In vivo technique for determining transcriptional mutagenesis

Large-scale preparation of fluorescence multiplex host cell reactivation (FM-HCR) reporters

Repair of DNA damage is a critical survival mechanism that affects susceptibility to various human diseases and represents a key target for cancer therapy. A major barrier to applying this knowledge in research and clinical translation has been the lack of efficient, quantitative functional assays for measuring DNA repair capacity in living primary cells. To overcome this barrier, we recently developed a technology termed 'fluorescence multiplex host cell reactivation' (FM-HCR). We describe a method for using standard molecular biology techniques to generate large quantities of FM-HCR reporter plasmids containing site-specific DNA lesions and using these reporters to assess DNA repair capacity in at least six major DNA repair pathways in live cells. We improve upon previous methodologies by (i) providing a universal workflow for generating reporter plasmids, (ii) improving yield and purity to enable large-scale studies that demand milligram quantities and (iii) reducing preparation time >ten-fold.

Transcriptional mutagenesis: causes and involvement in tumour development

The majority of human cells do not multiply continuously but are quiescent or slow-replicating and devote a large part of their energy to transcription. When DNA damage in the transcribed strand of an active gene is bypassed by a RNA polymerase, they can miscode at the damaged site and produce mutant transcripts. This process is known as transcriptional mutagenesis and, as discussed in this Perspective, could lead to the production of mutant proteins and might therefore be important in tumour development.

Stationary phase mutagenesis in B. subtilis: a paradigm to study genetic diversity programs in cells under stress

One of the experimental platforms to study programs increasing genetic diversity in cells under stressful or nondividing conditions is adaptive mutagenesis, also called stationary phase mutagenesis or stress-induced mutagenesis. In some model systems, there is evidence that mutagenesis occurs in genes that are actively transcribed. Some of those genes may be actively transcribed as a result of environmental stress giving the appearance of directed mutation. That is, cells under conditions of starvation or other stresses accumulate mutations in transcribed genes, including those transcribed because of the selective pressure. An important question concerns how, within the context of stochastic processes, a cell biases mutation to genes under selection pressure? Because the mechanisms underlying DNA transactions in prokaryotic cells are well conserved among the three domains of life, these studies are likely to apply to the examination of genetic programs in eukaryotes. In eukaryotes, increasing genetic diversity in differentiated cells has been implicated in neoplasia and cell aging. Historically, Escherichia coli has been the paradigm used to discern the cellular processes driving the generation of adaptive mutations; however, examining adaptive mutation in Bacillus subtilis has contributed new insights. One noteworthy contribution is that the B. subtilis' ability to accumulate chromosomal mutations under conditions of starvation is influenced by cell differentiation and transcriptional derepression, as well as by proteins homologous to transcription and repair factors. Here we revise and discuss concepts pertaining to genetic programs that increase diversity in B. subtilis cells under nutritional stress.

Assays for transcriptional mutagenesis in active genes

Cells exposed to DNA-damaging agents in their natural environment do not undergo continuous cycles of replication but are more frequently engaged in gene transcription. Despite the relatively high efficiency of the different DNA repair pathways, some lesions remain in DNA. During transcription, RNA polymerase can bypass DNA damage on the transcribed strand of an active gene. This bypass can be at the origin of the production of "mutated" mRNA because of the transcriptional miscoding (transcriptional mutagenesis) due to the altered pairing specificities of the lesion. In vivo consequences of transcriptional mutagenesis on normal cell physiology have not well been documented because of the lack of a robust system allowing for its study. We describe here a procedure that we developed using a plasmid-based luciferase reporter assay to analyze the transcriptional mutagenesis events induced by different types of DNA lesions. Introduction of the DNA lesion to be studied at a specific site on the plasmid is based on the synthesis of a complementary strand of a circular, single-stranded DNA (ssDNA) from a DNA lesion-containing oligonucleotide. Once obtained, this construct can be transformed into different Escherichia coli strains that can express the luciferase gene under nongrowth conditions. Quantification of luciferase activity and sequencing of luciferase cDNAs allow for the characterization of transcriptional mutagenesis both quantitatively and qualitatively.

Reliable method for generating double-stranded DNA vectors containing site-specific base modifications

Cells of all living organisms are continuously exposed to physical and chemical agents that damage DNA and alter the integrity of their genomes. Despite the relatively high efficiency of the different repair pathways, some lesions remain in DNA when it is replicated or transcribed. Lesion bypass by DNA and RNA polymerases has been the subject of numerous investigations. However, knowledge of the in vivo mechanism of transcription lesion bypass is very limited because no robust methodology is available. Here we describe a protocol based on the synthesis of a complementary strand of a circular, single-stranded DNA molecule, which allows for the production of large amounts of double-stranded DNA containing a lesion at a specific position in a transcribed sequence. Such constructs can subsequently be used for lesion bypass studies in vivo by RNA polymerase and to ascertain how these events can be affected by the genetic background of the cells.

Transcriptional Mutagenesis Induced by Uracil and 8-Oxoguanine in Escherichia coli

Cells exposed to DNA damaging agents in their natural environment do not undergo continuous cycles of replication but are more frequently engaged in gene transcription. Luciferase gene expression analysis with DNA templates containing uracil or 8-oxoguanine, placed at a defined position, indicated that in nondividing Escherichia coli cells, efficient mutagenic lesion bypass does occur in vivo during transcription. Sequence analyses of the transcript population revealed that RNA polymerase inserts adenine opposite to uracil, and adenine or cytosine opposite to 8-oxoguanine. Surprisingly, deletions were also detected for 8-oxoguanine-containing templates, indicating RNA polymerase slippage over this lesion. Genetic analyses showed that, in E. coli, 8-oxoguanine is subject to transcription-coupled repair. Consequently, DNA damages alter transcription fidelity in vivo, which may lead to the production of mutant proteins that have the potential to change the phenotype of nondividing cells.

Cell-selfish modes of evolution and mutations directed after transcriptional bypass

During transcription, prokaryotic and eukaryotic RNA polymerases bypass and misread (transcriptional mutagenesis) several classes of DNA lesions. For example, misreading of 8-OH-dG generates mRNAs containing G to T transversions. After translation, if the mutant protein briefly allowed the cell a growth-DNA replication advantage, then precocious DNA replication would bypass that unrepaired 8-OH-dG and misinsert dA opposite the directing DNA lesion with a higher probability than would be experienced for 8-OH-G lesions at other positions in otherwise identical neighboring cells. Such retromutations would have been tested for their imparted growth advantage as mRNA before they became heritable DNA mutations. The logical properties of a mode of evolution that utilizes directed-retromutagenesis were compared one by one with those of the standard neo-Darwinian mode. The retromutagenesis mode, while minimizing mutational load, is cell-selfish; fitness is for an immediate growth advantage rather than future reproductive potential. In prokaryotes, an evolutionary mode that involves standard Darwinian fitness testing of novel alleles in the genetic background of origin followed by clonal expansion also favors cell-selfish allele combinations when linkage disequilibrium is practiced. For metazoa and plants to have evolved organized tissues, cell-selfish modes of evolution represent systems-poisons that must be totally suppressed. The feedback loops that allow evolution to be cell-serving in prokaryotes are actively blocked in eukaryotes by traits that restrict fitness to future reproductive potential. These traits include (i) delay of fitness testing until after the mutation is made permanently heritable, (ii) diploidy to further delay fitness testing, (iii) segregation of somatic lines from germ lines, (iv) testing of novel alleles against randomized allele combinations constructed by obligate sex, and (v) obligate genetic death to insure that that the most basic systems unit of selfish allele combinatorial uniqueness is the species instead of the cell. The analyses indicate that modes of evolution in addition to our neo-Darwinian one could have existed utilizing known molecular mechanisms. The evolution of multicellularity was as much the discarding of old cell-selfish habits as the acquisition of new altruistic ones.

Translesion synthesis by RNA polymerases: occurrence and biological implications for transcriptional mutagenesis

The genes of all organisms are continuously damaged by extrinsic and intrinsic physical and chemical agents. If the resulting DNA damage is left unrepaired, a number of deleterious biological consequences may result including the production of mutant proteins which can change the cellular phenotype. The majority of DNA damage-induced mutagenesis studies are based on models of DNA polymerase errors occurring in the vicinity of the lesion. In contrast, few studies have addressed the possibility that mutagenesis at the level of transcription (i.e. when RNA polymerase bypasses a lesion and a misincorporation event occurs) may also be an important source of mutant proteins, particularly in nondividing cell populations. This article reviews a number of recent studies on translesion synthesis by RNA polymerases resulting in the production of mutant transcripts (transcriptional mutagenesis). Over a dozen different types of DNA damage are now known to be bypassed with various degrees of efficiency and miscoding abilities by the transcriptional elongation machinery. Some important biological implications of transcriptional mutagenesis are discussed.

Cancerous hyper-mutagenesis in p53 genes is possibly associated with transcriptional bypass of DNA lesions

The database of tumor-associated p53 base substitutions includes about 5% of tumors with two or more base substitutions. These multiplet base substitutions in one tumor are evidence for hyper-mutagenesis. Our retrospective analysis of this database indicates that most multiplets arise from a single transient hyper-mutagenic event in one cell that subsequently proliferated into a clonal tumor. The hyper-mutagenesis, 1.8 x 10(-4) substitutions per base pair, is detected as multiple mutations in p53 genes of tumors. It requires one strongly tumorigenic p53 substitution, usually missense, called the driver mutation. The occurrence frequencies of ancillary base substitutions, those that hitch-hike along with the driver mutation, are independent of their amino acid coding properties. In this respect, they act like neutral mutations. In support of this neutrality, we find that the frequency distribution of hitch-hiking CpG transitions along the p53 exons, their mutational spectrum, approximates the spontaneous pre-selection mutational spectrum of most human tissues and is correlated with the mutational spectrum of p53 pseudogenes in mammalian germ cells. The driver substitutions of multiplets predominantly originate along the transcribed strand while the ancillary substitutions tend to originate along the non-transcribed strand. This data is consistent with a model of time-dependent mutagenesis in non-dividing stem cells for generating multiple strand-asymmetric p53 mutations in tumors. By transcriptional bypass of DNA lesions with concomitant misincorporation, transcriptional mutagenesis generates a transient mutant p53 mRNA. The associated mutant p53 protein could allow the host cell a growth advantage, release from G1-arrest. Then, during subsequent DNA replication and misreading of the same lesion, the damaged base along the transcribed DNA strand would serve as the origin of the p53 base substitution that drives the hyper-mutagenic event leading to tumors with multiple p53 mutations.