The Experts below are selected from a list of 402 Experts worldwide ranked by ideXlab platform
Jeffrey J. Hayes - One of the best experts on this subject based on the ideXlab platform.
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the core histone n terminal tail domains negatively regulate binding of transcription factor iiia to a nucleosome containing a 5s rna gene via a novel mechanism
Molecular and Cellular Biology, 2005Co-Authors: Zungyoon Yang, Chunyang Zheng, Christophe Thiriet, Jeffrey J. HayesAbstract:Reconstitution of a DNA fragment containing a 5S RNA gene from Xenopus borealis into a nucleosome greatly restricts binding of the primary 5S transcription factor, TFIIIA. Consistent with transcription experiments using reconstituted templates, removal of the histone tail domains stimulates TFIIIA binding to the 5S nucleosome greater than 100-fold. However, we show that tail removal increases the probability of 5S DNA unwrapping from the core histone surface by only approximately fivefold. Moreover, using site-specific histone-to-DNA cross-linking, we show that TFIIIA binding neither induces nor requires nucleosome movement. Binding studies with COOH-terminal deletion mutants of TFIIIA and 5S nucleosomes reconstituted with native and tailless core histones indicate that the core histone tail domains play a direct role in restricting the binding of TFIIIA. Deletion of only the COOH-terminal transcription activation domain dramatically stimulates TFIIIA binding to the native nucleosome, while further C-terminal deletions or removal of the tail domains does not lead to further increases in TFIIIA binding. We conclude that the unmodified core histone tail domains directly negatively influence TFIIIA binding to the nucleosome in a manner that requires the C-terminal transcription activation domain of TFIIIA. Our data suggest an additional mechanism by which the core histone tail domains regulate the binding of trans-acting factors in chromatin.
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structural features of transcription factor iiia bound to a nucleosome in solution
Molecular and Cellular Biology, 2004Co-Authors: Joseph M Vitolo, Zungyoon Yang, Ravi Basavappa, Jeffrey J. HayesAbstract:Assembly of a DNA fragment containing a Xenopus borealis somatic-type 5S RNA gene into a nucleosome greatly restricts binding of the 5S gene-specific transcription factor IIIA (TFIIIA) to the 5S internal promoter. However, TFIIIA binds with high affinity to 5S nucleosomes lacking the N-terminal tail domains of the core histones or to nucleosomes in which these domains are hyperacetylated. The degree to which tail acetylation or removal improves TFIIIA binding cannot be simply explained by a commensurate change in the general accessibility of nucleosomal DNA. In order to investigate the molecular basis of how TFIIIA binds to the nucleosome and to ascertain if binding involves all nine zinc fingers and/or displacement of histone-DNA interactions, we examined the TFIIIA-nucleosome complex by hydroxyl radical footprinting and site-directed protein-DNA cross-linking. Our data reveal that the first six fingers of TFIIIA bind and displace approximately 20 bp of histone-DNA interactions at the periphery of the nucleosome, while binding of fingers 7 to 9 appears to overlap with histone-DNA interactions. Molecular modeling based on these results and the crystal structures of a nucleosome core and a TFIIIA-DNA cocomplex yields a precise picture of the ternary complex and a potentially important intermediate in the transition from naive chromatin structure to productive polymerase III transcription complex.
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core histone acetylation does not block linker histone binding to a nucleosome including a Xenopus borealis 5 s rrna gene
Journal of Biological Chemistry, 1994Co-Authors: Kiyoe Ura, Alan P. Wolffe, Jeffrey J. HayesAbstract:We demonstrate that acetylation of core histone tails does not significantly impair the ability of linker histones to bind preferentially and asymmetrically to a defined sequence mononucleosome core reconstituted in vitro. Thus a simple inhibition mechanism cannot explain models whereby acetylation is causal for the observed reduction in the linker histone content in chromatin. Other models to explain this correlation are discussed.
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Contacts of the globular domain of histone H5 and core histones with DNA in a "chromatosome"
Proceedings of the National Academy of Sciences of the United States of America, 1994Co-Authors: Jeffrey J. Hayes, Dmitry Pruss, Alan P. WolffeAbstract:Abstract The globular domain of histone H5 is found to asymmetrically associate with a nucleosome core including the Xenopus borealis somatic 5S RNA gene. Histones H2A and H2B are required for association of histone H5. Strong crosslinking of the globular domain of histone H5 to the 5S DNA in the nucleosome occurs at a single site to one side of the dyad axis. This site is also in contact with the core histones, and the interactions of the core histones with 5S DNA change as a result of association of the globular domain of histone H5. We discuss evidence for an allosteric change in core histone-5S DNA interactions following the association of the linker histone in the nucleosome.
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preferential and asymmetric interaction of linker histones with 5s dna in the nucleosome
Proceedings of the National Academy of Sciences of the United States of America, 1993Co-Authors: Jeffrey J. HayesAbstract:Abstract We establish that linker histones H1 and H5 bind preferentially to a Xenopus borealis somatic 5S RNA gene associated with an octamer of core histones rather than to naked 5S DNA. This preferential binding requires free linker DNA to either side of the nucleosome core. Incorporation of a single linker histone molecule into the nucleosome protects an additional 20 bp of linker DNA from micrococcal nuclease digestion. This additional DNA is asymmetrically distributed with respect to the nucleosome core. Incorporation of linker histones causes no change to the cleavage of DNA in the nucleosome by hydroxyl radical or DNase I.
Alan P. Wolffe - One of the best experts on this subject based on the ideXlab platform.
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a single high affinity binding site for histone h1 in a nucleosome containing the Xenopus borealis 5 s ribosomal rna gene
Journal of Biological Chemistry, 1996Co-Authors: Karl P Nightingale, Dmitry Pruss, Alan P. WolffeAbstract:Abstract We have reconstituted nucleosomes containing the Xenopus borealis 5 S rRNA gene, a single histone octamer, and 1 or 2 molecules of histone H1. We determine that the 1st molecule of histone H1 to associate with the 5 S nucleosome binds with high affinity (K 2 nM), and the 2nd molecule of H1 binds with a reduced affinity (K 10 nM). This latter binding is comparable with the association of histone H1 with naked DNA. Neither molecule of histone H1 alters the helical periodicity of DNA in the nucleosome as revealed by hydroxyl radical cleavage. We conclude that although multiple molecules of histone H1 can associate with nucleosomal DNA, there is only a single high affinity binding site for histone H1 within the 5 S nucleosome.
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methylation at cpg sequences does not influence histone h1 binding to a nucleosome including a Xenopus borealis 5 s rrna gene
Journal of Biological Chemistry, 1995Co-Authors: Karl P Nightingale, Alan P. WolffeAbstract:We demonstrate that methylation of the 12 dinucleotide CpGs within a GC-rich DNA fragment containing a Xenopus borealis 5 S rRNA gene does not influence histone H1 binding to naked or nucleosomal 5 S DNA. Thus a simple mechanism in which histone H1 selectively associates with nucleosomes containing methylated CpG cannot explain the repressive effects of methylation on gene activity.
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core histone acetylation does not block linker histone binding to a nucleosome including a Xenopus borealis 5 s rrna gene
Journal of Biological Chemistry, 1994Co-Authors: Kiyoe Ura, Alan P. Wolffe, Jeffrey J. HayesAbstract:We demonstrate that acetylation of core histone tails does not significantly impair the ability of linker histones to bind preferentially and asymmetrically to a defined sequence mononucleosome core reconstituted in vitro. Thus a simple inhibition mechanism cannot explain models whereby acetylation is causal for the observed reduction in the linker histone content in chromatin. Other models to explain this correlation are discussed.
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Contacts of the globular domain of histone H5 and core histones with DNA in a "chromatosome"
Proceedings of the National Academy of Sciences of the United States of America, 1994Co-Authors: Jeffrey J. Hayes, Dmitry Pruss, Alan P. WolffeAbstract:Abstract The globular domain of histone H5 is found to asymmetrically associate with a nucleosome core including the Xenopus borealis somatic 5S RNA gene. Histones H2A and H2B are required for association of histone H5. Strong crosslinking of the globular domain of histone H5 to the 5S DNA in the nucleosome occurs at a single site to one side of the dyad axis. This site is also in contact with the core histones, and the interactions of the core histones with 5S DNA change as a result of association of the globular domain of histone H5. We discuss evidence for an allosteric change in core histone-5S DNA interactions following the association of the linker histone in the nucleosome.
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histones h2a h2b inhibit the interaction of transcription factor iiia with the Xenopus borealis somatic 5s rna gene in a nucleosome
Proceedings of the National Academy of Sciences of the United States of America, 1992Co-Authors: Jeffrey J. Hayes, Alan P. WolffeAbstract:Abstract A Xenopus borealis somatic 5S RNA gene was assembled with either the complete octamer of histones, (H2A/H2B/H3/H4)2, or the (H3/H4)2 tetramer of histones that comprises the central protein kernel of the nucleosome. Gel-mobility shifts, DNase I protection, and immunoblotting assays demonstrate that the class III transcription factor IIIA (TFIIIA) readily interacts with 5S DNA associated with the tetramer but that little or no binding is detected when 5S DNA is associated with the full octamer of histones. Thus, the presence of histones H2A and H2B in the 5S nucleosome significantly inhibits the interaction of TFIIIA with its cognate binding site within the 5S RNA gene. We propose that either the depletion of histones H2A and H2B from preexisting nucleosomes or the staged assembly of chromatin after replication in which a tetramer of histones H3/H4 associates with DNA before histones H2A/H2B will facilitate the binding of transcription factors to their cognate DNA sequences.
Milena Mechkarska - One of the best experts on this subject based on the ideXlab platform.
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a comparison of host defense peptides in skin secretions of female Xenopus laevis Xenopus borealis and x borealis x laevis f1 hybrids
Peptides, 2013Co-Authors: Milena Mechkarska, Mohammed A Meetani, Hubert Vaudry, Jérôme Leprince, Ben J. Evans, Manju Prajeep, Michael J ConlonAbstract:Peptidomic analysis was used to compare the diversity of host-defense peptides in norepinephrine-stimulated skin secretions from laboratory-generated female F1 hybrids of Xenopus laevis and Xenopus borealis (Pipidae). Skin secretions of hybrids with maternal X. laevis (XLB) contained 12 antimicrobial peptides (AMPs), comprising 8 from X. laevis and 4 from X. borealis. Magainin-B1, XPF-B1, PGLa-B1 CPF-B2, CPF-B3 and CPF-B4 from X. borealis and XPF-1, XPF-2, and CPF-6 from X. laevis were not detected and CPF-1 and CPF-7 were present in low concentration. The secretions contained caerulein and caerulein-B1 derived from both parents but lacked X. laevis xenopsin and X. borealis caerulein-B2. Skin secretions of hybrids with maternal X. borealis (XBL) contained 14 AMPs comprising 6 from X. borealis and 8 from X. laevis. Magainin-B1, XPF-B1, PGLa-B1, CPF-B2, XPF-1, CPF-5, and CPF-7 were absent and CPF-B3, CPF-B4, CPF-1 and CPF-6 were present only in low concentration. Xenopsin and caerulein were identified in the secretions but caerulein-B2 was absent and caerulein-B1 was present in low concentration. No peptides were identified in secretions of either XLB or XBL hybrids that were not present in the parental species. The data indicate that hybridization between X. laevis and X. borealis results in increased diversity of host-defense peptides in skin secretions but point to extensive AMP gene silencing compared with previously studied female X. laevis×X. muelleri F1 hybrids and no novel peptide expression.
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Host-defense peptides in skin secretions of African clawed frogs (Xenopodinae, Pipidae).
General and Comparative Endocrinology, 2011Co-Authors: J. Michael Conlon, Milena Mechkarska, Jay D. KingAbstract:Abstract African clawed frogs of the Xenopodinae ( Xenopus + Silurana ) constitute a well-defined system in which to study the evolutionary trajectory of duplicated genes and are a source of antimicrobial peptides with therapeutic potential. Allopolyploidization events within the Xenopodinae have given rise to tetraploid, octoploid, and dodecaploid species. The primary structures and distributions of host-defense peptides from the tetraploid frogs Xenopus borealis , Xenopus clivii , Xenopus laevis , Xenopus muelleri , “X. muelleri West”, and Xenopus petersii may be compared with those from the octoploid frogs Xenopus amieti and X . andrei . Similarly, components in skin secretions from the diploid frog Silurana tropicalis may be compared with those from the tetraploid frog Silurana paratropicalis . All Xenopus antimicrobial peptides may be classified in the magainin, peptide glycine-leucine-amide (PGLa), caerulein-precursor fragment (CPF), and xenopsin-precursor fragment (XPF) families. However, the numbers of paralogs from the octoploid frogs were not significantly greater than the corresponding numbers from the tetraploid frogs. Magainins were not identified in skin secretions of Silurana frogs and the multiplicity of the PGLa, CPF, and XPF peptides from S . paratropicalis was not greater than that of S . tropicalis . The data indicate, therefore, that nonfunctionalization (gene silencing) has been the most common fate of antimicrobial peptide genes following polyploidization. While some duplicated gene products retain high antimicrobial potency (subfunctionalization), the very low activity of others suggests that they may be evolving towards a new biological role (neofunctionalization). CPF-AM1 and PGLa-AM1 from X . amieti show potential for development into anti-infective agents for use against antibiotic-resistant Gram-negative bacteria.
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caerulein and xenopsin related peptides with insulin releasing activities from skin secretions of the clawed frogs Xenopus borealis and Xenopus amieti pipidae
General and Comparative Endocrinology, 2011Co-Authors: Osama K. Zahid, Mohammed A Meetani, Milena Mechkarska, Yasser Abdelwahab, Peter R Flatt, Michael J ConlonAbstract:Caerulein-related peptides were identified in norepinephrine-stimulated skin secretions of the tetraploid frog Xenopus borealis and the octoploid frog Xenopus amieti using negative ion electrospray mass spectrometry and their primary structures determined by positive ion tandem (MS/MS) mass spectrometry. X. borealis caerulein-B1 (pGlu-Gln-Asp-Tyr(SO(3))-Gly-Thr-Gly-Trp-Met-Asp-Phe.NH2) contains an additional Gly(5) residue compared with X. laevis caerulein and caerulein-B2 (pGlu-Asp-Tyr(SO(3))-Thr-Gly-Trp-Met-Asp-Phe.NH2) contains a Gln(2) deletion. X. amieti caerulein was identical to the X. laevis peptide. In addition, xenopsin, identical to the peptide from X. laevis, together with xenopsin-AM2 (pGlu-Gly-Arg-Arg-Pro-Trp-Ile- Leu) that contains the substitution Lys(3) -> Arg were isolated from X. amieti secretions. X. borealis caerulein-B1, and X. amieti xenopsin and xenopsin-AM2 produced significant (P = 30 nM. The peptides did not stimulate the release of lactate dehydrogenase at concentrations up to 3 mu M demonstrating that the integrity of the plasma membrane had been preserved. While their precise biological role is unclear, the caerulein- and xenopsin-related peptides may constitute a component of the animal's chemical defenses against predators. (C) 2011 Elsevier Inc. All rights reserved.
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Antimicrobial peptides with therapeutic potential from skin secretions of the Marsabit clawed frog Xenopus borealis (Pipidae).
Comparative Biochemistry and Physiology C-toxicology & Pharmacology, 2010Co-Authors: Milena Mechkarska, Jay D. King, Eman Ahmed, Laurent Coquet, Hubert Vaudry, Thierry Jouenne, Jérôme Leprince, J. Michael ConlonAbstract:Abstract Nine peptides with differential growth inhibitory activity against Escherichia coli and Staphylococcus aureus were isolated from norepinephrine-stimulated skin secretions of the tetraploid frog Xenopus borealis Parker, 1936 (Pipidae). Structural characterization of the peptides demonstrated that they were orthologous to magainin-2 (1 peptide), peptide glycine–leucine-amide, PGLa (2 peptides), caerulein-precursor fragments, CPF (4 peptides), and xenopsin-precursor fragments, XPF (2 peptides), previously isolated from Xenopus laevis and X. amieti . In addition, a second magainin-related peptide (G**KFLHSAGKFGKAFLGEVMIG) containing a two amino acid residue deletion compared with magainin-2 was identified that had only weak antimicrobial activity. The peptide with the greatest potential for development into a therapeutically valuable anti-infective agent was CPF-B1 (GLGSLLGKAFKIGLKTVGKMMGGAPREQ) with MIC = 5 μM against E. coli , MIC = 5 μM against S. aureus , and MIC = 25 μM against Candida albicans , and low hemolytic activity against human erythrocytes (LC 50 > 200 μM). This peptide was also the most abundant antimicrobial peptide in the skin secretions. CPF-B1 was active against clinical isolates of the nosocomial pathogens, methicillin-resistant S. aureus (MRSA) and multidrug-resistant Acinetobacter baumannii (MDRAB) with MIC values in the range 4–8 μM.
Dmitry Pruss - One of the best experts on this subject based on the ideXlab platform.
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a single high affinity binding site for histone h1 in a nucleosome containing the Xenopus borealis 5 s ribosomal rna gene
Journal of Biological Chemistry, 1996Co-Authors: Karl P Nightingale, Dmitry Pruss, Alan P. WolffeAbstract:Abstract We have reconstituted nucleosomes containing the Xenopus borealis 5 S rRNA gene, a single histone octamer, and 1 or 2 molecules of histone H1. We determine that the 1st molecule of histone H1 to associate with the 5 S nucleosome binds with high affinity (K 2 nM), and the 2nd molecule of H1 binds with a reduced affinity (K 10 nM). This latter binding is comparable with the association of histone H1 with naked DNA. Neither molecule of histone H1 alters the helical periodicity of DNA in the nucleosome as revealed by hydroxyl radical cleavage. We conclude that although multiple molecules of histone H1 can associate with nucleosomal DNA, there is only a single high affinity binding site for histone H1 within the 5 S nucleosome.
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Contacts of the globular domain of histone H5 and core histones with DNA in a "chromatosome"
Proceedings of the National Academy of Sciences of the United States of America, 1994Co-Authors: Jeffrey J. Hayes, Dmitry Pruss, Alan P. WolffeAbstract:Abstract The globular domain of histone H5 is found to asymmetrically associate with a nucleosome core including the Xenopus borealis somatic 5S RNA gene. Histones H2A and H2B are required for association of histone H5. Strong crosslinking of the globular domain of histone H5 to the 5S DNA in the nucleosome occurs at a single site to one side of the dyad axis. This site is also in contact with the core histones, and the interactions of the core histones with 5S DNA change as a result of association of the globular domain of histone H5. We discuss evidence for an allosteric change in core histone-5S DNA interactions following the association of the linker histone in the nucleosome.
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histone dna contacts in a nucleosome core containing a Xenopus 5s rrna gene
Biochemistry, 1993Co-Authors: Dmitry PrussAbstract:We describe histone-DNA cross-linking in a nucleosome core containing a Xenopus borealis somatic 5S rRNA gene. Histones H3 and H4 are cross-linked to DNA within 30 bp to either side of the dyad axis. Histones H2A/H2B and H3 are cross-linked to DNA where it enters and exists, wrapping around the histone octamer. These latter interactions extend for 80 bp to one side of the dyad axis of the nucleosome core, including the entire binding site for transcription factor TFIIIA. These extensive interactions with linker DNA might account for inhibition of TFIIIA binding and also might assist in the folding of internucleosomal DNA within the chromatin fiber.
J. Michael Conlon - One of the best experts on this subject based on the ideXlab platform.
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Host-defense peptides in skin secretions of African clawed frogs (Xenopodinae, Pipidae).
General and Comparative Endocrinology, 2011Co-Authors: J. Michael Conlon, Milena Mechkarska, Jay D. KingAbstract:Abstract African clawed frogs of the Xenopodinae ( Xenopus + Silurana ) constitute a well-defined system in which to study the evolutionary trajectory of duplicated genes and are a source of antimicrobial peptides with therapeutic potential. Allopolyploidization events within the Xenopodinae have given rise to tetraploid, octoploid, and dodecaploid species. The primary structures and distributions of host-defense peptides from the tetraploid frogs Xenopus borealis , Xenopus clivii , Xenopus laevis , Xenopus muelleri , “X. muelleri West”, and Xenopus petersii may be compared with those from the octoploid frogs Xenopus amieti and X . andrei . Similarly, components in skin secretions from the diploid frog Silurana tropicalis may be compared with those from the tetraploid frog Silurana paratropicalis . All Xenopus antimicrobial peptides may be classified in the magainin, peptide glycine-leucine-amide (PGLa), caerulein-precursor fragment (CPF), and xenopsin-precursor fragment (XPF) families. However, the numbers of paralogs from the octoploid frogs were not significantly greater than the corresponding numbers from the tetraploid frogs. Magainins were not identified in skin secretions of Silurana frogs and the multiplicity of the PGLa, CPF, and XPF peptides from S . paratropicalis was not greater than that of S . tropicalis . The data indicate, therefore, that nonfunctionalization (gene silencing) has been the most common fate of antimicrobial peptide genes following polyploidization. While some duplicated gene products retain high antimicrobial potency (subfunctionalization), the very low activity of others suggests that they may be evolving towards a new biological role (neofunctionalization). CPF-AM1 and PGLa-AM1 from X . amieti show potential for development into anti-infective agents for use against antibiotic-resistant Gram-negative bacteria.
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Antimicrobial peptides with therapeutic potential from skin secretions of the Marsabit clawed frog Xenopus borealis (Pipidae).
Comparative Biochemistry and Physiology C-toxicology & Pharmacology, 2010Co-Authors: Milena Mechkarska, Jay D. King, Eman Ahmed, Laurent Coquet, Hubert Vaudry, Thierry Jouenne, Jérôme Leprince, J. Michael ConlonAbstract:Abstract Nine peptides with differential growth inhibitory activity against Escherichia coli and Staphylococcus aureus were isolated from norepinephrine-stimulated skin secretions of the tetraploid frog Xenopus borealis Parker, 1936 (Pipidae). Structural characterization of the peptides demonstrated that they were orthologous to magainin-2 (1 peptide), peptide glycine–leucine-amide, PGLa (2 peptides), caerulein-precursor fragments, CPF (4 peptides), and xenopsin-precursor fragments, XPF (2 peptides), previously isolated from Xenopus laevis and X. amieti . In addition, a second magainin-related peptide (G**KFLHSAGKFGKAFLGEVMIG) containing a two amino acid residue deletion compared with magainin-2 was identified that had only weak antimicrobial activity. The peptide with the greatest potential for development into a therapeutically valuable anti-infective agent was CPF-B1 (GLGSLLGKAFKIGLKTVGKMMGGAPREQ) with MIC = 5 μM against E. coli , MIC = 5 μM against S. aureus , and MIC = 25 μM against Candida albicans , and low hemolytic activity against human erythrocytes (LC 50 > 200 μM). This peptide was also the most abundant antimicrobial peptide in the skin secretions. CPF-B1 was active against clinical isolates of the nosocomial pathogens, methicillin-resistant S. aureus (MRSA) and multidrug-resistant Acinetobacter baumannii (MDRAB) with MIC values in the range 4–8 μM.
