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At least 19 recordsLinked to original sources
PubMed1996

Construction of a new system for separate expression of mutagenesis proteins: the abilities to promote UV mutagenesis and interchangeability of MucA', MucB, SamA' and SamB proteins in Salmonella typhimurium.

The two distinct mucAB and samAB operons originally isolated from the plasmids of Salmonella typhimurium encode proteins engaged in induced mutagenesis. They represent two extreme cases among the so far characterized members of the enterobacterial umuDC family in respect to both the strength and the specificity of their effect. It is suggested that the MucA and SamA proteins are post-translationally processed to MucA' and SamA', respectively, which lack the N-terminal 25 amino acids and are the active species in mutagenesis. For the purpose of characterizing the individual activities of these proteins, we developed a new system for their SOS-independent separate and controllable expression in enterobacteria. Besides the matured forms of MucA', SamA' as well as MucB and SamB proteins we also expressed hybrid HisTag-MucA' and HisTag-SamA' proteins in which a synthetic 24 amino acid HisTag region replaces the natural 25 amino acid N-terminal leader present in the MucA and SamA precursors. In this study, we analyzed the effect of the mutagenesis proteins on the UV mutability of S. typhimurium YG5144. None of the proteins, if expressed alone, promoted UV mutagenesis. Different combinations of the proteins promoted mutagenesis to different extents in the order MucA' + MucB > SamA' + SamB > or = HisTag-MucA' + MucB > or = SamA' + MucB > MucA' + SamB > HisTag-SamA' + SamB. The mutagenesis enhancing potential of the combinations with MucB protein decreased as the expression of the proteins increased while the mutagenesis enhancing potential of the combinations with SamB protein increased together with the increase in the expression. The artificially expressed MucA' + MucB proteins were as active as their MucAB counterparts expressed from the plasmid pKM101 in promoting UV mutagenesis, but they were remarkably more efficient than their pKM101-born counterparts in promoting spontaneous mutagenesis. We conclude that the MucA'B and SamA'B proteins are partly interchangeable and the functionality of the resulting A' + B complex is largely dependent on the appropriate B-protein.

Amino Acid Sequence↗
PubMed1998

Roles of the mutagenesis proteins SamA'B and MucA'B in chemically induced frameshift mutagenesis in Salmonella typhimurium hisD3052.

The mutagenesis induced by ultraviolet light and many chemicals in Escherichia coli is largely dependent upon the proteins encoded by the umuDC operon and their analogs. In Salmonella typhimurium, there are two sets of umuDC-like operons: the umuDC(ST) operon in the chromosome and the samAB operon located on the 60-MDa cryptic plasmid. The former operon, but not the latter, confers UV mutability on S. typhimurium. Nevertheless, the samAB operon, when carried on high-copy-number plasmids, can efficiently promote UV mutagenesis. In order to characterize the function of samAB in greater detail, we have compared the abilities of MucA'B and a putative activated form of SamAB, i.e. SamA'B, to promote chemically induced frameshift mutagenesis in S. typhimurium hisD3052. MucAB is an activated form of the products of mucAB, which is the most potent umuDC analog characterized so far. We have used four plasmids, each carrying samA', samB, mucA' or mucB with a lac promoter instead of their own promoters. The results indicated that under the conditions of elevated expression, SamA'B can promote chemically induced frameshift mutagenesis by furylfuramide, aflatoxin B1, 1-nitropyrene, and 1,8-dinitropyrene, with efficiencies comparable to, or even better than, MucA'B. Increase of the levels of expression enhanced the ability of SamA'B to promote the mutagenesis, while it decreased that of MucA'B. Surprisingly, the elevated expression of MucB alone significantly enhanced the frameshift mutagenesis induced by 1-nitropyrene and 1,8-dinitropyrene, whereas the elevated expression of SamB, MucA' and SamA' did not enhance it. These results suggest that the abilities of SamA'B and MucA'B to promote mutagenesis strongly depend on their levels of expression. The possible roles of these mutagenesis proteins in chemically induced frameshift mutagenesis are discussed.

Bacterial Proteins↗
PubMed1990

Proteolytic processing of MucA protein in SOS mutagenesis: both processed and unprocessed MucA may be active in the mutagenesis.

The mucAB operon carried on plasmid pKM101, which is an analogue of the umuDC operon of Escherichia coli, is involved in UV mutagenesis and mutagenesis induced by many chemicals. Mutagenesis dependent on either the umuDC or mucAB operon requires the function of the recA gene and is called SOS mutagenesis. By treating the cell with agents that damage DNA, RecA protein is activated by conversion into a form (RecA*) that mediates proteolytic cleavage of the LexA repressor and derepresses the SOS genes including mucAB. Since UmuD protein is proteolytically processed to an active form (UmuD*) in a RecA*-dependent fashion, and MucA shares extensive amino acid homology with UmuD, we examined whether MucA is similarly processed in the cell, using antiserum against a LacZ'-'MucA fusion protein. Like UmuD, MucA protein is indeed proteolytically processed in a RecA*-dependent fashion. In recA430 strains, MucAB but not UmuDC can mediate UV mutagenesis. However, MucA was not processed in the recA430 cells treated with mitomycin C. We constructed, by site-directed mutagenesis, several mutant mucA genes that encode MucA proteins with alterations in the amino acids flanking the putative cleavage site (Ala25-Gly26). MucA(Cys25) was processed and was as mutagenically active as wild-type MucA; MucA(Asp26) and MucA(Cys25,Asp26) were not processed, and were mutagenically inactive; MucA-(Thr25) was not processed, but was mutagenically as active as wild-type MucA. The mutant mucA gene that encoded the putative cleavage product of MucA was as active as mucA+ in UV mutagenesis. These results raise the possibility that both the nascent MucA and the processed product are active in mutagenesis.

Bacterial Proteins↗
PubMed2001

Structure-antimutagenic activity relationships of benzalacetone derivatives against UV-induced mutagenesis in E. coli WP2uvrA and gamma-induced mutagenesis in Salmonella typhimurium TA2638.

The antimutagenic activities of benzalacetone (4-phenyl-3-buten-2-one) and its structurally-related compounds were evaluated through their use as post-treatments for the UV-induced mutagenesis in Escherichia coli WP2s (uvrA) and the gamma-induced mutagenesis in Salmonella typhimurium TA2638, the latter of which is sensitive to oxidants. Structure-activity relationships were studied between IC(50) activity values, i.e. the dose (micromol/ml) at which the mutation frequency is reduced to 50% of the control, and electronic and hydrophobicity properties of the studied molecules. Benzalacetone and benzalacetone analogs, cinnamaldehyde and trans-1,1,1-trifluoro-4-phenyl-3-buten-2-one (TF), inhibited both forms of mutagenesis, but methyl cinnamate, cinnamic acid and cinnamamide did not. The IC(50) values of TF, for UV-induced mutagenesis and gamma-induced mutagenesis, were 0.028 and 0.045 micromol/ml, respectively, and one order of magnitude lower than those of cinnamaldehyde and benzalacetone. The three antimutagenic analogs listed in order of decreasing activity are: TF>>cinnamaldehyde>benzalacetone. This order is proportional to the electron-withdrawing property of the terminal group attached to an alpha,beta-unsaturated carbonyl moiety in the side chain that is known to play an important role in the antimutagenicities of benzalacetone and related compounds. In UV-induced mutagenesis in E. coli WP2s, mono-substituted benzalacetones - the ring-substituents of which have electron-withdrawing properties - showed antimutagenic activity that correlated with their electronic property. In gamma-induced mutagenesis in S. typhimurium TA2638, the antimutagenic activities of mono-substituted benzalacetones were proportional to the substituent hydrophobicities (pi). The different effects on both the mutation-induced systems is suggested to be related to the relative permeability of the cell membranes and the different sensitivities to mutagens between E. coli WP2s and S. typhimurium TA2638. In addition, the antimutagenic activity against gamma-induced mutagenesis could be due to the ability of parent compounds or their derivatives to scavenge long-lived organic radicals; the radicals have been described to be generated as a result of the X-irradiation of cells by Koyama et al. [Mutat. Res. 421 (1998) 45].

Antimutagenic Agents↗
PubMed1997

Multiple pathways for SOS-induced mutagenesis in Escherichia coli: an overexpression of dinB/dinP results in strongly enhancing mutagenesis in the absence of any exogenous treatment to damage DNA.

dinP is an Escherichia coli gene recently identified at 5.5 min of the genetic map, whose product shows a similarity in amino acid sequence to the E. coli UmuC protein involved in DNA damage-induced mutagenesis. In this paper we show that the gene is identical to dinB, an SOS gene previously localized near the lac locus at 8 min, the function of which was shown to be required for mutagenesis of nonirradiated lambda phage infecting UV-preirradiated bacterial cells (termed lambdaUTM for lambda untargeted mutagenesis). A newly constructed dinP null mutant exhibited the same defect for lambdaUTM as observed previously with a dinB::Mu mutant, and the defect was complemented by plasmids carrying dinP as the only intact bacterial gene. Furthermore, merely increasing the dinP gene expression, without UV irradiation or any other DNA-damaging treatment, resulted in a strong enhancement of mutagenesis in F'lac plasmids; at most, 800-fold increase in the G6-to-G5 change. The enhanced mutagenesis did not depend on recA, uvrA, or umuDC. Thus, our results establish that E. coli has at least two distinct pathways for SOS-induced mutagenesis: one dependent on umuDC and the other on dinB/P.

Bacterial Proteins↗
PubMed2004

[Development of retrovirus-mediated insertional mutagenesis in zebrafish and its application in saturation mutagenesis and gene screening].

The strategies of large-scale mutagenesis and gene screening include chemical mutagenesis, insertional mutagenesis and gene trap. Insertional mutagenesis is a method for identifying genes by using the integration of DNA as the mutagen, thereby facilitating the cloning of the mutated gene. The use of retrovirus-mediated insertional mutagenesis in zebrafish has led to the mutation and rapid identification of hundreds of genes required for embryonic development and cell growth. Gene trap elements are also used in the construction of retrovirus vectors. The whole system is likely to make zebrafish the first vertebrate to achieve saturation mutagenesis and gene screening.

Animals↗
PubMed1999

Mutagenesis induced by benzo[a]pyrene in lacZ mouse mammary and oral tissues: comparisons with mutagenesis in other organs and relationships to previous carcinogenicity assays.

Thus far, in vivo mutagenic assays have detected organ-specific effects of benzo[a]pyrene (B[a]P) in a number of organs, but not in oral tissues and breast. Previous studies have shown that the mouse tongue is a target for tumorigenesis induced by B[a]P when incorporated into feed, and polycyclic aromatic hydrocarbons are carcinogens in mouse mammary tissue. In order to evaluate the capacity of the lacZ mouse in vivo mutagenesis assay to detect mutations in these target tissues, we have measured mutagenesis induced by B[a]P in breast and oral tissues. The oral tissue consisted of either tongue or a mixture of oral tissues from several sites in the oral cavity. B[a]P was more mutagenic in breast tissue than in most other organs tested (liver, lung and kidney) when administered at relatively high dose by gavage, and more mutagenic than in liver, but not lung, at low dose. When administered in an emulsion in drinking water, B[a]P was more mutagenic in oral tissues than in liver, and somewhat less mutagenic than in lung. Regardless of dose, the mutagenic activity was greatest in colon where it was much higher than in other organs. A reasonable correlation was observed between mutagenesis observed here and carcinogenesis in previous studies although some differences were noted. To our knowledge, this represents the first report of in vivo mutagenesis in non-tumor mammary and oral tissue, and the results indicate these organs can efficiently metabolize B[a]P to genotoxic products, although some transport of active metabolites from the liver cannot be ruled out. The lacZ mouse mutagenesis assay may represent a shorter term alternative to carcinogenesis assays for investigations of factors affecting initiation of carcinogenesis in mammary and oral tissues. However, it is less predictive of actual tumor formation.

Animals↗
PubMed1976

Misrepair of overlapping daughter strand gaps as a possible mechanism for UV induced mutagenesis in UVR strains of Escherichia coli: a general model for induced mutagenesis by misrepair (SOS repair) of closely spaced DNA lesions.

It has been previously reported that an inducible form of post-replication repair appeared to be required for UV induced mutagenesis in a uvrA strain of Escherichia coli. It is shown here that the numbers of daughter strand gaps requiring inducible repair were similar to the numbers calculated to be overlapping one another in opposite daughter chromosomes. An estimation of survival with no repair of these gaps resembled the survival predicted with no mutagenesis. It is the thus proposed that inducible post-replication repair causes mutagenesis by the repair of overlapping daughter strand gaps. A general model for induced mutagenesis is presented. It is proposed that (a) some DNA lesions introduced by any DNA damaging agent may be close enough to interfere with constitutive repair replication of each other, (b) these lesions induce a repair system (SOS repair) which involves the recA+ lexA+ and polC+ genes (c) repair and concomitant mutagenesis occurs during repair replication by the insertion of mismatched bases opposite the noncoding DNA lesions.

Cell Survival↗
PubMed1981

Effects of inhibitors of de novo protein synthesis on UV-mutagenesis in Chinese hamster cells. Evidence against mutagenesis via inducible, error-prone DNA repair.

Experiments were designed to test whether UV-mutagenesis in animal cells requires an inducible error-phone DNA-repair system similar to the "SOS system" in E. coli. Chinese hamster (V79) cells were exposed to either 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole (DRB, a transcription inhibitor), cycloheximide, or puromycin for various times (3-6 h) following UV-irradiation (2-8 J/m2). Post-irradiation treatment with DRB resulted in a reproducible enhancement of UV-induced mutagenesis, whereas post-irradiation treatment with either cycloheximide or puromycin resulted in decreased UV-mutagenesis. Thus, the frequency of UV-mutagenesis does not appear to be dependent on an inducible error-prone DNA-repair pathway, since all 3 agents share the ability to inhibit de novo protein synthesis. In order to understand the effects of these inhibitors on mutation frequency, DNA synthesis in the presence of these agents was examined. DRB stimulated DNA synthesis in both irradiated and unirradiated cells. On the other hand, cycloheximide and puromycin caused an immediate inhibition of DNA synthesis in both irradiated and unirradiated cells. Therefore, it appears that UV-mutagenesis reflects changes in post-irradiation DNA synthesis rather than post-irradiation de novo protein synthesis.

Animals↗
PubMedDate not supplied

Perspective on mutagenesis and repair: the standard model and alternate modes of mutagenesis.

The basic ideas of replication, mutagenesis, and repair have outlined a picture of how point mutations occur that has provided a valuable framework for theory and experiment, much as the Standard Model of particle physics has done for our concept of fundamental particles. However, alternative modes of mutagenesis are being defined that are changing our perspective of the "Standard Model" of mutagenesis, requiring an expanded model. The genome is now envisioned as being in dynamic equilibrium between a multitude of forces for mutational change and forces that counteract such change. By maintaining a delicate balance between these forces, cells avoid unwanted or excessive mutations. Yet, cells allow mutagenesis to occur under certain conditions. We can define an emerging paradigm. Namely, mechanisms exist that can direct point mutations to specific designated genes or regions of genes. In some cases, this is achieved by specific enzymes, and in other cases high mutability is programmed into the sequence of certain genes to help generate diversity. In yet additional cases, general mutability is increased under stress, and selective forces allow the recovery of favorable mutants.

Animals↗
PubMed2001

Orthogonal combinatorial mutagenesis: a codon-level combinatorial mutagenesis method useful for low multiplicity and amino acid-scanning protocols.

We describe here a method to generate combinatorial libraries of oligonucleotides mutated at the codon-level, with control of the mutagenesis rate so as to create predictable binomial distributions of mutants. The method allows enrichment of the libraries with single, double or larger multiplicity of amino acid replacements by appropriate choice of the mutagenesis rate, depending on the concentration of synthetic precursors. The method makes use of two sets of deoxynucleoside-phosphoramidites bearing orthogonal protecting groups [4,4'-dimethoxytrityl (DMT) and 9-fluorenylmethoxycarbonyl (Fmoc)] in the 5' hydroxyl. These phosphoramidites are divergently combined during automated synthesis in such a way that wild-type codons are assembled with commercial DMT-deoxynucleoside-methyl-phosphoramidites while mutant codons are assembled with Fmoc-deoxynucleoside-methyl-phosphoramidites in an NNG/C fashion in a single synthesis column. This method is easily automated and suitable for low mutagenesis rates and large windows, such as those required for directed evolution and alanine scanning. Through the assembly of three oligonucleotide libraries at different mutagenesis rates, followed by cloning at the polylinker region of plasmid pUC18 and sequencing of 129 clones, we concluded that the method performs essentially as intended.

Amino Acid Substitution↗
PubMed2003

Roles of YqjH and YqjW, homologs of the Escherichia coli UmuC/DinB or Y superfamily of DNA polymerases, in stationary-phase mutagenesis and UV-induced mutagenesis of Bacillus subtilis.

YqjH and YqjW are Bacillus subtilis homologs of the UmuC/DinB or Y superfamily of DNA polymerases that are involved in SOS-induced mutagenesis in Escherichia coli. While the functions of YqjH and YqjW in B. subtilis are still unclear, the comparisons of protein structures demonstrate that YqjH has 36% identity to E. coli DNA polymerase IV (DinB protein), and YqjW has 26% identity to E. coli DNA polymerase V (UmuC protein). In this report, we demonstrate that both YqjH and the products of the yqjW operon are involved in UV-induced mutagenesis in this bacterium. Furthermore, resistance to UV-induced damage is significantly reduced in cells lacking a functional YqjH protein. Analysis of stationary-phase mutagenesis indicates that absences of YqjH, but not that of YqjW, decreases the ability of B. subtilis to generate revertants at the hisC952 allele via this system. These data suggest a role for YqjH in the generation of at least some types of stationary-phase-induced mutagenesis.

Bacillus subtilis↗
PubMed1980

Mutagenesis of ultraviolet-irradiated lambda phage by host cell irradiation: induction of Weigle mutagenesis is not an all-or-none process.

Ultraviolet mutagenesis of lambda phage to clear plaque formers is the same in the total phage population and in subpopulations of phage which have also mutated to gam- or at an amber codon. This is true for phage assayed in host cells in which Weigle mutagenesis has been either partially induced by low levels of ultraviolet irradiation, or fully induced by higher levels. If induction of Weigle mutagenesis were all-or-none, clear plaque formers in phage subpopulations selected for another mutation elsewhere would come mainly from induced cells; then the clear plaque mutation rate would always be that for fully induced host cells. Therefore, induction requires more than one lesion in host cell DNA. Although thymine starvation of cells induces synthesis of recA protein, it does not induce Weigle mutagenesis; in fact starvation inhibits induction of this process on subsequent ultraviolet irradiation of the cells.

Bacteriophage lambda↗
PubMed1981

cis-Platinum(II)diamminodichloride-induced mutagenesis in E. coli K12: crowding depression of mutagenesis.

Cis-Platinum(II)diamminodichloride (cis-PDD)-induced mutations to prototrophy were studied in Escherichia coli. Mutagenesis was not detected in a recA nor in a lexA mutant, but was greater in a uvrA strain than in a repair-proficient strain, at a given treatment of cis-PDD. Increasing the plating density above 10(5) cells per plate did not give an equivalent increase in revertants per plate [crowding depression of mutagenesis (Bockrath et al., 1980)]. Growth rates were similar at different plating densities and crowding depression of mutagenesis was observed in both excision-proficient and excision-deficient strains. A filtrate of a plate wash from crowded plates, of either treated or untreated cultures, further reduced the mutation frequencies over that due to crowding depression of mutagenesis.

Cisplatin↗
PubMed1987

Base substitution mutagenesis by terminal transferase: its role in somatic mutagenesis.

We have addressed the possibility of terminal transferase involvement in somatic mutagenesis and the creation of N-region diversity, by measuring the ability of TdT to enhance single-base substitution mutagenesis during in vitro DNA synthesis. Using 3 independent assays we find that terminal transferase produces only a small increase in base-substitution mutagenesis when assayed in the presence of DNA polymerase-beta. In the presence of either polymerase-alpha or E. coli polymerase-I, however, no detectable increase in TdT-induced mutagenesis is seen. Furthermore, in an assay capable of detecting a variety of mutational events, terminal transferase primarily produces complex addition/deletion mutations, as well as a few multiple, tightly-clustered, single-base mutations. We conclude that the majority of the scattered single-base changes that occur during antibody gene differentiation are not catalyzed by terminal transferase, but instead result from another error-prone DNA synthetic process (possibly utilizing DNA polymerase-beta).

Bacteriophage phi X 174↗
PubMed2000

Informatics for mutagenesis: the design of mutabase--a distributed data recording system for animal husbandry, mutagenesis, and phenotypic analysis.

The increasing use of high-throughput methods for the production of biologically important information and the increasing diversity of that information pose considerable bioinformatics challenges. These challenges will be met by implementing electronic data management systems not only to capture the data, but increasingly to provide a platform for data integration and mining as we enter the post-genomic era. We discuss the design and implementation of such a data capture system, 'Mutabase', as a model of how such electronic systems might be designed and implemented. Mutabase was created in support of a large-scale, phenotype-driven mouse mutagenesis program at MRC Mammalian Genetics Unit, Harwell, in collaboration with SmithKline Beecham Pharmaceuticals, Queen Mary and Westfield College, London, and Imperial College of Science, Technology and Medicine, London. The aim of this mutagenesis project is to make a significant contribution to the existing mouse mutant resource, closing the phenotype gap and providing many more models for fundamental research and disease modeling. Mutabase records experimental details at the 'point of generation' and provides a number of dissemination and analysis tools for the experimental data, as well as providing a means of assessing various aspects of progress of the program. Mutabase uses a hypertext-based interface to provide interaction between a number of intranet-based client workstations and a central industrial strength database. Mutabase utilizes a variety of techniques in order to implement the user interface system including Perl/CGI, Java Servlets, and an experimental CORBA server. We discuss the relative merits of these methods in the context of the need to provide sound informatics approaches for the support of systematic mutagenesis programs.

Animal Husbandry↗
PubMed1999

Transplacement mutagenesis: a novel in situ mutagenesis system using phage-plasmid recombination.

Site-specific mutagenesis provides the ability to alter DNA with precision so that the function of any given gene can be more fully understood. Several methods of in vitro mutagenesis are time-consuming and imprecise, requiring the subcloning and sequencing of products. Here we describe a rapid, high fidelity method of in situ mutagenesis in bacteriophage lambda using transplacement. Using this method, mutations are transferred from oligonucleotides to target phages using a plasmid interface. A small (50 bp) homology region bearing a centred point mutation is generated from oligonucleotides and subcloned into a transplacement plasmid bearing positive and negative phage selectable markers. Following a positive/negative selection cycle of integrative recombination and excision, the point mutation is transferred precisely from plasmid to phage in a subset ( approximately 25-50%) of recombinants. As the fidelity of both oligonucleotide synthesis and phage-plasmid recombination is great, this approach is extremely reliable. Using transplacement, point mutations can be accurately deposited within large phage clones and we demonstrate the utility of this technique in the construction of gene targeting vectors in bacteriophages.

Amino Acid Sequence↗