Reconstitution of the DNA base excision—repair pathway

Background: The base excision–repair pathway is the major cellular defence mechanism against spontaneous DNA damage. The enzymes involved have been highly conserved during evolution. Base excision–repair has been reproduced previously with crude cell-free extracts of bacterial or human origin. To further our understanding of base excision–repair, we have attempted to reconstitute the pathway in vitro using purified enzymes.Results We report here the successful reconstitution of the base excision–repair pathway with five purified enzymes from Escherichia coli: uracil-DNA glycosylase, a representative of the DNA glycosylases that remove various lesions from DNA; the AP endonuclease IV that specifically cleaves at abasic sites; RecJ protein which excises a 5′ terminal deoxyribose-phosphate residue; DNA polymerase I; and DNA ligase. The reaction proceeds with high efficiency in the absence of additional factors in the reconstituted system. Four of the enzymes are absolutely required for completion of the repair reaction. An unusual feature we have discovered is that the pathway branches after enzymatic incision at an abasic DNA site. RecJ protein is required for the major reaction, which involves replacement of only a single nucleotide at the damaged site; in its absence, an alternative pathway is observed, with generation of longer repair patches by the 5′ nuclease function of DNA polymerase I.Conclusion Repair of uracil in DNA is achieved by a very short-patch excision–repair process involving five different enzymes. No additional protein factors seem to be required. There is a minor, back-up pathway that uses replication factors to generate longer repair patches.     

Low-sulphated oligosaccharides derived from heparan sulphate inhibit normal angiogenesis

Heparin, with or without the addition of an adrenocorticosteroid,can inhibit normal angiogenesis in the chick embryo chorioallantoicmembrane. Low- or non-sulphated heparin fragments also haveanti-angiogenic effect. Attempts to define a saccharide structureresponsible for the anti-angiogenic effect implicated a -[GlcAß1,4-GlcNAc     

Induction of resistance to alkylating agents in E. coli: the ada+ gene product serves both as a regulatory protein and as an enzyme for repair of mutagenic damage.

The expression of several inducible enzymes for repair of alkylated DNA in Escherichia coli is controlled by the ada+ gene. This regulatory gene has been cloned into a multicopy plasmid and shown to code for a 37-kd protein. Antibodies raised against homogeneous O6-methylguanine-DNA methyltransferase (the main repair activity for mutagenic damage in alkylated DNA) were found to cross-react with this 37-kd protein. Cell extracts from several independently derived ada mutants contain variable amounts of an altered 37-kd protein after an inducing alkylation treatment. In addition, an 18-kd protein identical with the previously isolated O6-methyl-guanine-DNA methyltransferase has been identified as a product of the ada+ gene. The smaller polypeptide is derived from the 37-kd protein by proteolytic processing.     

Beta-2 microglobulin types in mice of wild origin

To determine the distribution of beta-2 microglobulin (B2m) alleles in wild mice we have typed mice derived from natural populations in Europe, North Africa, South America, and East Asia. Mus musculus domesticus mice from Germany, France, Italy, and Peru were all B2m ^a as were most from the United Kingdom. M.m. musculus mice from Denmark and Czechoslovakia, several stocks of M.m. molossinus from Japan, and M.m. castaneus from China, Thailand, and the Philippines were of B2m ^b type. This is consistent with the notion that C57BL/6 may have obtained some of its genes, including B2m, from Eastern mice. A BgII restriction site characteristic of B2m ^b was also found in mice from Czechoslovakia and Japan, confirming that B2m ^b is a naturally occurring allele of B2m. A new type of ₂m ( ₂m^w1) was found in four stocks of M. spretus from Portugal, Spain, and Morocco. This molecule differs in apparent size and charge from the a and b types. ₂m^w2 was found together with ₂ ma in one stock of M.m. domesticus (brevirostris) from Morocco. ₂m^w3 and ₂m^w4 were found in a few M. m. bactrianus from Pakistan. In all cases tested, these new ₂m molecules associate with class I histocompatibility antigens.Abbreviations used in this paper ₂m beta-2 microglobulin - B2m gene for beta-2 microglobulin - IEF isoelectric focusing - SDS-PAGE polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate - MHC major histocompatibility complex - T. E. Tris-EDTA buffer     

Some rRNA operons in E. coli have tRNA genes at their distal ends.

We have previously isolated seven rRNA operons on plasmids or lambda transducing phages and identified various tRNAs encoded by these operons. Each of the seven operons has one of two different spacer tRNA gene arrangements between the genes for 16S and 23S rRNA: either tRNAGlu2 or both tRNAIle1 and tRNAAla1B genes. In addition, various tRNA genes are located at or near the distal ends of rRNA operons. In particular, genes for tRNATrp and tRNAAsp1 are located at the distal end of rrnC at 83 min on the E. coli chromosome. Experiments with various hybrid plasmids, some of which lack the rRNA promoter, have now demonstrated that this promoter is necessary for expression of the distal tRNA genes. Rifampicin run-out experiments have also provided evidence that the tRNATrp gene is located farther from its promoter than the spacer tRNA gene or the 5S RNA gene. These results confirm the localization of genes for tRNATrp and tRNAAsp1 at the distal end of rrnC and strongly suggest that they are co-transcribed with the genes for 16S, tRNAGlu2, 23S and 5S RNA. Other such distal tRNAs have been identified, and it is suggested that they too are part of rRNA operons.     

Thermal Rearrangement of 4-Alkyl-1,2,4-triazoles. Rearrangements in the Crystalline State

Studies of the thermolyses of 4-alkyl substituted 1,2,4-triazoles was reviewed. They were observed to rearrange at 200–350 °C to the corresponding 1-alkylated triazoles. When substituted in the 4-position with aryl- or vinylic substituents the triazoles were inert to thermolysis, contrary to what was observed for the 4-alkyl- and 4-allyl substituted systems. The mechanisms for the reactions were elucidated, e.g., by studies of substituents effects and by kinetic measurements in solution as well as for the neat samples. Reactions in solutions were slow. The rearrangements in melts of the neat triazoles readily proceeded to the products, and were proposed to take place via a series of nucleophilic displacement steps. X-ray crystallographic measurements of selected structures, showed that the interatomic distances and angles between the relevant atoms in these structures, to a large degree resembled the geometry expected for the S_N2-type transition states proposed for the rearrangement mechanism. Thus, thermolyses of a series of triazole structures at temperatures below their melting points, confirmed that rearrangements actually did take place. The “kinetics” of the reactions in the crystalline state were investigated and rate constants and thermodynamic data were correlated with the structural characteristics of the crystals.     

Three distinct DNA ligases in mammalian cells

The major DNA ligase of proliferating mammalian cells, DNA ligase I, catalyzes the joining of single strand breaks in double stranded DNA and is active on a synthetic substrate of oligo(dT) hybridized to poly(dA). DNA ligase I does not catalyze the joining of an oligo(dT).poly(rA) substrate. Two additional DNA ligases, II and III, which can act on the latter substrate have been purified from calf thymus. DNA ligase II, which has been described previously, is a 72-kDa protein. DNA ligase III migrates as a 100-kDa protein in denaturing gel electrophoresis. Structural, immunochemical, and catalytic studies on the three DNA ligase activities strongly indicate that they are the products of three different genes.     

CO dehydrogenase from Clostridium thermoaceticum. EPR and electrochemical studies in CO2 and argon atmospheres

The EPR and redox properties of the metal complexes in CO dehydrogenase (CODH) from Clostridium thermoaceticum were studied. Controlled potential coulometric reductive titrations of CODH were performed under argon and CO2 atmospheres. In the titrations performed under argon, five to eight electrons/dimer were required for reduction, and four distinct EPR signals appeared. These included a signal with gave = 1.82 (Em approximately -220 mV), two signals with the same g values but different linewidths at gave = 1.94 (Em approximately -440 mV), and a signal at gave = 1.86 (Em approximately -530 mV). All of the S = 1/2 EPR signals had low spin concentrations; values between 0.2 and 0.3 spins/dimer were typically obtained for each signal. Features between g = 6 and 4, typical of S = 3/2 states, were also observed, and these may account, at least to some degree, for the low spin concentration values. Under CO2, and at negative potentials, CODH served as an electrocatalyst in the reduction of CO2 to CO. The apparent half-maximal activity for this reduction at pH 6.3 occurred at -430 mV, a potential near the thermodynamic value. An EPR signal, arising from a complex containing Ni, Fe, and the carbon from CO/CO2 developed along with this activity. The reduction of this complex is probably the last step to occur prior to the catalysis of CO2 reduction.