Effect of endogenous carotenoids on "adaptive" mutation in Escherichia coli FC40

Green Technology Approach for Reinforcement of Calcium Chloride Cured Sodium Alginate Films by Isolated Bacteria from Palm Oil Mill Effluent (POME)

The suitability of bacteria application as fillers to reinforce calcium chloride cured sodium alginate film was investigated through the determination of the physical, morphological and mechanical properties of composite films. There were six species of bacteria isolated from palm oil mill effluent sample. The bacteria sample selected for filler reinforcement has a sub-micron diameter of 0.83 ± 0.13 µm. The growth curve of selected bacteria revealed that four days of broth culture produced the maximum bacteria mass. The composite films were produced with reinforcement of 0.1 g, 0.2 g, 0.3 g and 0.4 g of bacteria respectively. Overall, the increment of bacteria mass resulted in the production of yellowish composite films with improved morphological, physical and mechanical properties. The results revealed that the composite films reinforced with 0.3 g and 0.4 g of bacteria appeared to have less curling on the surface of the film. The water absorption properties of the films were initially 140.74% and remained constant at an approximate of 200% after the reinforcement. The tensile strength properties showed a total increment of approximately 22.70% (from 36.10 ± 1.94 MPa to 44.29 ± 0.60 MPa). Based on the results, bacteria fillers were not able to enhance the elongation properties because only about 0.6% of overall increment was observed which was considered insignificant. It was concluded that the bacteria biomass has the potential to be used as fillers to reinforce calcium chloride cured sodium alginate film.

Metaproteomics Reveals Growth Phase-Dependent Responses of an In Vitro Gut Microbiota to Metformin

Metaproteomics has been used in combination with in vitro gut microbiota models to study drug-microbiome interactions. However, it remains unexplored whether the metaproteomics profile of in vitro gut microbiota responds differently to a same stimulus added at different growth phases. In this study, we cultured a human gut microbiota in 96-deep well plates using a previously validated model. Metformin was added during the lag, log, and stationary phases. Microbiome samples, collected at different time points, were analyzed by optical density and function by metaproteomic. The in vitro gut microbiota growth curves, taxonomy, and functional responses were different depending whether metformin was added during the lag, log, or stationary phases. The addition of drugs at the log phase may lead to the greatest decline of bacterial growth. Metaproteomic analysis suggests that the strength of the metformin effect on the gut microbiome functional profile may be ranked as lag phase > log phase > stationary phase. Metformin added at the lag phase may result in a significantly reduced level of the Clostridiales order and an increased level of the Bacteroides genus, which is different from stimulations during the rest of the growth phases. Metformin may also result in alterations of several pathways, including energy production and conversion, lipid transport and metabolism, translation, ribosomal structure, and biogenesis. Our results indicate that the timing for drug stimulation should be considered when studying drug-microbiome interactions in vitro.

Stress-Induced Mutagenesis

Early research on the origins and mechanisms of mutation led to the establishment of the dogma that, in the absence of external forces, spontaneous mutation rates are constant. However, recent results from a variety of experimental systems suggest that mutation rates can increase in response to selective pressures. This chapter summarizes data demonstrating that,under stressful conditions, Escherichia coli and Salmonella can increase the likelihood of beneficial mutations by modulating their potential for genetic change.Several experimental systems used to study stress-induced mutagenesis are discussed, with special emphasison the Foster-Cairns system for "adaptive mutation" in E. coli and Salmonella. Examples from other model systems are given to illustrate that stress-induced mutagenesis is a natural and general phenomenon that is not confined to enteric bacteria. Finally, some of the controversy in the field of stress-induced mutagenesis is summarized and discussed, and a perspective on the current state of the field is provided.

Stress-induced mutagenesis in bacteria

Bacteria spend their lives buffeted by changing environmental conditions. To adapt to and survive these stresses, bacteria have global response systems that result in sweeping changes in gene expression and cellular metabolism. These responses are controlled by master regulators, which include: alternative sigma factors, such as RpoS and RpoH; small molecule effectors, such as ppGpp; gene repressors such as LexA; and, inorganic molecules, such as polyphosphate. The response pathways extensively overlap and are induced to various extents by the same environmental stresses. These stresses include nutritional deprivation, DNA damage, temperature shift, and exposure to antibiotics. All of these global stress responses include functions that can increase genetic variability. In particular, up-regulation and activation of error-prone DNA polymerases, down-regulation of error-correcting enzymes, and movement of mobile genetic elements are common features of several stress responses. The result is that under a variety of stressful conditions, bacteria are induced for genetic change. This transient mutator state may be important for adaptive evolution.

Adaptive mutations in Salmonella typhimurium phenotypic of purR super-repression

Under non-lethal selective conditions, a non-dividing or very slowly dividing microbial population gives rise to mutations that relieve selective pressures. This process is described as adaptive mutation. Salmonella typhimurium strain 5-28 has been used as a system for studying adaptive mutations in the chromosomal regulatory gene purR and its target, the purD operator. When this strain is plated on a minimal lactose medium, no apparent growth of parent lawn is observed, yet the revertant colonies accumulate over a period of time. Analysis of the purR mutational spectra showed that the frequencies of transitions and transversions were not significantly different among the growth-dependent and adaptive mutations. But the frequencies for five kinds of -1 frameshifts were significantly different between the growth-dependent and adaptive types. Among the growth-dependent mutations, most one-base deletions occurred in non-iterated bases and were distributed randomly. Among adaptive mutations, the frequency of one-base deletions in small mononucleotide repeats was higher and mutations were concentrated at three hotspots. One-base deletion in small mononucleotide repeats are generally believed to result from DNA polymerase slippage errors, which are not corrected by DNA repair machinery. We further investigated the role of DNA repair on adaptive mutation. Our results showed that the mismatch repair (MMR) might function less efficiently during adaptive mutation. However, DNA oxidative damage repair seemed no less effective in correcting errors under selective pressures than during non-selective growth.

Stationary phase-induction of G-->T mutations in Escherichia coli

A series of Escherichia coli mutants, constructed originally by Cupples and Miller [C.G. Cupples, J.H. Miller, A set of lacZ mutations in Escherichia coli that allow rapid detection of each of the six base substitutions, Proc. Natl. Acad. Sci. U.S.A. 86 (1989) 5345-5349], provides a unique system for quantifying base-change mutations, and the repair processes that limit their establishment, in bacteria under selective and non-selective conditions. We focussed on one strain in which a T-->G replacement inactivates the lacZ gene. Reversions of this strain can occur through oxidation of G, leading to G-->T transversions. We show that spontaneous reversions occurred both in lactose (selective) and glucose (non-selective) medium. The number of revertants per viable cell was much greater in medium containing lactose or both sugars than glucose alone. In glucose medium, the rate of reversion was highest below 0.6% glucose and strongly inhibited at and above that level. Evidence that reversions occurred through G-->T transversions in both lactose and glucose media came from two observations: by sequence analysis of a series of revertants and by comparing the reversion rates in strains possessing and lacking the mutM gene (encoding formamidopyrimidine DNA glycosylase, FPG). However, the rate of reversion was stimulated by reducing O2 to 1% and inhibited or delayed by increasing O2 to 90%. In mutM- cells grown on glucose medium, the proportion of revertants increased over a 5-day period. In contrast, in mutM+ cells, revertants appeared primarily during the first 2-3 days after plating; few new revertants appeared in the following days. These data imply that base excision repair initiated by FPG was less effective in the first 2 days and more effective later in stationary phase.

General stress response regulator RpoS in adaptive mutation and amplification in Escherichia coli

Microbial cells under growth-limiting stress can generate mutations by mechanisms distinct from those in rapidly growing cells. These mechanisms might be specific stress responses that increase mutation rates, potentially altering rates of evolution, or might reflect non-stress-specific processes in rare growing cells. In an Escherichia coli model system, both frameshift reversion mutations and gene amplifications occur as apparent starvation-induced mutations. Whereas frameshift reversion ("point mutation") requires recombination proteins, the SOS response, and error-prone DNA polymerase IV (DinB), amplification requires neither SOS nor pol IV. We report that both point mutation and amplification require the stationary-phase and general stress response transcription factor RpoS (sigmaS). Growth-dependent mutation does not. Alternative interpretations are excluded. The results imply, first, that point mutation and amplification are stress responses that occur in differentiated stationary-phase (not rare growing) cells and, second, that transient genetic instability, producing both point mutation and genome rearrangement, may be a previously unrecognized component of the RpoS-dependent general stress response.

General Stress Response Regulator RpoS in Adaptive Mutation and Amplification in Escherichia coli

Microbial cells under growth-limiting stress can generate mutations by mechanisms distinct from those in rapidly growing cells. These mechanisms might be specific stress responses that increase mutation rates, potentially altering rates of evolution, or might reflect non-stress-specific processes in rare growing cells. In an Escherichia coli model system, both frameshift reversion mutations and gene amplifications occur as apparent starvation-induced mutations. Whereas frameshift reversion (“point mutation”) requires recombination proteins, the SOS response, and error-prone DNA polymerase IV (DinB), amplification requires neither SOS nor pol IV. We report that both point mutation and amplification require the stationary-phase and general stress response transcription factor RpoS (σS). Growth-dependent mutation does not. Alternative interpretations are excluded. The results imply, first, that point mutation and amplification are stress responses that occur in differentiated stationary-phase (not rare growing) cells and, second, that transient genetic instability, producing both point mutation and genome rearrangement, may be a previously unrecognized component of the RpoS-dependent general stress response.

Lethality of visible light for Escherichia coli hemH1 mutants influence of defects in DNA repair

The hemH gene encodes ferrochelatase, the final enzyme of the heme biosynthetic pathway. Defects of this enzyme lead to accumulation of protoporphyrin IX and an increase in reactive oxygen species, causing susceptibility to blue and white light in bacteria and protoporphyria in humans. Here we show that the photosensitivity of hemH1 strains is much increased when the bacteria are devoid of ability to repair abasic sites. The sensitivity is increased 10- or 50-fold, in mutants bearing single xth or triple xth-nth-nfo mutations, respectively, but is not changed in mutants bearing nth, fpg, mutY, and mutT that are positive or negative for uvrA. This may indicate that in hemH1 mutants abasic sites are accumulated to a greater degree than oxidised bases, and/or that protoporphyrin, in the presence of abasic sites, increases the photosensitivity of hemH1 cells. It was shown in this work that the level of abasic sites (and/or strand breaks) in DNA of hemH1 strains increases greatly. Abasic sites and oxidative bases are potential mutagenic lesions. Nevertheless, the sensitivity of hemH1 bacteria to the lethal effect of visible light is not accompanied by increase in mutations. One of the possible explanations is that the genotoxic effect due to damage of hemH, shortage of heme and/or accumulating of protoporphyrin IX makes mutagenesis impossible.