--Posttranscriptional control of bacterial gene expression--
All organisms must regulate the expression of their genes temporally, quantitatively, functionally, and oftentimes, spatially. Additionally, these regulatory processes must be responsive to a wide variety of chemical and physical cues. Exploration of the full range of regulatory possibilities and the biochemical mechanisms that they utilize will reveal the interconnectedness of metabolic pathways and elucidate life’s underlying genetic circuitry. Regulation of gene expression can occur through an alteration in any one of the steps that occur along the information processing pathways. Although control of transcription initiation is presumed to be the predominate mode of gene expression control, there is a growing appreciation for posttranscriptional regulatory mechanisms. Our laboratory is interested in the genetic and biochemical characterization of these regulatory strategies, as well as the discovery of novel regulatory mechanisms. We are using this data to develop biological engineering techniques that will be used for a variety of biomedical applications, including the development of novel drugs.
--Biology of riboswitch RNAs: molecular mechanisms and biological distribution--
Recent data indicate that, in bacteria, posttranscriptional regulatory strategies often employ specific RNA structures termed riboswitches, which are embedded within the 5’ untranslated region of mRNAs. These RNA sequences fold into specific three-dimensional shapes that act as molecular receptors for certain intracellular metabolites. Upon binding of the metabolite there is a change in conformation that ultimately results in a change in gene expression. Switching between conformations can influence mRNA stability, efficiency of translation initiation, or in some cases, the processivity of RNA polymerase. Riboswitches are widespread throughout biology and are utilized for genetic control over many fundamental genes. For these and other reasons, we are interested in exploring the biochemistry, biological distribution, and biomedical applications of riboswitch RNAs. We are particularly interested in a riboswitch that harnesses the self-cleavage ability of a ribozyme in order to regulate expression of a bacterial gene, glmS. We are working to uncover the molecular details for the novel mechanism by which this cleavage event results in a change in gene expression. We are also particularly interested in metalloregulatory RNAs that control gene expression in response to fluctuations in intracellular ion concentrations.
--Diverse roles for RNAs in biology--
When considering the assorted range of functions accomplished by RNAs in biology one has to consider more than just cis-acting RNA structures like riboswitches. RNAs are also involved in modification of other nucleic acids, as unstructured regulatory oligonucleotides, and as structured trans-acting regulatory RNAs. And this partial list may be just the beginning. Several billion years ago, organisms with surprisingly complex metabolisms were likely to have relied upon specific classes of RNAs for all of their genomic and catalytic requirements. Therefore, given the extensive precedence for present or past roles of RNA polymers, there is no reason not to expect that modern organisms are replete with biological RNAs enacting functions other than that of the ’passive mRNA’ transcript. Our lab is interested in discovering just how often, and in what capacity, these interesting and important RNA sequences are utilized inside a given cell.
RESEARCH INTERESTS
RNA biology
Biochemistry of gene regulation
RNA structure and function
Posttranscriptional genetic control
Microbial metabolism
RECENT PUBLICATIONS
Wickiser JK, Winkler WC, Breaker RR, and Crothers DM, "The speed of RNA transcription and metabolite binding kinetics operate an FMN riboswitch" Molecular Cell, 18(1):49-60, 2005
Winkler WC and Breaker RR, "Regulation of bacterial gene expression by riboswitches" Annual Review in Microbiology, 59:487-517, 2005
Irnov, Kertsburg A, and Winkler WC, "Genetic control by cis-acting regulatory RNAs in Bacillus subtilis: general principles and prospects for discovery" Cold Spring Harbor Symposium Quantitative Biology, 71:239-249, 2006
Roth A, Winkler WC, Regulski EE, Lee BW, Lim J, Jona I, Barrick JE, Ritwik A, Kim JN, Welz R, Iwata-Reuyl D, and Breaker RR, "A riboswitch selective for the queuosine precursor preQ1 contains an unusually small aptamer domain" Nature Structure and Molecular Biology, 14 (4):308-317, 2007
Dann CE, Wakeman CA, Sieling CE, Baker SC, Irnov I, and Winkler WC, "Structure and mechanism of a metal-sensing regulatory RNA" Cell, 130:878-892, 2007
SIGNIFICANT PUBLICATIONS
Winkler WC, Nahvi A, Roth A, Collins JA, Breaker RR, "Control of bacterial gene expression by a natural metabolite-responsive ribozyme" Nature, 428:281-286, 2004
Winkler WC, Cohen-Chalamish S, Breaker RR, "An mRNA structure that controls gene expression by binding FMN" Proceedings of the National Academy of Sciences, United States of America, 99:15908-15913, 2002
Winkler W, Nahvi A, Breaker RR, "Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression" Nature, 419:952-956, 2002
Grundy FJ, Winkler WC, Henkin TM, "tRNA-mediated transcription antitermination in vitro: Codon-anticodon pairing independent of the ribosome" Proceedings of the National Academy of Sciences, United States of America, 99:11121-11126, 2002
Dann CE, Wakeman CA, Sieling CE, Baker SC, Irnov I, and Winkler WC, "Structure and mechanism of a metal-sensing regulatory RNA" Cell, 130:878-892, 2007
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