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

Gene Deletion Algorithms for Minimum Reaction Network Design by Mixed-Integer Linear Programming for Metabolite Production in Constraint-Based Models: gDel_minRN

Genome-scale constraint-based metabolic networks play an important role in the simulation of growth-coupled production, which means that cell growth and target metabolite production are simultaneously achieved. For growth-coupled production, a minimal reaction-network-based design is known to be effective. However, the obtained reaction networks often fail to be realized by gene deletions due to conflicts with gene-protein-reaction (GPR) relations. Here, we developed gDel_minRN that determines gene deletion strategies using mixed-integer linear programming to achieve growth-coupled production by repressing the maximum number of reactions via GPR relations. The results of computational experiments showed that gDel_minRN could determine the core parts, which include only 30% to 55% of whole genes, for stoichiometrically feasible growth-coupled production for many target metabolites, which include useful vitamins such as biotin (vitamin B7), riboflavin (vitamin B2), and pantothenate (vitamin B5). Since gDel_minRN calculates a constraint-based model of the minimum number of gene-associated reactions without conflict with GPR relations, it helps biological analysis of the core parts essential for growth-coupled production for each target metabolite. The source codes, implemented in MATLAB using CPLEX and COBRA Toolbox, are available on https://github.com/MetNetComp/gDel-minRN

Ultrabright narrow-band telecom two-photon source for long-distance quantum communication

We demonstrate an ultrabright narrow-band two-photon source at the 1.5 -\mu m telecom wavelength for long-distance quantum communication. By utilizing a bow-tie cavity, we obtain a cavity enhancement factor of $4.06\times 10^4$. Our measurement of the second-order correlation function $G^{(2)} ({\tau})$ reveals that the linewidth of $2.4$ MHz has been hitherto unachieved in the 1.5 -\mu m telecom band. This two-photon source is useful for obtaining a high absorption probability close to unity by quantum memories set inside quantum repeater nodes. Furthermore, to the best of our knowledge, the observed spectral brightness of $3.94\times 10^5$ pairs/(s$\cdot$MHz$\cdot$mW) is also the highest reported over all wavelengths.Comment: 11 pages, 4 figures, 2 table

A compact frequency-stabilized pump laser for wavelength conversion in long-distance quantum communication

We demonstrate a compact frequency-stabilized laser at 1064 nm using Doppler-free saturation absorption spectroscopy of molecular iodine. The achieved laser frequency stability and linewidth are 5.7 10-12 (corresponding to an uncertainty of the laser frequency of 1.6 kHz) and 400 kHz, respectively. The developed frequency-stabilized laser can be used as a pump laser for wavelength conversion from visible to telecom (or vice versa) to connect quantum memories utilizing nitrogen-vacancy centers in diamond at remote nodes in fiber-based quantum communication.Comment: 5 pages, 6 figures, JOSAB accepte

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

Prognostic value of OCT4A and SPP1C transcript variant co-expression in early-stage lung adenocarcinoma

Background Octamer-binding transcription factor 4A (OCT4A) is essential for cell pluripotency and reprogramming both in humans and mice. To date, however, the function of human OCT4 in somatic and/or tumour tissues is largely unknown. Methods RT-PCR was used to identify full-length splice forms of OCT4 transcripts in normal and cancer cells. A FLAG-tagged OCT4 genomic transgene was used to identify OCT4-positive cancer cells. A potential role for OCT4 in somatic cancer cells was examined by cell ablation of OCT4-positive cells using promoter-driven diphtheria toxin A. OCT4 and secreted phosphoprotein 1 (SPP1) transcripts in early-stage lung adenocarcinoma tumours were analysed and compared with pathohistological features. Results The results show that, unlike in murine cells, OCT4A and OCT4B variants are transcribed in both human cancer cells and in adult tissues such as lung, kidney, uterus, breast, and eye. We found that OCT4A and SPP1C are co-expressed in highly aggressive human breast, endometrial, and lung adenocarcinoma cell lines, but not in mesothelial tumour cell lines. Ablation of OCT4-positive cells in lung adenocarcinoma cells significantly decreased cell migration and SPP1C mRNA levels. The OCT4A/SPP1C axis was found in primary, early-stage, lung adenocarcinoma tumours. Conclusions Co-expression of OCT4 and SPP1 may correlate with cancer aggressiveness, and the OCT4A/SPP1C axis may help identify early-stage high-risk patients with lung adenocarcinoma. Contrary to the case in mice, our data strongly suggest a critical role for OCT4A and SPP1C in the development and progression of human epithelial cancers

Potential of Thermotolerant Ethanologenic Yeasts Isolated from ASEAN Countries and Their Application in High- Temperature Fermentation

Thermotolerant ethanologenic yeasts receive attention as alternative bio-ethanol producers to traditionally used yeast, Saccharomyces cerevisiae. Their utilization is expected to provide several benefits for bio-ethanol production due to their characteristics and robustness. They have been isolated from a wide variety of environments in a number of ASEAN countries: Thailand, Vietnam, Laos, and Indonesia. One of these yeasts, Kluyveromyces marxianus has been investigated regarding characteristics. Some strains efficiently utilize xylose, which is a main component of the 2nd generation biomass. In addition, the genetic basis of K. marxianus has been revealed by genomic sequencing and is exploited for further improvement of the strains by thermal adaptation or gene engineering techniques. Moreover, the glucose repression of K. marxianus and its mechanisms has been investigated. Results suggest that K. marxianus is an alternative to S. cerevisiae in next-generation bio-ethanol production industry. Indeed, we have succeeded to apply K. marxianus for bio-ethanol production in a newly developed process, which combines high-temperature fermentation with simultaneous fermentation and distillation under low pressure. This chapter aims to provide valuable information on thermotolerant ethanologenic yeasts and their application, which may direct the economic bioproduction of ethanol and other useful materials in the future