Scaffold/matrix attachment regions (S/MARs): relevance for disease and therapy

There is increasing awareness that processes, such as development, aging and cancer, are governed, to a considerable extent, by epigenetic processes, such as DNA and histone modifications. The sites of these modifications in turn reflect their position and role in the nuclear architecture. Since epigenetic changes are easier to reverse than mutations, drugs that remove or add the chemical tags are at the forefront of research for the treatment of cancerous and inflammatory diseases. This review will use selected examples to develop a unified view that might assist the systematic development of novel therapeutic regimens.

A new search for restorer cytoplasm: the restorer cytoplasm for the gene ms10 most probably does not exist in maize

Since the suggestion concerning the hypothesis of the existence of restorer cytoplasms for some of the known and currently available male sterile (ms) genes in maize, a relatively limited amount of research effort has been made in order to test the hypothesis. Considering the importance of such a phenomenon, we designed a large, two-part experiment to test the idea more seriously. In the first part, 50 randomly chosen, medium-late open-pollinated (OP) varieties of maize from the Zemun Polje (ZP) collection were tested for the presence of the restorer cytoplasm in some currently known ms-genes in maize (ms1, ms2, ms3, ms4, ms5, ms6, ms7, ms8, ms9, ms11, ms12, ms13, ms17, ms22, ms23, and ms24). In the second part, the whole ZP collection of maize germplasm (more than 4,000 entries) was tested for the presence of the restorer cytoplasm for the gene ms10. After the first basic screening of OP varieties, more than 70 nonsegregating "candidates" were identified; however, after additional screening of the collection and the direct testing with respective homozygous ms-testers, all of them showed segregation, indicating that the restorer cytoplasm does not exist, especially the gene ms10. While performing this experiment, we discovered almost a hundred sources of male sterile cytoplasm, which were distinguished by their overwhelming frequency of male sterile plants in segregating test progenies.

Secondary structure and mutational analysis of the ribosomal frameshift signal of rous sarcoma virus

Expression of the Gag-Pol polyprotein of Rous sarcoma virus (RSV) requires a -1 ribosomal frameshifting event at the overlap region of the gag and pol open reading frames. The signal for frameshifting is composed of two essential mRNA elements; a slippery sequence (AAAUUUA) where the ribosome changes reading frame, and a stimulatory RNA structure located immediately downstream. This RNA is predicted to be a complex stem-loop but may also form an RNA pseudoknot. We have investigated the structure of the RSV frameshift signal by a combination of enzymatic and chemical structure probing and site-directed mutagenesis. The stimulatory RNA is indeed a complex stem-loop with a long stable stem and two additional stem-loops contained as substructures within the main loop region. The substructures are not however required for frameshifting. Evidence for an additional interaction between a stretch of nucleotides in the main loop and a region downstream to generate an RNA pseudoknot was obtained from an analysis of the frameshifting properties of RSV mutants translated in the rabbit reticulocyte lysate in vitro translation system. Mutations that disrupted the predicted pseudoknot-forming sequences reduced frameshifting but when the mutations were combined and should re-form the pseudoknot, frameshifting was restored to a level approaching that of the wild-type construct. It was also observed that the predicted pseudoknot-forming regions had reduced sensitivity to cleavage by the single-stranded probe imidazole. Overall, however, the structure probing data indicate that the pseudoknot interaction is weak and may form transiently. In comparison to other characterised RNA structures present at viral frameshift signals, the RSV stimulator falls into a novel group. It cannot be considered to be a simple hairpin-loop yet it is distinct from other well characterised frameshift-inducing RNA pseudoknots in that the overall contribution of the RSV pseudoknot to frameshifting is less dramatic.

Understanding the role of the essential Asp251 in cytochrome p450cam using site-directed mutagenesis, crystallography, and kinetic solvent isotope effect

Proton transfer in cytochromes P450 is a critical step in the activation of molecular oxygen. Extensive study of the P450cam active site has identified several residues that play a central role in dioxygen bond scission. A highly conserved carboxylate, aspartate-251 in P450cam in the distal helix I, participates in a series of hydrogen-bond/ion pairs near the molecular surface and has been implicated in the catalytic mechanism. Mutation of Asp251 is known to lower activity by 2 orders of magnitude and change the rate-limiting step in the catalytic cycle, suggesting a role for an acid functionality in generation of iron-oxygen reactive intermediates. The turnover rates of the Asp251Asn mutant in various protium-deuterium mixtures have been determined and show a significantly larger kinetic solvent isotope effect, with an overall magnitude of 10 compared to 1.8 for the wild-type P450cam. In addition, a much larger number of protons are involved in the rate-limiting step for the Asp251Asn mutant than in the wild-type enzyme. These results indicate that Asp251 is an essential part of the normal proton delivery machinery required for O-O bond scission. The crystal structure of the Aps251Asn mutant obtained from data collected at cryogenic temperatures has been refined to 1.9 A. Key hydrogen bonds required to hold Asp251 in position have been broken which allows the mutant Asn251 side chain to swing out and away from the O2 binding site leading to a more open active site. This change could allow easier access by water and thus contribute to the observed kinetic solvent isotope effects.

Electrostatic effects in electron transfer reactions of [2Fe-2S] ferredoxins with inorganic reagents

The kinetics of electron transfer from the reduced [2Fe-2S] ferredoxins from the cyanobacterium Anabaena 7120 and the protozoan Trichomonas vaginalis to select cobalt coordination compounds have been studied in order to gain insight into the mechanism of electron transfer and intrinsic reactivity of [2Fe-2S] active sites. With tripositive cobalt complexes, reactions of both proteins displayed saturation kinetics; values of association constants of 12,900 and 1,400 M-1 and limiting rate constants of 7.6 and 3.5 s-1 were found for oxidation of T. vaginalis and Anabaena ferredoxins, respectively, by Co(NH3)6(3+) at room temperature and I = 0.1 M. An activation enthalpy of 12.1 kcal/mol and activation entropy of -14.3 cal/mol K for oxidation of T. vaginalis ferredoxin by Co(NH3)6(3+) contrasted with corresponding values of 13.4 kcal/mol and -10.5 cal/mol K for the Spirulina platensis protein, which is homologous to Anabaena ferredoxin. The dependence of the reaction rates on ionic strength were measured to probe the importance of electrostatics on the reactivity of the proteins. Analysis of the ionic strength dependence of the oxidation of the proteins by Co(NH3)6(3+) by the "parallel plate" model of Watkins et al. (1994, Protein Sci 3:2104-2114) afforded values for active site charges of -0.7 and -1.1 and limiting rate constants at infinite ionic strength of 25,800 and 76 M-1 S-1 for T. vaginalis and Anabaena ferredoxins, respectively. These results suggest that the [2Fe-2S] center of the protozoal ferredoxin is more accessible and adjacent to a less highly charged, more compact patch of negative charges than the photosynthetic protein.

The environment of [2Fe-2S] clusters in ferredoxins: the role of residue 45 probed by site-directed mutagenesis

The biochemical and biophysical properties of the Ala45Ser mutant of the [2Fe-2S] ferredoxin from vegetative cells of the cyanobacterium Anabaena sp. 7120 are described. This novel protein, which incorporates the residue present in many higher plant ferredoxins into the analogous position of a typical cyanobacterial ferredoxin, was prepared to probe the origin of the characteristic spectrochemical and functional differences between the ferredoxins from these two sources. The variant protein was produced by site-directed mutagenesis and was expressed as the holoprotein in Escherichia coli. Although the UV-vis spectrum of the Ala45Ser mutant was indistinguishable from that of the wild-type (WT) protein, the circular dichroism (CD) spectrum of the mutant was distinct and similar in appearance to that of spinach ferredoxin, which possesses a Ser residue at the analogous position. The values of the principal g factors of the EPR spectrum of the dithionite-reduced mutant protein differed from those of the WT spectrum and resembled those of plant ferredoxins containing serine at position 45. Analysis of the mutant EPR spectrum according to the method of Blumberg indicated greater covalent interactions between the localized ferrous site of the cluster and the protein matrix relative to the WT protein. The resonance Raman spectrum of Ala45Ser Anabaena ferredoxin was distinct from the spectrum of the WT protein and showed exceptional similarity to the spectrum of higher plant ferredoxins, such as spinach ferredoxin. The mutant protein spectrum displayed considerably greater deuterium dependent isotope shifts for bands ascribed to terminal Fe-S stretching modes than did the WT spectrum.(ABSTRACT TRUNCATED AT 250 WORDS)