Mechanistic aspects of promoter binding and chain initiation by RNA polymerase

Summary The physicochemical properties of the interactions of RNA polymerase (RPase) with promoter and nonspecific DNA sequences have been investigated. These show that nonspecific binding is principally an ionic interaction and that promoter binding is more complex, involving nonionic interactions. Nonspecific binding has been shown to be very important in the promoter search, and one-dimensional diffusion can account for the rate at which RPase finds the promoter. Significant differences have been reported in the binding process for various promoters and in the effects of regulatory proteins. Further investigation of these differences will lead to a better understanding of the selectivity and regulation of the initiation process.The pathways of the initiation process have been outlined, by recent studies and considerable progress has been made in determining the rates of interconversion of the intermediate states. A number of questions remain about the detail of initiation and the effects of various parameters on the reactions. Of particular importance is the identification of the point at which the enzyme becomes truly processive. In addition, the step which is rate limiting has not been identified in either the productive or nonproductive process. The mechanistic features of the steps after bond formation are just beginning to yield to investigation.Use of substrate analogs with RPase has led to a picture of the polymerization site according to the ability of the enzyme to incorporate analogs. Base specificity appears to be determined primarily by interaction with the template rather than the enzyme, but the ribose moiety must interact with the site quite specifically. The orientation of the phosphate residues has been determined by NMR, which has also proved to be a valuable probe of the initiation site. At this site base specificity is resident in the enzyme and expressed through the interaction of the base and intrinsic metal, as shown by studies with the Cobalt substituted enzyme. In both initiation and polymerization, the reaction has been shown to proceed by inversion of configuration. Techniques similar to those used for initiation will probably be applied to the polymerization reaction as well, which has not recently received as much attention with respect to mechanism. Functional phenomena such as pausing make the polymerization process particularly promising for producing insight into RPase reactions.     

Polyacetylenes in Hawaiian bidens

Leaves and roots of 19 species and six subspecies of Hawaiian Bidens were examined for polyacetylenes. Eleven C₁₃ hydrocarbons, aromatic and thiophenyl derivatives, one C₁₄ tetrahydropyran and three C₁₇ hydrocarbons were isolated all identified. All can be derived from a common precursor, oleic acid. Polyacetylenes were not detected in the leaves of 13 taxa although they are found in the roots of all. The occurrence of 2-[2-phenyl-ethyne-1-yl]-5 acetoxymethyl thiopene in Bidens has not been previously reported. Its ubiquitous presence is consistent with other evidence that the Hawaiian species are all derived from a single ancestral immigrant to the islands. Most taxa could be distinguished by their complement of polyacetylenes in roots and leaves. No variation was found to occur within taxa except in B. torta, in which each population had a unique array of polyacetylenes. Above the species level there appeared to be no taxonomically significant pattern to the distribution of polyacetylenes in this group.     

Linkages between seagrass,mangrove and saltmarsh as fish habitat in the Botany Bay estuary,New South Wales

Shallow-water vegetated estuarine habitats, notably seagrass, mangrove and saltmarsh, are known to be important habitats for many species of small or juvenile fish in temperate Australia. However, the movement of fish between these habitats is poorly understood, and yet critical to the management of the estuarine fisheries resource. We installed a series of buoyant pop nets in adjacent stands of seagrass, mangrove and saltmarsh in order to determine how relative abundance of fishes varied through lunar cycles. Nets were released in all habitats at the peak of the monthly spring tide for 12 months, and in the seagrass habitat at the peak of the neap tide also. The assemblage of fish in each habitat differed during the spring tides. The seagrass assemblage differed between spring and neap tide, with the neap tide assemblage showing greater abundances of fish, particularly those species which visited the adjacent habitats when inundated during spring tides. The result supports the hypothesis that fish move from the seagrass to the adjacent mangrove and saltmarsh during spring tides, taking advantage of high abundances of zooplankton, and use seagrass as a refuge during lower tides. The restoration and preservation of mangrove and saltmarsh utility as fish habitat may in some situations be linked to the proximity of available seagrass.     

Unprocessed Bran in Treatment of Diverticular Disease of the Colon

Seventy patients with diverticular disease of the colon were treated with a high-residue, low-sugar diet including unprocessed bran. Follow-up for an average of 22 months showed marked relief of symptoms in 62 patients. Bowel habit was restored towards normal and abdominal discomfort relieved. Only seven patients were unable to give up the use of laxatives. Eight patients did not tolerate the bran diet, and one of these needed surgical treatment. None of the 62 patients who took the diet needed surgery.     

Identification of a new subpopulation of triad junctions isolated from skeletal muscle; Morphological correlations with intact muscle

Summary It has been previously recognized that a number of protocols may cause breakage of the triad junction and separation of the constituent organelles of skeletal muscle. We now describe a fraction of triad junctions which is refractory to the known protocols for disruption. Triads were passed through a French press and the dissociated organelles were separated on a sucrose density gradient, which was assayed for PN200-110, ouabain and ryanodine binding. Ryanodine binding showed a single peak at the density of heavy terminal cisternae. On the other hand, the PN200-110 and ouabain, which are external membrane ligands, bound in two peaks: one at the free transverse tubule region and the other at the light terminal cisternae. Similarly, a two peak pattern of PN200-110 and ouabain binding was observed when triad junctions were broken by the Ca²⁺-dependent protease, calpain, which selectively hydrolyzes the junctional foot protein. The light terminal cisternae vesicles were subjected to three different procedures of junctional breakage: French press, hypertonic salt treatment, and protease digestion using calpain or trypsin. The treated membranes were then centrifuged on density gradients. Only extensive trypsin digestion caused a partial shift of ouabain activity into the free transverse tubule region. These observations suggest that the triads are a composite mixture of breakage susceptible, weak, and breakage resistant, strong, triads. Scatchard analysis of PN200-110 suggests that the transverse tubules of strong triads contain a relatively high number of dihydropyridine receptors compared to those of weak triads. Thin section electron microscopic images of the strong triads comparable to those of intact muscle are presented.     

Photoaffinity Labeling with Progesterone-11α-Hemisuccinate-(2-[125I]Iodohistamine) Identifies Four Protein Bands in Mouse Brain Membranes

Abstract: The radiolabeled progesterone (PG) analogue progesterone-11α-hemisuccinate-(2-[¹²⁵I]iodohistamine) was used to label PG binding proteins in brain membranes from mouse cerebellum. Photoaffinity labeling and sodium dodecyl sulfate-polyacrylamide gel electrophoresis identified specific PG binding protein bands 1–4 of 64−29 kDa. Bands 1 and 4 were well resolved on the gel and easily quantified. Preincubation with PG inhibited photolabeling in a dose-dependent manner. The labeling was specific with respect to steroid structure. For band 1, the extent of inhibition of labeling by PG and 3α,5α-pregnanolone (3α) was pronounced. Other steroids such as testosterone (Tes), estradiol (Est), and corticosterone (Cor) were less effective, whereas pregnenolone sulfate (PS) and cholesterol (Cho) were ineffective. With respect to band 4, Est was the most effective; PG, 3α, and Tes were intermediate; and PS, Cho, and Cor were ineffective. The results describe specific membrane proteins that bind PG (band 1) and Est (band 4).