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Items: 46

1.

A dedicated diribonucleotidase resolves a key bottleneck for the terminal step of RNA degradation.

Kim SK, Lormand JD, Weiss CA, Eger KA, Turdiev H, Turdiev A, Winkler WC, Sondermann H, Lee VT.

Elife. 2019 Jun 21;8. pii: e46313. doi: 10.7554/eLife.46313.

2.

Single cell microscopy reveals that levels of cyclic di-GMP vary among Bacillus subtilis subpopulations.

Weiss CA, Hoberg JA, Liu K, Tu BP, Winkler WC.

J Bacteriol. 2019 May 28. pii: JB.00247-19. doi: 10.1128/JB.00247-19. [Epub ahead of print]

PMID:
31138629
3.

Ethanolamine Utilization and Bacterial Microcompartment Formation Are Subject to Carbon Catabolite Repression.

Kaval KG, Gebbie M, Goodson JR, Cruz MR, Winkler WC, Garsin DA.

J Bacteriol. 2019 Apr 24;201(10). pii: e00703-18. doi: 10.1128/JB.00703-18. Print 2019 May 15.

PMID:
30833356
4.

A Subset of Exoribonucleases Serve as Degradative Enzymes for pGpG in c-di-GMP Signaling.

Orr MW, Weiss CA, Severin GB, Turdiev H, Kim SK, Turdiev A, Liu K, Tu BP, Waters CM, Winkler WC, Lee VT.

J Bacteriol. 2018 Nov 26;200(24). pii: e00300-18. doi: 10.1128/JB.00300-18. Print 2018 Dec 15.

5.

Processive Antitermination.

Goodson JR, Winkler WC.

Microbiol Spectr. 2018 Sep;6(5). doi: 10.1128/microbiolspec.RWR-0031-2018. Review.

PMID:
30191803
6.

Loss of Ethanolamine Utilization in Enterococcus faecalis Increases Gastrointestinal Tract Colonization.

Kaval KG, Singh KV, Cruz MR, DebRoy S, Winkler WC, Murray BE, Garsin DA.

MBio. 2018 May 8;9(3). pii: e00790-18. doi: 10.1128/mBio.00790-18.

7.

LoaP is a broadly conserved antiterminator protein that regulates antibiotic gene clusters in Bacillus amyloliquefaciens.

Goodson JR, Klupt S, Zhang C, Straight P, Winkler WC.

Nat Microbiol. 2017 Feb 13;2:17003. doi: 10.1038/nmicrobiol.2017.3.

8.

Bacterial riboswitches cooperatively bind Ni(2+) or Co(2+) ions and control expression of heavy metal transporters.

Furukawa K, Ramesh A, Zhou Z, Weinberg Z, Vallery T, Winkler WC, Breaker RR.

Mol Cell. 2015 Mar 19;57(6):1088-1098. doi: 10.1016/j.molcel.2015.02.009.

9.

Riboswitches. A riboswitch-containing sRNA controls gene expression by sequestration of a response regulator.

DebRoy S, Gebbie M, Ramesh A, Goodson JR, Cruz MR, van Hoof A, Winkler WC, Garsin DA.

Science. 2014 Aug 22;345(6199):937-40. doi: 10.1126/science.1255091.

10.

Transport of magnesium by a bacterial Nramp-related gene.

Shin JH, Wakeman CA, Goodson JR, Rodionov DA, Freedman BG, Senger RS, Winkler WC.

PLoS Genet. 2014 Jun 26;10(6):e1004429. doi: 10.1371/journal.pgen.1004429. eCollection 2014 Jun.

11.

Metabolite-binding ribozymes.

Ramesh A, Winkler WC.

Biochim Biophys Acta. 2014 Oct;1839(10):989-994. doi: 10.1016/j.bbagrm.2014.04.015. Epub 2014 Apr 24. Review.

PMID:
24769284
12.

Assessment of the requirements for magnesium transporters in Bacillus subtilis.

Wakeman CA, Goodson JR, Zacharia VM, Winkler WC.

J Bacteriol. 2014 Mar;196(6):1206-14. doi: 10.1128/JB.01238-13. Epub 2014 Jan 10.

13.

Association of RNAs with Bacillus subtilis Hfq.

Dambach M, Irnov I, Winkler WC.

PLoS One. 2013;8(2):e55156. doi: 10.1371/journal.pone.0055156. Epub 2013 Feb 15.

14.

The mechanism for RNA recognition by ANTAR regulators of gene expression.

Ramesh A, DebRoy S, Goodson JR, Fox KA, Faz H, Garsin DA, Winkler WC.

PLoS Genet. 2012;8(6):e1002666. doi: 10.1371/journal.pgen.1002666. Epub 2012 Jun 7.

15.

Mechanism and distribution of glmS ribozymes.

McCown PJ, Winkler WC, Breaker RR.

Methods Mol Biol. 2012;848:113-29. doi: 10.1007/978-1-61779-545-9_8.

16.

The roles of metal ions in regulation by riboswitches.

Ferré-D'Amaré AR, Winkler WC.

Met Ions Life Sci. 2011;9:141-73. Review.

17.

Insights into metalloregulation by M-box riboswitch RNAs via structural analysis of manganese-bound complexes.

Ramesh A, Wakeman CA, Winkler WC.

J Mol Biol. 2011 Apr 8;407(4):556-70. doi: 10.1016/j.jmb.2011.01.049. Epub 2011 Feb 15.

18.

Identification of regulatory RNAs in Bacillus subtilis.

Irnov I, Sharma CM, Vogel J, Winkler WC.

Nucleic Acids Res. 2010 Oct;38(19):6637-51. doi: 10.1093/nar/gkq454. Epub 2010 Jun 4.

19.

A regulatory RNA required for antitermination of biofilm and capsular polysaccharide operons in Bacillales.

Irnov I, Winkler WC.

Mol Microbiol. 2010 May;76(3):559-75. doi: 10.1111/j.1365-2958.2010.07131.x. Epub 2010 Mar 31.

20.

Magnesium-sensing riboswitches in bacteria.

Ramesh A, Winkler WC.

RNA Biol. 2010 Jan-Feb;7(1):77-83. Epub 2010 Jan 1.

PMID:
20023416
21.

Multiple metal-binding cores are required for metalloregulation by M-box riboswitch RNAs.

Wakeman CA, Ramesh A, Winkler WC.

J Mol Biol. 2009 Sep 25;392(3):723-35. doi: 10.1016/j.jmb.2009.07.033. Epub 2009 Jul 17.

22.

Analysis of the RNA backbone: structural analysis of riboswitches by in-line probing and selective 2'-hydroxyl acylation and primer extension.

Wakeman CA, Winkler WC.

Methods Mol Biol. 2009;540:173-91. doi: 10.1007/978-1-59745-558-9_13.

PMID:
19381560
23.

Methods for analysis of ligand-induced RNA conformational changes.

Brautigam CA, Wakeman CA, Winkler WC.

Methods Mol Biol. 2009;540:77-95. doi: 10.1007/978-1-59745-558-9_7.

PMID:
19381554
24.

Structural probing techniques on natural aptamers.

Wakeman CA, Winkler WC.

Methods Mol Biol. 2009;535:115-33. doi: 10.1007/978-1-59745-557-2_8.

PMID:
19377977
25.

Expanding roles for metabolite-sensing regulatory RNAs.

Dambach MD, Winkler WC.

Curr Opin Microbiol. 2009 Apr;12(2):161-9. doi: 10.1016/j.mib.2009.01.012. Epub 2009 Feb 26. Review.

26.

Multiple posttranscriptional regulatory mechanisms partner to control ethanolamine utilization in Enterococcus faecalis.

Fox KA, Ramesh A, Stearns JE, Bourgogne A, Reyes-Jara A, Winkler WC, Garsin DA.

Proc Natl Acad Sci U S A. 2009 Mar 17;106(11):4435-40. doi: 10.1073/pnas.0812194106. Epub 2009 Feb 25.

27.

Mechanism of mRNA destabilization by the glmS ribozyme.

Collins JA, Irnov I, Baker S, Winkler WC.

Genes Dev. 2007 Dec 15;21(24):3356-68.

28.

Structure and mechanism of a metal-sensing regulatory RNA.

Dann CE 3rd, Wakeman CA, Sieling CL, Baker SC, Irnov I, Winkler WC.

Cell. 2007 Sep 7;130(5):878-92.

29.

Structural features of metabolite-sensing riboswitches.

Wakeman CA, Winkler WC, Dann CE 3rd.

Trends Biochem Sci. 2007 Sep;32(9):415-24. Epub 2007 Aug 30. Review.

30.

A riboswitch selective for the queuosine precursor preQ1 contains an unusually small aptamer domain.

Roth A, Winkler WC, Regulski EE, Lee BW, Lim J, Jona I, Barrick JE, Ritwik A, Kim JN, Welz R, Iwata-Reuyl D, Breaker RR.

Nat Struct Mol Biol. 2007 Apr;14(4):308-17. Epub 2007 Mar 25.

PMID:
17384645
31.

Genetic control by cis-acting regulatory RNAs in Bacillus subtilis: general principles and prospects for discovery.

Irnov, Kertsburg A, Winkler WC.

Cold Spring Harb Symp Quant Biol. 2006;71:239-49. Review.

PMID:
17381303
32.

RNA allostery glimpsed.

Winkler WC, Dann CE 3rd.

Nat Struct Mol Biol. 2006 Jul;13(7):569-71. No abstract available.

PMID:
16826230
33.

Molecular-recognition characteristics of SAM-binding riboswitches.

Lim J, Winkler WC, Nakamura S, Scott V, Breaker RR.

Angew Chem Int Ed Engl. 2006 Jan 30;45(6):964-8. No abstract available.

PMID:
16381055
34.

Riboswitches and the role of noncoding RNAs in bacterial metabolic control.

Winkler WC.

Curr Opin Chem Biol. 2005 Dec;9(6):594-602. Epub 2005 Oct 13. Review.

PMID:
16226486
35.

Regulation of bacterial gene expression by riboswitches.

Winkler WC, Breaker RR.

Annu Rev Microbiol. 2005;59:487-517. Review.

PMID:
16153177
36.

The speed of RNA transcription and metabolite binding kinetics operate an FMN riboswitch.

Wickiser JK, Winkler WC, Breaker RR, Crothers DM.

Mol Cell. 2005 Apr 1;18(1):49-60.

37.

Metabolic monitoring by bacterial mRNAs.

Winkler WC.

Arch Microbiol. 2005 Mar;183(3):151-9. Epub 2005 Mar 5. Review.

PMID:
15750802
38.

New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control.

Barrick JE, Corbino KA, Winkler WC, Nahvi A, Mandal M, Collins J, Lee M, Roth A, Sudarsan N, Jona I, Wickiser JK, Breaker RR.

Proc Natl Acad Sci U S A. 2004 Apr 27;101(17):6421-6. Epub 2004 Apr 19.

39.

Control of gene expression by a natural metabolite-responsive ribozyme.

Winkler WC, Nahvi A, Roth A, Collins JA, Breaker RR.

Nature. 2004 Mar 18;428(6980):281-6.

PMID:
15029187
40.

Genetic control by metabolite-binding riboswitches.

Winkler WC, Breaker RR.

Chembiochem. 2003 Oct 6;4(10):1024-32. Review. No abstract available.

PMID:
14523920
41.

An mRNA structure that controls gene expression by binding S-adenosylmethionine.

Winkler WC, Nahvi A, Sudarsan N, Barrick JE, Breaker RR.

Nat Struct Biol. 2003 Sep;10(9):701-7. Epub 2003 Aug 10.

PMID:
12910260
42.

Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria.

Mandal M, Boese B, Barrick JE, Winkler WC, Breaker RR.

Cell. 2003 May 30;113(5):577-86.

43.

An mRNA structure that controls gene expression by binding FMN.

Winkler WC, Cohen-Chalamish S, Breaker RR.

Proc Natl Acad Sci U S A. 2002 Dec 10;99(25):15908-13. Epub 2002 Nov 27.

44.

tRNA-mediated transcription antitermination in vitro: codon-anticodon pairing independent of the ribosome.

Grundy FJ, Winkler WC, Henkin TM.

Proc Natl Acad Sci U S A. 2002 Aug 20;99(17):11121-6. Epub 2002 Aug 6.

45.
46.

Nonsteric factors dominate binding of nitric oxide, azide, imidazole, cyanide, and fluoride to the rhizobial heme-based oxygen sensor FixL.

Winkler WC, Gonzalez G, Wittenberg JB, Hille R, Dakappagari N, Jacob A, Gonzalez LA, Gilles-Gonzalez MA.

Chem Biol. 1996 Oct;3(10):841-50.

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