The enzymatic cleavage of double-stranded RNA is an essential step in the maturation and degradation of diverse eukaryotic and prokaryotic RNAs, and is a key event in RNA interference (RNAi) and related gene silencing and genome maintenance mechanisms. dsRNA cleavage is catalyzed by members of the ribonuclease III (RNase III) family of endoribonucleases, which are highly conserved in bacterial and eukaryotic cells. Eukaryotic RNase III orthologs include Dicer and Drosha, which carry out the maturation of microRNAs and other gene-regulatory RNAs. RNase III also is a component of RNA editosomes in trypanosome mitochondria. dsRNA processing by bacterial ribonucleases III regulates cellular and phage gene expression, plasmid replication, antibiotic production, and virulence factor expression. Bacterial RNase substrates are cleaved in a highly site-specific manner, which is required for proper half-life or optimal function of the RNAs. There also is evidence that bacterial RNase III can regulate gene expression by binding RNA in a non-catalytic mode. The long-term objective of this project is to characterize the RNA sequence and structural elements and RNA-protein interactions that confer specificity in RNase III substrate recognition and cleavage.
Specific Aim 1 will employ in vitro selection, nucleotide analog interference mapping and site-directed mutagenesis to identify substrate functional groups essential for recognition.
Specific Aim 2 will characterize protein functional group contributions to substrate specificity and binding energy. Site-directed mutagenesis and polypeptide segment exchange experiments will identify RNase III domains involved in specificity of binding.
Specific Aim 3 will define the sequence and structural features of catalytic antideterminants in two specific RNAs. In vitro selection, site-directed mutagenesis, and RNA structure-probing will be used to determine the critical structural and functional features of an in vitro-selected, binding-competent RNA, and the lambda phage cIII mRNA 5'-leader. The mechanism of RNase III activation will be analyzed using an in vitro translation system. Along with Escherichia coli RNase III, this project will employ Aquifex aeolicus RNase III and Thermotoga maritima RNase III, for which structural data is available. These analyses will serve to define how specificity is achieved in dsRNA processing by RNase III, and ultimately determine the role of dsRNA processing in the cellular defense mechanisms, including RNAi and in specific disease states, including cancer and infectious diseases. ? ? ?

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
2R01GM056772-06A2
Application #
7322254
Study Section
Macromolecular Structure and Function C Study Section (MSFC)
Program Officer
Jones, Warren
Project Start
1999-05-01
Project End
2011-07-31
Budget Start
2007-09-10
Budget End
2008-07-31
Support Year
6
Fiscal Year
2007
Total Cost
$270,204
Indirect Cost
Name
Temple University
Department
Biology
Type
Schools of Arts and Sciences
DUNS #
057123192
City
Philadelphia
State
PA
Country
United States
Zip Code
19122
Gone, Swapna; Alfonso-Prieto, Mercedes; Paudyal, Samridhdi et al. (2016) Mechanism of Ribonuclease III Catalytic Regulation by Serine Phosphorylation. Sci Rep 6:25448
Paudyal, Samridhdi; Alfonso-Prieto, Mercedes; Carnevale, Vincenzo et al. (2015) Combined computational and experimental analysis of a complex of ribonuclease III and the regulatory macrodomain protein, YmdB. Proteins 83:459-72
Nicholson, Allen W (2014) Ribonuclease III mechanisms of double-stranded RNA cleavage. Wiley Interdiscip Rev RNA 5:31-48
Redhu, Shiv K; Castronovo, Matteo; Nicholson, Allen W (2013) Digital imprinting of RNA recognition and processing on a self-assembled nucleic acid matrix. Sci Rep 3:2550
Castronovo, M; Stopar, A; Coral, L et al. (2013) Effects of nanoscale confinement on the functionality of nucleic acids: implications for nanomedicine. Curr Med Chem 20:3539-57
Alla, Nageswara R; Nicholson, Allen W (2012) Evidence for a dual functional role of a conserved histidine in RNA·DNA heteroduplex cleavage by human RNase H1. FEBS J 279:4492-500
Gone, Swapna; Nicholson, Allen W (2012) Bacteriophage T7 protein kinase: Site of inhibitory autophosphorylation, and use of dephosphorylated enzyme for efficient modification of protein in vitro. Protein Expr Purif 85:218-23
Shi, Zhongjie; Nicholson, Rhonda H; Jaggi, Ritu et al. (2011) Characterization of Aquifex aeolicus ribonuclease III and the reactivity epitopes of its pre-ribosomal RNA substrates. Nucleic Acids Res 39:2756-68
Nathania, Lilian; Nicholson, Allen W (2010) Thermotoga maritima ribonuclease III. Characterization of thermostable biochemical behavior and analysis of conserved base pairs that function as reactivity epitopes for the Thermotoga 23S rRNA precursor. Biochemistry 49:7164-78
Pertzev, Alexandre V; Nicholson, Allen W (2006) Characterization of RNA sequence determinants and antideterminants of processing reactivity for a minimal substrate of Escherichia coli ribonuclease III. Nucleic Acids Res 34:3708-21

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