Long-term effects of inducible mutagenic DNA repair on relative fitness and phenotypic diversification in Pseudomonas cichorii 302959

Mutagenic DNA repair (MDR) employs low-fidelity DNA polymerases capable of replicating past DNA lesions resulting from exposure to high-energy ultraviolet radiation (UVR). MDR confers UVR tolerance and activation initiates a transient mutator phenotype that may provide opportunities for adaptation. To investigate the potential role of MDR in adaptation, we have propagated parallel lineages of the highly mutable epiphytic plant pathogen Pseudomonas cichorii 302959 with daily UVR activation (UVR lineages) for ~500 generations. Here we examine those lineages through the measurement of relative fitness and observation of distinct colony morphotypes that emerged. Isolates and population samples from UVR lineages displayed gains in fitness relative to the ancestor despite increased rates of inducible mutation to rifampicin resistance. Regular activation of MDR resulted in the maintenance of genetic diversity within UVR lineages, including the reproducible diversification and coexistence of “round” and “fuzzy” colony morphotypes. These results suggest that inducible mutability may present a reasonable strategy for adaptive evolution in stressful environments by contributing to gains in relative fitness and diversification.     

Growth parameter components of adaptive specificity during experimental evolution of the UVR-inducible mutator Pseudomonas cichorii 302959

Background

Mutagenic DNA repair (MDR) transiently increases mutation rate through the activation of low-fidelity repair polymerases in response to specific, DNA-damaging environmental stress conditions such as ultraviolet radiation (UVR) exposure. These repair polymerases also confer UVR tolerance, intimately linking mutability and survival in bacteria that colone habitats subject to regular UVR exposure.

Methodology/Principal Findings

Here, we investigate adaptive specificity in experimental lineages of the highly UVR-mutable epiphytic plant pathogen Pseudomonas cichorii 302959. Relative fitness measurements of isolates and population samples from replicate lineages indicated that adaptive improvements emerged early in all lineages of our evolution experiment and specific increases in relative fitness correlated with distinct improvements in doubling and lag times. Adaptive improvements gained under UVR and non-UVR conditions were acquired preferentially, and differentially contributed to relative fitness under varied growth conditions.

Conclusions

These results support our earlier observations that MDR activation may contribute to gains in relative fitness without impeding normal patterns of adaptive specificity in P. cichorii 302959.     

The consequences of growth of a mutator strain of Escherichia coli as measured by loss of function among multiple gene targets and loss of fitness

We have examined the composition of members of mutator populations of Escherichia coli by employing an extensive set of phenotypic screens that allow us to monitor the function of >700 genes, constituting approximately 15% of the genome. We looked at mismatch repair deficient cells after repeated cycles of single colony isolation on rich medium to generate lineages that are forced through severe bottlenecks, and compared the results to those for wild-type strains. The mutator lineages continued to accumulate mutations rapidly with each increasing cycle of colony isolation. By the end of the 40th cycle, after approximately 1000 generations, most of the lineages had reduced colony size, 4% had died out, 55% had auxotrophic requirements (increasing to 80% after 60 cycles), and 70% had defects in at least one sugar or catabolic pathway. In addition, 33% had a defect in cell motility, and 26% were either temperature-sensitive or cold-sensitive lethals. On the other hand, only 3% of the wild-type lineages had detectable mutations of any type after 40 cycles. By the 60th cycle, the typical mutator cell carried 4-5 inactive genes among the 15% of the genome being monitored, indicating that the average cell carried at least 24-30 inactivated genes distributed throughout the genome. Remarkably, 30% of the lineages had lost the ability to utilize xylose as a carbon source. DNA sequencing revealed that most of the Xyl(-) mutants had a frameshift in a run of eight G's (GGGGGGGG) in the xylB gene, either adding or deleting one -G-. Further analysis indicated that rendering E. coli deficient in mismatch repair unmasks hypermutable sites in certain genes or intergenic regions. Growth curves and competition tests on lineages that passed through 90 cycles of single colony isolation showed that all lineages suffered reduced fitness. We discuss these results in terms of the value of mutators in cellular evolution.     

Alterations in lymphocyte homing patterns within mice exposed to ultraviolet radiation

This report presents the results of an investigation designed to establish whether exposure of mice to ultraviolet radiation (UVR) is capable of influencing the factors that control the distribution of lymphoid cells in vivo. We found that such exposure resulted in a dramatic and long-lasting increase in the tropism of peripheral lymph nodes for circulating lymphoid cells. Termination of UVR exposure did not result in a reversal of this phenomenon. Since an increase in lymphocyte migration into the lymph nodes of UVR-exposed mice was apparent within 2 hr of infusion of the radiolabeled cells, we conclude that the homing assay data reflect a relatively increased binding of circulating lymphocytes to high endothelial venules (HEV) within the lymph nodes of irradiated animals. A histologic analysis of skin from UVR-exposed mice established that the dermal microvasculature had expanded in terms of size and number of vessels, a condition that also does not completely reverse after the termination of treatments. In spite of the increase in dermal microvasculature, very few inflammatory cells were detected in the irradiated skin site. These observations support our conclusion that the enhanced traffic of lymphocytes into peripheral lymph nodes of UVR-exposed mice occurs primarily via lymphocyte-HEV interactions rather than afferent drainage of the irradiated skin.     

Big-benefit mutations in a bacteriophage inhibited with heat

High temperature inhibits the growth of the wild-type bacteriophage phiX174. Three different point mutations were identified that each recovered growth at high temperature. Two affected the major capsid protein (residues F188 and F242), and one affected the internal scaffolding protein (B114). One of the major capsid mutations (F242) is located in a beta strand that contacts B114 in the procapsid during viral maturation, whereas the other capsid mutation (F188) is involved in subunit interactions at the threefold axis of symmetry. Selective coefficients of these mutations ranged from 13.9 to 3.8 in the inhibitory, hot environment, but all mutations reduced fitness at normal temperature. The selective effect of one of the mutations (F242) was evaluated at high temperature in four different genetic backgrounds and exhibited epistasis of diminishing returns: as log fitness of the background genotype increased from -0.1 to 4.1, the fitness boost provided by the F242 mutation decreased from 3.9 to 0. 8. These results support a model in which viral fitness is bounded by an upper limit and the benefit of a mutation is scaled according to the remaining opportunity for fitness improvement in the genome.     

Regulation of murine lymphokine production in vivo. Ultraviolet radiation exposure depresses IL-2 and enhances IL-4 production by T cells through an IL-1-dependent mechanism

The exposure of experimental animals to the inflammatory effects of ultraviolet radiation (UVR) is known to cause depressions in their ability to initiate and effectuate various types of cellular immune responses. Contact-type and delayed-type hypersensitivity, plus the ability to generate protective forms of anti-viral and anti-tumor immunity, are all affected by the prior exposure of normal animals to the effects of this physical agent. Presently, the cellular and molecular mechanism(s) responsible for mediating the changes in immune function observed in UVR-exposed animals is not fully understood. Herein we report that one reproducible consequence of exposing normal mice to low doses of UVR is a dramatic change in the pattern of lymphokines secreted by their activated T cells. Lymphocytes isolated from UVR-exposed donors produce/secrete greatly reduced levels of the T cell lymphokines IL-2 and IFN-gamma activation in vitro with protein Ag of the polyclonal T cell stimulant anti-CD3. The secretion of IL-4 by these lymphocyte cultures, however, is consistently elevated in comparison to normal controls. Further studies determined that a similar change in lymphokine production was induced when mice were treated with either bacterial LPS or rIL-1 beta, a cytokine known to be elevated in vivo after UVR or LPS exposure. The ability of IL-1 to facilitate a change in the capacity of T lymphocytes to produce/secrete lymphokines after in vitro activation does not appear to represent a direct effect of this cytokine on lymphocyte or accessory cell targets because addition of IL-1 beta to cultures of Ag-primed lymphocytes obtained from normal donors was incapable of altering the pattern of lymphokine production. Collectively, our present results add further support to the hypothesis that UVR-induced elevations in endogenous IL-1 are, in part, responsible for the immunomodulatory effects of UVR. These findings provide compelling evidence that UVR, plus other agents capable of endogenously stimulating the production of IL-1, may function to alter the expression of different effector mechanisms in vivo. This could be facilitated through selective reductions in lymphokines produced by Th-1-type cells (IL-2 and IFN-gamma) and a simultaneous augmentation in a lymphokine produced by Th-2-type cells (IL-4).     

Effects of UV radiation on the structure of Arctic macrobenthic communities

At present, information on the effects of ultraviolet radiation (UVR) on structure and diversity of polar, in particular Arctic, benthic communities is scarce. It is unclear whether and to what extent communities of different successional age are susceptible to UVR and whether UVR effects known to be detrimental at the species level can be buffered at the community level. In a subtidal field study on Spitsbergen (Norwegian Arctic), we investigated the potential effect of distinct UVR regimes on macrobenthic communities of different successional ages, grown on ceramic tiles. Total taxon cover, taxon composition, evenness, and richness were assessed after experimental exposure of 4 and 8 weeks. Overall, 17 algal and invertebrate taxa were encountered in the study and diatoms dominated the communities regardless of successional age or radiation treatment. UVR effects were dependent on both exposure time and community age. We did not find overall detrimental UVB effects. In contrast, abundance of several species increased in UVR-exposed communities. Especially, UVA seemed to have a beneficial effect in that several green and brown algal taxa increased in abundance (e.g. Ulothrix flacca, Chlorophyta, and Desmarestia sp., Phaeophyceae). In general, UVR effects depended on species composition and thus on successional age of communities, with later successional communities likely to be able to buffer and alleviate possible negative effects of UVR at species level. Overall, the presented study provides a first insight into the complex role UVR plays in structuring Arctic epibenthic communities.     

Disentangling population strategies of two cladocerans adapted to different ultraviolet regimes

Zooplankton have evolved several mechanisms to deal with environmental threats, such as ultraviolet radiation (UVR), and in order to identify strategies inherent to organisms exposed to different UVR environments, we here examine life‐history traits of two lineages of Daphnia pulex. The lineages differed in the UVR dose they had received at their place of origin from extremely high UVR stress at high‐altitude Bolivian lakes to low UVR stress near the sea level in temperate Sweden. Nine life‐history variables of each lineage were analyzed in laboratory experiments in the presence and the absence of sub‐lethal doses of UVR (UV‐A band), and we identified trade‐offs among variables through structural equation modeling (SEM). The UVR treatment was detrimental to almost all life‐history variables of both lineages; however, the Daphnia historically exposed to higher doses of UVR (HighUV) showed a higher overall fecundity than those historically exposed to lower doses of UVR (LowUV). The total offspring and ephippia production, as well as the number of clutches and number of offspring at first reproduction, was directly affected by UVR in both lineages. Main differences between lineages involved indirect effects that affected offspring production as the age at first reproduction. We here show that organisms within the same species have developed different strategies as responses to UVR, although no increased physiological tolerance or plasticity was shown by the HighUV lineage. In addition to known tolerance strategies to UVR, including avoidance, prevention, or repairing of damages, we here propose a population strategy that includes early reproduction and high fertility, which we show compensated for the fitness loss imposed by UVR stress.     

Induction of sister chromatid exchanges in xeroderma pigmentosum cells after exposure to ultraviolet light

The role of DNA repair mechanisms in the induction of sister chromatid exchanges (SCE) after exposure to ultraviolet radiation was investigated in xeroderma pigmentosum cells. Cells from different excision-deficient XP strains, representing the 5 complementation groups in XP, A, B, C, D and E, and from excision-proficient XP variant strains were irradiated with low doses of UVR (0-3.5 J/m2). The number of SCE was counted after two cycles in the presence of BUdR. In cells of the complementation groups A, B, C and D the number of SCE was significantly higher than in UV-exposed control cells. The frequencies of SCE in group E cells and in XP varient cells were not different from those in control cells. Treatment with caffeine (0-200 microgram/ml) did not result in a different response of variant cells compared with normal cells. A simple correlation between SCE frequency and residual excision-repair activity was not observed. The response of the excision-repair deficient cells suggest that unrepaired damage, produced by UVR is involved in the production of SCE.     

Host egg pigmentation protects developing parasitoids from ultraviolet radiation

Parasites rely on their hosts not only for nutrition and reproduction, but also for protection against natural enemies and adverse climatic conditions. In host‐parasite interactions, protective characteristics of both players are important to consider regarding damaging effects of environmental hazards. While ultraviolet radiation (UVR) is pervasive and harmful to organisms in general, its impact on parasite fitness remains understudied. Moreover, studies that do examine the effects of UV exposure on parasitic organisms tend to neglect host traits, which may vary inter‐ or intra‐specifically and thus confer different levels of environmental protection. We examined in the laboratory whether the UV‐protective value of host egg pigmentation could also benefit parasitoids, using the egg parasitoid Telenomus podisi and the predatory stink bug Podisus maculiventris. This host species lays eggs of variable pigmentation levels from light to dark grey, an adaptation protecting its own embryos from UVR. We showed that higher levels of host egg pigmentation protect parasitoids subjected to a developmental exposure to UVR, increasing emergence rates by up to 86% and reducing development time by up to 4%. This protective effect of host pigmentation was context‐dependent, being less pronounced at low UVR intensity and towards the end of parasitoid development. Parasitoids that emerged from darker‐coloured eggs exposed to UVR were of slightly larger size than those developing in light‐coloured eggs, but other fitness‐related traits (fecundity, longevity, sex ratio) were unaffected. This study provides the first experimental evidence that host pigmentation can increase host suitability for parasitic organisms, and emphasizes the importance of considering trait variation in interacting species when investigating the susceptibility of ecological communities to important abiotic environmental factors.     

Estimating fitness by competition assays between drug susceptible and resistant Mycobacterium tuberculosis of predominant lineages in Mumbai, India

Background

Multi Drug Resistant Tuberculosis (MDR TB) is a threat to global tuberculosis control. A significant fitness cost has been associated with DR strains from specific lineages. Evaluation of the influence of the competing drug susceptible strains on fitness of drug resistant strains may have an important bearing on understanding the spread of MDR TB. The aim of this study was to evaluate the fitness of MDR TB strains, from a TB endemic region of western India: Mumbai, belonging to 3 predominant lineages namely CAS, Beijing and MANU in the presence of drug susceptible strains from the same lineages.

Methodology

Drug susceptible strains from a single lineage were mixed with drug resistant strain, bearing particular non synonymous mutation (rpoB D516V; inhA, A16G; katG, S315T1/T2) from the same or different lineages. Fitness of M.tuberculosis (M.tb) strains was evaluated using the difference in growth rates obtained by using the CFU assay system.

Conclusion/Significance

While MANU were most fit amongst the drug susceptible strains of the 3 lineages, only Beijing MDR strains were found to grow in the presence of any of the competing drug susceptible strains. A disproportionate increase in Beijing MDR could be an alarm for an impending epidemic in this locale. In addition to particular non synonymous substitutions, the competing strains in an environment may impact the fitness of circulating drug resistant strains.     

Evolution of drug-resistant viral populations during interruption of antiretroviral therapy

Analysis of a large number of HIV-1 genomes at multiple time points after antiretroviral treatment (ART) interruption allows determination of the evolution of drug-resistant viruses and viral fitness in vivo in the absence of drug selection pressure. Using a parallel allele-specific sequencing (PASS) assay, potential primary drug-resistant mutations in five individual patients were studied by analyzing over 18,000 viral genomes. A three-phase evolution of drug-resistant viruses was observed after termination of ART. In the first phase, viruses carrying various combinations of multiple-drug-resistant (MDR) mutations predominated with each mutation persisting in relatively stable proportions while the overall number of resistant viruses gradually increased. In the second phase, viruses with linked MDR mutations rapidly became undetectable and single-drug-resistant (SDR) viruses emerged as minority populations while wild-type viruses quickly predominated. In the third phase, low-frequency SDR viruses remained detectable as long as 59 weeks after treatment interruption. Mathematical modeling showed that the loss in relative fitness increased with the number of mutations in each viral genome and that viruses with MDR mutations had lower fitness than viruses with SDR mutations. No single viral genome had seven or more drug resistance mutations, suggesting that such severely mutated viruses were too unfit to be detected or that the resistance gain offered by the seventh mutation did not outweigh its contribution to the overall fitness loss of the virus. These data provide a more comprehensive understanding of evolution and fitness of drug-resistant viruses in vivo and may lead to improved treatment strategies for ART-experienced patients.     

Direct and indirect effects of UV radiation on benthic communities: epilithic food quality and invertebrate growth in four montane lakes

The direct harmful effects of ultraviolet radiation (UVR) on benthic and planktonic organisms have been well studied in aquatic systems. Less clear, however, is how UVR might affect aquatic communities through its effects on trophic interactions. The focus of this study was twofold: first, to examine the direct effect of UVR on benthic invertebrates and epilithon, the rock-dwelling matrix of algae, bacteria, viruses, fungi and detritus, and second, to examine the indirect effect of UVR-mediated shifts in epilithic food quality on epilithic consumers. Food quality was assessed by measuring carbon to nutrient ratios and the concentration of polyunsaturated fatty acids (PUFA) in the epilithic matrix; the effect of its change on epilithic consumers was measured using a feeding experiment. The study was conducted in four montane lakes, where downwelling UVR can be intense. Of these lakes, the benthic community of only one was strongly affected by UVR. In this lake, exposure to UVR decreased epilithic accrual and invertebrate colonization, and, contrary to our expectations, increased food quality in the shallows through decreased carbon to phosphorus ratios and increased PUFA concentrations. In another of the four study lakes, the feeding experiment showed no significant difference in growth rates between invertebrates fed UVR-exposed and UVR-shielded epilithon, or invertebrates directly exposed to or shielded from UVR. This study demonstrates that although UVR can play an important role in structuring the trophic dynamics of benthic communities, its effects will not be constant across systems, or important in all environments.     

Effects of ultraviolet radiation and water motion on the reef coral, Porites compressa Dana: a transplantation experiment

Scleractinian corals have adapted to live in habitats were the level of ultraviolet radiation (UVR, 280–400 nm) is extremely high. The putative photoprotective molecules called mycosporine-like amino acids (MAAs) contained in the corals' tissues absorb UVR and release it harmlessly as heat. MAA concentration in corals is quite plastic and correlates well with UVR dose, but other ecological factors such as water motion may influence MAA production as well. In this study, the effects of ambient UVR and water motion on MAA concentration and several physiological parameters of the reef coral Porites compressa Dana were investigated in a two by two factorial transplantation experiment. Replicate branches from nine morphologically distinct colonies were transplanted from the windward side of Coconut Island (Kaneohe Bay, HI) to a control area on the windward side (ambient water motion) and to an area on the leeward side (low water motion). The transplanted corals were placed under UV-opaque (UVO) or UV-transparent (UVT) filters fixed to the reef. Initially and at 3 and 6 weeks, coral branches were weighed to determine calcification rate and tissues were extracted in methanol for photosynthetic pigment and MAA analysis via high performance liquid chromatography (HPLC). UVR was a significant factor determining MAA concentration. When UVR was screened from the corals' environment, total MAA concentration decreased by 33% over 6 weeks. However, UVR-exposed corals moved to low water motion also decreased MAA levels, while UVR-exposed corals moved to the control area retained initial levels. Photosynthetic pigments and calcification rate were also significantly reduced in corals moved to low water motion. There was no UVR effect on photosynthetic pigments or calcification rate. This study provides evidence that water motion is important for the maintenance of MAAs. However, there were interesting colony-specific patterns in MAA composition and response to the UVR treatment; some colonies had high total concentrations of MAAs in all treatments, while others displayed a pronounced UVR effect. Also, each genotype seemed to have its own signature MAA composition. These findings indicate a genetic (host, zooxanthellae or both) component to UVR resistance in this population of P. compressa.     

The cost of multiple drug resistance in Pseudomonas aeruginosa

The spread of bacterial antibiotic resistance mutations is thought to be constrained by their pleiotropic fitness costs. Here we investigate the fitness costs of resistance in the context of the evolution of multiple drug resistance (MDR), by measuring the cost of acquiring streptomycin resistance mutations (StrepR) in independent strains of the bacterium Pseudomonas aeruginosa carrying different rifampicin resistance (RifR) mutations. In the absence of antibiotics, StrepR mutations are associated with similar fitness costs in different RifR genetic backgrounds. The cost of StrepR mutations is greater in a rifampicin‐sensitive (RifS) background, directly demonstrating antagonistic epistasis between resistance mutations. In the presence of rifampicin, StrepR mutations have contrasting effects in different RifR backgrounds: StrepR mutations have no detectable costs in some RifR backgrounds and massive fitness costs in others. Our results clearly demonstrate the importance of epistasis and genotype‐by‐environment interactions for the evolution of MDR.     

Reversion and T Cell Escape Mutations Compensate the Fitness Loss of a CD8+ T Cell Escape Mutant in Their Cognate Transmitted/Founder Virus

Immune escape mutations that revert back to the consensus sequence frequently occur in newly HIV-1-infected individuals and have been thought to render the viruses more fit. However, their impact on viral fitness and their interaction with other immune escape mutations have not been evaluated in the background of their cognate transmitted/founder (T/F) viral genomes. To precisely determine the role of reversion mutations, we introduced reversion mutations alone or together with CD8⁺ T cell escape mutations in their unmodified cognate T/F viral genome and determined their impact on viral fitness in primary CD4⁺ T cells. Two reversion mutations, V247I and I64T, were identified in Gag and Tat, respectively, but neither had measurable effect on the fitness of their cognate T/F virus. The V247I and G248A mutations that were detected before and concurrently with the potent T cell escape mutation T242N, respectively, were selected by early T cell responses. The V247I or the G248A mutation alone partially restored the fitness loss caused by the T242N mutation. Together they could fully restore the fitness of the T242N mutant to the T/F level. These results demonstrate that the fitness loss caused by a T cell escape mutation could be compensated by preexisting or concurrent reversion and other T cell escape mutations. Our findings indicate that the overall viral fitness is modulated by the complex interplay among T cell escape, compensatory and reversion mutations to maintain the balance between immune escape and viral replication capacity.     

Fitness cost from fluctuating ultraviolet radiation in Daphnia magna

Solar ultraviolet radiation (UVR) is an important environmental threat for organisms in aquatic systems, but its temporally variable nature makes the understanding of its effects ambiguous. The aim of our study was to assess potential fitness costs associated with fluctuating UVR in the aquatic zooplankter Daphnia magna. We investigated individual survival, reproduction and behaviour when exposed to different UVR treatments. Individuals exposed to fluctuating UVR, resembling natural variations in cloud cover, had the lowest fitness (measured as the number of offspring produced during their lifespan). By contrast, individuals exposed to the same, but constant UVR dose had similar fitness to control individuals (not exposed to UVR), but they showed a significant reduction in daily movement. The re-occurring threat response to the fluctuating UVR treatment thus had strong fitness costs for D. magna, and we found no evidence for plastic behavioural responses when continually being exposed to UVR, despite the regular, predictable exposure schedule. In a broader context, our results imply that depending on how variable a stressor is in nature, populations may respond with alternative strategies, a framework that could promote rapid population differentiation and local adaptation.     

Life cycle replacement by gene introduction under an allee effect in periodical cicadas

Periodical cicadas (Magicicada spp.) in the USA are divided into three species groups (-decim, -cassini, -decula) of similar but distinct morphology and behavior. Each group contains at least one species with a 17-year life cycle and one with a 13-year cycle; each species is most closely related to one with the other cycle. One explanation for the apparent polyphyly of 13- and 17-year life cycles is that populations switch between the two cycles. Using a numerical model, we test the general feasibility of life cycle switching by the introduction of alleles for one cycle into populations of the other cycle. Our results suggest that fitness reductions at low population densities of mating individuals (the Allee effect) could play a role in life cycle switching. In our model, if the 13-year cycle is genetically dominant, a 17-year cycle population will switch to a 13-year cycle given the introduction of a few 13-year cycle alleles under a moderate Allee effect. We also show that under a weak Allee effect, different year-classes ("broods") with 17-year life cycles can be generated. Remarkably, the outcomes of our models depend only on the dominance relationships of the cycle alleles, irrespective of any fitness advantages.