Survival Strategy of <i>Escherichia coli</i> in Stationary Phase: Involvement of σE-Dependent Programmed Cell Death

In a natural habitat, microbes respond to alterations in the amounts of nutrients or to stresses such as osmotic stress and stresses caused by low or high pH, salt, heat, and antibiotics by changing their mode for proliferation or survival. Similarly, Escherichia coli cells in a test tube change the growth mode according to environmental conditions when they enter a stationary phase. Until a sufficient supply of nutrients, the organism survives under such stressful and nutrient-limited conditions by altering gene expression to be more protective against such conditions. The definite trigger of the onset of stationary phase is still unclear, but several lines of evidence indicate that the regulation mechanism is very complicated and involves several transcriptional factors including alternative sigma factors, σE and σS. In addition, E. coli cells behave as a community of species and give rise to programmed cell death (PCD) for ensuring survival by controlling the cell number and supplying nutrients to sibling cells in long-term stationary phase (LTSP). The main PCD is probably performed by σE in E. coli. In this chapter, physiological functions of σE and PCD are introduced and reviewed and their possible involvement in survival mechanisms in stationary phase, especially LTSP, is shown

Topographical characterization of the ubiquinone reduction site of glucose dehydrogenase in Escherichia coli using depth-dependent fluorescent inhibitors

AbstractMembrane-bound glucose dehydrogenase in Escherichia coli possesses a binding site for ubiquinone as well as glucose, metal ion and pyrroloquinoline quinone. To probe the depth of the ubiquinone binding site in the membrane environment, we synthesized two types of fluorenyl fatty acids which bear an inhibitor mimic moiety (i.e., specific inhibitor capsaicin) close to the fluorene located at different positions in the alkyl tail chain; one close to the polar carbonyl head group (α-(3,4-dimethoxyphenyl)acetyloxy-7-nonyl-2-fluoreneacetic acid, α-DFA), and the other in the middle of the chain (θ-(3,4-dimethoxyphenyl)acetyloxy-7-ethyl-2-fluorenenonanoic acid, θ-DFA). Mixed lipid vesicles consisting of phosphatidylcholine (PC) and α-DFA or θ-DFA were prepared by sonication method, and fluorescent quenching against a hydrophilic quencher, iodide anion, was examined. The vesicles containing α-DFA were more susceptible to quenching than those containing θ-DFA, indicating that the fluorene and consequently capsaicin mimic moiety are located at different depths in the lipid bilayer depending upon the position of attachment to the alkyl tail chain. The purified glucose dehydrogenase was reconstituted into PC vesicles which consisted of PC and α-DFA or θ-DFA with various molar ratios. For both types of reconstituted vesicles, the extent of inhibition of short-chain ubiquinone reduction activity increased with increases in the molar ratio of fluorenyl fatty acid to PC. The ubiquinone reduction activity was more significantly inhibited in the reconstituted vesicles containing α-DFA compared to those containing θ-DFA. Our findings strongly suggested that the ubiquinone reduction site in glucose dehydrogenase is located close to the membrane surface rather than in the hydrophobic membrane interior

11 地域社会と地方指導者 ＜神奈川大学創立三五周年記念論文集＞

第一

SIGMA: Scala Internal Domain-Specific Languages for Model Manipulations

International audienceModel manipulation environments automate model operations such as model consistency checking and model transformation. A number of external model manipulation Domain-Specific Languages (DSL) have been proposed, in particular for the Eclipse Modeling Framework (EMF). While their higher levels of abstraction result in gains in expressiveness over general-purpose languages, their limitations in versatility, performance, and tool support together with the need to learn new languages may significantly contribute to accidental complexities. In this paper, we present Sigma, a family of internal DSLs embedded in Scala for EMF model consistency checking, model-to-model and model-to-text transformations. It combines the benefits of external model manipulation DSLs with general-purpose programming taking full advantage of Scala versatility, performance and tool support. The DSLs are compared to the state-of-the-art Epsilon languages in non-trivial model manipulation tasks that resulted in 20% to 70% reduction in code size and significantly better performance

A Kluyveromyces marxianus 2-deoxyglucose-resistant mutant with enhanced activity of xylose utilization

Thermotolerant ethanologenic yeast Kluyveromyces marxianus is capable of fermenting various sugars including xylose but glucose represses to hamper the utilization of other sugars. To acquire glucose repression-defective strains, 33 isolates as 2-deoxyglucose (2-DOG)-resistant mutants were acquired from about 100 colonies grown on plates containing 2-DOG, which were derived from an efficient strain DMKU 3-1042. According to the characteristics of sugar consumption abilities and cell growth and ethanol accumulation along with cultivation time, they were classified into three groups. The first group (3 isolates) utilized glucose and xylose in similar patterns along with cultivation to those of the parental strain, presumably due to reduction of the uptake of 2-DOG or enhancement of its export. The second group (29 isolates) showed greatly delayed utilization of glucose, presumably by reduction of the uptake or initial catabolism of glucose. The last group, only one isolate, showed enhanced utilization ability of xylose in the presence of glucose. Further analysis revealed that the isolate had a single nucleotide mutation to cause amino acid substitution (G270S) in RAG5 encoding hexokinase and exhibited very low activity of the enzyme. The possible mechanism of defectiveness of glucose repression in the mutant is discussed in this paper. [Int Microbiol 18(4):235-244 (2015)]Keywords: Kluyveromyces marxianus &middot; glucose repression &middot; 2-deoxyglucose-resistant mutants &middot; ethanol fermentation on xylose &middot; thermotolerant yeas

Utilization capability of sucrose, raffinose and inulin and its less-sensitiveness to glucose repression in thermotolerant yeast Kluyveromyces marxianus DMKU 3-1042

Kluyveromyces marxianus possesses a useful potential to assimilate a wide variety of substrates at a high temperature, but the negative effect by coexisting glucose is critical for utilization of biomass containing various sugars. Such a negative effect on the activity of inulinase, which is the sole enzyme to hydrolyze sucrose, raffinose and inulin, has been demonstrated in K. marxianus without analysis at the gene level. To clarify the utilization capability of sucrose, raffinose and inulin and the glucose effect on inulinase in K. marxianus DMKU 3-1042, its growth and metabolite profiles on these sugars were examined with or without glucose under a static condition, in which glucose repression evidently occurs. Consumption of sucrose was not influenced by glucose or 2-deoxyglucose. On the other hand, raffinose and inulin consumption was hampered by glucose at 30°C but hardly hampered at 45°C. Unlike Saccharomyces cerevisiae, increase in glucose concentration had no effect on sucrose utilization. These sugar-specific glucose effects were consistent with the level of inulinase activity but not with that of the KmINU1 transcript, which was repressed in the presence of glucose via KmMig1p. This inconsistency may be due to sufficient activity of inulinase even when glucose is present. Our results encourage us to apply K. marxianus DMKU 3-1042 to high-temperature ethanol fermentation with biomass containing these sugars with glucose

Autoimmunity to citrullinated type II collagen in rheumatoid arthritis

The production of autoantibodies to citrullinated type II collagen and the citrullination of type II collagen were analyzed in rheumatoid arthritis. Autoantibodies to citrullinated type II collagen were detected in 78.5% of serum samples from 130 rheumatoid arthritis patients. Autoantibodies to native noncitrullinated type II collagen were detected in 14.6% of serum samples, all of which were positive for anti-citrullinated type II collagen antibodies. Serum samples were also positive for anti-citrullinated type II collagen antibodies in 1 of 31 systemic lupus erythematosus patients and 2 of 55 patients with osteoarthritis of the knee. In contrast, sera samples from 24 systemic sclerosis patients, 21 dermatomyositis/polymyositis patients, 21 ankylosing spondylitis patients, and 18 psoriatic arthritis patients were all negative for anti-citrullinated type II collagen antibodies. Anti-citrullinated type II collagen antibodies and fragments of citrullinated type II collagen were found in the synovial fluid obtained from affected knee joints of 15 rheumatoid arthritis patients. Moreover, anti-citrullinated type II collagen antibodies were isolated from the synovium of affected knee joints in 8 rheumatoid arthritis patients using antigen/antibody immunocomplex dissociation buffer but not by using standard buffers. These findings indicate that autoantibodies that react with citrullinated type II collagen are specifically produced and that immunocomplexes composed of fragments of citrullinated type II collagen and autoantibodies are deposited in the inflamed articular synovium in rheumatoid arthritis patients. Assaying for the presence of anti-citrullinated type II collagen antibodies may therefore be useful for diagnosing rheumatoid arthritis, and the deposition of these immunocomplexes in the articular synovium may be involved in pathogenesis