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RNA architecture and reactivity
Publications
2004
Przykorska A., Solecka K., Olszak K., Keith G., Nawrot B., Kuligowska E.
Wheat (Triticum vulgare) chloroplast nuclease ChSI exhibits 5' flap structure-specific endonuclease activity Journal Article
In: Biochemistry, vol. 43, no. 35, pp. 11283-94, 2004, (0006-2960 Journal Article).
Abstract | BibTeX | Tags: &, Acid, Catalysis, Chloroplasts/*enzymology, Conformation, Desorption-Ionization, DNA, Endonucleases/*chemistry/isolation, Exonucleases/chemistry/metabolism, Flap, Gov't, Hydrolysis, KEITH, Kinetics, Laser, Mass, Matrix-Assisted, Non-U.S., Nucleic, Oligonucleotides/chemical, Plant/chemistry/metabolism, purification/*metabolism, Relationship, Single-Stranded/chemistry/metabolism, Specificity, Spectrometry, Structure-Activity, Substrate, Support, synthesis/metabolism, Thermodynamics, Triticum/*enzymology
@article{,
title = {Wheat (Triticum vulgare) chloroplast nuclease ChSI exhibits 5' flap structure-specific endonuclease activity},
author = { A. Przykorska and K. Solecka and K. Olszak and G. Keith and B. Nawrot and E. Kuligowska},
year = {2004},
date = {2004-01-01},
journal = {Biochemistry},
volume = {43},
number = {35},
pages = {11283-94},
abstract = {The structure-specific ChSI nuclease from wheat (Triticum vulgare) chloroplast stroma has been previously purified and characterized in our laboratory. It is a single-strand-specific DNA and RNA endonuclease. Although the enzyme has been initially characterized and used as a structural probe, its biological function is still unknown. Localization of the ChSI enzyme inside chloroplasts, possessing their own DNA that is generally highly exposed to UV light and often affected by numerous redox reactions and electron transfer processes, might suggest, however, that this enzyme could be involved in DNA repair. The repair of some types of DNA damage has been shown to proceed through branched DNA intermediates which are substrates for the structure-specific DNA endonucleases. Thus we tested the substrate specificity of ChSI endonuclease toward various branched DNAs containing 5' flap, 5' pseudoflap, 3' pseudoflap, or single-stranded bulged structural motifs. It appears that ChSI has a high 5' flap structure-specific endonucleolytic activity. The catalytic efficiency (k(cat)/K(M)) of the enzyme is significantly higher for the 5' flap substrate than for single-stranded DNA. The ChSI 5' flap activity was inhibited by high concentrations of Mg(2+), Mn(2+), Zn(2+), or Ca(2+). However, low concentrations of divalent cations could restore the loss of ChSI activity as a consequence of EDTA pretreatment. In contrast to other known 5' flap nucleases, the chloroplast enzyme ChSI does not possess any 5'-->3' exonuclease activity on double-stranded DNA. Therefore, we conclude that ChSI is a 5' flap structure-specific endonuclease with nucleolytic activity toward single-stranded substrates.},
note = {0006-2960
Journal Article},
keywords = {&, Acid, Catalysis, Chloroplasts/*enzymology, Conformation, Desorption-Ionization, DNA, Endonucleases/*chemistry/isolation, Exonucleases/chemistry/metabolism, Flap, Gov't, Hydrolysis, KEITH, Kinetics, Laser, Mass, Matrix-Assisted, Non-U.S., Nucleic, Oligonucleotides/chemical, Plant/chemistry/metabolism, purification/*metabolism, Relationship, Single-Stranded/chemistry/metabolism, Specificity, Spectrometry, Structure-Activity, Substrate, Support, synthesis/metabolism, Thermodynamics, Triticum/*enzymology},
pubstate = {published},
tppubtype = {article}
}
The structure-specific ChSI nuclease from wheat (Triticum vulgare) chloroplast stroma has been previously purified and characterized in our laboratory. It is a single-strand-specific DNA and RNA endonuclease. Although the enzyme has been initially characterized and used as a structural probe, its biological function is still unknown. Localization of the ChSI enzyme inside chloroplasts, possessing their own DNA that is generally highly exposed to UV light and often affected by numerous redox reactions and electron transfer processes, might suggest, however, that this enzyme could be involved in DNA repair. The repair of some types of DNA damage has been shown to proceed through branched DNA intermediates which are substrates for the structure-specific DNA endonucleases. Thus we tested the substrate specificity of ChSI endonuclease toward various branched DNAs containing 5' flap, 5' pseudoflap, 3' pseudoflap, or single-stranded bulged structural motifs. It appears that ChSI has a high 5' flap structure-specific endonucleolytic activity. The catalytic efficiency (k(cat)/K(M)) of the enzyme is significantly higher for the 5' flap substrate than for single-stranded DNA. The ChSI 5' flap activity was inhibited by high concentrations of Mg(2+), Mn(2+), Zn(2+), or Ca(2+). However, low concentrations of divalent cations could restore the loss of ChSI activity as a consequence of EDTA pretreatment. In contrast to other known 5' flap nucleases, the chloroplast enzyme ChSI does not possess any 5'-->3' exonuclease activity on double-stranded DNA. Therefore, we conclude that ChSI is a 5' flap structure-specific endonuclease with nucleolytic activity toward single-stranded substrates.
2001
Wilhelm M., Uzun O., Mules E. H., Gabriel A., Wilhelm F. X.
Polypurine tract formation by Ty1 RNase H Journal Article
In: J Biol Chem, vol. 276, no. 50, pp. 47695-701, 2001, (0021-9258 Journal Article).
Abstract | BibTeX | Tags: *Purines, *Retroelements, Base, Binding, Calf, Data, DNA, DNA/metabolism, Factors, Gov't, H, Hydrolysis, Molecular, Mutation, Non-U.S., P.H.S., Polymerase/*chemistry/*metabolism, Primers/pharmacology, Protein, Proteins/metabolism, Recombinant, Ribonuclease, RNA-Directed, RNA/metabolism, Sequence, Sites, Support, Thymus/*chemistry/*genetics/metabolism, time, U.S.
@article{,
title = {Polypurine tract formation by Ty1 RNase H},
author = { M. Wilhelm and O. Uzun and E. H. Mules and A. Gabriel and F. X. Wilhelm},
year = {2001},
date = {2001-01-01},
journal = {J Biol Chem},
volume = {276},
number = {50},
pages = {47695-701},
abstract = {To better understand the mechanism by which Ty1 RNase H creates the polypurine tract (PPT) primer, we have demonstrated the polymerase-dependent hydrolytic activity of Ty1 reverse transcriptase (RT) during minus-strand synthesis. Using RNase H and polymerase mutants of the recombinant Ty1 RT protein, we show that the two domains of Ty1 RT can act independently of one another. Our results indicate that RNA/DNA substrates containing a short RNA PPT, which serve as primers for plus-strand DNA synthesis, are relatively resistant to RNase H cleavage. RNA substrates with a correct 5' end but with 3' end extending beyond the plus-strand initiation site were cleaved specifically to generate the correct 3' end of the PPT. Using long RNA/DNA duplexes containing the PPT, we show that Ty1 RT is able to make specific internal cleavages that could generate the plus-strand primer with correct 5' and 3' ends. Long RNA/DNA duplexes with mutations in the PPT or in a U-rich region upstream of the PPT, which abolish plus-strand initiation in vivo, were not cleaved specifically at the 5' end of the PPT. Our work demonstrates that the in vitro enzyme can recapitulate key processes that control proper replication in vivo.},
note = {0021-9258
Journal Article},
keywords = {*Purines, *Retroelements, Base, Binding, Calf, Data, DNA, DNA/metabolism, Factors, Gov't, H, Hydrolysis, Molecular, Mutation, Non-U.S., P.H.S., Polymerase/*chemistry/*metabolism, Primers/pharmacology, Protein, Proteins/metabolism, Recombinant, Ribonuclease, RNA-Directed, RNA/metabolism, Sequence, Sites, Support, Thymus/*chemistry/*genetics/metabolism, time, U.S.},
pubstate = {published},
tppubtype = {article}
}
To better understand the mechanism by which Ty1 RNase H creates the polypurine tract (PPT) primer, we have demonstrated the polymerase-dependent hydrolytic activity of Ty1 reverse transcriptase (RT) during minus-strand synthesis. Using RNase H and polymerase mutants of the recombinant Ty1 RT protein, we show that the two domains of Ty1 RT can act independently of one another. Our results indicate that RNA/DNA substrates containing a short RNA PPT, which serve as primers for plus-strand DNA synthesis, are relatively resistant to RNase H cleavage. RNA substrates with a correct 5' end but with 3' end extending beyond the plus-strand initiation site were cleaved specifically to generate the correct 3' end of the PPT. Using long RNA/DNA duplexes containing the PPT, we show that Ty1 RT is able to make specific internal cleavages that could generate the plus-strand primer with correct 5' and 3' ends. Long RNA/DNA duplexes with mutations in the PPT or in a U-rich region upstream of the PPT, which abolish plus-strand initiation in vivo, were not cleaved specifically at the 5' end of the PPT. Our work demonstrates that the in vitro enzyme can recapitulate key processes that control proper replication in vivo.
1987
Debono M, Barnhart M, Carrell C B, Hoffmann Jules A, Occolowitz J L, Abbott B J, Fukuda D S, Hamill R L, Biemann K, Herlihy W C
A21978C, a complex of new acidic peptide antibiotics: isolation, chemistry, and mass spectral structure elucidation Journal Article
In: J. Antibiot., vol. 40, no. 6, pp. 761–777, 1987, ISSN: 0021-8820.
Abstract | BibTeX | Tags: Acylation, Amino Acids, Anti-Bacterial Agents, Chemical Phenomena, Chemistry, Chromatography, Cyclic, Fatty Acids, Gas Chromatography-Mass Spectrometry, High Pressure Liquid, hoffmann, Hydrolysis, M3i, Magnetic Resonance Spectroscopy, Mass Spectrometry, Molecular Conformation, Peptides, Spectrophotometry, Streptomyces
@article{debono_a21978c_1987,
title = {A21978C, a complex of new acidic peptide antibiotics: isolation, chemistry, and mass spectral structure elucidation},
author = {M Debono and M Barnhart and C B Carrell and Jules A Hoffmann and J L Occolowitz and B J Abbott and D S Fukuda and R L Hamill and K Biemann and W C Herlihy},
issn = {0021-8820},
year = {1987},
date = {1987-01-01},
journal = {J. Antibiot.},
volume = {40},
number = {6},
pages = {761--777},
abstract = {A21978C, produced by Streptomyces roseosporus, NRRL 11379, is a complex of new acidic lipopeptolide antibiotics which inhibits Gram-positive bacteria. HPLC separation of the various components from the purified complex resulted in the isolation of A21978C1, -C2 and -C3 (major components) and -C4, -C5, and -C0 (minor components). Each of these components was fermented with cultures of Actinoplanes utahensis (NRRL 12052) to give the identical inactive peptide ("A21978C nucleus") by removal of the fatty acid acyl groups from the N-terminus. This peptide was composed of 13 amino acids: L-kynurenine, L-threo-3-methylglutamic acid, L-asparagine, L-aspartic acid (3 residues), glycine (2 residues), L-tryptophan, L-ornithine, D-alanine, D-serine and L-threonine. The amino acid sequence was determined using a combination of the Edman degradation and gas chromatography mass spectrum (GC-MS) analysis of appropriately derivatized peptides obtained from partial hydrolysis. Each major component was shown to be acylated with a branched chain fatty acid at the N-terminus and the structure of this fatty acid was determined by 1H NMR and mass spectral methods. A structure for A21978C was assigned on the basis of this degradative and physico-chemical information.},
keywords = {Acylation, Amino Acids, Anti-Bacterial Agents, Chemical Phenomena, Chemistry, Chromatography, Cyclic, Fatty Acids, Gas Chromatography-Mass Spectrometry, High Pressure Liquid, hoffmann, Hydrolysis, M3i, Magnetic Resonance Spectroscopy, Mass Spectrometry, Molecular Conformation, Peptides, Spectrophotometry, Streptomyces},
pubstate = {published},
tppubtype = {article}
}
A21978C, produced by Streptomyces roseosporus, NRRL 11379, is a complex of new acidic lipopeptolide antibiotics which inhibits Gram-positive bacteria. HPLC separation of the various components from the purified complex resulted in the isolation of A21978C1, -C2 and -C3 (major components) and -C4, -C5, and -C0 (minor components). Each of these components was fermented with cultures of Actinoplanes utahensis (NRRL 12052) to give the identical inactive peptide ("A21978C nucleus") by removal of the fatty acid acyl groups from the N-terminus. This peptide was composed of 13 amino acids: L-kynurenine, L-threo-3-methylglutamic acid, L-asparagine, L-aspartic acid (3 residues), glycine (2 residues), L-tryptophan, L-ornithine, D-alanine, D-serine and L-threonine. The amino acid sequence was determined using a combination of the Edman degradation and gas chromatography mass spectrum (GC-MS) analysis of appropriately derivatized peptides obtained from partial hydrolysis. Each major component was shown to be acylated with a branched chain fatty acid at the N-terminus and the structure of this fatty acid was determined by 1H NMR and mass spectral methods. A structure for A21978C was assigned on the basis of this degradative and physico-chemical information.
1973
Koolman J, Hoffmann Jules A, Karlson P
Sulphage esters as inactivation products of ecdysone in Locusta migratoria Journal Article
In: Hoppe-Seyler's Z. Physiol. Chem., vol. 354, no. 9, pp. 1043–1048, 1973, ISSN: 0018-4888.
BibTeX | Tags: Animals, Biological, Cattle, Chromatography, Ecdysone, Electrophoresis, Esterases, Glucosidases, Glucuronidase, Grasshoppers, hoffmann, Hydrogen-Ion Concentration, Hydrolysis, Ion Exchange, Isotope Labeling, Kinetics, Larva, Liver, M3i, Metamorphosis, Paper, Plants, Saccharomyces cerevisiae, Snails, Sulfatases, Sulfur Radioisotopes, Sulfuric Acids, Swine, Thin Layer, Time Factors, Tritium
@article{koolman_sulphage_1973,
title = {Sulphage esters as inactivation products of ecdysone in Locusta migratoria},
author = {J Koolman and Jules A Hoffmann and P Karlson},
issn = {0018-4888},
year = {1973},
date = {1973-09-01},
journal = {Hoppe-Seyler's Z. Physiol. Chem.},
volume = {354},
number = {9},
pages = {1043--1048},
keywords = {Animals, Biological, Cattle, Chromatography, Ecdysone, Electrophoresis, Esterases, Glucosidases, Glucuronidase, Grasshoppers, hoffmann, Hydrogen-Ion Concentration, Hydrolysis, Ion Exchange, Isotope Labeling, Kinetics, Larva, Liver, M3i, Metamorphosis, Paper, Plants, Saccharomyces cerevisiae, Snails, Sulfatases, Sulfur Radioisotopes, Sulfuric Acids, Swine, Thin Layer, Time Factors, Tritium},
pubstate = {published},
tppubtype = {article}
}