Expression, identification and purification of Dictyostelium acetoacetyl-coa thiolase expressed in Escherichia coli

Studies of the molecular mechanisms that are involved in stress responses (environmental or physiological) have long been used to make links to disease states in humans. The nematode model organism, Caenorhabditis elegans, undergoes a state of hypometabolism called the ''dauer'' stage. This period of developmental arrest is characterized by a significant reduction in metabolic rate, triggered by ambient temperature increase and restricted oxygen/ nutrients. C. elegans employs a number of signal transduction cascades in order to adapt to these unfavourable conditions and survive for long times with severely reduced energy production. The suppression of cellular metabolism, providing energetic homeostasis, is critical to the survival of nematodes through the dauer period. This transition displays molecular mechanisms that are fundamental to control of hypometabolism across the animal kingdom. In general, mammalian systems are highly inelastic to environmental stresses (such as extreme temperatures and low oxygen), however, there is a great deal of conservation between the signal transduction pathways of nematodes and mammals. Along with conserving many of the protein targets in the stress response, many of the critical regulatory mechanisms are maintained, and often differ only in their level of expression. Hence, the C. elegans model outlines a framework of critical molecular mechanisms that may be employed in the future as therapeutic targets for addressing disease states.     

Molecular characterization of inorganic sulfur‐compound metabolism in the deep‐sea epsilonproteobacterium Sulfurovum sp. NBC37‐1

The molecular components involved in energy metabolism of deep‐sea Epsilonproteobacteria were characterized in the mesophilic hydrogen‐ and sulfur‐oxidizing chemolithoautotroph Sulfurovum sp. NBC37‐1. Previous whole‐genome analysis of strain NBC37‐1 identified key genes likely to be associated with both sulfur reduction (psr gene families) and oxidation (two sox gene clusters). However, the sox gene clusters showed unique organizations and low homologies to those in other bacteria. Therefore, the biochemical mechanism of inorganic sulfur metabolism has been uncertain. Enzymatic activity measurements and partial protein purification indicated that the Sox enzyme system was constitutively expressed, whereas the expression of sulfur‐reduction enzymes varied depending on the culture conditions. The operative Sox system in strain NBC37‐1 required membrane components. The molecular basis of energy metabolism reported in this study provides important insight into how deep‐sea Epsilonproteobacteria change their energy metabolism in response to variable physical and chemical conditions in mixing zones between hydrothermal fluid and ambient seawater.     

Versatile Solidified Nanofibrous Cellulose-Containing Media for Growth of Extremophiles

Solidified media that employ a porous matrix of nanofibrous cellulose are described. The physicochemical stability of the porous structure allows the development of solidified media that can support the growth of extremophiles, such as acidophilic Acidiphilium, alkaliphilic Bacillus, thermophilic Geobacillus and Thermus, alkalithermophilic Bacillus, and acidothermophilic Sulfolobus microbes. The cellulose-supported media have several advantages over agar- and gellan gum-derived media, including versatility and stability.Solidified media using agar as a solidifying agent are indispensable in microbiology. For solid cultures of mesophilic microorganisms, agar is an ideal solidifying agent and has been used essentially unchanged since it was first introduced in the late 19th century (2, 15). However, the situation is very different when it comes to culturing extremophiles on solidified media. For example, agar media are not suitable for culturing thermophiles and hyperthermophiles because the solidification of agar is thermoreversible at around 50 to 60°C (21), and the media are unstable at temperatures much above 70°C for extended periods (1). Culturing extremophiles on solidified media under acidic or alkaline conditions presents a similar problem of instability.We reported previously the use of porous plates made of nanofibrous cellulose for microbial culture (4). Detailed accounts of the preparation procedure, fine structure of the cellulose plate, and its application to culturing representative mesophilic microorganisms (Escherichia coli, Bacillus subtilis, and Saccharomyces cerevisiae) appeared in that paper.Interestingly, the porous structure of the cellulose plate has a structural robustness comparable to that of highly crystalline cellulose (6-8) despite its seemingly fragile structure (4). In situ optical microscopic observation in hot and compressed water (5, 18) revealed that the cellulose plate remained unchanged in water up to 260°C at 25 MPa (4, 7). This finding suggested that the cellulose plate could be used, in principle, as a versatile platform for developing solidified media that support the growth of extremophilic microbes under a wide range of extreme culture conditions. A proof-of-concept experiment was done by successfully culturing Thermus thermophilus on the cellulose plate at 80°C (4), but its true potential, especially its versatility, still remained to be corroborated.In this paper, we show that a wide variety of extremophiles, including an acidophile, an alkaliphile, thermophiles, an acidothermophile, and an alkalithermophile, can be cultured on the cellulose plates. Another advantage of the cellulose-supported media, that no solidifying aid is needed for solidification regardless of culture conditions, is also discussed.     

Tacrolimus differentially regulates the proliferation of conventional and regulatory CD4<Superscript>+</Superscript> T cells

Tacrolimus is a widely used T cell targeted immunosuppressive drug, known as a calcineurin inhibitor. However, the exact pharmacological effects of tacrolimus on CD4⁺ T cells have yet to be elucidated. This study investigated the effects of tacrolimus on CD4⁺ T cell subsets. Mouse or human CD4⁺ T cells were cultured with immobilized anti-CD3/CD28 antibodies in the presence of tacrolimus. The cell division of CD4⁺ T cells was analyzed using a flow cytometer according to the expression of Foxp3. The gene expression patterns of tacrolimus-exposed T cells were examined by quantitative PCR. In the case of conventional CD4⁺ T cells (Tconv cells), tacrolimus inhibited T cell receptor stimulation-induced cell division. In contrast, the cell division of regulatory CD4⁺ T cells (Treg cells) was even promoted in the presence of tacrolimus, especially in humans. Tacrolimus did not promote conversion of Tconv to Treg cells in mice. Furthermore, tacrolimus modified the expression levels of Foxp3-regulated T cell receptor signal related-genes, PTPN22 and Itk, in human Treg cells. Immunosuppressive effect of tacrolimus may be attributed to the relatively enhanced proliferation of Treg cells in association with altered gene expression levels of TCR signaling molecules.     

The Impact of Using Mature Compost on Nitrous Oxide Emission and the Denitrifier Community in the Cattle Manure Composting Process

The diversity and dynamics of the denitrifying genes (nirS, nirK, and nosZ) encoding nitrite reductase and nitrous oxide (N₂O) reductase in the dairy cattle manure composting process were investigated. A mixture of dried grass with a cattle manure compost pile and a mature compost-added pile were used, and denaturing gradient gel electrophoresis was used for denitrifier community analysis. The diversity of nirK and nosZ genes significantly changed in the initial stage of composting. These variations might have been induced by the high temperature. The diversity of nirK was constant after the initial variation. On the other hand, the diversity of nosZ changed in the latter half of the process, a change which might have been induced by the accumulation of nitrate and nitrite. The nirS gene fragments could not be detected. The use of mature compost that contains nitrate and nitrite promoted the N₂O emission and significantly affected the variation of nosZ diversity in the initial stage of composting, but did not affect the variation of nirK diversity. Many Pseudomonas-like nirK and nosZ gene fragments were detected in the stage in which N₂O was actively emitted.     

Zyxin Is a Transforming Growth Factor-β (TGF-β)/Smad3 Target Gene That Regulates Lung Cancer Cell Motility via Integrin α5β1

Although TGF-β acts as a tumor suppressor in normal tissues and in early carcinogenesis, these tumor suppressor effects are lost in advanced malignancies. Single cell migration and epithelial-mesenchymal transition (EMT), both of which are regulated by TGF-β, are critical steps in mediating cancer progression. Here, we sought to identify novel direct targets of TGF-β signaling in lung cancer cells and have indentified the zyxin gene as a target of Smad3-mediated TGF-β1 signaling. Zyxin concentrates at focal adhesions and along the actin cytoskeleton; as such, we hypothesized that cytoskeletal organization, motility, and EMT in response to TGF-β1 might be regulated by zyxin expression. We show that TGF-β1 treatment of lung cancer cells caused rapid phospho-Smad3-dependent expression of zyxin. Zyxin expression was critical for the formation and integrity of cell adherens junctions. Silencing of zyxin decreased expression of the focal adhesion protein vasodilator-activated phospho-protein (VASP), although the formation and morphology of focal adhesions remained unchanged. Zyxin-depleted cells displayed significantly increased integrin α5β1 levels, accompanied by enhanced adhesion to fibronectin and acquisition of a mesenchymal phenotype in response to TGF-β1. Zyxin silencing led to elevated integrin α5β1-dependent single cell motility. Importantly, these features are mirrored in the K-ras-driven mouse model of lung cancer. Here, lung tumors revealed decreased levels of both zyxin and phospho-Smad3 when compared with normal tissues. Our data thus demonstrate that zyxin is a novel functional target and effector of TGF-β signaling in lung cancer. By regulating cell-cell junctions, integrin α5β1 expression, and cell-extracellular matrix adhesion, zyxin may regulate cancer cell motility and EMT during lung cancer development and progression.     

Population viability analysis predicts decreasing genetic diversity in <Emphasis Type="Italic">ex situ</Emphasis> populations of the Itasenpara bitterling <Emphasis Type="Italic">Acheilognathus longipinnis</Emphasis> from the Kiso River,Japan

To conserve endangered species, the maintenance of ex situ captive populations with sustainable genetic diversity is often required, in combination with population viability analysis (PVA). Since 2010, the threatened Itasenpara bitterling Acheilognathus longipinnis lineages in the Kiso region, Japan, have been maintained in ex situ rearing facilities to allow for conservation efforts. In this study, we obtained microsatellite data from DNA extracted from these captive populations to elucidate their genetic diversity and effective population size. The populations of several initial generations indicated a deviation from Hardy–Weinberg equilibrium, probably due to the limited number of extracted founder individuals analyzed. The effective population size of the captive population tended to increase over the course of generations, although the degree of genetic diversity tended to decrease highlighting the concern for the progression of inbreeding. Our prediction based on the PVA suggests that the maintenance of the captive population under the current conditions could lead to extinction of the Itasenpara bitterling in 50 years. In contrast, simultaneously increasing the carrying capacity and individual exchange among populations appears to enhance the effective management of captive Itasenpara bitterling populations.     

Molecular phylogenetic and isotopic evidence of two lineages of chemoautotrophic endosymbionts distinct at the subdivision level harbored in one host-animal type: the genus Alviniconcha (Gastropoda: Provannidae)

The hydrothermal-vent gastropod Alviniconcha hessleri from the Alice Springs deep-sea hydrothermal field in the Mariana Back-Arc Basin in the Western Pacific houses an intracellular bacterial endosymbiont in its gill. Although enzymatic analysis has revealed that the endosymbiont is a sulfur-oxidizing chemoautotroph using the Calvin-Benson cycle for the fixation of carbon dioxide, the phylogenetic affiliation of, and the trophic relationship of A. hessleri with, the chemoautotrophic endosymbiont remains undetermined. A single 16S rRNA gene sequence was obtained from the DNA extract of the gill, and phylogenetic analysis placed the source organism within the lineage of the gamma subdivision of the Proteobacteria that consists of many chemoautotrophic endosymbionts of marine invertebrates. Fluorescence in situ hybridization analysis showed the bacterium densely colonizing the gill filaments. The fatty acid profile of the symbiont-free mantle contains the high level of the 16:1 fatty acid originating from the endosymbiont, which indicates that the endosymbiont cells are digested by, and incorporated into, the host. Compound-specific carbon isotopic analysis revealed that fatty acids from the gastropod tissues are all (13)C-depleted relative to the gastropod biomass. This fractionation pattern is consistent with chemoautotrophy based on the Calvin-Benson cycle and subsequent fatty-acid biosynthesis from (13)C-depleted acetyl coenzyme A. The results from the present study are clearly different from those from our previous study for A. aff. hessleri from the Indian Ocean that harbors a chemoautotrophic endosymbiont belonging to the epsilon subdivision of the Proteobacteria, which mediates the reductive tricarboxylic acid cycle for carbon fixation. Thus, it is concluded here that two lineages of chemoautotrophic bacteria, phylogenetically distinct at the subdivision level, occur as the primary endosymbiont in one host-animal type, which is unknown for the other metazoans.     

Molecular analyses of the sediment of the 11000-m deep Mariana Trench

We have obtained sediment samples from the world's deepest sea-bottom, the Mariana Trench challenger point at a depth of 10 898 m, using the new unmanned submersible Kaiko. DNA was extracted from the sediment, and DNA fragments encoding several prokaryotic ribosomal RNA small-subunit sequences and pressure-regulated gene clusters, typically identifed in deep-sea adapted bacteria, were amplifed by the polymerase chain reaction. From the sequencing results, at least two kinds of bacterial 16S rRNAs closely related to those of the genus Pseudomonas and deep-sea adapted marine bacteria, and archaeal 16S rRNAs related to that of a planktonic marine archaeon were identifed. The sequences of the amplifed pressure-regulated clusters were more similar to those of deep-sea barophilic bacteria than those of barotolerant bacteria. These results suggest that deep-sea adapted barophilic bacteria, planktonic marine archaea, and some of the world's most widespread bacteria (the genus Pseudomonas) coexist on the world's deepest sea-bottom. Received: October 10, 1996 / Accepted: March 3, 1997     

Microbial Diversity in Sediments Collected from the Deepest Cold-Seep Area, the Japan Trench

The Japan Trench land slope at a depth of 6,400 m is the deepest cold-seep environment with Calyptogena communities. Sediment samples from inside and beside the Calyptogena communities were collected, and the microbial diversity in the sediment samples was studied by molecular phylogenetic techniques. From DNA extracted directly from the sediment samples, 16S rDNAs were amplified by the polymerase chain reaction method. The sequences of the amplified 16S rDNAs selected by restriction fragment length polymorphism analysis were determined and compared with sequences in DNA databases. The results showed that 33 different bacterial 16S rDNA sequences from the two samples analyzed fell into similar phylogenetic categories, the α-, γ-, δ-, and ɛ-subdivisions of Proteobacteria, Cytophaga, and gram-positive bacteria; some of the 16S rDNA sequences were common to both samples. δ- and ɛ-Proteobacteria-related sequences were abundant in both sediments. These sequences are mostly related to sulfate-reducing or sulfur-reducing bacteria and epibionts, respectively. Eight different archaeal 16S rDNA sequences were cloned from the sediments. The majority of the archaeal 16S rDNA sequences clustered in Crenarchaeota and showed high similarities to marine group I archaeal rDNA. A Methanococcoides burtonii–related sequence obtained from the sediment clustered in the Euryarchaeota indicating that M. burtonii–related strains in the area of Calyptogena communities may contribute to production of methane in this environment. From these results, we propose a possible model of sulfur circulation within the microbial community and that of Calyptogena clams in the cold-seep environment. Received June 15, 1998; accepted November 10, 1998.