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Journal articles on the topic 'RNA Cleavage'

Author: Grafiati

Published: 4 June 2021

Last updated: 18 February 2022

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1

Pantaleo, Vitantonio, György Szittya, and József Burgyán. "Molecular Bases of Viral RNA Targeting by Viral Small Interfering RNA-Programmed RISC." Journal of Virology 81, no. 8 (January 31, 2007): 3797–806. http://dx.doi.org/10.1128/jvi.02383-06.

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ABSTRACT RNA silencing is conserved in a broad range of eukaryotes and operates in the development and maintenance of genome integrity in many organisms. Plants have adapted this system for antiviral defense, and plant viruses have in turn developed mechanisms to suppress RNA silencing. RNA silencing-related RNA inactivation is likely based on target RNA cleavage or translational arrest. Although it is widely assumed that virus-induced gene silencing (VIGS) promotes the endonucleolytic cleavage of the viral RNA genome, this popular assumption has never been tested experimentally. Here we analyzed the viral RNA targeting by VIGS in tombusvirus-infected plants, and we show evidence that antiviral response of VIGS is based on viral RNA cleavage by RNA-induced silencing effector complex (RISC) programmed by virus-specific small interfering RNAs (siRNAs). In addition, we found that the RISC-mediated cleavages do not occur randomly on the viral genome. Indeed, sequence analysis of cloned cleavage products identified hot spots for target RNA cleavage, and the regions of specific RISC-mediated cleavages are asymmetrically distributed along the positive- and negative-sense viral RNA strands. In addition, we identified viral siRNAs containing high-molecular-mass protein complexes purified from the recovery leaves of the silencing suppressor mutant virus-infected plants. Strikingly, these large nucleoproteins cofractionated with microRNA-containing complexes, suggesting that these nucleoproteins are silencing related effector complexes.

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2

Desroches, Alexandre, and Jean-Bernard Denault. "Characterization of caspase-7 interaction with RNA." Biochemical Journal 478, no. 13 (July 16, 2021): 2681–96. http://dx.doi.org/10.1042/bcj20210366.

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Apoptosis is a regulated form of cell death essential to the removal of unwanted cells. At its core, a family of cysteine peptidases named caspases cleave key proteins allowing cell death to occur. To do so, each caspase catalytic pocket recognizes preferred amino acid sequences resulting in proteolysis, but some also use exosites to select and cleave important proteins efficaciously. Such exosites have been found in a few caspases, notably caspase-7 that has a lysine patch (K38KKK) that binds RNA, which acts as a bridge to RNA-binding proteins favoring proximity between the peptidase and its substrates resulting in swifter cleavage. Although caspase-7 interaction with RNA has been identified, in-depth characterization of this interaction is lacking. In this study, using in vitro cleavage assays, we determine that RNA concentration and length affect the cleavage of RNA-binding proteins. Additionally, using binding assays and RNA sequencing, we found that caspase-7 binds RNA molecules regardless of their type, sequence, or structure. Moreover, we demonstrate that the N-terminal peptide of caspase-7 reduces the affinity of the peptidase for RNA, which translates into slower cleavages of RNA-binding proteins. Finally, employing engineered heterodimers, we show that a caspase-7 dimer can use both exosites simultaneously to increase its affinity to RNA because a heterodimer with only one exosite has reduced affinity for RNA and cleavage efficacy. These findings shed light on a mechanism that furthers substrate recognition by caspases and provides potential insight into its regulation during apoptosis.

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3

Dorner, S., and A. Barta. "Probing Ribosome Structure by Europium-Induced RNA Cleavage." Biological Chemistry 380, no. 2 (February 1, 1999): 243–51. http://dx.doi.org/10.1515/bc.1999.032.

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AbstractDivalent metal ions are absolutely required for the structure and catalytic activities of ribosomes. They are partly coordinated to highly structured RNA, which therefore possesses high-affinity metal ion binding pockets. As metalion induced RNA cleavages are useful for characterising metal ion binding sites and RNA structures, we analysed europium (Eu3+) induced specific cleavages in both 16S and 23S rRNA ofE. coli. The cleavage sites were identified by primer extension and compared to those previously identified for calcium, lead, magnesium, and manganese ions. Several Eu3+cleavage sites, mostly those at which a general metal ion binding site had been already identified, were identical to previously described divalent metal ions. Overall, the Eu3+cleavages are most similar to the Ca2+cleavage pattern, probably due to a similar ion radius. Interestingly, several cleavage sites which were specific for Eu3+were located in regions implicated in the binding of tRNA and antibiotics. The binding of erythromycin and chloramphenicol, but not tetracycline and streptomycin, significantly reduced Eu3+cleavage efficiencies in the peptidyl transferase center. The identification of specific Eu3+binding sites near the active sites on the ribosome will allow to use the fluorescent properties of europium for probing the environment of metal ion binding pockets at the ribosome's active center.

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4

Westhof, E. "RNA CATALYSIS:Chemical Diversity in RNA Cleavage." Science 286, no. 5437 (October 1, 1999): 61–62. http://dx.doi.org/10.1126/science.286.5437.61.

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5

Altman, Sidney, Madeline Baer, Cecilia Guerrier-Takada, and Agustin Vioque. "Enzymatic cleavage of RNA by RNA." Trends in Biochemical Sciences 11, no. 12 (December 1986): 515–18. http://dx.doi.org/10.1016/0968-0004(86)90086-1.

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6

Altman, Sidney. "Enzymatic cleavage of RNA by RNA." Bioscience Reports 10, no. 4 (August 1, 1990): 317–37. http://dx.doi.org/10.1007/bf01117232.

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7

Suhasini, Avvaru N., and Ravi Sirdeshmukh. "Transfer RNA Cleavages by Onconase Reveal Unusual Cleavage Sites." Journal of Biological Chemistry 281, no. 18 (February 23, 2006): 12201–9. http://dx.doi.org/10.1074/jbc.m504488200.

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8

Rusk, Nicole. "Another player for RNA-guided RNA cleavage." Nature Methods 14, no. 3 (March 2017): 222–23. http://dx.doi.org/10.1038/nmeth.4213.

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9

Saleem, M., and L. E. Pelcher. "Site-specific cleavage of tobacco mosaic virus RNA: A study of factors influencing the cleavage." Canadian Journal of Biochemistry and Cell Biology 63, no. 5 (May 1, 1985): 382–86. http://dx.doi.org/10.1139/o85-055.

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DNA oligomer directed ribonuclease H (RNase H) methodology is applied to specifically cleave tobacco mosaic virus (TMV) RNA. Using a synthetic DNA oligomer P(dT8)dCdC, complementary to a region from nucleotide 5545 to nucleotide 5554 at the 3′ end of TMV RNA, we have cleaved the RNA at the site of polynucleotides complementary to the DNA oligomer. Factors such as secondary structure of the RNA, concentrations of DNA oligomer, RNase H and magnesium ions in the reaction mixture, and time of incubation were optimized for the RNase H cleavage of TMV RNA – DNA oligomer complex. Denaturation of TMV RNA with 50% dimethyl sulphoxide at 50 °C is essential for the site-specific cleavage.

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10

Ryan, Kevin. "Pre-mRNA 3’ Cleavage is Reversibly Inhibited in Vitro by Cleavage Factor Dephosphorylation." RNA Biology 4, no. 1 (January 2007): 26–33. http://dx.doi.org/10.4161/rna.4.1.4365.

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11

Otsuka, Yuichi, Hiroyuki Ueno, and Tetsuro Yonesaki. "Escherichia coli Endoribonucleases Involved in Cleavage of Bacteriophage T4 mRNAs." Journal of Bacteriology 185, no. 3 (February 1, 2003): 983–90. http://dx.doi.org/10.1128/jb.185.3.983-990.2003.

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ABSTRACT The dmd mutant of bacteriophage T4 has a defect in growth because of rapid degradation of late-gene mRNAs, presumably caused by mutant-specific cleavages of RNA. Some such cleavages can occur in an allele-specific manner, depending on the translatability of RNA or the presence of a termination codon. Other cleavages are independent of translation. In the present study, by introducing plasmids carrying various soc alleles, we could detect cleavages of soc RNA in uninfected cells identical to those found in dmd mutant-infected cells. We isolated five Escherichia coli mutant strains in which the dmd mutant was able to grow. One of these strains completely suppressed the dmd mutant-specific cleavages of soc RNA. The loci of the E. coli mutations and the effects of mutations in known RNase-encoding genes suggested that an RNA cleavage activity causing the dmd mutant-specific mRNA degradation is attributable to a novel RNase. In addition, we present evidence that 5′-truncated soc RNA, a stable form in T4-infected cells regardless of the presence of a dmd mutation, is generated by RNase E.

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12

Rusché, L. N., K. J. Piller, and B. Sollner-Webb. "Guide RNA-mRNA chimeras, which are potential RNA editing intermediates, are formed by endonuclease and RNA ligase in a trypanosome mitochondrial extract." Molecular and Cellular Biology 15, no. 6 (June 1995): 2933–41. http://dx.doi.org/10.1128/mcb.15.6.2933.

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RNA editing in kinetoplast mitochondrial transcripts involves the insertion and/or deletion of uridine residues and is directed by guide RNAs (gRNAs). It is thought to occur through a chimeric intermediate in which the 3' oligo(U) tail of the gRNA is covalently joined to the 3' portion of the mRNA at the site being edited. Chimeras have been proposed to be formed by a transesterification reaction but could also be formed by the known mitochondrial site-specific nuclease and RNA ligase. To distinguish between these models, we studied chimera formation in vitro directed by a trypanosome mitochondrial extract. This reaction was found to occur in two steps. First, the mRNA is cleaved in the 3' portion of the editing domain, and then the 3' fragment derived from this cleavage is ligated to the gRNA. The isolated mRNA 3' cleavage product is a more efficient substrate for chimera formation than is the intact mRNA, inconsistent with a transesterification mechanism but supporting a nuclease-ligase mechanism. Also, when normal mRNA cleavage is inhibited by the presence of a phosphorothioate, normal chimera formation no longer occurs. Rather, this phosphorothioate induces both cleavage and chimera formation at a novel site within the editing domain. Finally, levels of chimera-forming activity correlate with levels of mitochondrial RNA ligase activity when reactions are conducted under conditions which inhibit the ligase, including the lack of ATP containing a cleavable alpha-beta bond. These data show that chimera formation in the mitochondrial extract occurs by a nuclease-ligase mechanism rather than by transesterification.

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13

Sampson, J. R., F. X. Sullivan, L. S. Behlen, A. B. DiRenzo, and O. C. Uhlenbeck. "Characterization of Two RNA-catalyzed RNA Cleavage Reactions." Cold Spring Harbor Symposia on Quantitative Biology 52 (January 1, 1987): 267–75. http://dx.doi.org/10.1101/sqb.1987.052.01.032.

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14

Altman, Sidney. "Enzymatic Cleavage of RNA by RNA(Nobel Lecture)." Angewandte Chemie International Edition in English 29, no. 7 (July 1990): 749–58. http://dx.doi.org/10.1002/anie.199007491.

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15

van Aken, Danny, Jessika Zevenhoven-Dobbe, Alexander E. Gorbalenya, and Eric J. Snijder. "Proteolytic maturation of replicase polyprotein pp1a by the nsp4 main proteinase is essential for equine arteritis virus replication and includes internal cleavage of nsp7." Journal of General Virology 87, no. 12 (December 1, 2006): 3473–82. http://dx.doi.org/10.1099/vir.0.82269-0.

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The positive-stranded RNA genome of the arterivirus Equine arteritis virus (order Nidovirales) encodes the partially overlapping replicase polyproteins pp1a (1727 aa) and pp1ab (3175 aa). Previously, three viral proteinases were reported to cleave these large polyproteins into 12 non-structural proteins (nsps). The chymotrypsin-like viral main proteinase residing in nsp4 is responsible for eight of these cleavages. Processing of the C-terminal half of pp1a (the nsp3–8 region) was postulated to occur following either of two alternative proteolytic pathways (the ‘major’ and ‘minor’ pathways). Here, the importance of these two pathways was investigated by using a reverse-genetics system and inactivating each of the cleavage sites by site-directed mutagenesis. For all of these pp1a cleavage sites, mutations that prevented cleavage by the nsp4 proteinase were found to block or severely inhibit EAV RNA synthesis. Furthermore, our studies identified a novel nsp4 cleavage site (Glu-1575/Ala-1576) that is located within nsp7 and is conserved in arteriviruses. The N-terminal nsp7 fragment (nsp7α) derived from this cleavage was detected in lysates of both EAV-infected cells and cells transiently expressing pp1a. Mutagenesis of the novel cleavage site in the context of an EAV full-length cDNA clone proved to be lethal, underlining the fact that the highly regulated, nsp4-mediated processing of the C-terminal half of pp1a is a crucial event in the arterivirus life cycle.

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16

Bashkin, James K. "Introduction to RNA/DNA Cleavage." Chemical Reviews 98, no. 3 (May 1998): 937–38. http://dx.doi.org/10.1021/cr970415b.

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17

Barrangou, Rodolphe. "RNA-mediated programmable DNA cleavage." Nature Biotechnology 30, no. 9 (September 2012): 836–38. http://dx.doi.org/10.1038/nbt.2357.

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18

Kirsebom, Leif A., and Stefan Trobro. "RNase P RNA-mediated cleavage." IUBMB Life 61, no. 3 (March 2009): spcone. http://dx.doi.org/10.1002/iub.191.

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19

Kirsebom, Leif A., and Stefan Trobro. "RNase P RNA-mediated cleavage." IUBMB Life 61, no. 3 (March 2009): 189–200. http://dx.doi.org/10.1002/iub.160.

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20

Shibahara, Susumu, Sachiko Mukai, Tohru Nishihara, Hideo Inoue, Eiko Ohtsuka, and Hirokazu Morisawa. "Site-directed cleavage of RNA." Nucleic Acids Research 15, no. 11 (1987): 4403–15. http://dx.doi.org/10.1093/nar/15.11.4403.

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21

Battigello, Jean-Marc A., Mei Cui, Stacie Roshong, and Barbara J. Carter. "Enediyne-mediated cleavage of RNA." Bioorganic & Medicinal Chemistry 3, no. 6 (June 1995): 839–49. http://dx.doi.org/10.1016/0968-0896(95)00046-j.

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22

Morrow, Janet R., and Olga Iranzo. "Synthetic metallonucleases for RNA cleavage." Current Opinion in Chemical Biology 8, no. 2 (April 2004): 192–200. http://dx.doi.org/10.1016/j.cbpa.2004.02.006.

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23

Wu, H. N., and M. M. Lai. "RNA conformational requirements of self-cleavage of hepatitis delta virus RNA." Molecular and Cellular Biology 10, no. 10 (October 1990): 5575–79. http://dx.doi.org/10.1128/mcb.10.10.5575.

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Hepatitis delta virus (HDV) RNA subfragments undergo self-cleavage at varying efficiencies. We have developed a procedure of using repeated cycles of heat denaturation and renaturation of RNA to achieve a high efficiency of cleavage. This effect can also be achieved by gradual denaturation of RNA with heat or formamide. These results suggest that only a subpopulation of the catalytic RNA molecules assumes the active conformation required for self-cleavage. This procedure could be of general use for detecting catalytic RNA activities.

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24

Wu, H. N., and M. M. Lai. "RNA conformational requirements of self-cleavage of hepatitis delta virus RNA." Molecular and Cellular Biology 10, no. 10 (October 1990): 5575–79. http://dx.doi.org/10.1128/mcb.10.10.5575-5579.1990.

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Hepatitis delta virus (HDV) RNA subfragments undergo self-cleavage at varying efficiencies. We have developed a procedure of using repeated cycles of heat denaturation and renaturation of RNA to achieve a high efficiency of cleavage. This effect can also be achieved by gradual denaturation of RNA with heat or formamide. These results suggest that only a subpopulation of the catalytic RNA molecules assumes the active conformation required for self-cleavage. This procedure could be of general use for detecting catalytic RNA activities.

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25

GOILA, Ritu, and Akhil C. BANERJEA. "Inhibition of hepatitis B virus X gene expression by novel DNA enzymes." Biochemical Journal 353, no. 3 (January 25, 2001): 701–8. http://dx.doi.org/10.1042/bj3530701.

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Two mono- and a di-RNA-cleaving DNA enzymes with the 10–23 catalytic motif were synthesized that were targeted to cleave at the conserved site/sites of the X gene of the hepatitis B virus. In each case, protein-independent but Mg2+-dependent cleavage of in vitro-synthesized full-length X RNA was obtained. Specific cleavage products were obtained with two different mono- and a di-DNA enzyme, with the latter giving rise to multiple RNA fragments that retained the cleavage specificity of the mono-DNA enzymes. A relatively less efficient cleavage was also obtained under simulated physiological conditions by the two mono-DNA enzymes but the efficiency of the di-DNA enzyme was significantly reduced. A single nucleotide change (G to C) in the 10–23 catalytic motif of the DNA enzyme 307 abolished its ability to cleave target RNA completely. Both, mono- and di-DNA enzymes, when introduced into a mammalian cell, showed specific inhibition of X-gene-mediated transactivation of reporter-gene expression. This decrease was due to the ability of these DNA enzymes to cleave X RNA intracellularly, which was also reflected by significant reduction in the levels of X protein in a liver-specific cell line, HepG2. Ribonuclease protection assay confirmed the specific reduction of X RNA in DNA-enzyme-treated cells. Potential in vivo applications of mono- and di-DNA enzymes in interfering specifically with the X-gene-mediated pathology are discussed.

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26

Kuyumcu-Martinez, Muge, Gaël Belliot, Stanislav V. Sosnovtsev, Kyeong-Ok Chang, Kim Y. Green, and Richard E. Lloyd. "Calicivirus 3C-Like Proteinase Inhibits Cellular Translation by Cleavage of Poly(A)-Binding Protein." Journal of Virology 78, no. 15 (August 1, 2004): 8172–82. http://dx.doi.org/10.1128/jvi.78.15.8172-8182.2004.

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ABSTRACT Caliciviruses are single-stranded RNA viruses that cause a wide range of diseases in both humans and animals, but little is known about the regulation of cellular translation during infection. We used two distinct calicivirus strains, MD145-12 (genus Norovirus) and feline calicivirus (FCV) (genus Vesivirus), to investigate potential strategies used by the caliciviruses to inhibit cellular translation. Recombinant 3C-like proteinases (r3CLpro) from norovirus and FCV were found to cleave poly(A)-binding protein (PABP) in the absence of other viral proteins. The norovirus r3CLpro PABP cleavage products were indistinguishable from those generated by poliovirus (PV) 3Cpro cleavage, while the FCV r3CLpro products differed due to cleavage at an alternate cleavage site 24 amino acids downstream of one of the PV 3Cpro cleavage sites. All cleavages by calicivirus or PV proteases separated the C-terminal domain of PABP that binds translation factors eIF4B and eRF3 from the N-terminal RNA-binding domain of PABP. The effect of PABP cleavage by the norovirus r3CLpro was analyzed in HeLa cell translation extracts, and the presence of r3CLpro inhibited translation of both endogenous and exogenous mRNAs. Translation inhibition was poly(A) dependent, and replenishment of the extracts with PABP restored translation. Analysis of FCV-infected feline kidney cells showed that the levels of de novo cellular protein synthesis decreased over time as virus-specific proteins accumulated, and cleavage of PABP occurred in virus-infected cells. Our data indicate that the calicivirus 3CLpro, like PV 3Cpro, mediates the cleavage of PABP as part of its strategy to inhibit cellular translation. PABP cleavage may be a common mechanism among certain virus families to manipulate cellular translation.

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27

Hale, Caryn R., Peng Zhao, Sara Olson, Michael O. Duff, Brenton R. Graveley, Lance Wells, Rebecca M. Terns, and Michael P. Terns. "RNA-Guided RNA Cleavage by a CRISPR RNA-Cas Protein Complex." Cell 139, no. 5 (November 2009): 945–56. http://dx.doi.org/10.1016/j.cell.2009.07.040.

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28

Shibata, Hirotaka S., Hiroaki Takaku, Masamichi Takagi, and Masayuki Nashimoto. "The T Loop Structure Is Dispensable for Substrate Recognition by tRNase ZL." Journal of Biological Chemistry 280, no. 23 (April 11, 2005): 22326–34. http://dx.doi.org/10.1074/jbc.m502048200.

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tRNA 3′-processing endoribonucleases (tRNase Z, or 3′-tRNase; EC 3.1.26.11) are enzymes that remove 3′-trailers from pre-tRNAs. An about 12-base-pair stem, a T loop-like structure, and a 3′-trailer were considered to be the minimum requirements for recognition by the long form (tRNase ZL) of tRNase Z; tRNase ZL can recognize and cleave a micro-pre-tRNA or a hooker/target RNA complex that resembles a micro-pre-tRNA. We examined four hook RNAs containing systematically weakened T stems for directing target RNA cleavage by tRNase ZL. As expected, the cleavage efficiency decreased with the decrease in T stem stability, and to our surprise, even the hook RNA that forms no T stem-loop-directed slight cleavage of the target RNA, suggesting that the T stem-loop structure is important but dispensable for substrate recognition by tRNase ZL. To analyze the effect of the T loop on substrate recognition, we compared the cleavage reaction for a micro-pre-tRNA with that for a 12-base-pair double-stranded RNA, which is the same as the micro-pre-tRNA except for the lack of the T loop structure. The observed rate constant value for the double-stranded RNA was comparable with that for the micro-pre-tRNA, whereas the Kd value for the complex with the double-stranded RNA was much higher than that for the complex with the micro-pre-tRNA. These results suggest that the T loop structure is not indispensable for the recognition, although the interaction between the T loop and the enzyme exists. Cleavage assays for such double-stranded RNA substrates of various lengths suggested that tRNase ZL can recognize and cleave double-stranded RNA substrates that are longer than 5 base pairs and shorter than 20 base pairs. We also showed that double-stranded RNA is not a substrate for the short form of tRNase Z.

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29

Gao, Hong-Qiang, Stefan G. Sarafianos, Edward Arnold, and Stephen H. Hughes. "RNase H Cleavage of the 5′ End of the Human Immunodeficiency Virus Type 1 Genome." Journal of Virology 75, no. 23 (December 1, 2001): 11874–80. http://dx.doi.org/10.1128/jvi.75.23.11874-11880.2001.

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ABSTRACT The synthesis of retroviral DNA is initiated near the 5′ end of the RNA. DNA synthesis is transferred from the 5′ end to the 3′ end of viral RNA in an RNase H-dependent step. In the case of human immunodeficiency virus type 1 (HIV-1) (and certain other retroviruses that have complex secondary structures at the ends of the viral RNA), there is the possibility that DNA synthesis can lead to a self-priming event that would block viral replication. The extent of RNase H cleavage must be sufficient to allow the strand transfer reaction to occur, but not so extensive that self-priming occurs. We have used a series of model RNA substrates, with and without a 5′ cap, to investigate the rules governing RNase H cleavage at the 5′ end of the HIV-1 genome. These in vitro RNase H cleavage reactions produce an RNA fragment of the size needed to block self-priming but still allow strand transfer. The cleavages seen in vitro can be understood in light of the structure of HIV-1 reverse transcriptase in a complex with an RNA/DNA substrate.

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30

Ro, Young-Tae, and Jean L. Patterson. "Identification of the Minimal Essential RNA Sequences Responsible for Site-Specific Targeting of theLeishmania RNA Virus 1-4 Capsid Endoribonuclease." Journal of Virology 74, no. 1 (January 1, 2000): 130–38. http://dx.doi.org/10.1128/jvi.74.1.130-138.2000.

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ABSTRACT The Leishmania RNA virus 1-4 capsid protein possesses an endoribonuclease activity responsible for single-site-specific cleavage within the 450-nucleotide 5′ untranslated region of its own viral RNA transcript. To characterize the minimal essential RNA determinants required for site-specific cleavage, mutated RNA transcripts were examined for susceptibility to cleavage by the virus capsid protein in an in vitro assay. Deletion analyses revealed that all determinants necessary for accurate cleavage are encoded in viral nucleotides 249 to 342. Nuclease mapping and site-specific mutagenesis of the minimal RNA sequence defined a stem-loop structure that is located 40 nucleotides upstream from the cleavage site (nucleotide 320) and that is essential for accurate RNA cleavage. Abrogation of cleavage by disruption of base pairing within the stem-loop was reversed through the introduction of complementary nucleotide substitutions that reestablished the structure. We also provide evidence that divalent cations, essential components of the cleavage reaction, stabilized the stem-loop structure in solution. That capsid-specific antiserum eliminated specific RNA cleavage provides further evidence that the virus capsid gene encodes the essential endoribonuclease activity.

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31

Agback, Peter, Corine Glemarec, Lee Yin, Anders Sandström, Janez Plavec, Christian Sund, Shun-ichi Yamakage, et al. "The self-cleavage of lariat-RNA." Tetrahedron Letters 34, no. 24 (June 1993): 3929–32. http://dx.doi.org/10.1016/s0040-4039(00)79266-5.

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32

Yamanishi, Haruyo, and Tetsuro Yonesaki. "RNA Cleavage Linked With Ribosomal Action." Genetics 171, no. 2 (July 14, 2005): 419–25. http://dx.doi.org/10.1534/genetics.105.042515.

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33

Breslow, R. "Kinetics and mechanism in RNA cleavage." Proceedings of the National Academy of Sciences 90, no. 4 (February 15, 1993): 1208–11. http://dx.doi.org/10.1073/pnas.90.4.1208.

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34

Kuimelis, Robert G., and Larry W. McLaughlin. "Mechanisms of Ribozyme-Mediated RNA Cleavage." Chemical Reviews 98, no. 3 (May 1998): 1027–44. http://dx.doi.org/10.1021/cr960426p.

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35

Pan, Tao. "Probing RNA Structure by Lead Cleavage." Current Protocols in Nucleic Acid Chemistry 00, no. 1 (February 2000): 6.3.1–6.3.9. http://dx.doi.org/10.1002/0471142700.nc0603s00.

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36

Belousoff, Matthew J., Bim Graham, Leone Spiccia, and Yitzhak Tor. "Cleavage of RNA oligonucleotides by aminoglycosides." Org. Biomol. Chem. 7, no. 1 (2009): 30–33. http://dx.doi.org/10.1039/b813252f.

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37

Pyshnyi, D., M. Repkova, S. Lokhov, E. Ivanova, A. Venyaminova, and V. Zarytova. "Oligonucleotide-Peptide Conjjugates for RNA Cleavage." Nucleosides and Nucleotides 16, no. 7-9 (July 1997): 1571–74. http://dx.doi.org/10.1080/07328319708006232.

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38

Hecht, Sidney M., Chris E. Holmes, Robert J. Duff, Michael A. Morgan, Barbara J. Carter, Erik de Vroom, and Eric C. Long. "RNA recognition and cleavage by Fe·bleomycin." Journal of Inorganic Biochemistry 51, no. 1-2 (July 1993): 514. http://dx.doi.org/10.1016/0162-0134(93)85540-o.

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39

Tuschl, Thomas, James B. Thomson, and Fritz Eckstein. "RNA cleavage by small catalytic RNAs." Current Opinion in Structural Biology 5, no. 3 (June 1995): 296–302. http://dx.doi.org/10.1016/0959-440x(95)80090-5.

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40

Sperry, A. O., and S. M. Berget. "In vitro cleavage of the simian virus 40 early polyadenylation site adjacent to a required downstream TG sequence." Molecular and Cellular Biology 6, no. 12 (December 1986): 4734–41. http://dx.doi.org/10.1128/mcb.6.12.4734.

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Exogenous RNA containing the simian virus 40 early polyadenylation site was efficiently and accurately polyadenylated in in vitro nuclear extracts. Correct cleavage required ATP. In the absence of ATP, nonpoly(A)+ products accumulated which were 18 to 20 nucleotides longer than the RNA generated by correct cleavage; the longer RNA terminated adjacent to the downstream TG element required for polyadenylation. In the presence of ATP analogs, alternate cleavage was not observed; instead, correct cleavage without poly(A) addition occurred. ATP-independent cleavage of simian virus 40 early RNA had many of the same properties as correct cleavage including requirements for an intact AAUAAA element, a proximal 3' terminus, and extract small nuclear ribonucleoproteins. This similarity in reaction parameters suggested that ATP-independent cleavage is an activity of the normal polyadenylation machinery. The ATP-independent cleavage product, however, did not behave as an intermediate in polyadenylation. The alternate RNA did not preferentially chase into correctly cleaved material upon readdition of ATP; instead, poly(A) was added to the 3' terminus of the cleaved RNA during a chase. Purified ATP-independent cleavage RNA, however, was a substrate for correct cleavage when reintroduced into the nuclear extract. Thus, alternate cleavage of polyadenylation sites adjacent to a required downstream sequence element is directed by the polyadenylation machinery in the absence of ATP.

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41

Sperry, A. O., and S. M. Berget. "In vitro cleavage of the simian virus 40 early polyadenylation site adjacent to a required downstream TG sequence." Molecular and Cellular Biology 6, no. 12 (December 1986): 4734–41. http://dx.doi.org/10.1128/mcb.6.12.4734-4741.1986.

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Abstract:

Exogenous RNA containing the simian virus 40 early polyadenylation site was efficiently and accurately polyadenylated in in vitro nuclear extracts. Correct cleavage required ATP. In the absence of ATP, nonpoly(A)+ products accumulated which were 18 to 20 nucleotides longer than the RNA generated by correct cleavage; the longer RNA terminated adjacent to the downstream TG element required for polyadenylation. In the presence of ATP analogs, alternate cleavage was not observed; instead, correct cleavage without poly(A) addition occurred. ATP-independent cleavage of simian virus 40 early RNA had many of the same properties as correct cleavage including requirements for an intact AAUAAA element, a proximal 3' terminus, and extract small nuclear ribonucleoproteins. This similarity in reaction parameters suggested that ATP-independent cleavage is an activity of the normal polyadenylation machinery. The ATP-independent cleavage product, however, did not behave as an intermediate in polyadenylation. The alternate RNA did not preferentially chase into correctly cleaved material upon readdition of ATP; instead, poly(A) was added to the 3' terminus of the cleaved RNA during a chase. Purified ATP-independent cleavage RNA, however, was a substrate for correct cleavage when reintroduced into the nuclear extract. Thus, alternate cleavage of polyadenylation sites adjacent to a required downstream sequence element is directed by the polyadenylation machinery in the absence of ATP.

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42

Carte, J., N. T. Pfister, M. M. Compton, R. M. Terns, and M. P. Terns. "Binding and cleavage of CRISPR RNA by Cas6." RNA 16, no. 11 (September 30, 2010): 2181–88. http://dx.doi.org/10.1261/rna.2230110.

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RajanBabu, Suganthan, Y. Sato, S. Yagi, Ampaabeng Gyedu, and N. Shimamoto. "1P123 Unexpected cleavage occurred in modified sigma7O subunit of active E. coli RNA polymerase." Seibutsu Butsuri 45, supplement (2005): S62. http://dx.doi.org/10.2142/biophys.45.s62_3.

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Hannon, G. J., P. A. Maroney, A. Branch, B. J. Benenfield, H. D. Robertson, and T. W. Nilsen. "Accurate processing of human pre-rRNA in vitro." Molecular and Cellular Biology 9, no. 10 (October 1989): 4422–31. http://dx.doi.org/10.1128/mcb.9.10.4422.

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We report here that the mature 5' terminus of human 18S rRNA is generated in vitro by a two-step processing reaction. In the first step, SP6 transcripts were specifically cleaved in HeLa cell nucleolar extract at three positions near the external transcribed spacer (ETS)-18S boundary. Of these cleavage sites, two were major and the other was minor. RNase T1 fingerprint and secondary nuclease analyses placed the two major cleavage sites 3 and 8 bases upstream from the mature 5' end of 18S rRNA and the minor cleavage site 1 base into the 18S sequence. All three cleavages yielded 5'-hydroxyl, 2'-3'-cyclic phosphate termini and were 5' of adenosine residues in the sequence UACCU, which was repeated three times near the ETS-18S boundary. In the second step, the initial cleavage product containing 3 bases of ETS was converted to an RNA with a 5' terminus identical to that of mature 18S RNA by an activity found in HeLa cell cytoplasmic extracts.

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45

Hannon, G. J., P. A. Maroney, A. Branch, B. J. Benenfield, H. D. Robertson, and T. W. Nilsen. "Accurate processing of human pre-rRNA in vitro." Molecular and Cellular Biology 9, no. 10 (October 1989): 4422–31. http://dx.doi.org/10.1128/mcb.9.10.4422-4431.1989.

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We report here that the mature 5' terminus of human 18S rRNA is generated in vitro by a two-step processing reaction. In the first step, SP6 transcripts were specifically cleaved in HeLa cell nucleolar extract at three positions near the external transcribed spacer (ETS)-18S boundary. Of these cleavage sites, two were major and the other was minor. RNase T1 fingerprint and secondary nuclease analyses placed the two major cleavage sites 3 and 8 bases upstream from the mature 5' end of 18S rRNA and the minor cleavage site 1 base into the 18S sequence. All three cleavages yielded 5'-hydroxyl, 2'-3'-cyclic phosphate termini and were 5' of adenosine residues in the sequence UACCU, which was repeated three times near the ETS-18S boundary. In the second step, the initial cleavage product containing 3 bases of ETS was converted to an RNA with a 5' terminus identical to that of mature 18S RNA by an activity found in HeLa cell cytoplasmic extracts.

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46

Kuznetsova, A. A., D. S. Novopashina, O. S. Fedorova, and N. A. Kuznetsov. "Effect of the Substrate Structure and Metal Ions on the Hydrolysis of Undamaged RNA by Human AP Endonuclease APE1." Acta Naturae 12, no. 2 (August 7, 2020): 74–85. http://dx.doi.org/10.32607/actanaturae.10864.

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Human apurinic/apyrimidinic (AP) endonuclease APE1 is one of the participants in the DNA base excision repair. The main biological function of APE1 is to hydrolyzethe phosphodiester bond on the 5-side of the AP sites. It has been shown recently that APE1 acts as an endoribonuclease and can cleave mRNA, thereby controlling the level of some transcripts. The sequences of CA, UA, and UG dinucleotides are the cleavage sites in RNA. In the present work, we performed a comparative analysis of the cleavage efficiency of model RNA substrates with short hairpin structures in which the loop size and the location of the pyrimidinepurine dinucleotide sequence were varied. The effect of various divalent metal ions and pH on the efficiency of the endoribonuclease reaction was analyzed. It was shown that site-specific hydrolysis of model RNA substrates depends on the spatial structure of the substrate. In addition, RNA cleavage occured in the absence of divalent metal ions, which proves that hydrolysis of DNA- and RNA substrates occurs via different catalytic mechanisms.

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47

Peach, Sally E., Kerri York, and Jay R. Hesselberth. "Global analysis of RNA cleavage by 5′-hydroxyl RNA sequencing." Nucleic Acids Research 43, no. 17 (May 22, 2015): e108-e108. http://dx.doi.org/10.1093/nar/gkv536.

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Liu, Liang, Xueyan Li, Jun Ma, Zongqiang Li, Lilan You, Jiuyu Wang, Min Wang, Xinzheng Zhang, and Yanli Wang. "The Molecular Architecture for RNA-Guided RNA Cleavage by Cas13a." Cell 170, no. 4 (August 2017): 714–26. http://dx.doi.org/10.1016/j.cell.2017.06.050.

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49

Lee, Eva, Christine E. Stocks, Sean M. Amberg, Charles M. Rice, and Mario Lobigs. "Mutagenesis of the Signal Sequence of Yellow Fever Virus prM Protein: Enhancement of Signalase Cleavage In Vitro Is Lethal for Virus Production." Journal of Virology 74, no. 1 (January 1, 2000): 24–32. http://dx.doi.org/10.1128/jvi.74.1.24-32.2000.

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ABSTRACT Proteolytic processing at the C-prM junction in the flavivirus polyprotein involves coordinated cleavages at the cytoplasmic and luminal sides of an internal signal sequence. We have introduced at the COOH terminus of the yellow fever virus (YFV) prM signal sequence amino acid substitutions (VPQAQA mutation) which uncoupled efficient signal peptidase cleavage of the prM protein from its dependence on prior cleavage in the cytoplasm of the C protein mediated by the viral NS2B-3 protease. Infectivity assays with full-length YFV RNA transcripts showed that the VPQAQA mutation, which enhanced signal peptidase cleavage in vitro, was lethal for infectious virus production. Revertants or second-site mutants were recovered from cells transfected with VPQAQA RNA. Analysis of these viruses revealed that single amino acid substitutions in different domains of the prM signal sequence could restore viability. These variants had growth properties in vertebrate cells which differed only slightly from those of the parent virus, despite efficient signal peptidase cleavage of prM in cell-free expression assays. However, the neurovirulence in mice of the VPQAQA variants was significantly attenuated. This study demonstrates that substitutions in the prM signal sequence which disrupt coordinated cleavages at the C-prM junction can impinge on the biological properties of the mutant viruses. Factors other than the rate of production of prM are vitally controlled by regulated cleavages at this site.

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Fu, William, Que Dang, Kunio Nagashima, Eric O. Freed, Vinay K. Pathak, and Wei-Shau Hu. "Effects of Gag Mutation and Processing on Retroviral Dimeric RNA Maturation." Journal of Virology 80, no. 3 (February 1, 2006): 1242–49. http://dx.doi.org/10.1128/jvi.80.3.1242-1249.2006.

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ABSTRACT After their release from host cells, most retroviral particles undergo a maturation process, which includes viral protein cleavage, core condensation, and increased stability of the viral RNA dimer. Inactivating the viral protease prevents protein cleavage; the resulting virions lack condensed cores and contain fragile RNA dimers. Therefore, protein cleavage is linked to virion morphological change and increased stability of the RNA dimer. However, it is unclear whether protein cleavage is sufficient for mediating virus RNA maturation. We have observed a novel phenotype in a murine leukemia virus capsid mutant, which has normal virion production, viral protein cleavage, and RNA packaging. However, this mutant also has immature virion morphology and contains a fragile RNA dimer, which is reminiscent of protease-deficient mutants. To our knowledge, this mutant provides the first evidence that Gag cleavage alone is not sufficient to promote RNA dimer maturation. To extend our study further, we examined a well-defined human immunodeficiency virus type 1 (HIV-1) Gag mutant that lacks a functional PTAP motif and produces immature virions without major defects in viral protein cleavage. We found that the viral RNA dimer in the PTAP mutant is more fragile and unstable compared with those from wild-type HIV-1. Based on the results of experiments using two different Gag mutants from two distinct retroviruses, we conclude that Gag cleavage is not sufficient for promoting RNA dimer maturation, and we propose that there is a link between the maturation of virion morphology and the viral RNA dimer.

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