Asp537, Asp812 are essential and Lys631, His811 are catalytically significant in bacteriophage T7 RNA polymerase activity.

To define catalytically essential residues of bacteriophage T7 RNA polymerase, we have generated five mutants of the polymerase, D537N, K631M, Y639F, H811Q and D812N, by site-directed mutagenesis and purified them to homogeneity. The choice of specific amino acids for mutagenesis was based upon photoaffinity-labeling studies with 8-azido-ATP and homology comparisons with the Klenow fragment and other DNA/RNA polymerases. Secondary structural analysis by circular dichroism indicates that the protein folding is intact in these mutants. The mutants D537N and D812N are totally inactive. The mutant K631M has 1% activity, confined to short oligonucleotide synthesis. The mutant H811Q has 25% activity for synthesis of both short and long oligonucleotides. The mutant Y639F retains full enzymatic activity although individual kinetic parameters are somewhat different. Kinetic parameters, (kcat)app and (Km)app for the nucleotides, reveal that the mutation of Lys to Met has a much more drastic effect on (kcat)app than on (Km)app, indicating the involvement of K631 primarily in phosphodiester bond formation. The mutation of His to Gln has effects on both (kcat)app and (Km)app; namely, three- to fivefold reduction in (kcat)app and two- to threefold increase in (Km)app, implying that His811 may be involved in both nucleotide binding and phosphodiester bond formation. The ability of the mutant T7 RNA polymerases to bind template has not been greatly impaired. We have shown that amino acids D537 and D812 are essential, that amino acids K631 and H811 play significant roles in catalysis, and that the active site of T7 RNA polymerase is composed of different regions of the polypeptide chain. Possible roles for these catalytically significant residues in the polymerase mechanism are discussed.     

Oxygen concentration profiles and exchange in sediment cores with circulated overlying water

SUMMARY. 1. The overlying water of intact sediment cores was constantly stirred with an impeller at a rate sufficient to mix turbulently the water column and maintain the diffusive boundary layer at a determined thickness. The system allowed standardization of water circulation in laboratory sediment core experiments.
2. Both oxygen concentration and oxygen penetration depth in the sediments decreased, the former by 70% and the latter from 4.2 mm to 2.0 mm, when the overlying water was not stirred for 24 h, as measured with oxygen microelectrodes in a lake sediment core.
3. Oxygen profiles measured in sediment cores in the laboratory were similar to those measured in situ when the overlying water was stirred with an impeller at such a rate that a similar thickness of the diffusive boundary layer at the sediment-water interface developed in the laboratory as that in situ.
4. Sediment oxygen consumption was calculated from: (1) measured oxygen profiles in the diffusive boundary layer and the molecular diffusion coefficient for oxygen in water; (2) the measured oxygen decrease in the top of the sediments and the estimated diffusion coefficient in the sediment; and (3) by oxygen differences in the overlying water after incubation of sediment cores.     

The effects of cervical dilation on plasma PGFM, progesterone and the duration of luteal function in diestrous mares

Transcervical diagnostic techniques may alter the length of the equine estrous cycle and affect subsequent luteal function. Therefore, nine mares were used to determine the effect of cervical dilation on plasma 13, 14-dihydro, 15-keto-prostaglandin F(2) (PGFM), progesterone (P(4)) and posttreatment duration of luteal function. Mares were given a daily score of 0 to 4 based on sexual receptivity. Five days following the end of receptivity, mares were randomly assigned to one of three, 3 x 3 latin squares. Control mares received no cervical dilation. Cervically stimulated mares recieved cervical dilation for 60 sec. Cervically stimulated plus inhibitor mares were dilated similarly to cervically stimulated mares, but received a prostaglandin synthetase inhibitor 30 min prior to treatment. Each mare completed all three treatments in three consecutive estrous cycles. Plasma PGFM and P(4) were determined by RIA. Plasma PGFM was lower (P<0.05) in cervically stimulated plus inhibitor than control and cervically stimulated mares. In addition, plasma P(4) was lower (P<0.10) in cervically stimulated plus inhibitor than in control and cervically stimulated mares. Luteal function following treatments did not differ. These data indicate that neither plasma PGFM and P(4) nor the duration of luteal function were affected by cervical dilation. However, administration of a prostaglandin synthetase inhibitor prior to cervical dilation decreased plasma PGFM and P(4) concentrations.     

Measles-specific T cell clones derived from a twin with multiple sclerosis: genetic restriction studies

The association between multiple sclerosis (MS) and HLA-DR2 suggests that the disease may be associated with an aberrant immune response, likely directed against an antigen of either viral or host origin. We have used measles virus-specific T cell clones derived from a patient with MS to study genetic restriction patterns of antigen presentation by macrophage-enriched (E-) populations. Twenty-two clones proliferated in response to measles-infected Vero cells but not to mumps-infected or uninfected Veros. E- cells from both the autologous subject and her healthy, measles nonresponder identical twin were capable of presenting antigen to all clones. Studies with E- cells obtained from a panel of cell donors demonstrated clones which recognized antigen in association with D2/DR2, DR4, subgroups of DR4, and SB3. Three clones recognized antigen only in association with the autologous or twin's cells, but not with other sets of HLA-matched E-cells obtained from healthy donors or from other patients with MS. These studies indicate that the differing responses to measles virus demonstrated by these two identical twins are not explained by alterations in the interactions between antigen-presenting cells and T cells. Furthermore, at the clonal level, no preferential role is seen for HLA-DR2 as the restricting element for presentation of measles virus to these clones.     

Photoaffinity labeling of DNA-dependent RNA polymerase from Escherichia coli with 8-azidoadenosine 5'-triphosphate

A photoaffinity analogue of adenosine 5'-triphosphate (ATP), 8-azidoadenosine 5'-triphosphate (8-N3ATP), has been used to elucidate the role of the various subunits involved in forming the active site of Escherichia coli DNA-dependent RNA polymerase. 8-N3ATP was found to be a competitive inhibitor of the enzyme with respect to the incorporation of ATP with Ki = 42 microM, while uridine 5'-triphosphate (UTP) incorporation was not affected. UV irradiation of the reaction mixture containing RNA polymerase and [gamma-32P]-8-N3ATP induced covalent incorporation of radioactive label into the enzyme. Analysis by gel filtration and nitrocellulose filter binding indicated specific binding. Subunit analysis by sodium dodecyl sulfate and sodium tetradecyl sulfate gel electrophoresis and autoradiography of the labeled enzyme showed that the major incorporation of radioactive label was in beta' and sigma, with minor incorporation in beta and alpha. The same pattern was observed in both the presence and absence of poly[d(A-T)] and poly[d(A-T)] plus ApU. Incorporation of radioactive label in all bands was significantly reduced by 100-150 microM ATP, while 100-200 microM UTP did not show a noticeable effect. Our results indicate major involvement of the beta' and sigma subunits in the active site of RNA polymerase. The observation of a small extent of labeling of the beta and alpha subunits, which was prevented by saturating levels of ATP, suggests that these subunits are in close proximity to the catalytic site.     

Living Vessel Elements in the Late Metaxylem of Sheathed Maize Roots

The two types of nodal roots of field-grown maize, sheathedand bare, were found to have such different water conductivitiesthat an investigation of the anatomy of their large metaxylemvessels was made. While the vessels of the bare roots were openfor scores of centimetres, those of the sheathed roots werefound to be not vessels but developing vessel elements, withcross walls at 1 mm intervals, and protoplasts. The cross wallsbetween the elements had several unique histochemical properties.Previous investigators have often failed to find the cross wallsbecause they are very easily dislodged during the usual methodsof tissue preparation. They are best identified by microdissectionof fresh xylem. The living elements persist in the late metaxylemup to 20 – 30 cm from the tip. As the roots become longerthan this both the cross walls and the soil sheaths disappearand there is a transition to a bare root with open vessels inthe proximal region. The soil sheath persists a little longerthan the cross walls. The two types are thus stages in a developmentalsequence through which all nodal roots pass. A fundamental differencebetween the two types is in their water status, since the estimatedconductive capacity of a bare root is about 100 times greaterthan that of a sheathed root. These observations point to theneed for a reassessment of the published work on transport ofions into the xylem of grass roots through a reinvestigationof the ‘maturity’ of their xylem vessels. Grass roots, dimorphic roots, ion secretion to xylem, soil sheaths, xylem vessels, xylem differentiation, water conduction, Zea mays L     

A simple model for the optical properties of chiral amides

The intramolecular charge-transfer model for the electronic structure of amides has been extended to include the effects of torsion about the peptide bond (Δω = ω – 180) and pyramidalization at the peptide nitrogen (θ_N). The model is used to calculate the absorption and CD spectra of nonplanar amides as a function of the angles Δω and θ_N. For cis-amides, the rotational strengths of the nπ* and ππ* transitions are much more sensitive to θ_N for a given value of Δω than is the case for trans-amides. The results from the model are compared with available experimental and previous theoretical treatments of such systems. The contributions of nonplanarity in amides to the CD of various polypeptide conformations is discussed. The effects should be negligible for α-helixes but may be quite significant in β-sheets and β-turns. The CD spectrum of unordered peptides would be readily explained if there were a significant bias toward negative Δω values in polypeptides of L-amino acids. However, the evidence currently available does not indicate such a bias.     

Reconstitution of a GTPase Activity a 50S Ribosomal Protein from <Emphasis Type="Italic">E. coli</Emphasis>

DURING each step of peptide chain elongation the ribosome shifts up one triplet along the messenger RNA with concomitant movement of the peptidyl-transfer RNA from the donor to the acceptor site. This process, commonly known as translocation, is triggered by a supernatant protein, factor G, which in association with the ribosome cleaves GTP into GDP and inorganic phosphate^1,2 and it has been argued that the energy liberated in this reaction is used “to carry the complex one triplet forward”³.