Specificity of restriction endonucleases and methylases--a review

The properties and sources of all known restriction endonucleases and methylases are listed. The enzymes are cross-indexed (Table I), classified according to their recognition sequence homologies (Table II), and characterized within Table II by the cleavage and methylation positions, the number of recognition sites on the double-stranded DNA of the bacteriophages lambda, phi X174 and M13mp7, the viruses Ad2 and SV40, the plasmids pBR322 and pBR328, and the microorganisms from which they originate. Other tabulated properties of the restriction endonucleases include relaxed specificities (integrated into Table II), the structure of the generated fragment ends (Table III), and the sensitivity to different kinds of DNA methylation (Table V). In Table IV the conversion of two- and four-base 5'-protruding ends into new recognition sequences is compiled which is obtained by the fill-in reaction with Klenow fragment of the Escherichia coli DNA polymerase I or additional nuclease S1 treatment followed by ligation of the modified fragment termini [P3]. Interconversion of restriction sites generates novel cloning sites without the need of linkers. This should improve the flexibility of genetic engineering experiments. Table VI classifies the restriction methylases according to the nature of the methylated base(s) within their recognition sequences. This table also comprises restriction endonucleases which are known to be inhibited or activated by the modified nucleotides. The detailed sequences of those overlapping restriction sites are also included which become resistant to cleavage after the sequential action of corresponding restriction methylases and endonucleases [N11, M21]. By this approach large DNA fragments can be generated which is helpful in the construction of genomic libraries. The data given in both Tables IV and VI allow the design of novel sequence specificities. These procedures complement the creation of universal cleavage specificities applying class IIS enzymes and bivalent DNA adapter molecules [P17, S82].     

Increased carbohydrate substitution of lipoteichoic acid during inhibition of protein synthesis.

Decreases in electrophoretic mobilities of intracellular lipoteichoic acid, intracellular deacylated lipoteichoic acid, and extracellular deacylated lipoteichoic acid were observed during inhibition of protein synthesis in Streptococcus faecium after exposure to chloramphenicol or valine deprivation. Increased carbohydrate content, and thus an increased mass-to-charge ratio, rather than changes in ester alanine content or novel fatty acid substitutions, appeared to account for the decreased electrophoretic mobilities. The increase in carbohydrate content, as judged from mobility measurements, was progressive over time and appeared to occur on biosynthetically new lipoteichoic acid as well as on lipoteichoic acid made before inhibition of protein synthesis.     

Gallium-67 Scans in the Diagnosis of Pyelonephritis

Gallium-67 (⁶⁷Ga) citrate was administered intravenously (50 microcuries per kg of body weight) to patients in whom acute and chronic urinary tract infections were suspected. Scanning was done, using both the Anger-type scintillation camera and the rectilinear scanner, 24 to 78 hours after injection of the isotope.The preliminary results imply that ⁶⁷Ga renal uptake is present in patients with pyelonephritis whether overt or silent, as well as in patients with uretero-sigmoidostomies. However, ⁶⁷Ga renal uptake is not present in patients with radiographic evidence of chronic pyelonephritis without active infection and in patients without renal disease.     

Cold-sensitive Mutations in Salmonella typhimurium Which Affect Ribosome Synthesis

A number of mutations (45) expressed as cold-sensitive conditional lethal pheno-types were screened by transduction for their linkage to the streptomycin-resistance locus; 7 showed such linkage. Of these, two were studied in greater detail. The sedimentation profiles of ribosomes from cultures grown at low temperature differed from wild type and from one another. Both mutants lost ribonucleic acid control at low temperature. It is suggested that a high proportion of mutants expressing a cold-sensitive phenotype harbor mutations in genes affecting ribosome synthesis or regulation.     

Physiologische und biochemische Beiträge zur Taxonomie der Gattung Chlorella

Zusammenfassung Es wurde die Verwendbarkeit von Glutaminsäure, Glutamin, Nicotinsäure, Nicotinsäureamid und Purin als Stickstoffquelle für die Kultur von 71 autotrophen Chlorella-Stämmen, die 8 Arten angehören, untersucht. Im Licht zeigen mit Glutaminsäure 63 und mit Glutamin 67 Stämme gutes Wachstum. Nicotinsäure wird dagegen nur von 1 Stamm, Nicotinsäureamid von 9 und Purin von 16 Stämmen verwertet. Die Verwendbarkeit der 5 geprüften organischen Stickstoffverbindungen als N-Quelle ist innerhalb der Gattung Chlorella als taxonomisches Merkmal zur Charakterisierung von Arten nicht geeignet. Lediglich die 7 Stämme von Chlorella kessleri unterscheiden sich durch gutes Wachstum mit Nicotinsäureamid von der sonst recht ähnlichen Chlorella luteoviridis sowie von den übrigen Arten.

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Physiological and biochemical contributions to the taxonomy of the genus Chlorella IV. Utilization of organic nitrogen compounds

Summary The utilization of glutamic acid, glutamine, nicotinic acid, nicotinamide, and purine as sources of nitrogen for growth in the light of 71 autotrophic Chlorella strains belonging to 8 species was studied. Whereas 63 strains grow well with glutamic acid and 67 with glutamine, nicotinic acid is used by 1, nicotinamide by 9, and purine by 16 strains only. Utilization of the 5 organic nitrogen compounds tested cannot serve as a taxonomic character in the genus Chlorella. However, the 7 strains of Chlorella kessleri differ in their good growth with nicotinamide from the otherwise rather similar Chlorella luteoviridis and from the other species.

     

Inhibition of nitrite assimilation by uncouplers of phosphorylation

Summary Carbonyl cyanide m-chlorophenylhydrazone (CCCP) and pentachlorophenol (PCP), two powerful uncouplers of phosphorylation, specifically inhibit the assimilation of nitrite in the course of nitrate reduction. These results support our former conclusion that high-energy phosphate is involved in the metabolism of nitrite.     

Characterization of Opioid Receptors in Cultured Neurons

The appearance of mu-, delta-, and kappa-opioid receptors was examined in primary cultures of embryonic rat brain. Membranes prepared from striatal, hippocampal, and hypothalamic neurons grown in dissociated cell culture each exhibited high-affinity opioid binding sites as determined by equilibrium binding of the universal opioid ligand (-)-[3H]bremazocine. The highest density of binding sites (per mg of protein) was found in membranes prepared from cultured striatal neurons (Bmax = 210 +/- 40 fmol/mg protein); this density is approximately two-thirds that of adult striatal membranes. By contrast, membranes of cultured cerebellar neurons and cultured astrocytes were devoid of opioid binding sites. The opioid receptor types expressed in cultured striatal neurons were characterized by equilibrium binding of highly selective radioligands. Scatchard analysis of binding of the mu-specific ligand [3H]D-Ala2,N-Me-Phe4,Gly-ol5-enkephalin to embryonic striatal cell membranes revealed an apparent single class of sites with an affinity (KD) of 0.4 +/- 0.1 nM and a density (Bmax) of 160 +/- 20 fmol/mg of protein. Specific binding of (-)-[3H]bremazocine under conditions in which mu- and delta-receptor binding was suppressed (kappa-receptor labeling conditions) occurred to an apparent single class of sites (KD = 2 +/- 1 nM; Bmax = 40 +/- 15 fmol/mg of protein). There was no detectable binding of the selective delta-ligand [3H]D-Pen2,D-Pen5-enkephalin. Thus, cultured striatal neurons expressed mu- and kappa-receptor sites at densities comparable to those found in vivo for embryonic rat brain, but not delta-receptors.     

A Glycine Site Associated with N-Methyl-d-Aspartic Acid Receptors: Characterization and Identification of a New Class of Antagonists

Membranes from rat telencephalon contain a single class of strychnine-insensitive glycine sites. That these sites are associated with N-methyl-D-aspartic acid (NMDA) receptors is indicated by the observations that [3H]glycine binding is selectively modulated by NMDA receptor ligands and, conversely, that several amino acids interacting with the glycine sites increase [3H]N-[1-(2-thienyl)cyclohexyl]piperidine ([3H]TCP) binding to the phencyclidine site of the NMDA receptor. The endogenous compound kynurenate and several related quinoline and quinoxaline derivatives inhibit glycine binding with affinities that are much higher than their affinities for glutamate binding sites. In contrast to glycine, kynurenate-type compounds inhibit [3H]TCP binding and thus are suggested to form a novel class of antagonists of the NMDA receptor acting through the glycine site. These results suggest the existence of a dual and opposite modulation of NMDA receptors by endogenous ligands.     

Biochemical analysis of CRM 66. A nonfunctional Pseudomonas aeruginosa exotoxin A

Pseudomonas aeruginosa exotoxin A (ETA) is an ADP-ribosyltransferase which inactivates protein synthesis by covalently attaching the ADP-ribose portion of NAD+ onto eucaryotic elongation factor 2 (EF-2). A direct biochemical comparison has been made between ETA and a nonenzymatically active mutant toxin (CRM 66) using highly purified preparations of each protein. The loss of ADP-ribosyltransferase activity and subsequent cytotoxicity have been correlated with the presence of a tyrosine residue in place of a histidine at position 426 in CRM 66. In the native conformation, CRM 66 demonstrated a limited ability (by a factor or at least 100,000) to modify EF-2 covalently and lacked in vitro and in vivo cytotoxicity, yet CRM 66 appeared to be normal with respect to NAD+ binding. Upon activation with urea and dithiothreitol, CRM 66 lost ADP-ribosyltransferase activity entirely yet CRM 66 retained the ability to bind NAD+. Replacement of Tyr-426 with histidine in CRM 66 completely restored cytotoxicity and ADP-ribosyltransferase activity. These results support previous findings from this laboratory (Wozniak, D. J., Hsu, L.-Y., and Galloway, D. R. (1988) Proc. Natl. Acad. Sci. U. S. A. 85, 8880-8884) which suggest that the His-426 residue of ETA is not involved in NAD+ binding but appears to be associated with the interaction between ETA and EF-2.