Comparison of the nucleotide and amino acid sequences of the RsrI and EcoRI restriction endonucleases

The RsrI endonuclease, a type-II restriction endonuclease (ENase) found in Rhodobacter sphaeroides, is an isoschizomer of the EcoRI ENase. A clone containing an 11-kb BamHI fragment was isolated from an R. sphaeroides genomic DNA library by hybridization with synthetic oligodeoxyribonucleotide probes based on the N-terminal amino acid (aa) sequence of RsrI. Extracts of E. coli containing a subclone of the 11-kb fragment display RsrI activity. Nucleotide sequence analysis reveals an 831-bp open reading frame encoding a polypeptide of 277 aa. A 50% identity exists within a 266-aa overlap between the deduced aa sequences of RsrI and EcoRI. Regions of 75-100% aa sequence identity correspond to key structural and functional regions of EcoRI. The type-II ENases have many common properties, and a common origin might have been expected. Nevertheless, this is the first demonstration of aa sequence similarity between ENases produced by different organisms.     

Tolerance of snakes to hypergravity

Sensitivity of carotid blood flow to increased gravitational force acting in the head-to-tail direction(+Gz) was studied in diverse species of snakes hypothesized to show adaptive variation of response. Tolerance to increased gravity was measured red as the maximum graded acceleration force at which carotid blood flow ceased and was shown to vary according to gravitational adaptation of species defined by their ecology and behavior. Multiple regression analysis showed that gravitational habitat, but not body length, had a significant effect on Gz tolerance. At the extremes, carotid blood flow decreased in response to increasing G force and approached zero near +1 Gz in aquatic and ground-dwelling species, whereas in climbing species carotid flow was maintained at forces in excess of +2 Gz. Tolerant (arboreal) species were able to withstand hypergravic forces of +2 to +3 Gz for periods up to 1 h without cessation of carotid blood flow or loss of body movement and tongue flicking. Data suggest that the relatively tight skin characteristic of tolerant species provides a natural antigravity suit and is of prime importance in counteracting Gz stress on blood circulation.     

Blood vessel adaptation to gravity in a semi-arboreal snake

The effects of vasoactive agonists on systemic blood vessels were examined with respect to anatomical location and gravity acclimation in the semi-arboreal snake, Elaphe Obsoleta. Major blood vessels were reactive to putative neurotransmitters, hormones or local factors in vessel specific patterns. Catecholamines, adenosine triphosphate, histamine and high potassium (80 mM) stimulated significantly greater tension per unit vessel mass in posterior than anterior arteries. Anterior vessels were significantly more sensitive to catecholamines than midbody and posterior vessels. Angiotensin II stimulated significantly greater tension in carotid artery than in midbody and posterior dorsal aorta. Arginine vasotocin strongly contracted the left and right aortic arches and anterior dorsal aorta. Veins were strongly contracted by catecholamines, high potassium and angiotensin II, but less so by adenosine triphosphate, arginine vasotocin and histamine. Precontracted vessels were relaxed by acetylcholine and sodium nitroprusside, but not by atrial natriuretic peptide or bradykinin. Chronic exposure of snakes to intermittent hypergravity stress (+1.5 G_z at tail) did not affect the majority of vessel responses. These data demonstrate that in vitro tension correlates with known patterns of sympathetic innervation and suggest that catecholamines, as well as other agonists, are important in mediating vascular responses to gravitational stresses in snakes.Abbreviations ACH acetylcholine - ADA anterior dorsal aorta - ANG II salmon asn¹-val⁵-angiotensin II - ANP rat ile²⁶-atrial natriuretic peptide - ATP adenosine triphosphate - AVT arginine vasotocin - BK human bradykinin - BL total body length - CA carotid artery - CONT control - EC ₅₀ effective concentration producing 50% maximal response - EPI epinephrine - + G _z earth's gravity force - HI-G high gravity acclimation - HI K ⁺ 80 mM high potassium - JV jugular vein - LAA left aortic arch - MDA midbody dorsal aorta - MPV midbody portal vein - MS Mackenzie's solution - NEPI norepinephrine - pD ₂ log EC₅₀ - PDA posterior dorsal aorta - PPV posterior portal vein - RAA right aortic arch - SNP sodium nitroprusside     

Reduced Variation in Drosophila Simulans Mitochondrial DNA

We investigated the evolutionary dynamics of infection of a Drosophila simulans population by a maternally inherited insect bacterial parasite, Wolbachia, by analyzing nucleotide variability in three regions of the mitochondrial genome in four infected and 35 uninfected lines. Mitochondrial variability is significantly reduced compared to a noncoding region of a nuclear-encoded gene in both uninfected and pooled samples of flies, indicating a sweep of genetic variation. The selective sweep of mitochondrial DNA may have been generated by the fixation of an advantageous mitochondrial gene mutation in the mitochondrial genome. Alternatively, the dramatic reduction in mitochondrial diversity may be related to Wolbachia.     

Genomic concatemerization/deletion in rotaviruses: a new mechanism for generating rapid genetic change of potential epidemiological importance.

Three variants of group A rotavirus with large changes in their gene 5 structures have been analyzed at the molecular level. The first of these, P9 delta 5, was obtained during plaque purification undertaken as part of the biological cloning of a field isolate of virus. The gene 5 homolog in this isolate migrated just ahead of the normal segment 6 RNA, giving an estimated size of 1,300 bp. Molecular cloning and sequencing of this homolog revealed it to have a single 308-bp deletion in the center of the normal gene 5 sequence extending between nucleotides 460 and 768 of the normal gene sequence. This deletion caused a frameshift in the gene such that a stop codon was encountered 8 amino acids downstream of the deletion point, giving a predicted size for the protein product of this gene of 150 amino acids compared with the 490 amino acids of its normal-size counterpart. Attempts to detect this shortened protein in virus-infected cells were not successful, indicating that it was much less stable than the full-length protein and/or had suffered a large change in its antigenicity. The second two variants, brvA and brvE, were generated in an earlier study following the high-multiplicity passage of the UKtc strain of bovine rotavirus. Polyacrylamide gel electrophoresis analysis of these nondefective variants showed that brvA had a gene 5 homolog approximately equal in size to the normal RNA segment 2 (approximately 2,700 bp) and that brvE had a size of approximately 2,300 bp. Both variants showed changes in their gene 5 protein products, with brvA mimicking P9 delta 5 in failing to produce a detectable product whereas brvE produced a new virus-specific protein approximately 80 kDa in size. Full-length cDNA clones of the brvE gene 5 homolog were isolated, and analysis of their structure revealed a head-to-tail concatemerization of the normal gene 5 sequence with the first copy of the concatemer covering nucleotides 1 to 808 and the second covering nucleotides 92 to 1579, giving a total length of 2,296 bp. Sequencing across the junction region of the two copies of the gene showed that they were joined in frame to give a predicted combined open reading frame of 728 amino acids with the amino-terminal region consisting of amino acids 1 to 258 fused at the carboxy terminus to amino acids 21 to 490.(ABSTRACT TRUNCATED AT 400 WORDS)     

Low codon bias and high rates of synonymous substitution in Drosophila hydei and D. melanogaster histone genes

We have evaluated codon usage bias in Drosophila histone genes and have obtained the nucleotide sequence of a 5,161-bp D. hydei histone gene repeat unit. This repeat contains genes for all five histone proteins (H1, H2a, H2b, H3, and H4) and differs from the previously reported one by a second EcoRI site. These D. hydei repeats have been aligned to each other and to the 5.0-kb (i.e., long) and 4.8-kb (i.e., short) histone repeat types from D. melanogaster. In each species, base composition at synonymous sites is similar to the average genomic composition and approaches that in the small intergenic spacers of the histone gene repeats. Accumulation of synonymous changes at synonymous sites after the species diverged is quite high. Both of these features are consistent with the relatively low codon usage bias observed in these genes when compared with other Drosophila genes. Thus, the generalization that abundantly expressed genes in Drosophila have high codon bias and low rates of silent substitution does not hold for the histone genes.      

DNA binding properties of the Saccharomyces cerevisiae DAT1 gene product.

The DAT1 gene of Saccharomyces cerevisiae encodes a DNA binding protein (Dat1p) that specifically recognizes the minor groove of non-alternating oligo(A).oligo(T) tracts. Sequence-specific recognition requires arginine residues found within three perfectly repeated pentads (G-R-K-P-G) of the Dat1p DNA binding domain [Reardon, B. J., Winters, R. S., Gordon, D., and Winter, E. (1993) Proc. Natl. Acad. Sci. USA 90, 11327-1131]. This report describes a rapid and simple method for purifying the Dat1p DNA binding domain and the biochemical characterization of its interaction with oligo(A).oligo(T) tracts. Oligonucleotide binding experiments and the characterization of yeast genomic Dat1p binding sites show that Dat1p specifically binds to any 11 base sequence in which 10 bases conform to an oligo(A).oligo(T) tract. Binding studies of different sized Dat1p derivatives show that the Dat1p DNA binding domain can function as a monomer. Competition DNA binding assays using poly(I).poly(C), demonstrate that the minor groove oligo(A).oligo(T) constituents are not sufficient for high specificity DNA binding. These data constrain the possible models for Dat1p/oligo(A).oligo(T) complexes, suggest that the DNA binding domain is in an extended structure when complexed to its cognate DNA, and show that Dat1p binding sites are more prevalent than previously thought.     

Distribution and partial purification of a liver membrane protein capable of inactivating cytosol enzymes.

1. The inactivation of cytosol enzymes in liver extracts was carried out by several subcellular fractions, with plasma membranes having the highest specific activity. Rough and smooth microsomal fractions were both active, whereas lysosmal inactivation capacity appeared to be derived entirely from contaminating plasma-membrane fragments. 2. Inactivation capacity in liver fractions was derived from parenchymal cells. Of the non-liver cells tested, plasma membranes from H35 hepatoma cells were able to inactivate glucose 6-phosphate dehydrogenase (EC 1.1.1.49), adipocyte "ghosts" showed slight activity and erythrocyte and reticulocyte "ghosts" were inactive. 3. Liposomes prepared from pure lipids with net negative, positive or neutral charge did not possess inactivation capacity. 4. Liver plasma-membrane inactivation capacity was destroyed by heating at 50 degrees C. 5. Inactivation factor solubilized from membranes by trypsin plus Triton X-100 treatment was partially purified by (NH4)2SO4 fractionation, gel filtration, ion-exchange chromatography and hydroxyapatite chromatography. 6. Partially purified inactivation factor analysed by gel electrophoresis gave a major protein band that co-migrated with capacity for inactivation of glucose 6-phosphate dehydrogenase. 7. It is concluded that inactivation factor is a membrane protein whose intracellular distribution and other properties are consistent with a possible role for this activity in the initial step of protein degradation.