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PubMed1983

Expression vehicles used in recombinant DNA technology.

We survey cloning vehicles whose function is to carry and express a gene in host cells including Escherichia coli, Saccharomyces cerevisiae and mammalian cells. In E. coli these include vehicles based on the lac operon, the trp operon, the rho leftward operon, and the recA gone; open reading frame cloning vehicles are also discussed, as are steps that can be taken to extrude a gene product from the cell and the use of plasmids with runaway replication. In S. cerevisiae we discuss vehicles based on the PGK gene, the ADH1 gene, the acid phosphatase gene and the GAL1-GAL10 gene cluster. In mammalian cells we discuss vehicles based on SV40 promoters, the metallothionein gene, retroviral LTR promoters, bovine papilloma virus and vaccinia virus.

Journal Article↗
PubMed1988

Yersinia enterocolitica O:9 as a potential live oral carrier for protective antigens.

Yersinia enterocolitica has the capacity to invade the intestinal tissue and to resist the primary host resistance. The former is chromosome coded while the second largely depends on the presence of a 70 kb plasmid called pYV. This plasmid directs the conditional synthesis of high amounts of proteins (YOPs) that are secreted and inserted in the outer membrane. In order to evaluate Y. enterocolitica W22703 as a potential live carrier for immunization, three strains expressing beta-galactosidase (GZ), were tested for their ability to induce an antibody response to this antigen in mice. The first strain contained plasmid pGC1256, a mutated pYV plasmid containing lacZ transcribed from a yop gene promoter. This strain produced high amounts of GZ instead of a YOP protein and was shown to be hypovirulent. The other strains tested were W22703 pYV+ and pYV- containing a derepressed lac operon carried on an independent plasmid. Immunoblot analysis of sera of mice having received by oral inoculation, W22703(pGC1256) or the pYV+ GZ producing strain revealed the presence of antibodies to GZ. The response to GZ after inoculation of W22703(pGC1256) was shown by ELISA to be only slightly inferior to that obtained by subcutaneous injection of GZ. No response was obtained after oral inoculation of the pYV-GZ producing strain. This showed that the presence of pYV was necessary to obtain an antibody response in this system.

Administration, Oral↗
PubMed1987

A DNA probe for detecting Mycoplasma genitalium in clinical specimens.

Despite decades of careful study, the etiologies of all cases of pelvic inflammatory disease (PID) and non-gonococcal urethritis (NGU) have yet to be described. Mycoplasma genitalium is a newly described organism which has been implicated as a cause of both PID and NGU. Because of fastidious growth requirements, prolonged incubation time and frequent overgrowth in clinical specimens by Mycoplasma hominis, non-culture methods need to be developed for its detection. We have cloned M. genitalium DNA by transfection into Escherichia coli using M13 as the vector. Using these segments as templates, we synthesized radiolabelled cDNAs that were tested for specific hybridization with M. genitalium, and clinically isolated genital mycoplasmas presumptively identified as M. hominis, and Ureaplasma urealyticum. A 256 base-pair segment was found to hybridize with M. genitalium with a sensitivity of 10(2) colour-changing units (CCUs). No cross-hybridization was observed with M. hominis, and cross-hybridization was observed only with large concentrations (greater than 10(6) CCUs) of U. urealyticum. Because of our choice of M13 as the vector, which contains the Lac Operon of E. coli, slight hybridization occurred with E. coli as well. This cDNA can be used against clinical specimens to determine the ecologic niche and spectrum of disease caused by M. genitalium.

DNA, Bacterial↗
PubMed1995

Factors affecting somatic mutation frequencies in vivo.

The factors that influence the spontaneous mutant frequencies in mammalian tissues have been ranked on the basis of data from our laboratory together with published data. Some of the data come from the endogenous hprt and Dlb-1 loci, but most come from transgenic mice carrying the bacterial lacI and lacZ genes in recoverable lambda phage vectors. Since there is evidence that these bacterial loci are selectively neutral, the mutant frequency observed is the integral of the mutation rates from the formation of the zygote. The factors that affect the inferred mutation rate, in decreasing order of importance are: site of integration of the transgene, age, tissue, and strain. Insufficient data exist to determine the influence of gender (probably small) and inter-laboratory variables (probably at least as important as age). The two most surprising results are (1) that about half of all mutations arise during development (and half of these in utero) and (2) that most somatic tissues, whether queiscent or actively proliferating, have similar mutant frequencies and similar increases during adult life.

Aging↗
PubMed2004

Quorum sensing and bacterial cross-talk in biotechnology.

Only a decade ago, the secretion and perception of small signalling molecules that in turn are transduced to coordinate behaviour of a 'minimal unit' of microorganisms was termed quorum sensing by EP Greenberg and colleagues. Since then, an explosion (or exponential growth) in understanding and prevalence of quorum-sensing systems has ensued, with sightings ranging from virulence in human and plant pathogens to degradative capacity of activated sludge. Not surprisingly, regulatory mechanisms span traditional inducer/repressor motifs homologous to the lac operon to the recently discovered interfering RNAs. Further characterisation of signalling circuits, coupled with creative niche applications, suggest a wealth of opportunity for advancing commercial biotechnology.

Animals↗
PubMed2006

Computational models for neurogenic gene expression in the Drosophila embryo.

The early Drosophila embryo is emerging as a premiere model system for the computational analysis of gene regulation in development because most of the genes, and many of the associated regulatory DNAs, that control segmentation and gastrulation are known. The comprehensive elucidation of Drosophila gene networks provides an unprecedented opportunity to apply quantitative models to metazoan enhancers that govern complex patterns of gene expression during development. Models based on the fractional occupancy of defined DNA binding sites have been used to describe the regulation of the lac operon in E. coli and the lysis/lysogeny switch of phage lambda. Here, we apply similar models to enhancers regulated by the Dorsal gradient in the ventral neurogenic ectoderm (vNE) of the early Drosophila embryo. Quantitative models based on the fractional occupancy of Dorsal, Twist, and Snail binding sites raise the possibility that cooperative interactions among these regulatory proteins mediate subtle differences in the vNE expression patterns. Variations in cooperativity may be attributed to differences in the detailed linkage of Dorsal, Twist, and Snail binding sites in vNE enhancers. We propose that binding site occupancy is the key rate-limiting step for establishing localized patterns of gene expression in the early Drosophila embryo.

Animals↗
PubMedDate not supplied

Molecular dynamics and nuclear receptor function.

The development of live cell and biochemical analysis methods has led to an increase in our understanding of the dynamic regulation of transcription. Live single cell studies using photobleaching techniques indicate that many proteins have a high nuclear mobility. Pioneering work using promoter array systems based on the lac operon or the mouse mammary tumor virus promoter enabled the study of chromatin structure, promoter occupancy and protein-chromatin interaction dynamics in relation to transcription. Chromatin immunoprecipitation (ChIP)-based assays allow an exhaustive analysis of the temporal recruitment of proteins to an endogenous promoter and provide evidence of cyclic protein-protein and protein-promoter interactions. Although reflecting different timescales, both ChIP and live cell studies indicate a highly dynamic control of transcription that until now has gone undetected and unappreciated.

Animals↗
PubMed1988

Characterization of a recombinant murine interleukin-6: assignment of disulfide bonds.

Murine interleukin 6 (mIL-6) has been synthesized as a fusion protein using a lac operon inducible plasmid in Escherichia coli. The first 8 amino acids are from the N-terminus of bacterial beta-galactosidase and the last 175 amino acids are from residue number 12 to the end of native mIL-6. This fusion protein is equipotent with the native molecule in the hybridoma growth factor assay and has comparable receptor binding characteristics. The two disulfide bridges in mIL-6 have been identified by Staphylococcus aureus V8 protease peptide mapping and Edman degradation of cystine-containing peptides. It has been shown that there are disulfide bonds between Cys46-Cys52 and Cys75-Cys85.

Animals↗
PubMed1996

Is there an error correcting code in the base sequence in DNA?

Modern methods of encoding information into digital form include error check digits that are functions of the other information digits. When digital information is transmitted, the values of the error check digits can be computed from the information digits to determine whether the information has been received accurately. These error correcting codes make it possible to detect and correct common errors in transmission. The sequence of bases in DNA is also a digital code consisting of four symbols: A, C, G, and T. Does DNA also contain an error correcting code? Such a code would allow repair enzymes to protect the fidelity of nonreplicating DNA and increase the accuracy of replication. If a linear block error correcting code is present in DNA then some bases would be a linear function of the other bases in each set of bases. We developed an efficient procedure to determine whether such an error correcting code is present in the base sequence. We illustrate the use of this procedure by using it to analyze the lac operon and the gene for cytochrome c. These genes do not appear to contain such a simple error correcting code.

Base Sequence↗
PubMed2000

Epigenes: design and construction of new hereditary units.

A plasmid digene construction designed before [Tchuraev, R.N. (1982) J. Gen. Biol. 43, 79-87] has been realised, including feedback by repressing proteins with given trigger regime of gene functioning. Experimental tests of the expected epigene properties of the obtained pECPI recombinant plasmid involving lacI and cI(857) regulatory genes have shown a phenomenon of steady inheritance of two alternative epigenotypes lacI(1)cI(0) and lacI(0)cI(1), as well as an external toggle switch through metabolitic and temperature signals from one inherited functional state of the cyclic digene system into another. Thus, we have constructed a hereditary unit of a specific kind, namely, a two-component stationary epigene with preset properties.

Bacterial Proteins↗
PubMed2000

In vivo formation and repair of cyclobutane pyrimidine dimers and 6-4 photoproducts measured at the gene and nucleotide level in Escherichia coli.

In vivo formation and repair of the major UV-induced DNA photoproducts, cyclobutane pyrimidine dimers (CPDs) and 6-4 pyrimidine-pyrimidone photoproducts (6-4 PPs), have been examined at the gene and nucleotide level in Escherichia coli. Each type of DNA photoproduct has individually been studied using photoreactivation and two newly developed assays; the multiplex QPCR assay for damage detection at the gene level and the reiterative primer extension (PE) assay for damage detection at the nucleotide level. In the E. coli lacI and lacZ genes, CPDs and 6-4 PPs form in a 2:1 ratio, respectively, during UV irradiation. Repair of 6-4 PPs is more efficient than repair of CPDs since, on the average, 42% of 6-4 PPs are repaired in both genes in the first 40 min following 200 J/m(2) UV irradiation, while 1% of CPDs are repaired. The location, relative frequency of formation, and efficiency of repair of each type of photoproduct was examined in the first 52 codons of the E. coli lacI gene at the nucleotide level. Hotspots of formation were found for each type of lesion. Most photoproducts are at sites where both CPDs and 6-4 PPs are formed. Allowing 40 min of recovery following 200 J/m(2) shows that in vivo repair of 6-4 PPs is about fourfold more efficient than the repair of CPDs. Comparison of the lesion-specific photoproduct distribution of the lacI gene with a UV-induced mutation spectrum from wild-type cells shows that most mutational hotspots are correlated with sites of a majority of CPD formation. However, 6-4 PPs are also formed at some of these sites with relatively high frequency. This information, taken together with the observation that 6-4 PPs are repaired faster than CPDs, suggest that the cause of mutagenic hotspots in wild-type E. coli is inefficient repair of CPDs.

Bacterial Proteins↗
PubMed2000

Differential mutation of transgenic and endogenous loci in vivo.

Although chemicals usually induce very similar frequencies of mutations in transgenes and endogenous genes in vivo when given acutely, chronic exposure to N-ethyl-N-nitrosourea (ENU) produced a more complex pattern in which the endogenous locus was spared many mutations. Here, we demonstrate that the effect is neither ENU-specific nor locus-specific, and thus, may be important in the extrapolations of risk assessment and in understanding mutational mechanisms. During chronic mutagen exposure, mutations at the transgene accumulate linearly with time, i.e. in direct proportion to the dose received. In contrast, mutations at the endogenous gene are much less frequent than those of the transgene early in the exposure period and the accumulation is not linear with time, but rather accelerates as the exposure continues. Previous comparisons involved the endogenous Dlb-1 locus and the lacI transgene from the Big BlueMouse in the small intestine. These experiments involved the Dlb-1 locus and the lacZ transgene from the MutaMouse in the small intestine and the hprt locus and the lacZ transgene in splenocytes. Comparisons were made in both tissues after acute and chronic exposures to ENU, the original mutagen, and in the small intestine after exposures to benzo(a)pyrene. All comparisons showed that during chronic exposures mutations at the transgene accumulate linearly with the increasing duration of exposure, whereas induced mutations of the endogenous gene initially accumulate at a slower rate. Thus, the difference in mutational response observed during low chronic treatment is not unique to a particular transgene, endogenous gene, tissue, or mutagen used, but may be a general phenomenon of such genes.

Animals↗
PubMed1998

Mutation spectrum in the lacI gene, induced by gamma-radiation in aqueous solution under oxic conditions.

Irradiation of DNA in a cellular environment leads to many types of DNA damage, resulting from various effects of gamma-radiation. One of these effects is the formation of water-derived radicals (e.g., .OH radicals), which are formed in the vicinity of DNA (indirect effect). To study the influence of the indirect effect on gamma-radiation-induced mutations, a newly constructed plasmid, containing the lacI gene as a target gene, was irradiated with 60Co gamma-radiation in aqueous solution, in the presence of oxygen. Under these circumstances, only .OH radicals will be responsible for the induced mutations. Sequence analysis of the gamma-radiation-induced mutations showed that 96% of all mutations were base pair substitutions, 87% of which occurred in the lacI gene, the others are formed in the lac operator part. All gamma-radiation-induced mutations in the lacI gene occurred exclusively on G:C base pairs, and no mutations at A:T base pairs could be detected. In the spontaneous mutation spectrum, 83% of all mutations were base pair substitutions, 35% of which occurred in the lacI gene and 48% in the lac operator part. Base pair substitutions on G:C base pairs were very similar in the gamma-radiation-induced and in the spontaneous mutation spectrum, implying a high contribution of .OH radicals to spontaneous mutagenesis. A:T to G:C transitions accounted for 10% of all spontaneous base pair substitutions in the lacI gene and are probably the result of effects, other than just .OH radicals. It can be concluded that .OH radicals are an important source for mutations at G:C base pairs. In this paper, the extracellular gamma-radiation-induced mutation spectrum is also compared to the previously obtained, intracellular gamma-radiation-induced mutation spectrum of the lacI gene. Comparison shows some differences, such as relative high amounts of mutations at A:T base pairs, G:C to T:A transversions and frameshift mutations in the intracellular gamma-radiation-induced mutation spectrum, as compared to the extracellular gamma-radiation-induced mutation spectrum. Since the extracellular gamma-radiation-induced mutation spectrum shows that .OH radicals are mainly responsible for base pair substitutions on G:C base pairs, mutations at A:T base pairs in the intracellular gamma-radiation-induced mutation spectrum are apparently the result of additional or other factors.

Aerobiosis↗
PubMed1998

Lactose repressor protein: functional properties and structure.

The lactose repressor protein (LacI), the prototype for genetic regulatory proteins, controls expression of lactose metabolic genes by binding to its cognate operator sequences in E. coli DNA. Inducer binding elicits a conformational change that diminishes affinity for operator sequences with no effect on nonspecific binding. The release of operator is followed by synthesis of mRNA encoding the enzymes for lactose utilization. Genetic, chemical and physical studies provided detailed insight into the function of this protein prior to the recent completion of X-ray crystallographic structures. The structural information can now be correlated with the phenotypic data for numerous mutants. These structures also provide the opportunity for physical and chemical studies on mutants designed to examine various aspects of lac repressor structure and function. In addition to providing insight into protein structure-function correlations, LacI has been utilized in a wide variety of applications both in prokaryotic gene expression and in eukaryotic gene regulation and studies of mutagenesis.

Amino Acid Sequence↗
PubMed1997

Methods for predicting carcinogenic hazards: new opportunities coming from recent developments in molecular oncology and SAR studies.

Without epidemiological evidence, and prior to either short-term tests of genotoxicity or long-term tests of carcinogenicity in rodents, an initial level of information about the carcinogenic hazard of a chemical that perhaps has been designed on paper, but never synthesized, can be provided by structure-activity relationship (SAR) studies. Herein, we have reviewed the interesting strategies developed by human experts and/or computerized approaches for the identification of structural alerts that can denote the possible presence of a carcinogenic hazard in a novel molecule. At a higher level of information, immediately below epidemiological evidence, we have discussed carcinogenicity experiments performed in new types of genetically engineered small rodents. If a dominant oncogene is already mutated, or if an allele of a recessive oncogene is inactivated, we have a model animal with (n-1) stages in the process of carcinogenesis. Both genotoxic and receptor-mediated carcinogens can induce cancers in 20-40% of the time required for classical murine strains. We have described the first interesting results obtained using these new artificial animal models for carcinogenicity studies. We have also briefly discussed other types of engineered mice (lac operon transgenic mice) that are especially suitable for detecting mutagenic effects in a broad spectrum of organs and tissues and that can help to establish mechanistic correlations between mutations and cancer frequencies in specific target organs. Finally, we have reviewed two complementary methods that, while obviously also feasible in rodents, are especially suitable for biomonitoring studies. We have illustrated some of the advantages and drawbacks related to the detection of DNA adducts in target and surrogate tissues using the 32P-DNA postlabeling technique, and we have discussed the possibility of biomonitoring mutations in different human target organs using a molecular technique that combines the activity of restriction enzymes with polymerase chain reaction (RFLP/PCR). Prediction of carcinogenic hazard and biomonitoring are very wide-ranging areas of investigation. We have therefore selected five different subfields for which we felt that interesting innovations have been introduced in the last few years. We have made no attempt to systematically cover the entire area: such an endeavor would have produced a book instead of a review article.

Animals↗
PubMedDate not supplied

DNA replication and indirect induction of the SOS response in Escherichia coli.

The SOS response can be induced indirectly in Escherichia coli by infection with UV irradiated bacteriophage P1, lambda or M13. Induction, monitored quantitatively by means of a sfiA::lac operon fusion, was stronger with the plasmid phage P1 than with lambda, but the kinetics were similar, showing that plasmid and non-plasmid phages are not fundamentally different in their ability to produce indirect induction. In the absence of lambda DNA replication the level of induction was strongly reduced, indicating that the attempt to replicate damaged DNA results in induction of the SOS response. The slight residual induction observed in the absence of DNA replication suggests the existence of a second pathway leading from DNA lesions to induction of the SOS response.

Coliphages↗
PubMed1986

Genetic and physiological characterization of new Escherichia coli mutants impaired in hydrogenase activity.

The Mu dl (ApR lac) bacteriophage was used to generate mutants of Escherichia coli which were defective in formate hydrogenlyase. Three mutants were chosen for further analysis: they lacked hydrogenase (hydrogen: benzyl viologen oxidoreductase) activity, but produced normal levels of fumarate reductase activity and two- to three-fold reduced levels of benzyl viologen (BV)-dependent formate dehydrogenase activity. Two of them (hydC) were shown to contain about 4-fold reduced amounts of formate hydrogenlyase and fumarate-dependent H2 uptake activities. The third one (hydD) was totally devoid of both activities. Their insertion sites were located at 77 min on the E. coli map. Subdivision of these mutants into two classes was subsequently based on the restoration capacity of hydrogenase activity with high concentration of nickel in the growth media. Addition of 500 microM NiCl2 led to a complete recovery of hydrogenase activity, and to the concomitant restoration of normal BV-linked formate dehydrogenase, formate hydrogenlyase and fumarate-dependent H2 uptake activities in the hydC mutants. The hydD mutant was insensitive to the effect of nickel. Expression of the lac operon in hydC and hydD mutants was induced by anaerobiosis. It was not increased by the addition of formate under anaerobic conditions. The presence of nitrate resulted in slightly reduced beta-galactosidase activities in the hydC mutants, whereas those found in the hydD mutant reached only one third of the level obtained in its absence. Fumarate had no effect on both classes. Moreover, in contrast to the hydD locus, the hydC::Mu dl fusions were found to be dependent upon the positive control exerted by the nirR gene product and were totally repressed by an excess of nickel. In addition, the low levels of overall hydrogenase-dependent activities found in a nirR strain were also relieved by the presence of nickel. Our results strongly suggest that the pleiotropic regulatory gene nirR is essential for the expression of a gene (hydC) involved in either transport or processing of nickel in the cell, whose alteration leads to a loss of hydrogenase activity.

Alleles↗