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Regulation of Iron Storage by CsrA Supports Exponential Growth of Escherichia coli.

Pourciau C, Pannuri A, Potts A, Yakhnin H, Babitzke P, Romeo T.

MBio. 2019 Aug 6;10(4). pii: e01034-19. doi: 10.1128/mBio.01034-19.


Posttranscription Initiation Control of Gene Expression Mediated by Bacterial RNA-Binding Proteins.

Babitzke P, Lai YJ, Renda AJ, Romeo T.

Annu Rev Microbiol. 2019 Sep 8;73:43-67. doi: 10.1146/annurev-micro-020518-115907. Epub 2019 May 17.


In vivo RNA structural probing of uracil and guanine base-pairing by 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC).

Mitchell D 3rd, Renda AJ, Douds CA, Babitzke P, Assmann SM, Bevilacqua PC.

RNA. 2019 Jan;25(1):147-157. doi: 10.1261/rna.067868.118. Epub 2018 Oct 19.


Global Regulation by CsrA and Its RNA Antagonists.

Romeo T, Babitzke P.

Microbiol Spectr. 2018 Mar;6(2). doi: 10.1128/microbiolspec.RWR-0009-2017. Review.


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

Potts AH, Vakulskas CA, Pannuri A, Yakhnin H, Babitzke P, Romeo T.

Nat Commun. 2017 Nov 17;8(1):1596. doi: 10.1038/s41467-017-01613-1.


Glyoxals as in vivo RNA structural probes of guanine base-pairing.

Mitchell D 3rd, Ritchey LE, Park H, Babitzke P, Assmann SM, Bevilacqua PC.

RNA. 2018 Jan;24(1):114-124. doi: 10.1261/rna.064014.117. Epub 2017 Oct 13.


Circuitry Linking the Global Csr- and σE-Dependent Cell Envelope Stress Response Systems.

Yakhnin H, Aichele R, Ades SE, Romeo T, Babitzke P.

J Bacteriol. 2017 Oct 31;199(23). pii: e00484-17. doi: 10.1128/JB.00484-17. Print 2017 Dec 1.


Translational Repression of the RpoS Antiadapter IraD by CsrA Is Mediated via Translational Coupling to a Short Upstream Open Reading Frame.

Park H, McGibbon LC, Potts AH, Yakhnin H, Romeo T, Babitzke P.

MBio. 2017 Aug 29;8(4). pii: e01355-17. doi: 10.1128/mBio.01355-17.


Modular Organization of the NusA- and NusG-Stimulated RNA Polymerase Pause Signal That Participates in the Bacillus subtilis trp Operon Attenuation Mechanism.

Mondal S, Yakhnin AV, Babitzke P.

J Bacteriol. 2017 Jun 27;199(14). pii: e00223-17. doi: 10.1128/JB.00223-17. Print 2017 Jul 15.


Noncanonical Translation Initiation Comes of Age.

Babitzke P, O'Connor M.

J Bacteriol. 2017 Jun 27;199(14). pii: e00295-17. doi: 10.1128/JB.00295-17. Print 2017 Jul 15.


Eliminating blurry bands in gels with a simple cost-effective repair to the gel cassette.

Bingaman JL, Frankel EA, Hull CM, Leamy KA, Messina KJ, Mitchell D 3rd, Park H, Ritchey LE, Babitzke P, Bevilacqua PC.

RNA. 2016 Dec;22(12):1929-1930. Epub 2016 Oct 19.


NusA-dependent transcription termination prevents misregulation of global gene expression.

Mondal S, Yakhnin AV, Sebastian A, Albert I, Babitzke P.

Nat Microbiol. 2016 Jan 11;1:15007. doi: 10.1038/nmicrobiol.2015.7.


Circuitry Linking the Catabolite Repression and Csr Global Regulatory Systems of Escherichia coli.

Pannuri A, Vakulskas CA, Zere T, McGibbon LC, Edwards AN, Georgellis D, Babitzke P, Romeo T.

J Bacteriol. 2016 Oct 7;198(21):3000-3015. Print 2016 Nov 1.


FliW antagonizes CsrA RNA binding by a noncompetitive allosteric mechanism.

Mukherjee S, Oshiro RT, Yakhnin H, Babitzke P, Kearns DB.

Proc Natl Acad Sci U S A. 2016 Aug 30;113(35):9870-5. doi: 10.1073/pnas.1602455113. Epub 2016 Aug 11.


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

Vakulskas CA, Leng Y, Abe H, Amaki T, Okayama A, Babitzke P, Suzuki K, Romeo T.

Nucleic Acids Res. 2016 Sep 19;44(16):7896-910. doi: 10.1093/nar/gkw484. Epub 2016 May 27.


Toxin MqsR cleaves single-stranded mRNA with various 5' ends.

Chowdhury N, Kwan BW, McGibbon LC, Babitzke P, Wood TK.

Microbiologyopen. 2016 Jun;5(3):370-7. doi: 10.1002/mbo3.335. Epub 2016 Feb 5.


NusG Is a Sequence-specific RNA Polymerase Pause Factor That Binds to the Non-template DNA within the Paused Transcription Bubble.

Yakhnin AV, Murakami KS, Babitzke P.

J Biol Chem. 2016 Mar 4;291(10):5299-308. doi: 10.1074/jbc.M115.704189. Epub 2016 Jan 7.


Regulation of CsrB/C sRNA decay by EIIA(Glc) of the phosphoenolpyruvate: carbohydrate phosphotransferase system.

Leng Y, Vakulskas CA, Zere TR, Pickering BS, Watnick PI, Babitzke P, Romeo T.

Mol Microbiol. 2016 Feb;99(4):627-39. doi: 10.1111/mmi.13259. Epub 2015 Nov 17.


CsrA Participates in a PNPase Autoregulatory Mechanism by Selectively Repressing Translation of pnp Transcripts That Have Been Previously Processed by RNase III and PNPase.

Park H, Yakhnin H, Connolly M, Romeo T, Babitzke P.

J Bacteriol. 2015 Dec;197(24):3751-9. doi: 10.1128/JB.00721-15. Epub 2015 Oct 5.


Ribosomal protein L10(L12)4 autoregulates expression of the Bacillus subtilis rplJL operon by a transcription attenuation mechanism.

Yakhnin H, Yakhnin AV, Babitzke P.

Nucleic Acids Res. 2015 Aug 18;43(14):7032-43. doi: 10.1093/nar/gkv628. Epub 2015 Jun 22.


csrR, a Paralog and Direct Target of CsrA, Promotes Legionella pneumophila Resilience in Water.

Abbott ZD, Yakhnin H, Babitzke P, Swanson MS.

MBio. 2015 Jun 9;6(3):e00595. doi: 10.1128/mBio.00595-15.


Regulation of bacterial virulence by Csr (Rsm) systems.

Vakulskas CA, Potts AH, Babitzke P, Ahmer BM, Romeo T.

Microbiol Mol Biol Rev. 2015 Jun;79(2):193-224. doi: 10.1128/MMBR.00052-14. Review.


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

Vakulskas CA, Pannuri A, Cortés-Selva D, Zere TR, Ahmer BM, Babitzke P, Romeo T.

Mol Microbiol. 2014 Jun;92(5):945-58. doi: 10.1111/mmi.12606. Epub 2014 Apr 24.


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

Yakhnin AV, Babitzke P.

Curr Opin Microbiol. 2014 Apr;18:68-71. doi: 10.1016/j.mib.2014.02.005. Epub 2014 Mar 12. Review.


CsrA activates flhDC expression by protecting flhDC mRNA from RNase E-mediated cleavage.

Yakhnin AV, Baker CS, Vakulskas CA, Yakhnin H, Berezin I, Romeo T, Babitzke P.

Mol Microbiol. 2013 Feb;87(4):851-66. doi: 10.1111/mmi.12136. Epub 2013 Jan 11.


Dual posttranscriptional regulation via a cofactor-responsive mRNA leader.

Patterson-Fortin LM, Vakulskas CA, Yakhnin H, Babitzke P, Romeo T.

J Mol Biol. 2013 Oct 9;425(19):3662-77. doi: 10.1016/j.jmb.2012.12.010. Epub 2012 Dec 28.


FliW and FliS function independently to control cytoplasmic flagellin levels in Bacillus subtilis.

Mukherjee S, Babitzke P, Kearns DB.

J Bacteriol. 2013 Jan;195(2):297-306. doi: 10.1128/JB.01654-12. Epub 2012 Nov 9.


Gel mobility shift assays to detect protein-RNA interactions.

Yakhnin AV, Yakhnin H, Babitzke P.

Methods Mol Biol. 2012;905:201-11. doi: 10.1007/978-1-61779-949-5_12.


Post-transcriptional regulation on a global scale: form and function of Csr/Rsm systems.

Romeo T, Vakulskas CA, Babitzke P.

Environ Microbiol. 2013 Feb;15(2):313-24. doi: 10.1111/j.1462-2920.2012.02794.x. Epub 2012 Jun 5. Review.


Translational repression of NhaR, a novel pathway for multi-tier regulation of biofilm circuitry by CsrA.

Pannuri A, Yakhnin H, Vakulskas CA, Edwards AN, Babitzke P, Romeo T.

J Bacteriol. 2012 Jan;194(1):79-89. doi: 10.1128/JB.06209-11. Epub 2011 Oct 28.


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.

Yakhnin H, Baker CS, Berezin I, Evangelista MA, Rassin A, Romeo T, Babitzke P.

J Bacteriol. 2011 Nov;193(22):6162-70. doi: 10.1128/JB.05975-11. Epub 2011 Sep 9.


CsrA-FliW interaction governs flagellin homeostasis and a checkpoint on flagellar morphogenesis in Bacillus subtilis.

Mukherjee S, Yakhnin H, Kysela D, Sokoloski J, Babitzke P, Kearns DB.

Mol Microbiol. 2011 Oct;82(2):447-61. doi: 10.1111/j.1365-2958.2011.07822.x. Epub 2011 Sep 19.


Complex regulation of the global regulatory gene csrA: CsrA-mediated translational repression, transcription from five promoters by Eσ⁷⁰ and Eσ(S), and indirect transcriptional activation by CsrA.

Yakhnin H, Yakhnin AV, Baker CS, Sineva E, Berezin I, Romeo T, Babitzke P.

Mol Microbiol. 2011 Aug;81(3):689-704. doi: 10.1111/j.1365-2958.2011.07723.x. Epub 2011 Jun 23.


Integration of a complex regulatory cascade involving the SirA/BarA and Csr global regulatory systems that controls expression of the Salmonella SPI-1 and SPI-2 virulence regulons through HilD.

Martínez LC, Yakhnin H, Camacho MI, Georgellis D, Babitzke P, Puente JL, Bustamante VH.

Mol Microbiol. 2011 Jun;80(6):1637-56. doi: 10.1111/j.1365-2958.2011.07674.x. Epub 2011 May 12.


Circuitry linking the Csr and stringent response global regulatory systems.

Edwards AN, Patterson-Fortin LM, Vakulskas CA, Mercante JW, Potrykus K, Vinella D, Camacho MI, Fields JA, Thompson SA, Georgellis D, Cashel M, Babitzke P, Romeo T.

Mol Microbiol. 2011 Jun;80(6):1561-80. doi: 10.1111/j.1365-2958.2011.07663.x. Epub 2011 May 5.


A genome-wide analysis of small regulatory RNAs in the human pathogen group A Streptococcus.

Perez N, Treviño J, Liu Z, Ho SC, Babitzke P, Sumby P.

PLoS One. 2009 Nov 2;4(11):e7668. doi: 10.1371/journal.pone.0007668.


Molecular geometry of CsrA (RsmA) binding to RNA and its implications for regulated expression.

Mercante J, Edwards AN, Dubey AK, Babitzke P, Romeo T.

J Mol Biol. 2009 Sep 18;392(2):511-28. doi: 10.1016/j.jmb.2009.07.034. Epub 2009 Jul 17.


Regulation of translation initiation by RNA binding proteins.

Babitzke P, Baker CS, Romeo T.

Annu Rev Microbiol. 2009;63:27-44. doi: 10.1146/annurev.micro.091208.073514. Review.


Molecular basis of TRAP-5'SL RNA interaction in the Bacillus subtilis trp operon transcription attenuation mechanism.

McGraw AP, Mokdad A, Major F, Bevilacqua PC, Babitzke P.

RNA. 2009 Jan;15(1):55-66. doi: 10.1261/rna.1314409. Epub 2008 Nov 25.


Function of the Bacillus subtilis transcription elongation factor NusG in hairpin-dependent RNA polymerase pausing in the trp leader.

Yakhnin AV, Yakhnin H, Babitzke P.

Proc Natl Acad Sci U S A. 2008 Oct 21;105(42):16131-6. doi: 10.1073/pnas.0808842105. Epub 2008 Oct 13.


Mechanism of hcnA mRNA recognition in the Gac/Rsm signal transduction pathway of Pseudomonas fluorescens.

Lapouge K, Sineva E, Lindell M, Starke K, Baker CS, Babitzke P, Haas D.

Mol Microbiol. 2007 Oct;66(2):341-56. Epub 2007 Sep 10.


CsrA of Bacillus subtilis regulates translation initiation of the gene encoding the flagellin protein (hag) by blocking ribosome binding.

Yakhnin H, Pandit P, Petty TJ, Baker CS, Romeo T, Babitzke P.

Mol Microbiol. 2007 Jun;64(6):1605-20.


CsrA inhibits translation initiation of Escherichia coli hfq by binding to a single site overlapping the Shine-Dalgarno sequence.

Baker CS, Eöry LA, Yakhnin H, Mercante J, Romeo T, Babitzke P.

J Bacteriol. 2007 Aug;189(15):5472-81. Epub 2007 May 25.


CsrB sRNA family: sequestration of RNA-binding regulatory proteins.

Babitzke P, Romeo T.

Curr Opin Microbiol. 2007 Apr;10(2):156-63. Epub 2007 Mar 23. Review.


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