Academic literature on the topic 'Ribonuclease III'
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Journal articles on the topic "Ribonuclease III"
Lorenc-Kubis, Irena, and Bronisława Morawiecka. "Preliminary studies on ribonucleases from Poa pratensis seeds." Acta Societatis Botanicorum Poloniae 43, no. 4 (2015): 471–78. http://dx.doi.org/10.5586/asbp.1974.044.
Full textMacRae, Ian J., and Jennifer A. Doudna. "Ribonuclease revisited: structural insights into ribonuclease III family enzymes." Current Opinion in Structural Biology 17, no. 1 (February 2007): 138–45. http://dx.doi.org/10.1016/j.sbi.2006.12.002.
Full textConrad, Christian, and Reinhard Rauhut. "Ribonuclease III: new sense from nuisance." International Journal of Biochemistry & Cell Biology 34, no. 2 (February 2002): 116–29. http://dx.doi.org/10.1016/s1357-2725(01)00112-1.
Full textWu, Chang-Xian, Xian-Jin Xu, Ke Zheng, Fang Liu, Xu-Dong Yang, Chuang-Fu Chen, Huan-Chun Chen, and Zheng-Fei Liu. "Characterization of ribonuclease III from Brucella." Gene 579, no. 2 (April 2016): 183–92. http://dx.doi.org/10.1016/j.gene.2015.12.068.
Full textJi, Xinhua. "Ruler-based mechanisms of ribonuclease III enzymes." Acta Crystallographica Section A Foundations and Advances 73, a1 (May 26, 2017): a5. http://dx.doi.org/10.1107/s0108767317099949.
Full textChelladurai, Bhadrani, Honglin Li, Kejing Zhang, and Allen W. Nicholson. "Mutational analysis of a ribonuclease III processing signal." Biochemistry 32, no. 29 (July 1993): 7549–58. http://dx.doi.org/10.1021/bi00080a029.
Full textFranch, Thomas, Thomas Thisted, and Kenn Gerdes. "Ribonuclease III Processing of Coaxially Stacked RNA Helices." Journal of Biological Chemistry 274, no. 37 (September 10, 1999): 26572–78. http://dx.doi.org/10.1074/jbc.274.37.26572.
Full textNicholson, Allen W. "Ribonuclease III mechanisms of double-stranded RNA cleavage." Wiley Interdisciplinary Reviews: RNA 5, no. 1 (September 30, 2013): 31–48. http://dx.doi.org/10.1002/wrna.1195.
Full textSchweisguth, David C., Bhadrani S. Chelladurai, Allen W. Nicholson, and Peter B. Moore. "Structural characterization of a ribonuclease III processing signal." Nucleic Acids Research 22, no. 4 (1994): 604–12. http://dx.doi.org/10.1093/nar/22.4.604.
Full textFanning, Ann-Marie, Sally E. Plush, and Thorfinnur Gunnlaugsson. "Tri- and tetra-substituted cyclen based lanthanide(iii) ion complexes as ribonuclease mimics: a study into the effect of log Ka, hydration and hydrophobicity on phosphodiester hydrolysis of the RNA-model 2-hydroxypropyl-4-nitrophenyl phosphate (HPNP)." Organic & Biomolecular Chemistry 13, no. 20 (2015): 5804–16. http://dx.doi.org/10.1039/c4ob02384f.
Full textDissertations / Theses on the topic "Ribonuclease III"
Saramago, Ana Margarida Teixeira. "The Relevance of Ribonuclease III in Pathogenic Bacteria." Doctoral thesis, Universidade Nova de Lisboa. Instituto de Tecnologia Química e Biológica, 2013. http://hdl.handle.net/10362/12027.
Full textRibonucleases (RNases) are key factors in the control of all biological processes, since they modulate the stability of RNA transcripts, allowing rapid changes in gene expression. Some RNases are up-regulated under stress situations and are involved in virulence processes in pathogenic microorganisms. RNases also control the levels of regulatory RNAs, which play very important roles in cell physiology.(...)
Malloch, Richard Anthony. "Ribonuclease III processing of Escherichia coli rpoBC messenger RNA." Thesis, University of Edinburgh, 1990. http://hdl.handle.net/1842/15259.
Full textPedroso, Dora Cristina. "Study of a novel ribonuclease III-like protein (RNR) from Arabidopsis thaliana and development of a ribonuclease III-enhanced antisense gene silencing system." Thesis, King's College London (University of London), 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.732701.
Full textShi, Zhongjie. "Biochemical properties and substrate reactivities of Aquifex Aeolicus Ribonuclease III." Diss., Temple University Libraries, 2012. http://cdm16002.contentdm.oclc.org/cdm/ref/collection/p245801coll10/id/213666.
Full textPh.D.
Ribonuclease III is a highly-conserved bacterial enzyme that cleaves double-stranded (ds) RNA structures, and participates in diverse RNA maturation and decay pathways. Essential insight on the RNase III mechanism of dsRNA cleavage has been provided by crystallographic studies of the enzyme from the hyperthermophilic bacterium, Aquifex aeolicus. However, those crystals involved complexes containing either cleaved RNA, or a mutant RNase III that is catalytically inactive. In addition, neither the biochemical properties of A. aeolicus (Aa)-RNase III, nor the reactivity epitopes of its cognate substrates are known. The goal of this project is to use Aa-RNase III, for which there is atomic-level structural information, to determine how RNase III recognizes its substrates and selects the target site. I first purified recombinant Aa-RNase III and defined the conditions that support its optimal in vitro catalytic activity. The catalytic activity of purified recombinant Aa-RNase III exhibits a temperature optimum of 70-85°C, a pH optimum of 8.0, and with either Mg2+ or Mn2+ supports efficient catalysis. Cognate substrates for Aa-RNase III were identified and their reactivity epitopes were characterized, including the specific bp sequence elements that determine processing reactivity and selectivity. Small RNA hairpins, based on the double-stranded structures associated with the Aquifex 16S and 23S rRNA precursors, are cleaved in vitro at sites that are consistent with production of the immediate precursors to the mature rRNAs. Third, the role of the dsRBD in scissile bond selection was examined by a mutational analysis of the conserved interactions of RNA binding motif 1 (RBM1) with the substrate proximal box (pb). The individual contributions towards substrate recognition were determined for conserved amino acid side chains in the RBM1. It also was shown that the dsRBD plays key dual roles in both binding energy and selectivity, through RBM1 responsiveness to proximal box bp sequence. The dsRBD is specifically responsive to an antideterminant (AD) bp in pb position 2. The relative structural rigidity of both dsRNA and dsRBD rationalizes the strong effect of an inhibitory bp at pb position 2: disruption of one RBM1 side chain interaction can effectively disrupt the other RBM1 side chain interactions. Finally, a cis-acting model was developed for subunit involvement in substrate recognition by RNase III. Structurally asymmetric mutant heterodimers of Escherichia coli (Ec)-RNase III were constructed, and asymmetric substrates were employed to reveal how RNase III can bind and deliver hairpin substrates to the active site cleft in a pathway that requires specific binding configurations of both enzyme and substrate.
Temple University--Theses
Nathania, Lilian. "Biochemical Analysis of Thermotoga maritima Ribonuclease III and its Ribosomal RNA Substrates." Diss., Temple University Libraries, 2011. http://cdm16002.contentdm.oclc.org/cdm/ref/collection/p245801coll10/id/140013.
Full textPh.D.
The site-specific cleavage of double-stranded (ds) RNA is a conserved early step in bacterial ribosomal RNA (rRNA) maturation that is carried out by ribonuclease III. Studies on the RNase III mechanism of dsRNA cleavage have focused mainly on the enzymes from mesophiles such as Escherichia coli. In contrast, little is known of the RNA processing pathways and the functions of associated ribonucleases in the hyperthermophiles. Therefore, structural and biochemical studies of proteins from hyperthermophilic bacteria are providing essential insight on the sources of biomolecular thermostability, and how enzymes function at high temperatures. The biochemical behavior of RNase III of the hyperthermophilic bacterium Thermotoga maritima is analyzed using purified recombinant enzyme and the cognate pre-ribosomal RNAs as substrates. The T. maritima genome encodes a ~5,000 nucleotide (nt) transcript, expressed from the single ribosomal RNA (rRNA) operon. RNase III processing sites are expected to form through base-pairing of complementary sequences that flank the 16S and 23S rRNAs. The Thermotoga pre-16S and pre-23S processing stems are synthesized in the form of small hairpins, and are efficiently and site-specifically cleaved by Tm-RNase III at sites consistent with an in vivo role of the enzyme in producing the immediate precursors to the mature rRNAs. T. maritima (Tm)-RNase III activity is dependent upon divalent metal ion, with Mg^2+ as the preferred species, at concentrations >= 1 mM. Mn^2+, Co^2+ and Ni^2+ also support activity, but with reduced efficiency. The enzyme activity is also supported by salt (Na^+, K^+, or NH4^+) in the 50-80 mM range, with an optimal pH of ~8. Catalytic activity exhibits a broad temperature maximum of ~40-70 deg C, with significant activity retained at 95 deg C. Comparison of the Charged-versus-Polar (C-vP) bias of the protein side chains indicates that Tm-RNase III thermostability is due to large C-vP bias. Analysis of pre-23S substrate variants reveals a dependence of reactivity on the base-pair (bp) sequence in the proximal box (pb), a site of protein contact that functions as a positive determinant of recognition of E. coli (Ec)-RNase III substrates. The pb sequence dependence of reactivity is similar to that observed with the Ec-RNase III pb. Moreover, Tm-RNase III cleaves an Ec-RNase III substrate with identical specificity, and is inhibited by pb antideterminants that also inhibit Ec-Rnase III. These studies reveal the conservation acrosss a broad phylogenetic distance of substrate reactivity epitopes, both the positive and negative determinants, among bacterial RNase III substrates.
Temple University--Theses
Gone, Swapna. "Functional analysis of Ribonuclease III regulation by a viral protein kinase." Diss., Temple University Libraries, 2011. http://cdm16002.contentdm.oclc.org/cdm/ref/collection/p245801coll10/id/159409.
Full textPh.D.
The bacteriophage T7 protein kinase enhances T7 growth under suboptimal growth conditions, including elevated temperature or limiting carbon source. T7PK phosphorylates numerous E. coli proteins, and it has been proposed that phosphorylation of these proteins is responsible for supporting T7 replication under stressful growth conditions. How the phosphorylation of host proteins supports T7 growth is not understood. Escherichia coli (Ec) RNase III is phosphorylated on serine in bacteriophage T7-infected cells. Phosphorylation of Ec-RNase III induces a ~4-fold increase in catalytic activity in vitro. Ec-RNase III is involved in the maturation of several T7 mRNAs, and it has been shown that RNase III processing controls the translational activity and stability of the T7 mRNAs. Perhaps T7PK phosphorylation of Ec- RNase III ensures optimal processing of T7 mRNAs under suboptimal growth conditions. In this study a biochemical analysis was performed on the N-terminal portion of the 0.7 gene (T7PK), exhibiting only the protein kinase activity. In addition to phosphotransferase activity, T7PK also undergoes self-phosphorylation on serine, which down-regulates catalytic activity by an unknown mechanism. Mass spectral analysis revealed that Ser216 is the autophosphorylation site in T7PK. The serine residue is highly conserved, which in turn suggests that autophosphorylation is a conserved reaction with functional importance. Phosphorylated T7PK exhibits reduced phosphotransferase activity, compared to its dephosphorylated counterpart (dT7PK). The dT7PK exhibits enhanced ability to phosphorylate proteins, as well as undergo autophosphorylation. The mechanism by which autophosphorylation inhibits T7PK activity is unknown. An in vitro phosphorylation assay revealed that T7PK directly phosphorylates RNase III. Ec-RNase III processing activity is stimulated from two to ten-fold upon phosphorylation by the T7PK. The primary site of phosphorylation in RNase III is found to be Ser33, and Ser34 may act as the recognition determinant for T7PK. This was established by Ser →Ala mutations at the concerned site. The enhancement of catalytic activity is primarily due to a larger turnover number (kcat), with some additional contribution from a greater substrate binding affinity, as revealed by lower Km and K‟D values. Substrate cleavage assays under single turn over conditions established that the product release is the rate limiting step. Since there is no significant increase in the kcat as measured under single-turnover (enzyme excess) conditions, the increase in the kcat in the steady-state is due to enhancement of the product release step, and not due to an enhancement of the hydrolysis (chemical) step.
Temple University--Theses
Grelier, Gaël. "Dicer, Enzyme clef de l'interférence ARN : études de son intérêt dans les cancers du sein et implication dans la réponse au stress réplicatif." Lyon 1, 2008. http://www.theses.fr/2008LYO10290.
Full textBreast cancers are the first cause of mortality in occidental women population. Breast tumours can show various forms which are frequently resistant to therapeutics and prone to late relapse. Thus, the current clinical challenge consists in refining individual therapeutics management by employing tools provided by the study of molecular basis of mammary tumorigenesis. Besides, chromosomal instability (CIN) is a hallmark of breast cancer and recent data showed that Dicer, a key ribonuclease of the RNA interference mechanism, could be a regulator of chromosomal stability in human cells. We thus hypothesized that alteration of this protein could be associated with mammary tumorigenesis. In order to test this hypothesis, we assessed dicer transcription and expression in breast cancer cell lines and tissues corresponding to different phases of tumor progression. We further investigated the consequences of dicer knock-down on cell cycle and response to replicative stress. Our results show that dicer expression has an independent prognostic value for metastatic relapse prediction and is correlated with hormonal receptors expression. Furthermore, cells harbouring dicer inactivation presented defects in cell cycle and DNA breaks response pathways. Altogether, our data indicate that dicer inactivation could favour CIN during mammary tumorigenesis and this feature could represent a useful tool in breast cancer management
Paudyal, Samridhdi. "FUNCTIONAL ANALYSIS OF THE BACTERIAL MACRODOMAIN PROTEIN YMDB AND ITS INTERACTION WITH RIBONUCLEASE III." Diss., Temple University Libraries, 2014. http://cdm16002.contentdm.oclc.org/cdm/ref/collection/p245801coll10/id/271085.
Full textPh.D.
The Escherichia coli ymdB gene encodes a ~19 kDa protein that binds ADP-ribose (ADPR) and metabolites related to NAD+. As such, it has been termed a macrodomain protein, referring to a conserved fold that binds ADPR. YmdB can catalyze the hydrolysis of O-acetyl-ADP-ribose (OAADPR), forming acetate and ADPR. OAADPR is a product of sirtuin action on lysine-acetylated proteins, which involves NAD+ as a cosubstrate. There is evidence that YmdB interacts with other proteins, including the conserved enzyme, ribonuclease III. Ribonuclease III (RNase III) is a double-strand(ds)-specific enzyme that processes diverse RNA precursors in bacterial cells to form the mature, functional forms that participate in protein synthesis and gene regulation. RNase III is involved in the maturation, turnover, and action of small noncoding RNAs (sRNAs), which play key roles in regulating bacterial gene expression in response to environmental inputs and changes in growth conditions. A mass-spectroscopy-based analysis of the E. coli proteome has shown that YmdB and RNase III interact in vivo. However, the functional importance of this interaction is not known. There is preliminary evidence that YmdB regulates RNase III activity during specific stress inputs. Thus, during cellular entry into stationary phase (nutrient limitation), or during the cold shock response, YmdB levels increase, which is correlated with a downregulation of RNase III activity. Inhibition of RNase III may alter the maturation and turnover of sRNAs, as well as other RNAs, during the adaptive response to stress. However, it is unclear whether the inhibition is a direct or indirect effect of YmdB on RNase III activity. Moreover, since YmdB binds ADPR, this (or related) metabolite may influence RNase III activity in an YmdB-dependent manner. If the YmdB-RNase III interaction in fact regulates RNase III, this interaction may connect post-transcriptional regulatory pathways with the cellular metabolic state, as reflected by NAD+ and ADPR levels. The goal of this project is to characterize the YmdB interaction with RNase III, with the long-range goal of understanding the mechanism and role of YmdB regulation of RNase III. Since both YmdB and RNase III are conserved bacterial proteins, characterization of YmdB and its influence on RNase III activity would provide insight on a conserved interaction in bacterial cells in general as well as reveal a potentially novel mechanism of post-transcriptional gene regulation.
Temple University--Theses
Han, Bo W. "Using Experimental and Computational Strategies to Understand the Biogenesis of microRNAs and piRNAs: A Dissertation." eScholarship@UMMS, 2007. http://escholarship.umassmed.edu/gsbs_diss/782.
Full textHan, Bo W. "Using Experimental and Computational Strategies to Understand the Biogenesis of microRNAs and piRNAs: A Dissertation." eScholarship@UMMS, 2015. https://escholarship.umassmed.edu/gsbs_diss/782.
Full textBook chapters on the topic "Ribonuclease III"
Schomburg, Dietmar, and Margit Salzmann. "Ribonuclease III." In Enzyme Handbook 3, 853–56. Berlin, Heidelberg: Springer Berlin Heidelberg, 1991. http://dx.doi.org/10.1007/978-3-642-76463-9_180.
Full textNicholson, Allen W. "Ribonuclease III and the Role of Double-Stranded RNA Processing in Bacterial Systems." In Nucleic Acids and Molecular Biology, 269–97. Berlin, Heidelberg: Springer Berlin Heidelberg, 2011. http://dx.doi.org/10.1007/978-3-642-21078-5_11.
Full textMeersman, F., and K. Heremans. "Pressure Unfolded States of Ribonuclease A under Native and Reducing Conditions have Identical Conformations." In Advances in High Pressure Bioscience and Biotechnology II, 69–72. Berlin, Heidelberg: Springer Berlin Heidelberg, 2003. http://dx.doi.org/10.1007/978-3-662-05613-4_13.
Full text"Ribonuclease III (RNase III)." In Encyclopedia of Genetics, Genomics, Proteomics and Informatics, 1706. Dordrecht: Springer Netherlands, 2008. http://dx.doi.org/10.1007/978-1-4020-6754-9_14639.
Full textRobertson, Hugh D. "Escherichia coli ribonuclease III." In RNA Processing Part B: Specific Methods, 189–202. Elsevier, 1990. http://dx.doi.org/10.1016/0076-6879(90)81121-a.
Full textMeng, Wenzhao, Rhonda H. Nicholson, Lilian Nathania, Alexandre V. Pertzev, and Allen W. Nicholson. "Chapter 7 New Approaches to Understanding Double‐Stranded RNA Processing by Ribonuclease III." In RNA Turnover in Bacteria, Archaea and Organelles, 119–29. Elsevier, 2008. http://dx.doi.org/10.1016/s0076-6879(08)02207-6.
Full textAmarasinghe, Asoka K., Irina Calin-Jageman, Ahmed Harmouch, Weimei Sun, and Allen W. Nicholson. "Escherichia coli Ribonuclease III: Affinity Purification of Hexahistidine-Tagged Enzyme and Assays for Substrate Binding and Cleavage." In Methods in Enzymology, 143–58. Elsevier, 2001. http://dx.doi.org/10.1016/s0076-6879(01)42542-0.
Full textConference papers on the topic "Ribonuclease III"
Sheng, Jinghao, Chi Luo, Yuxiang Jiang, Philip W. Hinds, Zhengping Xu, and Guo-fu Hu. "Abstract 1401: Transcription of angiogenin and ribonuclease 4 is regulated by RNA polymerase III elements and a CTCF-dependent intragenic chromatin loop." In Proceedings: AACR Annual Meeting 2014; April 5-9, 2014; San Diego, CA. American Association for Cancer Research, 2014. http://dx.doi.org/10.1158/1538-7445.am2014-1401.
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