Human DNA topoisomerase I is encoded by a single-copy gene that maps to chromosome region 20q12-13.2

cDNA clones of the human TOP1 gene encoding DNA topoisomerase I (EC 5.99.1.2) have been obtained by immunochemical screening of phage lambda libraries expressing human cDNA segments, using rabbit antibodies raised against purified HeLa DNA topoisomerase I. Hybridization patterns between the cloned cDNA sequences and human cellular DNA and cytoplasmic mRNAs indicate that human TOP1 is a single-copy gene. The chromosomal location of the gene has been mapped to the long arm of chromosome 20, in the region q12-13.2, by hybridization of a radioactively labeled TOP1 cDNA probe to human metaphase chromosomes and to a panel of rodent-human somatic hybrids retaining overlapping subsets of human chromosomes.

The primary structure of chicken liver cytochrome b5 deduced from the DNA sequence of a cDNA clone

A cDNA clone encoding the chicken liver cytochrome b5 was isolated by probing a library with synthetic oligonucleotides based on a partial amino acid sequence of the protein. Determination of the DNA sequence indicated a 414-nucleotide open reading frame which encodes a 138-amino acid residue polypeptide. The open reading frame contains 6 amino acids at the amino terminus which were not present on any of the cytochrome b5 polypeptides for which the amino acid sequence has been determined directly, suggesting that the protein is proteolytically processed to the mature form. The results of genomic Southern analysis were consistent with the presence of two structurally different genes in the chicken genome, raising the possibility that the soluble and membrane-bound forms of the protein are the products of separate genes.

pK shift of functional group in mechanochemical coupling due to hydrophobic effect: evidence for an apolar-polar repulsion free energy in water

In the sequential polypeptide poly[4(VPGVG),(VPGEG)] and its more hydrophobic analog poly[4(IPGVG),(IPGEG)] when the material is gamma-irradiation cross-linked to form an elastomeric matrix, mechanochemical coupling occurs on changing the pH, that is, motion and mechanical work are achieved by a change in proton chemical potential. The temperature dependence of aggregation at different pH values in phosphate buffered saline demonstrates the pK to be shifted approximately one pH unit higher for the more hydrophobic sequential polypeptide. The pH dependence of contraction or relaxation for each elastomer shows a similar shift. Data are reviewed and 2D-NMR data are presented which argue that the pK shift is not due to different conformations of the polypentapeptides. Specifically it is proposed that there exist a competition between carboxylates and hydrophobic side chains for mutually incompatible water structures; this results in an apolar-polar repulsion free energy in water with the difference in free energy reflecting the difference in the lle and Val hydrophobicities.

Mechanochemical coupling in synthetic polypeptides by modulation of an inverse temperature transition

For the polypentapeptide of elastin, (L-Val-L-Pro-Gly-L-Val-Gly)n, and appropriate analogs when suitably cross-linked, it has been previously demonstrated that development of elastomeric force at fixed length and length changes at fixed load occur as the result of an inverse temperature transition, with the temperature of the transition being inversely dependent on the hydrophobicity of the polypeptide. This suggests that at fixed temperature a chemical means of reversibly changing the hydrophobicity could be used for mechanochemical coupling. Evidence for this mechanism of mechanochemical coupling is given here with a 4%-Glu-polypentapeptide, in which the valine in position 4 is replaced in 1 out of 5 pentamers by a glutamic acid residue. Before cross-linking, the temperature for aggregation of 4%-Glu-polypentapeptide is remarkably sensitive to pH, shifting from 25 degrees C at pH 2 to 70 degrees C at pH 7.4 in phosphate-buffered saline (PBS). At 37 degrees C, the cross-linked 4%-Glu-polypentapeptide matrix in PBS undergoes a pH-modulated contraction and relaxation with a change from pH 4.3 to 3.3 and back. The mean distance between carboxylates at pH 4.3 in the elastomeric matrix is greater than 40 A, twice the mean distance between negatively charged species in PBS. Accordingly, charge-charge repulsion is expected to make little or no contribution to the coupling. Mechanochemical coupling is demonstrated at fixed load by monitoring pH dependence of length and at constant length by monitoring pH dependence of force. To our knowledge, this is the first demonstration of mechanochemical coupling in a synthetic polypeptide and the first system to provide a test of the recent proposal that chemical modulation of an inverse temperature transition can be a mechanism for mechanochemical coupling. It is suggested that phosphorylation and dephosphorylation may modulate structure and forces in proteins by locally shifting the temperatures of inverse temperature transitions.

Lethality of a dut (deoxyuridine triphosphatase) mutation in Escherichia coli

A chloramphenicol resistance gene was cloned into a plasmid-borne dut gene, producing an insertion mutation that was then transferred to the chromosome by allelic exchange. The mutation could not be acquired by haploid strains through substitutive recombination, even when two flanking markers were simultaneously transduced. The insertion was easily transferred, via generalized transduction, into the chromosomal dut region of strains harboring a lambda dut + transducing phage; however, the resulting dut mutant/lambda dut + merodiploid could not then be cured of the prophage. This apparent lethality of the mutation could not be explained by effects on adjacent genes; the dfp gene retained complementing activity, and a ttk insertion mutant was viable. The dut gene product, deoxyuridine triphosphatase, is known to reduce incorporation of uracil into DNA and to be required in the de novo synthesis of thymidylate. Therefore, an attempt was made to determine whether the dut insertion would be tolerated in strains carrying the following compensatory mutations: dcd (dCTP deaminase) and cdd (deoxycytidine deaminase), which should reduce dUTP formation; ung (uracil-DNA glycosylase), which should reduce fatally excessive excision repair; deoA (thymidine phosphorylase), which should enhance the utilization of exogenous thymidine; and sulA, which should reduce the lethal side effects of SOS regulon induction. These mutations, either alone or in various combinations, did not permit the survival of a haploid dut insertion mutant, suggesting that the dut gene product might have an essential function apart from its deoxyuridine triphosphatase activity.

Double stranded DNA sequencing as a choice for DNA sequencing

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Spatial heterogeneity of local blood flow and metabolite content in dog hearts

Spatial variation (heterogeneity) of myocardial blood flow was studied under basal conditions in relation to four biochemical markers: creatine kinase (CK), lactate dehydrogenase (LDH), ATP, and glycogen. A total of 508 individual 0.5-g samples from the left ventricular free wall was studied in 12 dogs. Myocardial blood flow was measured by radioactive microspheres (15 micron diam) injected via a pigtail catheter into the left ventricle during light sedation (closed-chest flow measurements); following thoracotomy, a second set of microspheres was injected via a catheter into the left atrium (open-chest flow measurements, n = 5). In 27-54 samples/heart, myocardial blood flow, CK, LDH, protein, ATP, and glycogen were determined, permitting a direct correspondence between local blood flow and metabolic markers in each sample and an assessment of the spatial heterogeneity of flow and metabolite content. Correlations between myocardial blood flow per gram tissue and metabolite concentration per gram tissue in pooled data were weak but significant: partial correlation coefficients were 0.137 for CK (P = 0.024), 0.167 for LDH (P = 0.006), 0.341 for ATP (P less than 0.001), 0.123 for glycogen (P = 0.053), but not significant for protein vs. myocardial blood flow. The coefficient of variation, which defines the extent of spatial heterogeneity, averaged 20% for closed-chest flow measurements, 19% for open-chest flow measurements, 22% for CK, 17% for LDH, 15% for protein, 8% for ATP, and 18% for glycogen; these values are over and above the variability due to the technique error, indicating a definite physiological spatial variability. The correlation between local blood flow and the studied metabolites can only explain a minor portion of the spatial heterogeneity of myocardial blood flow. Although a physiological link between blood flow and metabolite content for small regions of the heart is demonstrated, the true local variability of blood flow may be modulated predominantly by other factors.

Involvement of DNA topoisomerase I in transcription of human ribosomal RNA genes

Treatment of HeLa cells with a DNA topoisomerase I-specific inhibitor, camptothecin, results in rapid cessation of the synthesis of the 45S rRNA precursor. The inhibition of rRNA synthesis is reversible following drug removal and correlates with the presence of camptothecin-trapped topoisomerase I-DNA abortive complexes, which can be detected as topoisomerase I-linked DNA breaks upon lysis with sodium dodecyl sulfate. These breaks were found to be concentrated within the transcribed region of human rRNA genes. No such sites can be detected in the inactive human rRNA genes in mouse-human hybrid cells, suggesting a preferential association of topoisomerase I with actively transcribed genes. The distribution of RNA polymerase molecules along the transcription unit of human rRNA genes in camptothecin-treated HeLa cells, as assayed by nuclear run-on transcription, shows a graded decrease of the RNA polymerase density toward the 3' end of the transcription unit; the density is minimally affected near the 5' start of the transcription unit. These results suggest that DNA topoisomerase I is normally involved in the elongation step of transcription, especially when the transcripts are long, and that camptothecin interferes with this role.

Profound structural alterations of the extracellular collagen matrix in postischemic dysfunctional ("stunned") but viable myocardium

Ultrastructural studies of the extracellular collagen matrix were made on the "stunned" myocardium using scanning, conventional and high voltage transmission electron microscopy and light microscopy. Regional myocardial dysfunction was produced by 12 sequential 5 minute occlusions of the left anterior descending coronary artery, separated by 10 minute intervals of reperfusion. A final 90 minute reperfusion period documented persistent myocardial dysfunction. At the end of the final reperfusion period, the percent systolic shortening, measured by sonomicrometers, was depressed significantly to 35 +/- 9% of baseline. The heart was then perfusion fixed, and samples were taken from both control and stunned areas. No changes associated with irreversible cellular damage were noted in the stunned region. However, scanning electron microscopy of the stunned area showed that the extracellular collagen matrix underwent profound structural changes. Collagen cables were roughened, uncoiled and discontinuous. Linear grooves on the surface of the myocytes were frequently seen, indicating complete loss of collagen cables. The usual dense collagen weave surrounding myocytes became patchy or absent. Myocyte to myocyte struts were sparse and frequently absent, with remnant nodular or nublike structures indicative of breakage. High voltage electron microscopy of the stunned area showed that the collagen struts were discontinuous and vacuolated with rounded tips. Light microscopy of silver-stained sections of the stunned tissue demonstrated large patchy areas that were devoid of silver, indicating absence of the collagen matrix. There was a progressive increase in percent systolic bulging during each sequential coronary occlusion, suggesting increasing myocardial compliance. These results indicate that the myocardial collagen matrix is severely damaged from reversible ischemic cell injury. The greater myocardial compliance and less effective contractile effort in the stunned myocardium might be explained on a structural basis: disruption of the mechanical coupling function provided by the extracellular collagen matrix.