Directed Evolution of Ionizing Radiation Resistance in Escherichia coli

We have generated extreme ionizing radiation resistance in a relatively sensitive bacterial species, Escherichia coli, by directed evolution. Four populations of Escherichia coli K-12 were derived independently from strain MG1655, with each specifically adapted to survive exposure to high doses of ionizing radiation. D₃₇ values for strains isolated from two of the populations approached that exhibited by Deinococcus radiodurans. Complete genomic sequencing was carried out on nine purified strains derived from these populations. Clear mutational patterns were observed that both pointed to key underlying mechanisms and guided further characterization of the strains. In these evolved populations, passive genomic protection is not in evidence. Instead, enhanced recombinational DNA repair makes a prominent but probably not exclusive contribution to genome reconstitution. Multiple genes, multiple alleles of some genes, multiple mechanisms, and multiple evolutionary pathways all play a role in the evolutionary acquisition of extreme radiation resistance. Several mutations in the recA gene and a deletion of the e14 prophage both demonstrably contribute to and partially explain the new phenotype. Mutations in additional components of the bacterial recombinational repair system and the replication restart primosome are also prominent, as are mutations in genes involved in cell division, protein turnover, and glutamate transport. At least some evolutionary pathways to extreme radiation resistance are constrained by the temporally ordered appearance of specific alleles.A survey of bacteria and archaea identifies 11 phyla that contain species with unusually high resistance to the lethal effects of ionizing radiation (IR). These phyla are not closely related to each other and do not share a common lineage, and all include genera that are considered radiosensitive (9). The existence of so many unrelated and isolated radioresistant species in the phylogenetic tree argues that the molecular mechanisms that protect against IR-induced damage evolved independently in these organisms, suggesting that at least some species have the capacity to acquire radioresistance through evolutionary processes if they are subjected to appropriate selective pressure.The first of these species to be discovered, and the best studied to date, is the bacterium Deinococcus radiodurans. The molecular basis of the extraordinary radioresistance of Deinococcus has not been elucidated, but well-constructed proposals abound. Radioresistance has variously been attributed to the condensed structure of the nucleoid (29, 40, 56), the elevated levels of Mn ion present in the cytosol as a mechanism to control protein oxidation (11, 12), a specialized RecA-independent DNA repair process (54), and other species attributes (9). Radioresistance in Deinococcus is probably mechanistically related to desiccation resistance derived from evolution in arid environments (37, 45), although this may not be the origin of the phenotype in all relevant species (9).An understanding of the genetic underpinnings of bacterial radiation resistance holds promise for yielding insights into the mechanistic basis of radiation toxicity, along with the potential for new approaches to facilitate recovery from radiation injury in other organisms, including humans. To better define the genetic, biochemical, and physiological characteristics most important for radioresistance, we employed a strategy to allow the cells to inform us. In brief, we generated radioresistant variants of radiosensitive bacteria and defined the genetic changes underlying the new phenotype.In 1946, Evelyn Witkin established that it was possible to increase the resistance of Escherichia coli B to DNA damage (50). She exposed cultures to high doses of UV light, killing most of the population and selecting for variants better able to tolerate UV. In the 6 decades since the Witkin report, additional investigators have repeated this result, demonstrating that iterative cycles of high-dose exposure to a DNA damaging agent can heritably enhance a culture''s ability to tolerate that DNA damaging agent. Increases in IR resistance have been reported for E. coli (17), Salmonella enterica serovar Typhimurium (14), and Bacillus pumulis (44), organisms that are otherwise considered radiosensitive. Davies and Sinskey (14) showed that for S. enterica serovar Typhimurium LT2, the number of cycles of exposure and recovery correlates with the level of radioresistance achieved. After 84 cycles, they generated a strain displaying inactivation kinetics similar to that of Deinococcus radiodurans, with a D₁₀ value (the dose needed to inactivate 90% of the population) 200-fold higher than that of the parental strain.For this study, we expanded on these earlier studies by independently generating four IR-resistant populations of Escherichia coli K-12 MG1655 (4). Our effort included an important innovation relative to the earlier studies—we characterized the evolved populations with an experimental program that included the complete genomic resequencing of multiple strains purified from three of the populations, taking advantage of new sequencing technologies. The result is an increasingly detailed data set—based on a single robust model system—that allows us to (i) explore the molecular basis of radiation resistance in bacteria and (ii) test current hypotheses and search for novel mechanisms of radiation resistance.     

Reaction wood – a key cause of variation in cell wall recalcitrance in willow

Background

The recalcitrance of lignocellulosic cell wall biomass to deconstruction varies greatly in angiosperms, yet the source of this variation remains unclear. Here, in eight genotypes of short rotation coppice willow (Salix sp.) variability of the reaction wood (RW) response and the impact of this variation on cell wall recalcitrance to enzymatic saccharification was considered.

Results

A pot trial was designed to test if the ‘RW response’ varies between willow genotypes and contributes to the differences observed in cell wall recalcitrance to enzymatic saccharification in field-grown trees. Biomass composition was measured via wet chemistry and used with glucose release yields from enzymatic saccharification to determine cell wall recalcitrance. The levels of glucose release found for pot-grown control trees showed no significant correlation with glucose release from mature field-grown trees. However, when a RW phenotype was induced in pot-grown trees, glucose release was strongly correlated with that for mature field-grown trees. Field studies revealed a 5-fold increase in glucose release from a genotype grown at a site exposed to high wind speeds (a potentially high RW inducing environment) when compared with the same genotype grown at a more sheltered site.

Conclusions

Our findings provide evidence for a new concept concerning variation in the recalcitrance to enzymatic hydrolysis of the stem biomass of different, field-grown willow genotypes (and potentially other angiosperms). Specifically, that genotypic differences in the ability to produce a response to RW inducing conditions (a ‘RW response’) indicate that this RW response is a primary determinant of the variation observed in cell wall glucan accessibility. The identification of the importance of this RW response trait in willows, is likely to be valuable in selective breeding strategies in willow (and other angiosperm) biofuel crops and, with further work to dissect the nature of RW variation, could provide novel targets for genetic modification for improved biofuel feedstocks.

     

Oligonucleotides blocking glucosylceramide synthase expression selectively reverse drug resistance in cancer cells

High glucosylceramide synthase (GCS) activity is one factor contributing to multidrug resistance (MDR) in breast cancer. Enforced GCS overexpression has been shown to disrupt ceramide-induced apoptosis and to confer resistance to doxorubicin. To examine whether GCS is a target for cancer therapy, we have designed and tested the effects of antisense oligodeoxyribonucleotides (ODNs) to GCS on gene expression and chemosensitivity in multidrug-resistant cancer cells. Here, we demonstrate that antisense GCS (asGCS) ODN-7 blocked cellular GCS expression and selectively increased the cytotoxicity of anticancer agents. Pretreatment with asGCS ODN-7 increased doxorubicin sensitivity by 17-fold in MCF-7-AdrR (doxorubicin-resistant) breast cancer cells and by 10-fold in A2780-AD (doxorubicin-resistant) ovarian cancer cells. In MCF-7 drug-sensitive breast cancer cells, asGCS ODN-7 only increased doxorubicin sensitivity by 3-fold, and it did not influence doxorubicin cytotoxicity in normal human mammary epithelial cells. asGCS ODN-7 was shown to be more efficient in reversing drug resistance than either the GCS chemical inhibitor d-threo-1-phenyl-2-decanoylamino-3-morpholino-1-propanol or the P-glycoprotein blocking agents verapamil and cyclosporin A. Experiments defining drug transport and lipid metabolism parameters showed that asGCS ODN-7 overcomes drug resistance mainly by enhancing drug uptake and ceramide-induced apoptosis. This study demonstrates that a 20-mer asGCS oligonucleotide effectively reverses MDR in human cancer cells.     

Pincher,a pinocytic chaperone for nerve growth factor/TrkA signaling endosomes

A central tenet of nerve growth factor (NGF) action that is poorly understood is its ability to mediate cytoplasmic signaling, through its receptor TrkA, that is initiated at the nerve terminal and conveyed to the soma. We identified an NGF-induced protein that we termed Pincher (pinocytic chaperone) that mediates endocytosis and trafficking of NGF and its receptor TrkA. In PC12 cells, overexpression of Pincher dramatically stimulated NGF-induced endocytosis of TrkA, unexpectedly at sites of clathrin-independent macropinocytosis within cell surface ruffles. Subsequently, a system of Pincher-containing tubules mediated the delivery of NGF/TrkA-containing vesicles to cytoplasmic accumulations. These vesicles selectively and persistently mediated TrkA-erk5 mitogen-activated protein kinase signaling. A dominant inhibitory mutant form of Pincher inhibited the NGF-induced endocytosis of TrkA, and selectively blocked TrkA-mediated cytoplasmic signaling of erk5, but not erk1/2, kinases. Our results indicate that Pincher mediates pinocytic endocytosis of functionally specialized NGF/TrkA endosomes with persistent signaling potential.     

Expression of lauroyl-acyl carrier protein thioesterase in brassica napus seeds induces pathways for both fatty acid oxidation and biosynthesis and implies a set point for triacylglycerol accumulation

Expression of a California bay lauroyl-acyl carrier protein thioesterase (MCTE) in developing seeds of transgenic oilseed rape alters the fatty acid composition of the mature seed, resulting in up to 60 mol% of laurate in triacylglycerols. In this study, we examined the metabolism of lauric acid and 14C-acetate in developing seeds of oilseed rape that express high levels of MCTE. Lauroyl-CoA oxidase activity but not palmitoyl-CoA oxidase activity was increased several-fold in developing seeds expressing MCTE. In addition, isocitrate lyase and malate synthase activities were six- and 30-fold higher, respectively, in high-laurate developing seeds. Control seeds incorporated 14C-acetate almost entirely into fatty acids, whereas in seeds expressing MCTE, only 50% of the label was recovered in lipids and the remainder was in a range of water-soluble components, including sucrose and malate. Together, these results indicate that the pathways for beta-oxidation and the glyoxylate cycle have been induced in seeds expressing high levels of MCTE. Although a substantial portion of the fatty acid produced in these seeds is recycled to acetyl-CoA and sucrose through the beta-oxidation and glyoxylate cycle pathways, total seed oil is not reduced. How is oil content maintained if lauric acid is inefficiently converted to triacylglycerol? The levels of acyl carrier protein and several enzymes of fatty acid synthesis were increased two- to threefold at midstage development in high-laurate seeds. These results indicate that a coordinate induction of the fatty acid synthesis pathway occurs, presumably to compensate for the lauric acid lost through beta-oxidation or for a shortage of long-chain fatty acids.