Specific Base Substitutions Research Articles

Bias in somatic hypermutation of human VH genes.

Translationally silent mutations, which are not antigen selected, of human VH6 Ig gene rearrangements isolated from human spleen were analyzed for bias to gain insight into intrinsic features of the mutation process. Sixty-three clones representing 38 VH6DJ rearrangements had an overall mutation frequency of 4.5%, a replacement/silent (R/S) mutation ratio of 2.1 and 167 unique silent mutations. The silent mutations showed bias in: (i) targeting to CDR1 and CDR2, (ii) an increased frequency of mutations of A compared to T nucleotide bases on the coding strand, and (iii) an increased frequency of transitions versus transversions. Bias of C-->G over C-->A, of G-->C over G-->T and of A-->C over A-->T transversions was also present. Hot spots of mutation were observed, some which corresponded to potential sites of stem-loop formation. The results suggest that the somatic mutation process in man may be targeted to the complementarity determining region for some V genes, exhibits specific base substitutions favoring transitions and specific types of transversions, and may be occurring on only one DNA strand.

Mutation spectra in salmonella of complex mixtures: Comparison of urban air to benzo[a]pyrene

We used an ion-exchange procedure coupled to the Salmonella assay to fractionate the dichloromethane-extractable particulate organics from an urban air sample collected in Boise, Idaho. A resulting base/neutral fraction contained 81% of the mutagenic activity but only 36% of the mass of the unfractionated sample. Chemical analysis showed that polycyclic aromatic hydrocarbons (PAHs) accounted for much of the mutagenic activity of the air sample. Colony probe hybridization, PCR, and DNA sequence analysis were then used to determine the mutations induced by the complex mixtures and a model PAH, benzo[a]pyrene (BAP) in approximately 900 revertants of the frameshift hisD3052 allele and approximately 400 revertants of the base-substitution hisG46 allele. The majority (93-94%) of the mutations induced at the frameshift allele in strain TA98 by the whole or base/neutral fraction of the urban air sample was a hotspot 2-base deletion of a CG or GC within the sequence CGCGCGCG. The remaining mutations were complex frameshifts that consisted of -2 or +1 frameshifts associated with a flanking base substitution. BAP induced a somewhat similar pattern of mutations, with 70% being the hotspot mutation, 23% being complex frameshifts, and the remaining being deletions. The inferred base-substitution specificity associated with the complex frameshifts at the hisD3052 allele (primarily G.C-->T.A transversions) was consistent with the observation that this same transversion was the primary mutation induced by the whole urban air sample and BAP at the base-substitution allele in strain TA100. At the frameshift allele, adducts that promote correct incorporation/slippage could account for hotspot mutations, whereas those that promote misincorporation/slippage could account for complex frameshifts. At the base-substitution allele, a mixture of adducts or of adducts with multiple conformations could account for the observed proportion of transitions and transversions. Combined with the bioassay-directed chemical analysis, these results from the first mutation spectra of a complex mixture suggest that such spectra reflect the dominance of particular classes of chemical mutagens within the mixture.

Passenger transgenes reveal intrinsic specificity of the antibody hypermutation mechanism: clustering, polarity, and specific hot spots.

We have analyzed somatic hypermutation in mice carrying an immunoglobulin kappa transgene in order to discriminate mutations that reflect the intrinsic specificity of the hypermutation mechanism from those highlighted by antigenic selection. We have immunized animals with three different immunogens. With one immunogen, the antigen-specific B cells express a transgenic kappa chain, which does not form part of the antibody; the transgene is a passenger free to accumulate unselected mutations. With the other two immunogens, the transgenic kappa chain constitutes the light chain of the expressed antibody. A comparison of the transgene mutations obtained under these different circumstances allows us to identify common features that we attribute to the intrinsic specificity of the hypermutation process. In particular, it yields only base substitutions and leads to hot spots occurring in individual positions (e.g., the second base of the Ser-31 codon). The mutations preferentially accumulate around the first complementarity-determining region. The process exhibits specific base substitution preferences with transitions being favored over transversions. We propose that these substitution preferences can be used to discriminate intrinsic from antigen-selected hot spots. We also note that hypermutation distinguishes between the coding and noncoding strands since pyrimidines (particularly thymidines) mutate less frequently than purines.

Use of mutant RNAs in studies on yeast 5S rRNA structure and function

The expression of mutant yeast 5S rRNA genes in vivo is reviewed as a basis for further studies on the structure, function, and regulation of the ribosomal 5S rRNA. Specific base substitutions, insertions, or deletions can result in substantial structural changes which can be detected readily by gel electrophoresis, permitting the assay of mutant RNA synthesis and utilization. Furthermore, the use of high and low copy shuttle vectors, as well as alternate growth conditions, permits a wide adjustment of the mutant RNA concentration. Under optimized conditions more than 80% of the cell's RNA can be replaced with mutant molecules. The application of this strategy to studies on the biosynthesis and structure of the 5S rRNA are demonstrated through recently isolated mutations.

Mouse transgenes in human cells detect specific base substitutions.

We describe a system of transgenic human cell lines that detects and identifies specific point mutations at defined positions within a gene. The target transgenome is a mouse adenine phosphoribosyltransferase (APRT) gene rendered nonfunctional by introduction of a substitution at either of two bases that comprise a splice acceptor site. Reversion at a mutated site results in the expression of wild-type mouse APRT and consequent growth of APRT+ transgenic cell colonies. Site-specific reversion to wild-type sequence is confirmed by regeneration of a previously destroyed diagnostic Pst I site. Two independent cell clones, each with mutant transgenomes bearing an A----G transition, exhibited an up to 7500-fold, dose-dependent induction of reversion following treatment with ethyl methanesulfonate. Treatment of these clones with 2-aminopurine resulted in no induction of revertants. In contrast, another transgenic cell clone, bearing a G----A transition, reverted as a consequence of 2-aminopurine, but not ethyl methanesulfonate, treatment. These data confirm for human cells the proposed mechanisms of action of these mutagens and provide evidence for the utility of our site-specific reversion method for mutagenesis studies.

Efficient expression and utilization of mutant 5 S rRNA in Saccharomyces cerevisiae.

The expression of mutant 5 S rRNA genes in vivo is examined as a basis for further studies on the control, structure, and function of the ribosomal 5 S RNA. Specific single base substitutions (e.g. positions 98 or 99) or short insertions can result in substantial structural changes that can easily be detected by gel electrophoresis and permit the assay of mutant RNA synthesis and utilization. In addition, the use of high and low copy shuttle vectors as well as alternate growth conditions permits the adjustment of mutant RNA levels in vivo. Despite the high genomic copy number for the 5 S rRNA gene, under optimized conditions as much as 80% of the cellular 5 S RNA can be mutant, and RNA structure analyses indicate that some of these RNAs can readily be assembled into the ribosome structure resulting in an in vivo ribosome population which is also approximately 80% mutant. The results indicate that plasmid integrated 5 S rRNA genes are preferentially expressed and suggest that additional features of the chromosome structure regulate 5 S rRNA gene expression in vivo.

Control of mRNA stability in chloroplasts by 3′ inverted repeats: effects of stem and loop mutations on degradation ofpsbA mRNAin vitro

To investigate the role of mRNA 3' inverted repeats (IRs) in stabilizing plant chloroplast mRNAs, we have measured the processing and stability of wild-type and mutant RNAs corresponding to the 3' end of the spinach chloroplast psbA mRNA. wild-type and mutant 3' IR-RNA precursors were processed at similar rates in a homologous in vitro system, but RNAs with either a mutant loop sequence CUUCGG or a specific base substitution in the IR exhibited an enhanced accumulation of mature product. Incubation of mature products in the in vitro system demonstrated that this was due to an increased stability of the product. These mutant RNAs displayed the same order of stabilities when their decay was measured following electroporation into intact chloroplasts. We found that the in vitro system contains an endonuclease activity that cleaves the wild-type 3' IR-RNA within the loop and also in single-stranded regions, suggesting a possible role for the loop sequence in determining RNA longevity in vitro. Interestingly, the altered loop sequence CUUCGG, which enhances RNA stability in bacteria (1), prolonged the half-life of psbA 3' IR-RNA in vitro and also resulted in an altered endonuclease cleavage pattern. Such nucleases could potentially play an important role in plastid mRNA decay in vivo.

Mutagenesis by transient misalignment.

Based upon a consideration of two mutational hot spots produced during DNA synthesis by a eukaryotic DNA repair polymerase, we suggested that certain base substitution errors result not from direct miscoding but from correct coding by a transiently misaligned template-primer (Kunkel, T. A., and Alexander, P. S. (1986) J. Biol. Chem. 261, 160-166). This model, which we called dislocation mutagenesis, has been directly tested. Introducing a single, phenotypically silent G----A base change into the template switches the base substitution specificity at the immediately adjacent hot spot, a T residue, from T----G transversions to T----A transversions. The cumulative change in frequency, represented by the disappearance of the T----G events and the appearance of the T----A events, is greater than 300-fold. These data demonstrate that during DNA synthesis in vitro, a base at one position can code a mutation at another position. This mechanism can operate over greater distances to produce complex mutations as well. We present one example in which a 123-base deletion containing three base changes at one end of the deletion can be precisely explained by transient misalignment. It remains to be established whether mutagenesis by dislocation operates in vivo to produce biologically significant changes in genetic information.

Identification of Base Substitutions in the Promoter Regions of the xγ- and Gγ-Globin Genes in xγ- (or cγ-) β+-HPFH Heterozygotes Using the DNA-Amplification-Synthetic Oligonucleotide Procedure

DNA amplification combined with hybridization with 32P-labeled synthetic oligonucleotide probes has been used to identify base substitutions in the 5' promoter region of the A gamma globin gene in members of eleven families from China, Sardinia, Canada, and the United States who had a heterozygosity for the A gamma-beta+-hereditary persistence of fetal hemoglobin (HPFH), and in members of six black families with a possible G gamma-beta+-HPFH heterozygosity. All three known A gamma types were observed, ie, the British type (-198, T----C), the Chinese type (-196, C----T), and the Green type (-117, G----A); the latter has been found in a black family. Of the six families with G gamma-beta+-HPFH, three had C----G at -202 and none T----C -175. Conditions for hybridization of amplified DNA with the specific probes are provided and the usefulness of the technique is discussed. The increase in numbers of A gamma(G gamma)-beta+-HPFH heterozygotes with specific base substitutions greatly enhances the probability of a direct correlation between these substitutions and the increase in the production of a specific gamma chain.

Identification of base substitutions in the promoter regions of the A gamma- and G gamma-globin genes in A gamma- (or G gamma-) beta+-HPFH heterozygotes using the DNA-amplification-synthetic oligonucleotide procedure

DNA amplification combined with hybridization with 32P-labeled synthetic oligonucleotide probes has been used to identify base substitutions in the 5′ promoter region of the A gamma globin gene in members of eleven families from China, Sardinia, Canada, and the United States who had a heterozygosity for the A gamma-beta+-hereditary persistence of fetal hemoglobin (HPFH), and in members of six black families with a possible G gamma-beta+-HPFH heterozygosity. All three known A gamma types were observed, ie, the British type (-198, T----C), the Chinese type (-196, C----T), and the Green type (-117, G----A); the latter has been found in a black family. Of the six families with G gamma-beta+-HPFH, three had C----G at -202 and none T----C -175. Conditions for hybridization of amplified DNA with the specific probes are provided and the usefulness of the technique is discussed. The increase in numbers of A gamma(G gamma)-beta+-HPFH heterozygotes with specific base substitutions greatly enhances the probability of a direct correlation between these substitutions and the increase in the production of a specific gamma chain.

Synthesis of mutant parathyroid hormone genes via site-specific recombination directed by crossover linkers

A synthetic ‘crossover linker’ technique has been designed for gene modification. The linker has (i) a restriction end for an initial ‘cohesive end’ ligation with one terminus of a linearized plasmid, (ii) a middle section carrying modified sequence information, and (iii) an ‘homology-searching’ sequence of 20 bp at its other end, that is homologous to a specific region in the opposite terminus of the plasmid. Inside the Escherichia coli transformation host, intramolecular recombination between the homologous ends of the resultant plasmid intermediate completes the integration of the Unker. Using different crossover Unkers, a human parathyroid hormone gene which had previously been cloned into plasmid pUC8 was converted to mutant coding sequences via specific (i) base substitution, (ii) sequence deletion and (iii) sequence insertion.

Classifying mutagens as to their specificity in causing the six possible transitions and transversions: A simple analysis using the salmonella mutagenicity assay

The standard Salmonella tester strains used to detect base substitution mutations carry the hisG428 ochre mutation (TA102 and TA104) and the hisG46 missense mutation (TA100). These mutations can be reverted by base changes at their mutant his loci or at extragenic suppressor loci. The base changes resulting in each class of revertants of these mutations have been identified, and simple phenotypic screens have been developed to distinguish among them. Revertants at extragenic suppressor loci are distinguished from those at the his loci by their sensitivity to inhibitory histidine analogs. The four ochre suppressor loci of hisG428 are distinguished by their ability to support growth of nonsense mutants of phage P22. These screens are the basis for a rapid and simple system for determining the base substitution specificity of mutagens using hisG428- and hisG46-containing tester strains. Diagnostic mutagens specific for each of the six possible base changes (transitions and transversions) have been identified. Using these diagnostic mutagens, two additional strains, each specifically reverted by a single base substitution mutation, have been developed to provide a minimum of two loci at which to detect each type of base change. The ability of this system to provide detailed information about mutational specificity in a variety of DNA repair backgrounds will allow further elucidation of the mechanisms of mutagenesis and DNA repair.

Mutations that affect utilization of a promoter in stationary-phase Bacillus subtilis.

Transcription of the ctc gene in Bacillus subtilis is activated only after exponentially growing cells enter stationary phase. The promoter of the ctc gene is utilized in vitro by two minor forms of RNA polymerase, E sigma 37 and E sigma 32, but not by the most abundant form of RNA polymerase, E sigma 55. We have used the ctc promoter to direct transcription of the xylE gene on plasmid pLC4 and observed that xylE was expressed only in stationary-phase B. subtilis. We also have constructed a series of homologous plasmids that differ only by specific base substitutions in the ctc promoter. We observed that the base substitutions that affected utilization of the ctc promoter in vivo (xylE expression) were the same as those that we had previously shown to affect utilization of the promoter in vitro by E sigma 37 and E sigma 32. We conclude that it is likely that the ctc promoter is utilized in vivo by E sigma 37 or E sigma 32.

Vesicular stomatitis virus defective interfering particles can contain extensive genomic sequence rearrangements and base substitutions.

We sequenced the 5' and 3' RNA termini of 16 defective interfering (DI) particles of vesicular stomatitis virus (VSV) isolated at intervals from persistent infections and from a series of undiluted lytic passages. All DI RNAs exhibited complementary termini, but sequences internal to these termini were extensively rearranged in a variety of ways. Despite extensive rearrangement, these internal sequences (in addition to the termini) apparently are important for DI particle interference properties. Some of these DI particles are derived from multiple intrastrand and interstrand recombination events, and the generation of each can be explained by current replicase error models. During viral evolution in persistent and acute infections, DI particles with specific termini base substitutions are selected. One DI particle exhibits a remarkable clustering of specific A----G (and complementary U----C) substitutions, apparently as a result of repetitive misincorporations by an error-prone viral polymerase complex.

TRNA gene transcription in yeast: Effects of specified base substitutions in the intragenic promoter

The yeast SUP53 gene encodes a leucine-inserting amber suppressor tRNA. We have introduced specific base substitutions into both 5′ and 3′ elements of the intragenic promoter of this tRNA gene. The influence of these sequence changes on promoter function has been investigated by transcription of the mutant genes in a homologous cell-free system. Our results do not support the idea that tertiary intragenic structure is important in tRNA gene transcription. For one of the SUP53 mutants we are able to suggest a plausible molecular basis for defective transcription: a single base substitution in the 3′ element of the intragenic promoter prevents the interaction of this element with a putative transcription factor.

Pollen Genetic Markers for Detection of Mutagens in the Environment

To utilize and exploit pollen for in situ mutagen monitoring, screening and toxicology, the range of genetic traits in pollen must be identified and analyzed. Traits that can be considered include ornamentation, shape and form, male sterility viability, intraspecific incompatibility, proteins and starch deposition. To be useful for the development of mutagen detection systems proteins should be: (1) activity stainable or immunologically identifiable in the pollen, (2) the products of one to three loci, and (3) gametophytic and nuclear in origin. Several proteins including alcohol dehydrogenase in maize, which meet those criteria will be discussed. The waxy locus in barley and maize which controls starch deposition has been characterized genetically and methods have been developed for pollen screening and mutant detection. At Washington State University a waxy pollen system is being developed in barley for in situ mutagen monitoring. The basis is an improved method for staining and scoring waxy pollen mutants. Specific base substitution, frameshift, and deletion mutant lines are being developed to provide information about the nature of the mutations induced by environmental mutagens. Thirty waxy mutant lines, induced by sodium azide and gamma-rays have been selected and are being characterized for spontaneous and induced reversion frequencies, allelism, karyotype, amylose content, and UDP glucose glucosyltransferase (waxy gene product) activity. Twelve mutant alleles are being mapped by recombinant frequencies.

Pollen genetic markers for detection of mutagens in the environment.

To utilize and exploit pollen for in situ mutagen monitoring, screening and toxicology, the range of genetic traits in pollen must be identified and analyzed. Traits that can be considered include ornamentation, shape and form, male sterility viability, intraspecific incompatibility, proteins and starch deposition. To be useful for the development of mutagen detection systems proteins should be: (1) activity stainable or immunologically identifiable in the pollen, (2) the products of one to three loci, and (3) gametophytic and nuclear in origin. Several proteins including alcohol dehydrogenase in maize, which meet those criteria will be discussed. The waxy locus in barley and maize which controls starch deposition has been characterized genetically and methods have been developed for pollen screening and mutant detection. At Washington State University a waxy pollen system is being developed in barley for in situ mutagen monitoring. The basis is an improved method for staining and scoring waxy pollen mutants. Specific base substitution, frameshift, and deletion mutant lines are being developed to provide information about the nature of the mutations induced by environmental mutagens. Thirty waxy mutant lines, induced by sodium azide and gamma-rays have been selected and are being characterized for spontaneous and induced reversion frequencies, allelism, karyotype, amylose content, and UDP glucose glucosyltransferase (waxy gene product) activity. Twelve mutant alleles are being mapped by recombinant frequencies.