Archaeal histones and nucleosomes.
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Archaea↗
Biomedical subjects
S L Pereira
Publications and source records attributed to S L Pereira.
Colposcopy 101: a didactic curriculum to complement the clinical experience.
The family medicine faculty who perform colposcopy at the University of Missouri-Columbia have developed an innovative didactic curriculum that is used as an adjunct to the clinical experience in teaching family practice residents about colposcopy. The curriculum is taught weekly during a colposcopy conference that is held in the family practice center and includes core topic lectures, pathology-correlate lectures, and a journal club. The core lecture series has 26 topics that range from basic to advanced colposcopy. Pathology-correlate lectures combine pathologic evaluation with the clinical colposcopic examination. The journal club systematically reviews and evaluates the colposcopy literature.
Clinical Competence↗
Archaeal histone selection of nucleosome positioning sequences and the procaryotic origin of histone-dependent genome evolution.
Archaeal histones and the eucaryal (eucaryotic) nucleosome core histones have almost identical histone folds. Here, we show that DNA molecules selectively incorporated by rHMfB (recombinant archaeal histone B from Methanothermus fervidus) into archaeal nucleosomes from a mixture of approximately 10(14) random sequence molecules contain sequence motifs shown previously to direct eucaryal nucleosome positioning. The dinucleotides GC, AA (=TT) and TA are repeated at approximately 10 bp intervals, with the GC harmonic displaced approximately 5 bp from the AA and TA harmonics [(GCN(3)AA or TA)(n)]. AT and CG were not strongly selected, indicating that TA not equalAT and GC not equalCG in terms of facilitating archaeal nucleosome assembly. The selected molecules have affinities for rHMfB ranging from approximately 9 to 18-fold higher than the level of affinity of the starting population, and direct the positioned assembly of archaeal nucleosomes. Fourier-transform analyses have revealed that AA dinucleotides are much enriched at approximately 10. 1 bp intervals, the helical repeat of DNA wrapped around a nucleosome, in the genomes of Eucarya and the histone-containing Euryarchaeota, but not in the genomes of Bacteria and Crenarchaeota, procaryotes that do not have histones. Facilitating histone packaging of genomic DNA has apparently therefore imposed constraints on genome sequence evolution, and since archaeal histones have no structure in addition to the histone fold, these constraints must result predominantly from histone fold-DNA contacts. Based on the three-domain universal phylogeny, histones and histone-dependent genome sequence evolution most likely evolved after the bacterial-archaeal divergence but before the archaeal-eucaryal divergence, and were subsequently lost in the Crenarchaeota. However, with lateral gene transfer, the first histone fold could alternatively have evolved after the archaeal-eucaryal divergence, early in either the euryarchaeal or eucaryal lineages.
Archaea↗
MJ1647, an open reading frame in the genome of the hyperthermophile Methanococcus jannaschii, encodes a very thermostable archaeal histone with a C-terminal extension.
All archaeal histones studied to date have similar lengths, 66 to 69 amino acid residues that form three alpha-helices separated by two beta-strand loop regions which together constitute a histone fold. In contrast, the eukaryal nucleosome core histones are larger, 102 to 135 residues in length, with N-terminal and C-terminal extensions flanking the histone fold that participate in gene regulation and higher-order chromatin assembly. In the Methanococcus jannaschii genome, MJ1647 was annotated as an open reading frame predicted to encode an archaeal histone with an approximately 27-amino-acid C-terminal extension, and we here document the DNA binding and assembly properties and thermodynamic stability parameters of the recombinant product of MJ1647 synthesized in Escherichia coli with (rMJ1647) and without (rMJ1647delta) the C-terminal extension. The presence of the C-terminal extension did not prevent homodimer formation or inhibit DNA binding, but the complexes formed by rMJ1647, presumably archaeal nucleosomes containing a (rMJ1647)4 tetramer, were apparently less stable than those formed by (rMJ1647delta)4. The presence of the C-terminal extension increased the thermostability of rMJ1647 when compared with rMJ1647delta in 0.2 M KCl at pH 4 but not in the absence of KCl at pH 1. Based on thermal unfolding transitions, rMJ1647 and rHAfB generated by expression of AF0337 cloned from the genome of the related hyperthermophile Archaeoglobus fulgidus in E. coli were found to have higher thermodynamic stabilities than all previously studied archaeal histones.
Amino Acid Sequence↗
Guided tissue regeneration with a bioabsorbable polylactic acid membrane in gingival recessions. A histometric study in dogs.
BACKGROUND: The goal of this investigation was to histologically and histometrically evaluate the healing process of gingival recessions treated by guided tissue regeneration with bioabsorbable polylactic acid membranes (GTR group) and to compare it to that obtained with coronally positioned flaps (CPF group). METHODS: Gingival recessions were surgically created on the buccal aspect of the upper cuspids of 5 mongrel dogs. The defects (5x7 mm) were exposed to plaque accumulation for 3 months. The contralateral defects were then randomly assigned to each group. After 3 months of healing, the dogs were sacrificed and the blocks were processed. The histometric parameters evaluated included length of sulcular and junctional epithelium, connective tissue adaptation, new cementum, new bone, and defect coverage. RESULTS: The extension of the epithelium was 1.9 +/- 0.8 mm for the GTR-group and 3.0 +/- 0.9 mm for the CPF-group (P = 0.16). The connective tissue adaptation was 0.1 +/- 0.1 and 0.8 +/- 0.5 mm in the GTR group and CPF group, respectively (P = 0.051). The new cementum was 3.8 +/- 1.5 mm and 2.4 +/- 0.3 mm in the GTR group and CPF group, respectively (P= 0.16). Bone formation was 1.1 +/- 0.5 mm in the GTR group and 1.4 +/- 0.2 mm in the CPF group (P = 0.53). Histologically, the defect coverage observed was similar, 90.5% and 91.9% for the GTR group and the CPF group, respectively. No statistical differences in any of the parameters could be detected. CONCLUSIONS: Within the limits of this study, it can be concluded that both procedures resulted in a favorable healing response with no significant difference between the treatments.
Absorbable Implants↗
Archaeal nucleosome positioning sequence from Methanothermus fervidus.
DNA in Methanothermus fervidus, a hyperthermophilic archaeon, is constrained into archaeal nucleosomes in vivo by the archaeal histones HMfA and HMfB. Here, we document the translational and rotational positioning of archaeal nucleosome assembly in vitro by a sequence from the 7S RNA encoding region of the M. fervidus genome. The minor groove of the DNA at the center of the DNA sequence, protected from micrococcal nuclease digestion by incorporation into a positioned archaeal nucleosome, faces away from the archaeal histone core.
Archaea↗
[Paradoxical expansive lesions of cerebral tuberculosis during antitubercular drug therapy].
Central nervous system involvement by tuberculosis presents two main types: tuberculosis meningitis or tuberculoma. This second condition has nowadays ideal conditions for development. We report three patients who developed paradoxical brain tuberculosis expansive lesion during the use of tuberculostatic drugs. The cases point out the importance of tomography follow up of patients who present neurological signs in the course of treatment for tuberculosis. The first two patients presented onset of the a neurological symptoms, associated with lung tuberculosis. The third patient previously had tuberculous meningitis. Computerized tomography was used to follow up these patients. Tuberculostatic and corticoid drugs were used for treatment.
Adult↗
Diversity of prokaryotic chromosomal proteins and the origin of the nucleosome.
All cells employ architectural proteins to confine and organize their chromosomes, and to prevent the otherwise thermodynamically favored collapse of concentrated DNA into compact structures. To accomplish this, prokaryotes have evolved a variety of phylogenetically unrelated, small, basic, sequence-independent DNA-binding proteins that include histones in Euryarchaeota, and members of the HU family in many Bacteria. In contrast, virtually, all Eukarya employ histones, and recently a metabolism-based hypothesis proposed that the eukaryal nucleus originated from a hydrogen-consuming, histone-containing Archaeon. Histones may have prevailed during the evolution of the Eukarya because of their extended interactions with DNA and, as noted, the histone fold now exists not only in histones but also as a structural motif in eukaryal transcription factors.
Amino Acid Sequence↗
Histones and nucleosomes in Archaea and Eukarya: a comparative analysis.
Archaeal histones from mesophilic, thermophilic, and hyperthermophilic members of the Euryarchaeota have primary sequences, the histone fold, tertiary structures, and dimer formation in common with the eukaryal nucleosome core histones H2A, H2B, H3, and H4. Archaeal histones form nucleoprotein complexes in vitro and in vivo, designated archaeal nucleosomes, that contain histone tetramers and protect approximately 60 base pairs of DNA from nuclease digestion. Based on the sequence and structural homologies and experimental data reviewed here, archaeal nucleosomes appear similar, and may be homologous in evolutionary terms and function, to the structure at the center of the eukaryal nucleosome formed by the histone (H3 + H4)2 tetramer.
Amino Acid Sequence↗
Archaeal nucleosomes.
Archaea contain histones that have primary sequences in common with eukaryal nucleosome core histones and a three-dimensional structure that is essentially only the histone fold. Here we report the results of experiments that document that archaeal histones compact DNA in vivo into structures similar to the structure formed by the histone (H3+H4)2 tetramer at the center of the eukaryal nucleosome. After formaldehyde cross-linking in vivo, these archaeal nucleosomes have been isolated from Methanobacterium thermoautotrophicum and Methanothermus fervidus, visualized by electron microscopy on plasmid and genomic DNAs, and shown by immunogold labeling, SDS/PAGE, and immunoblotting to contain archaeal histones, cross-linked into tetramers. Archaeal nucleosomes protect approximately 60 bp of DNA and multiples of approximately 60 bp from micrococcal nuclease digestion, and immunoprecipitation has demonstrated that most, but not all, M. fervidus genomic DNA sequences are associated in vivo with archaeal histones.
Archaea↗
DNA fingerprinting in the rare black-fronted piping guan Pipile jacutinga (Cracidae, Aves).
Brazilian Cracidae are threatened by heavy environmental degradation and hunting. The Black-fronted piping-guan (Pipile jacutinga) used to inhabit the Atlantic coastal highland forests. Now it occurs in limited forest areas where it is rarely seen. Interative management, including captive breeding, might be an important action for its survival. We present data on DNA fingerprinting using Jeffreys' human minisatellite probes 33.6 and 33.15. Our results show that this technique is useful for estimating the genetic variability of natural populations and may help to maintain the genetic variability of captive bred individuals of this species. A linkage analysis of the fingerprint profiles in a family with 7 chicks was performed (to estimate the number of independently segregating loci detected in this species) and at least 16 highly polymorphic independent loci were identified for each probe.
Animals↗