Removal of the RecA C-terminus results in a conformational change in the RecA-DNA filament

The Escherichia coli RecA protein catalyzes homologous recombination of DNA molecules, and the active form of the protein is a helical polymer that it forms around DNA. Previous image analysis of electron micrographs has revealed the RecA protein to be organized into two domains or lobes within the RecA-DNA filament. We have now been able to show that a small modification of the RecA protein by proteolysis results in a significant shift in the internal mass in the RecA filament. We have cleaved approximately 18 residues from the C-terminus of the RecA protein, producing a roughly 36K MW RecA core protein that binds DNA and polymerizes normally. A three-dimensional reconstruction of this complex has been computed, and has been compared with a previous reconstruction of the intact protein. The main difference is consistent with a 15 A outward movement of the lobe that was at an inner radius in the wild-type protein. These observations yield additional evidence about the conformational flexibility of the RecA filament, and will aid in understanding the structural mechanics and dynamics of the RecA filament.

Characterization of developmentally regulated and retina-specific nuclear protein binding to a site in the upstream region of the rat opsin gene

DNase I protection and gel retardation assays have identified a sequence 5' to the transcription start site of the rat opsin gene that interacts with nuclear proteins from mammalian retinas but not from a variety of other neural and non-neural tissues. Following sodium dodecyl sulfate-polyacrylamide gel electrophoresis and transfer to nitrocellulose the protein(s) responsible for this binding were identified with an oligonucleotide probe and were found to migrate with an apparent molecular size of 40 kilodaltons. The binding complex eluted from fast protein liquid chromatography gel filtration as a peak centered at 100 kilodaltons, suggesting the presence of more than one subunit. Binding activity could be detected in postnatal day 1 retinal extracts and increased over the next 2 weeks of development, a time course coincident with opsin gene expression and maturation of rod photoreceptors. Synthetic oligonucleotides with altered sequences showed that the binding was dependent upon residues in a CTAAT motif and was facilitated by surrounding GGCCCC sequences. The specificity of the binding interaction was measured by inhibition of complex formation in a gel retardation assay. The unaltered sequence was over 2 orders of magnitude more effective at inhibiting complex formation than either an unrelated DNA sequence or a concensus sequence corresponding to a known CCAAT box binding protein NF1.

[Studies and comparisons on chemical components of essential oils from Clematis hexapetala Pall. and Inula nervosa Wall]

Chemical components of the essential oils from clematis hexapetala and Inula nervosa were analyzed by using GC-MS-DS. The result shows that the major components of the essential oil from Inula nervosa are thymol and thymol isobutyrate, while the major components of the essential oil from Clematis hexapetala are palmitic acid and 3-hydroxy-4-methoxyl benzaldehyde.

Image analysis reveals that Escherichia coli RecA protein consists of two domains

The Escherichia coli RecA protein catalyzes homologous genetic recombination by forming helical polymers around DNA molecules. These polymers have an ATPase activity, which is essential for the movement of strands between two DNA molecules. One obstacle to structural studies of the RecA filament has been that the ATPase results in a dynamical polymer containing a mixture of states with respect to the bound ATP and its hydrolytic products. We have formed filaments which are trapped in the ADP-Pi state by substituting AIF4- for the Pi, and have used these stable filaments to generate a three-dimensional reconstruction from electron micrographs. The resolution of the reconstruction is sufficient to resolve the 38-k RecA subunit into two nearly equal domains. This reconstruction provides the most detailed view yet of the RecA protein, and serves as a framework within which existing biochemical data on RecA can be understood.

The location of DNA in RecA-DNA helical filaments

The helical filament that the RecA protein of Escherichia coli forms around DNA is the active apparatus in protein-catalyzed homologous genetic recombination. The actual position of DNA within this complex has been unknown. Image analysis has been performed on electron micrographs of filaments of RecA on double-stranded DNA and on single-stranded DNA to visualize a difference that is consistent with one strand of the double-stranded DNA. This localization of the DNA gives additional information about the unusual structure of DNA in the complex with RecA protein.

Mechanism of soft X-ray radiation damage on glycine by XPS

This paper reports the behaviour of radiation damage of solid glycine in a XPS spectrometer equipped with Mg and Al X-ray sources. The main results are as follows: (i) the kinetics of the damage process obeys the first-order rate law, (ii) decarboxylation can be deduced, and (iii) deamination does not occur, but the nitrogen atoms in original molecules are transformed into a new chemical form with higher electron density by photo-reduction.