzke, P., J. Yealy, and D. Campanelli. Interaction of the trp RNA-binding Attenuation Protein (TRAP) of Bacillus subtilis with RNA: Effects of the Number of GAG Repeats, the Nucleotide Sequence Separating Adjacent Repeats, and RNA Secondary Structure. J. Bacteriol. 178:5159-5163.

1995

Babitzke, P. and C. Yanofsky. Structural Features of L-Tryptophan Required for Activation of TRAP, the trp RNA-Binding Attenuation Protein of Bacillus subtilis. J. Biol. Chem. 270:12452-12456.

Babitzke, P., D.G. Bear, and C. Yanofsky. TRAP, the trp RNA-binding Attenuation Protein of Bacillus subtilis, is a Toroid-shaped Molecule that Binds Transcripts Containing GAG or UAG Repeats Separated by Two Nucleotides. Proc. Natl. Acad. Sci. USA. 92:1-5.

Enrique, M., P. Babitzke, and C. Yanofsky. trp RNA-Binding Attenuation Protein (TRAP)-trp Leader RNA Interactions Mediate Translational as well as Transcriptional Regulation of the Bacillus subtilis trp Operon. J. Bacteriol. 177:6362-6370.

1994

Babitzke, P., J.T. Stults, S.J. Shire, and C. Yanofsky. TRAP, the trp RNA-binding Attenuation Protein of Bacillus subtilis, is a Multisubunit Complex that Appears to Recognize G/UAG Repeats in the trpEDCFBA and trpG Transcripts. J. Biol. Chem. 269:16597-16604.