Regulatory systems that recognize and response to oxygen and reactive oxygen species are essential for the survival of bacteria in air. Various sensing systems have been reported in bacteria, and findings of these sensing systems have provided the concept that how organisms recognize these molecules. Although oxygen sensing mechanisms have been studied in aerobic bacteria, recent studies have shown that the presence of sensing systems in anaerobic bacteria. Lactic acid bacteria (LAB) are used industrially for their fermentation properties, and as such, have been generally regarded as anaerobic bacteria. However, recent studies have shown that LAB has unique oxygen metabolisms and adaptation mechanisms to oxygen rich environments. This manuscript presents an overview of oxygen sensing mechanisms in bacteria and recent advances in LAB.

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Lactic acid bacteria (LAB) species like L. lactis are traditionally considered as obligate fermentative bacteria because even in aerobiosis they use sugar degradation for substrate-level phosphorylation, i.e. ATP production. However, recent studies revealed that this bacterium and some other LAB are capable of activating a heme-dependent cytochrome oxidase (CydAB) and thus undergo a respiration metabolism. Nevertheless, respiratory chain activation is allowed only when cells have access to heme (and additionally menaquinone for some LAB) in the environment because they cannot synthesize these compounds. Respiration increases the biomass yield and extends the long term survival of stored cells. These benefits of respiration are explained in different ways: i) Respiratory chain activity consumes oxygen, limiting the formation of toxic reactive oxygen species. ii) Respiratory chain generates a pH gradient, which potentially increases ATP production via H⁺-ATPase activity. iii) Respiration metabolism decreases lactic acid production, limiting acid stress. However, LAB have to cope with heme toxicity. Although heme has clear metabolic benefits the intracellular pool of free heme must be stringently controlled to prevent damage to macromolecules like DNA. In L. lactis, a potential efflux pump system, consisting of an ATPase (YgfA) and a permease (YgfB), is specifically highly induced in response to exogenous heme. Interestingly, the ygfA and ygfB genes are in an operon with ygfC, a potential regulator of the TetR family. Our studies implicate the ygfCBA operon is involved in modulating the free heme level and is regulated by YgfC.

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There have been known various mechanisms in response to environmental stresses in bacteria. Upon serious stress like heat shock, usually independent cellular machineries start functioning at the same time and try to protect their own targets. Those machineries involve molecular chaperones, a stress sigma (SigB) regulon, extra-cytoplasmic function (ECF) sigma networks, two-component regulatory systems (TCS), subsets of transcription factors, and so on. In this review, I introduce some of our recent results with respect to the new aspects of stress response machineries. Those are an essential function of DnaK chaperone machine, a new regulation of SigB activation cascade, a general structure of ECF sigma and anti-sigma relationship, and findings from extraordinary- multiple knockout of TCS genes. These machineries are, at least in part, dependent on one another by sharing one or more components or transferring signals to other machineries. These phenomena demonstrate a functional network among stress response machineries.

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During infection of mammalian hosts, Salmonella enterica serovar Typhimurium, a facultative intracellular pathogen, has to adjust rapidly to different environmental conditions encountered in passage through the gastrointestinal tract and following uptake into epithelial cells and macrophages. Successful establishment within the host therefore requires the coordinated expression of a large number of virulence genes necessary for the adaptation between the extracellular and intracellular phases of infection. The stringent response is a global bacterial response to nutritional stress that is mediated by accumulation of the alarmone guanosine tetraphosphate (ppGpp). It has been reported that ppGpp is required for the expression of nearly all known S. enterica virulence genes. However, the function of many proteins that are annotated on the genome of S. enterica serovar Typhimurium are still putative or unknown, and the complicated regulatory mechanism of the virulence by ppGpp is not well understood. Here, we constructed an agarose 2-dementinal electrophoresis reference map of S. enterica serovar Typhimurium strain ATCC 14028 for an exhaustive identification of ppGpp-regulated genes. We successfully identified 320 proteins on the reference map, and 155 proteins including a number of known virulence factors, which are more highly expressed in S. enterica serovar Typhimurium wild-type strain than the ppGpp⁰ mutant strain by comparative proteomics. Furthermore, using a mouse model of infection, two proteins, STM3169 and STM4242, were identified as novel virulence factors required for the complete mouse systemic infection by Salmonella. These results provide unequivocal evidence of the role of ppGpp in Salmonella virulence.

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We have reviewed the molecular mechanism of the two-component signal transduction (TCS) network in Escherichia coli that were clarified using a DNA microarray. Focusing on the EvgS/EvgA and PhoQ/PhoP systems, we identified a small membrane protein, SafA (sensor associating factor A), which regulated the signal transduction cascade between the two systems. Furthermore, novel drug discovery systems for developing inhibitors targeting the WalK/WalR TCS essential for bacterial growth have been described.

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We investigated the anti-allergic effect of a new strain (Pediococcus pentosaceus Sn26 strain (Sn26 strain)) among 59 strains of lactic acid bacteria isolated from the Japanese traditional fermented vegetable pickle, the 'Sunki pickle'. Oral administration of the Sn26 strain decreased the serum OVA-specific IgE level and ameliorated the appearance of diarrhea in OVA-induced allergic diarrhea mice. A positive relationship was recognized between the serum IgE level and the occurrence of allergic diarrhea. Furthermore, we examined immunological effects of Peyer's patch (PP) cells, splenocytes and lamina propria lymphocytes (LPL) by oral administration of the Sn26 strain. The ability of IL-12 and IFN- productions of PP cells in the Sn26 group were significantly higher than those in the control group, and the total IgE level in the Sn26 group was significantly lower than in the control group. The ability of IL-4 and OVA-specific IgE productions of LPL in the Sn26 group was significantly lower than those in the control group. However, the immune response in splenocytes did not differ between the Sn26 and control groups. These results suggested that the orally administrated Sn26 strain ameliorated allergic diarrhea through improvement of the Th1/Th2 balance in PP cells and subsequent inhibition of IgE production of LPL.

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