Stress-induced mutation via DNA breaks in Escherichia coli: A molecular mechanism with implications for evolution and medicine

Evolutionary theory assumed that mutations occur constantly, gradually, and randomly over time. This formulation from the "modern synthesis" of the 1930s was embraced decades before molecular understanding of genes or mutations. Since then, our labs and others have elucidated mutation mechanisms activated by stress responses. Stress-induced mutation mechanisms produce mutations, potentially accelerating evolution, specifically when cells are maladapted to their environment, that is, when they are stressed. The mechanisms of stress-induced mutation that are being revealed experimentally in laboratory settings provide compelling models for mutagenesis that propels pathogen-host adaptation, antibiotic resistance, cancer progression and resistance, and perhaps much of evolution generally. We discuss double-strand-break-dependent stress-induced mutation in Escherichia coli. Recent results illustrate how a stress response activates mutagenesis and demonstrate this mechanism's generality and importance to spontaneous mutation. New data also suggest a possible harmony between previous, apparently opposed, models for the molecular mechanism. They additionally strengthen the case for anti-evolvability therapeutics for infectious disease and cancer.     

适应性突变的遗传学特征

基于大肠杆菌FC40菌株的研究结果表明,适应性突变依赖RecBCD重组途径的酶,要求SOS反应的部分基因功能,lac+回复突变序列都是在单核苷酸短重复序列处的一个碱基缺失。有证据表明有的适应性突变来自一个或多个暂时性的超突变的细胞亚群,它们的基因组发生大量的突变,转座子高频丢失。产生这种暂时性的超突变的增变子可能是因为细胞的MMR活性暂时不足,或是因错误翻译产生丧失了校读活性的DNA聚合酶III。其他一些研究系统虽然得到了一些同FC40菌株不一致的结论,但所有实验证据都表明,在饥饿等环境胁迫因子作用下,非生长或缓慢生长的细胞可以产生突变,这种突变具有生长依赖的自发突变所不同的一些遗传学特征。 Abstract:The research based on the Escherichia coli FC40 showed that adaptive mutations required the enzymes of RecBCD recombination pathway and some unknown proteins of SOS response,and the mutation spectrum of lac+ revertants is single-base deletions in the small mononucleotide repeats.Some evidence showed that the revertants with adaptive mutations partly come from one (or some) subset of transient hypermutable subpopulation of cells,in which high frequently losing of transposons and genome-wide mutations were observed.It was suggested that this kind of transient hypermutability may be due to the transient deficient activity of mismatch repair (MMR) system,or a defective epsilon unit of DNA polymerase III generated by mistranslation.Although other systems demonstrated some different mechanisms from FC40,all research works suggested that,adaptive mutations occurred in nondividing or nongrowing cells under environmental stresses,for example,starvation,displayed different genetic features from growth-dependent spontaneous mutation.     

Controlling Mutation: Intervening in Evolution as a Therapeutic Strategy

ABSTRACT

Mutation is the driving force behind many processes linked to human disease, including cancer, aging, and the evolution of drug resistance. Mutations have traditionally been considered the inevitable consequence of replicating large genomes with polymerases of finite fidelity. Observations over the past several decades, however, have led to a new perspective on the process of mutagenesis. It has become clear that, under some circumstances, mutagenesis is a regulated process that requires the induction of pro-mutagenic enzymes and that, at least in bacteria, this induction may facilitate evolution. Herein, we review what is known about induced mutagenesis in bacteria as well as evidence that it contributes to the evolution of antibiotic resistance. Finally, we discuss the possibility that components of induced mutation pathways might be targeted for inhibition as a novel therapeutic strategy to prevent the evolution of antibiotic resistance.     

Inducible SOS response system of DNA repair and mutagenesis in Escherichia coli

Chromosomal DNA is exposed to continuous damage and repair. Cells contain a number of proteins and specific DNA repair systems that help maintain its correct structure. The SOS response was the first DNA repair system described in Escherichia coli induced upon treatment of bacteria with DNA damaging agents arrest DNA replication and cell division. Induction of the SOS response involves more than forty independent SOS genes, most of which encode proteins engaged in protection, repair, replication, mutagenesis and metabolism of DNA. Under normal growth conditions the SOS genes are expressed at a basal level, which increases distinctly upon induction of the SOS response. The SOS-response has been found in many bacterial species (e.g., Salmonella typhimurium, Caulobacter crescentus, Mycobacterium tuberculosis), but not in eukaryotic cells. However, species from all kingdoms contain some SOS-like proteins taking part in DNA repair that exhibit amino acid homology and enzymatic activities related to those found in E. coli. but are not organized in an SOS system. This paper presents a brief up-to-date review describing the discovery of the SOS system, the physiology of SOS induction, methods for its determination, and the role of some SOS-induced genes.     

Pathways of Genetic Adaptation: Multistep Origin of Mutants Under Selection Without Induced Mutagenesis in Salmonella enterica

In several bacterial systems, mutant cell populations plated on growth-restricting medium give rise to revertant colonies that accumulate over several days. One model suggests that nongrowing parent cells mutagenize their own genome and thereby create beneficial mutations (stress-induced mutagenesis). By this model, the first-order induction of new mutations in a nongrowing parent cell population leads to the delayed accumulation of visible colonies. In an alternative model (selection only), selective conditions allow preexisting small-effect mutants to initiate clones that grow and give rise to faster-growing mutants. By the selection-only model, the delay in appearance of revertant colonies reflects (1) the time required for initial clones to reach a size sufficient to allow the second mutation plus (2) the time required for growth of the improved subclone. We previously characterized a system in which revertant colonies accumulate slowly and contain cells with two mutations, one formed before plating and one after. This left open the question of whether mutation rates increase under selection. Here we measure the unselected formation rate and the growth contribution of each mutant type. When these parameters are used in a graphic model of revertant colony development, they demonstrate that no increase in mutation rate is required to explain the number and delayed appearance of two of the revertant types.     

Environmental regulation of mutation rates at specific sites

Recent studies on bacterial adaptation to stress suggest that bacteria can regulate the generation of mutations at specific sites in response to environmental conditions. Here, we review these findings and discuss the circumstances under which these mechanisms might prove advantageous.     

Plasmid Copy Number Underlies Adaptive Mutability in Bacteria

The origin of mutations under selection has been intensively studied using the Cairns-Foster system, in which cells of an Escherichia coli lac mutant are plated on lactose and give rise to 100 Lac⁺ revertants over several days. These revertants have been attributed variously to stress-induced mutagenesis of nongrowing cells or to selective improvement of preexisting weakly Lac⁺ cells with no mutagenesis. Most revertant colonies (90%) contain stably Lac⁺ cells, while others (10%) contain cells with an unstable amplification of the leaky mutant lac allele. Evidence is presented that both stable and unstable Lac⁺ revertant colonies are initiated by preexisting cells with multiple copies of the F′lac plasmid, which carries the mutant lac allele. The tetracycline analog anhydrotetracycline (AnTc) inhibits growth of cells with multiple copies of the tetA gene. Populations with tetA on their F′lac plasmid include rare cells with an elevated plasmid copy number and multiple copies of both the tetA and lac genes. Pregrowth of such populations with AnTc reduces the number of cells with multiple F′lac copies and consequently the number of Lac⁺ colonies appearing under selection. Revertant yield is restored rapidly by a few generations of growth without AnTc. We suggest that preexisting cells with multiple F′lac copies divide very little under selection but have enough energy to replicate their F′lac plasmids repeatedly until reversion initiates a stable Lac⁺ colony. Preexisting cells whose high-copy plasmid includes an internal lac duplication grow under selection and produce an unstable Lac⁺ colony. In this model, all revertant colonies are initiated by preexisting cells and cannot be stress induced.     

Cystathionine β-Synthase (CBS) Domain-containing Pyrophosphatase as a Target for Diadenosine Polyphosphates in Bacteria

Among numerous proteins containing pairs of regulatory cystathionine β-synthase (CBS) domains, family II pyrophosphatases (CBS-PPases) are unique in that they generally contain an additional DRTGG domain between the CBS domains. Adenine nucleotides bind to the CBS domains in CBS-PPases in a positively cooperative manner, resulting in enzyme inhibition (AMP or ADP) or activation (ATP). Here we show that linear P¹,Pⁿ-diadenosine 5′-polyphosphates (Ap_nAs, where n is the number of phosphate residues) bind with nanomolar affinity to DRTGG domain-containing CBS-PPases of Desulfitobacterium hafniense, Clostridium novyi, and Clostridium perfringens and increase their activity up to 30-, 5-, and 7-fold, respectively. Ap₄A, Ap₅A, and Ap₆A bound noncooperatively and with similarly high affinities to CBS-PPases, whereas Ap₃A bound in a positively cooperative manner and with lower affinity, like mononucleotides. All Ap_nAs abolished kinetic cooperativity (non-Michaelian behavior) of CBS-PPases. The enthalpy change and binding stoichiometry, as determined by isothermal calorimetry, were ∼10 kcal/mol nucleotide and 1 mol/mol enzyme dimer for Ap₄A and Ap₅A but 5.5 kcal/mol and 2 mol/mol for Ap₃A, AMP, ADP, and ATP, suggesting different binding modes for the two nucleotide groups. In contrast, Eggerthella lenta and Moorella thermoacetica CBS-PPases, which contain no DRTGG domain, were not affected by Ap_nAs and showed no enthalpy change, indicating the importance of the DTRGG domain for Ap_nA binding. These findings suggest that Ap_nAs can control CBS-PPase activity and hence affect pyrophosphate level and biosynthetic activity in bacteria.     

Emergence of a mutagenic ochre suppressor mutation under lactose selection in appm mutant ofEscherichia coli harbouring the F′lacZU118 episome

WhenEscherichia coli harbouring theppm (earlier calledadi) mutation and the F′lacZU118 episome is subjected to lactose selection in the presence of suboptimal concentrations of glycerol, Lac⁺ colonies emerge after 5–6 days. They are shown to harbour an ochre suppressor mutation at 15.15 min. Inactivation ofrecA results in approximately four-fold reduction in the response. In theppm — ochre suppressor double mutant background the leakiness of thelacZ allele carried by F′ CC105 is enhanced, suggesting misreading of a valine codon (GUG) as glutamic acid codon (GAG). This is accompanied by reversion of thelacZ mutation tolacZ ⁺ (GTG → GAG). In LB medium both the leakiness and reversion are inhibited by streptomycin. Inactivation ofrecA did not affect leakiness but abolished reversion. These data are discussed in relation to the importance of allele leakiness and restricted growth in stationary-phase (adaptive) mutagenesis.     

多聚磷酸盐及其在分枝杆菌中的生理功能

结核病仍然是全球性传染病。缩短疗程的新药和新疫苗是控制结核病的关键。研究分枝杆菌的生理功能有助于实现上述目的。多聚磷酸盐在细菌胁迫应答中发挥重要作用。结核分枝杆菌具有两类多聚磷酸盐代谢酶以控制细胞内多聚磷酸盐的动态平衡:多聚磷酸盐激酶和多聚磷酸酸盐水解酶。本文综述多聚磷酸盐在分枝杆菌中的代谢及其生理功能,以期为研究多聚磷酸盐在结核分枝杆菌中的生理功能提供参考。     

EMS诱变技术在植物育种中的研究进展

甲基磺酸乙酯（Ethyl methane sulfonate,EMS）是一种常用的化学诱变剂,能诱发产生高密度的系列等位基因点突变。在当前种质资源极为匮乏,基因资源日益枯竭的状况下,采用EMS诱发突变技术创造有用基因资源具有极其重要的意义。本文通过对EMS的诱变原理和技术要领、应用实例、以及该技术在现代分子生物学中的应用前景加以阐述,对EMS诱变技术在农业生产中的应用具有重要作用。     

Dietary Restraint and Stress-Induced Snacking in Youth

Objective: To determine whether dietary restraint modifies stress-induced eating in youth. Research Methods and Procedures: Snacking was measured in boys (9.5 ± 0.3 years) and girls (9.0 ± 0.3 years), with and without dietary restraint, across a control day after reading children's magazines and/or coloring, and on a stress day after giving a videotaped speech, with order of conditions counterbalanced. Children were divided into four groups based on dietary restraint and changes in perceived stress: low-restraint/low-reactive (n = 9), low-restraint/high-reactive (n = 13), high-restraint/low-reactive (n = 10), and high-restraint/high-reactive (n = 8). Body composition was estimated by skinfolds. Results: Energy intake of snack foods was influenced differently by dietary restraint and stress reactivity in the stress and control conditions (p < 0.01). After being stressed, low-restraint/low-reactive children ate fewer snacks and high-restraint/high-reactive children ate more snacks compared with the control condition. After covarying for percentage of body fat, the interactions remained (p < 0.01). Girls ate less than boys (p < 0.001), but sex did not influence eating in control and stress conditions. Discussion: Dietary restraint occurs in children and may influence the effect of stress on eating. Interpersonal stress decreases snacking in low dietary restrained youth but increases snacking in high dietary restrained children, perhaps because of stress-induced disinhibition.     

The SOS response increases bacterial fitness,but not evolvability,under a sublethal dose of antibiotic

Exposure to antibiotics induces the expression of mutagenic bacterial stress–response pathways, but the evolutionary benefits of these responses remain unclear. One possibility is that stress–response pathways provide a short-term advantage by protecting bacteria against the toxic effects of antibiotics. Second, it is possible that stress-induced mutagenesis provides a long-term advantage by accelerating the evolution of resistance. Here, we directly measure the contribution of the Pseudomonas aeruginosa SOS pathway to bacterial fitness and evolvability in the presence of sublethal doses of ciprofloxacin. Using short-term competition experiments, we demonstrate that the SOS pathway increases competitive fitness in the presence of ciprofloxacin. Continued exposure to ciprofloxacin results in the rapid evolution of increased fitness and antibiotic resistance, but we find no evidence that SOS-induced mutagenesis accelerates the rate of adaptation to ciprofloxacin during a 200 generation selection experiment. Intriguingly, we find that the expression of the SOS pathway decreases during adaptation to ciprofloxacin, and this helps to explain why this pathway does not increase long-term evolvability. Furthermore, we argue that the SOS pathway fails to accelerate adaptation to ciprofloxacin because the modest increase in the mutation rate associated with SOS mutagenesis is offset by a decrease in the effective strength of selection for increased resistance at a population level. Our findings suggest that the primary evolutionary benefit of the SOS response is to increase bacterial competitive ability, and that stress-induced mutagenesis is an unwanted side effect, and not a selected attribute, of this pathway.     

肉类工业微生物诱变及应用研究进展

随着分子生物学、细胞生物学及分子遗传学等学科的迅猛发展,对微生物诱变分子机理的研究也日益完善。从微生物诱变分子机理出发,着重介绍了DNA损伤分子机理、基因突变分子机理和诱变剂的种类及遗传效应,同时,列举了诱变菌在肉类工业中的应用。     

胁迫诱导抗性基因转移导致细菌耐药的分子机制研究进展

抗性基因转移是细菌形成耐药性的重要原因.近年来的研究表明胁迫因子可通过多种机制诱导抗性基因转移.DNA损伤可导致细菌产生SOS应激反应,进而诱导接合DNA介导的抗性基因转移.在一些缺乏SOS系统的细菌中,抗生素胁迫可诱导细菌建立自然转化感受态.此外,作者最近的研究表明普通胁迫应答因子RpoS调控一种由双链质粒DNA介导的固体基质表面的抗性基因转移方式.本文在总结SOS依赖和非依赖型胁迫因子诱导细菌接合和转化介导的DNA转移以及RpoS调控固体基质表面双链质粒DNA转移的基础上,提出今后需重点研究胁迫因子如何激活关键调控蛋白以及这些调控蛋白如何影响DNA转移相关基因表达等关键问题.解决上述问题将为寻找合适的分子靶标用于防控抗性基因转移导致的细菌耐药奠定基础.