Potential of Phototrophic Purple Nonsulfur Bacteria to Fix Nitrogen in Rice Fields

Biological nitrogen fixation catalyzed by Mo-nitrogenase of symbiotic diazotrophs has attracted interest because its potential to supply plant-available nitrogen offers an alternative way of using chemical fertilizers for sustainable agriculture. Phototrophic purple nonsulfur bacteria (PNSB) diazotrophically grow under light anaerobic conditions and can be isolated from photic and microaerobic zones of rice fields. Therefore, PNSB as asymbiotic diazotrophs contribute to nitrogen fixation in rice fields. An attempt to measure nitrogen in the oxidized surface layer of paddy soil estimates that approximately 6–8 kg N/ha/year might be accumulated by phototrophic microorganisms. Species of PNSB possess one of or both alternative nitrogenases, V-nitrogenase and Fe-nitrogenase, which are found in asymbiotic diazotrophs, in addition to Mo-nitrogenase. The regulatory networks control nitrogenase activity in response to ammonium, molecular oxygen, and light irradiation. Laboratory and field studies have revealed effectiveness of PNSB inoculation to rice cultures on increases of nitrogen gain, plant growth, and/or grain yield. In this review, properties of the nitrogenase isozymes and regulation of nitrogenase activities in PNSB are described, and research challenges and potential of PNSB inoculation to rice cultures are discussed from a viewpoint of their applications as nitrogen biofertilizer.

Utilizing Cattle Manure Compost Increases Ammonia Monooxygenase A Gene Expression and Ammonia-oxidizing Activity of Both Bacteria and Archaea in Biofiltration Media for Ammonia Deodorization

Malodorous emissions are a crucial and inevitable issue during the decomposition of biological waste and contain a high concentration of ammonia. Biofiltration technology is a feasible, low-cost, energy-saving method that reduces and eliminates malodors without environmental impact. In the present study, we evaluated the effectiveness of compost from cattle manure and food waste as deodorizing media based on their removal of ammonia and the expression of ammonia-oxidizing genes, and identified the bacterial and archaeal communities in these media. Ammonia was removed by cattle manure compost, but not by food waste compost. The next-generation sequencing of 16S ribosomal RNA obtained from cattle manure compost revealed the presence of ammonia-oxidizing bacteria (AOB), including Cytophagia, Alphaproteobacteria, and Gammaproteobacteria, and ammonia-oxidizing archaea (AOA), such as Thaumarchaeota. In cattle manure compost, the bacterial and archaeal ammonia monooxygenase A (amoA) genes were both up-regulated after exposure to ammonia (fold ratio of 14.2±11.8 after/before), and the bacterial and archaeal communities were more homologous after than before exposure to ammonia, which indicates the adaptation of these communities to ammonia. These results suggest the potential of cattle manure compost as an efficient biological deodorization medium due to the activation of ammonia-oxidizing microbes, such as AOB and AOA, and the up-regulation of their amoA genes.

Biosyntheses of geranic acid and citronellic acid from monoterpene alcohols by Saccharomyces cerevisiae

Geraniol is one of the important aromatic ingredients in alcoholic beverages. Bioconversions of geraniol to other terpenoids and genes involved in the oxidation of geraniol were investigated. Geranic acid and citronellic acid were detected in yeast culture, where geraniol or nerol was added. Addition of citral, a mixture of geranial and neral, resulted in the production of geranic acid and citronellic acid, whereas the addition of citral or citronellal resulted in the production of citronellic acid, suggesting that citronellic acid might be produced through the conversion of citral to citronellal followed by the oxidation of citronellal. Consumption of geraniol and production of geranic acid, citronellic acid, and citronellol were affected in adh1Δ, adh3Δ, adh4Δ, and sfa1Δ yeast strains, which possess single deletion of a gene encoding alcohol dehydrogenase. This is the first report of the bioconversion of monoterpene alcohols, geraniol and nerol, to geranic acid and citronellic acid in yeast culture.

Linoleic acid, α-linolenic acid, and monolinolenins as antibacterial substances in the heat-processed soybean fermented with Rhizopus oligosporus

Antibacterial activities against Staphylococcus aureus and Bacillus subtilis were found in an ethanol fraction of tempe, an Indonesian fermented soybean produced using Rhizopus oligosporus. The ethanol fraction contained free fatty acids, monoglycerides, and fatty acid ethyl esters. Among these substances, linoleic acid and α-linolenic acid exhibited antibacterial activities against S. aureus and B. subtilis, whereas 1-monolinolenin and 2-monolinolenin exhibited antibacterial activity against B. subtilis. The other free fatty acids, 1-monoolein, monolinoleins, ethyl linoleate, and ethyl linolenate did not exhibit bactericidal activities. These results revealed that R. oligosporus produced the long-chain polyunsaturated fatty acids and monolinolenins as antibacterial substances against the Gram-positive bacteria during the fungal growth and fermentation of heat-processed soybean.

Effect of increased feeding of dietary α-linolenic acid by grazing on formation of the cis9,trans11-18:2 isoform of conjugated linoleic acid in bovine milk

Feeding systems such as grazing affect the fatty acid profile of bovine milk fat. In addition, milk fat is formed as the product of fatty acid metabolism in cow bodies before being secreted into milk. However, how grazing influences milk fatty acid profile through the metabolism has not been completely characterized. When fatty acid concentrations in Holstein milk were compared between grazing and non-grazing periods, α-linolenic acid was significantly higher in the grazing period than in the non-grazing period. This could be explained with an increase in α-linolenic acid feeding with grazing. α-linolenic acid had a linear positive correlation with conjugated linoleic acid (9c,11t-18:2) (CLA) and vaccenic acid (VA) during the grazing period, whereas CLA had higher correlation with linoleic acid rather than with α-linolenic acid during the non-grazing period. These data indicate that the high content of dietary α-linolenic acid affects CLA and VA formation in milk of grazing periods via α-linolenic acid metabolism into VA.

Light-enhanced bioaccumulation of molybdenum by nitrogen-deprived recombinant anoxygenic photosynthetic bacterium Rhodopseudomonas palustris

As molybdenum (Mo) is an indispensable metal for plant nitrogen metabolisms, accumulation of dissolved Mo into bacterial cells may connect to the development of bacterial fertilizers that promote plant growth. In order to enhance Mo bioaccumulation, nitrogen removal and light illumination were examined in anoxygenic photosynthetic bacteria (APB) because APB possess Mo nitrogenase whose synthesis is strictly regulated by ammonium ion concentration. In addition, an APB, Rhodopseudomonas palustris, transformed with a gene encoding Mo-responsive transcriptional regulator ModE was constructed. Mo content was most markedly enhanced by the removal of ammonium ion from medium and light illumination while their effects on other metal contents were limited. Increases in contents of trace metals including Mo by the genetic modification were observed. Thus, these results demonstrated an effective way to enrich Mo in the bacterial cells by the culture conditions and genetic modification.

Evaluation of bacterial communities by bacteriome analysis targeting 16S rRNA genes and quantitative analysis of ammonia monooxygenase gene in different types of compost

Biofiltration technology based on microbial degradation and assimilation is used for the removal of malodorous compounds, such as ammonia. Microbes that degrade malodorous and/or organic substances are involved in composting and are retained after composting; therefore, mature composts can serve as an ideal candidate for a biofilter medium. In this study, we focused on different types of raw compost materials, as these are important factors determining the bacterial community profile and the chemical component of the compost. Therefore, bacterial community profiles, the abundance of the bacterial ammonia monooxygenase gene (amoA), and the quantities of chemical components were analyzed in composts produced from either food waste or cattle manure. The community profiles with the lowest beta diversity were obtained from single type of cattle manure compost. However, cattle manure composts showed greater alpha diversity, contained higher amounts of various rRNA gene fragments than those of food waste composts and contained the amoA gene by relative quantification, and Proteobacteria were abundantly found and nitrifying bacteria were detected in it. Nitrifying bacteria are responsible for ammonia oxidation and mainly belong to the Proteobacteria or Nitrospira phyla. The quantities of chemical components, such as salt, phosphorus, and nitrogen, differed between the cattle manure and food waste composts, indicating that the raw materials provided different fermentation environments that were crucial for the formation of different community profiles. The results also suggest that cattle manure might be a more suitable raw material for the production of composts to be used in the biofiltration of ammonia.

Combinatorial parallel display of polypeptides using bacteriophage T7 for development of fluorescent nano-bioprobes

Application of nano-particles to diagnostic fields has attracted much attention. Biotechnology can contribute to produce useful nano-materials by engineering bacteriophage nano-particles, which are easily prepared by infecting phages to bacterial host cells. In this study, establishment of nano-bioprobes was demonstrated, based on the T7 phage display system, by constructing phage particles displaying a ligand polypeptide S-tag and a green fluorescent protein (GFP) at the same time on the surface of phage head. To achieve this purpose, two types of phage particles were tested: One displayed S-tag and GFP as a single polypeptide (tandem display), and another displayed these molecules as two different polypeptides (parallel display). Only the parallelly displayed phage could be detected with ligand blotting using S-protein and with immunoblotting using an anti-GFP antibody. S-protein-coated magnetic beads and nano-particles were successively labeled with fluorescence using the parallelly displayed phage but could not be labeled with the tandemly displayed phage. Thus, the parallel display of a ligand molecule and fluorescent protein on the head surface of bacteriophage T7 could provide a new scheme of producing fluorescent nano-bioprobes for diagnostic applications.

Fluorescent bioassays for toxic metals in milk and yoghurt

Background

From a human health viewpoint, contaminated milk and its products could be a source of long-term exposure to toxic metals. Simple, inexpensive, and on-site assays would enable constant monitoring of their contents. Bioassays that can measure toxic metals in milk or yoghurt might reduce the risk. For this purpose, the green fluorescent protein (GFP)-tagged trans factors, ArsR-GFP and CadC-GFP, together with their cis elements were used to develop such bioassays.

Results

ArsR-GFP or CadC-GFP, which binds either toxic metal or DNA fragment including cis element, was directly mixed with cow’s milk or yoghurt within a neutral pH range. The fluorescence of GFP, which is reflected by the association/dissociation ratio between cis element and trans factor, significantly changed with increasing externally added As (III) or Cd (II) whereas smaller responses to externally added Pb (II) and Zn (II) were found. Preparation and dilution of whey fraction at low pH were essential to intrinsic zinc quantification using CadC-GFP. Using the extraction procedure and bioassay, intrinsic Zn (II) concentrations ranging from 1.4 to 4.8 mg/l for milk brands and from 1.2 to 2.9 mg/kg for yoghurt brands were determined, which correlated to those determined using inductively coupled plasma atomic emission spectroscopy.

Conclusions

GFP-tagged bacterial trans factors and cis elements can work in the neutralized whole composition and diluted whey fraction of milk and yoghurt. The feature of regulatory elements is advantageous for establishment of simple and rapid assays of toxic metals in dairy products.

Monitoring of environmental arsenic by cultures of the photosynthetic bacterial sensor illuminated with a near-infrared light emitting diode array

Recombinant Rhodopseudomonas palustris, harboring the carotenoid-metabolizing gene crtI (CrtIBS), and whose color changes from greenish yellow to red in response to inorganic As(III), was cultured in transparent microplate wells illuminated with a light emitting diode (LED) array. The cells were seen to grow better under near-infrared light, when compared with cells illuminated with blue or green LEDs. The absorbance ratio of 525 to 425 nm after cultivation for 24 h, which reflects red carotenoid accumulation, increased with an increase in As(III) concentrations. The detection limit of cultures illuminated with near-infrared LED was 5 microgram/l, which was equivalent to that of cultures in test tubes illuminated with an incandescent lamp. A near-infrared LED array, in combination with a microplate, enabled the simultaneous handling of multiple cultures, including CrtIBS and a control strain, for normalization by the illumination of those with equal photon flux densities. Thus, the introduction of a near-infrared LED array to the assay is advantageous for the monitoring of arsenic in natural water samples that may contain a number of unknown factors and, therefore, need normalization of the reporter event.

Genetic modification in Bacillus subtilis for production of C30 carotenoids

C30 carotenoids, which have shorter backbones than C40 carotenoids, are known to be produced in the pathogenic bacterium Staphylococcus aureus that causes opportunistic infection. The first committed enzyme in the C30 carotenoid synthetic pathway is dehydrosqualene synthase CrtM. CrtM converts farnesyl pyrophosphate to dehydrosqualene. Dehydrosqualene desaturase CrtN then converts dehydrosqualene to the yellow C30 carotenoid, 4,4'-diaponeurosporene. This chapter describes a method to synthesize C30 carotenoids in Bacillus subtilis, which is generally recognized as a safe (GRAS) organism. Introduction of S. aureus crtM and crtN genes into B. subtilis results in yellow pigmentation. The B. subtilis transformant accumulates two C30 carotenoids, 4,4'-diapolycopene and 4,4'-diaponeurosporene. Furthermore, together with crtMN, introduction of S. aureus crtP and crtQ genes, which encode mixed function oxidase and glycosyltransferase, respectively, donates the ability to produce glycosylated C30 carotenoic acid. Thus, carotenoid biosynthesis genes of S. aureus is applicable to genetically modify B. subtilis in order to construct a safe organism producing C30 carotenoids.

P5-17-04: Association between Breast Cancer and Osteoporosis among Women 85 Years or Older

Background: The pathogenesis of breast cancer in very elderly women is of interest, because estrogen levels are likely to be extremely low during the development of the disease. Estrogens have opposing effects on the pathogenesis of breast cancer and osteoporosis. In an effort to understand the significance of estrogens in the pathogenesis of breast cancer in this group, we examined the association between breast cancer and osteoporosis in women at least 85 years old, taking body mass index (BMI) and hormone receptors status into consideration.

Methods:Clinical records of consecutive elderly women (≥ 85 y/o) who underwent breast cancer surgery at Tokyo Metropolitan Geriatric Hospital (BC) and control women of the same age group (Cont) were reviewed; osteoporosis and BMI status in both groups were recorded and compared. The status of estrogen receptor (ER) and progesterone receptor (PR) of breast cancers was examined immunohistochemically and compared between BC with and without osteoporosis (BC-OP and BC-nonOP, respectively).

Results:Frequency of osteoporosis was significantly lower among BC than Cont. There was no difference in BMI measured after 85 y/o between BC and Cont; however, percentage of women, whose BMI measured when they were in their sixties or seventies was ≥ 20% higher than BMI measured when they were 85 y/o or older, was significantly higher among BC than Cont (31% and 2%, respectively. P = 0.0001). ER positivity of breast cancer did not differ between BC-OP and BC-nonOP, whereas PR positivity was significantly higher among BC-nonOP than BC-OP (P = 0.0359).

Discussion: The inverse relationship between the incidence of breast cancer and osteoporosis suggests an important role for estrogens in the pathogenesis of breast cancer in the very elderly women. Our finding that one third of BC had ≥ 20% higher BMI when they were in their sixties or seventies suggests they may also had elevated serum estrogens during these earlier years, because increased BMI has been reported to be associated with increased serum estrogens in postmenopausal women. Expression of PR is regulated by estrogen-ER signaling, and PR positivity is considered to reflect the effectiveness of estrogen-ER pathway. Significant difference of PR positivity between BC-nonOP and BC-OP suggests the more importance of estrogens in BC-nonOP than BC-OP.

Conclusion:Estrogens seem to play an important role in the pathogenesis of breast cancers in very elderly women, especially without osteoporosis. With increasing aging population in developed countries, those findings may have implications for breast cancer prevention in this age group.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P5-17-04.

Solid phase biosensors for arsenic or cadmium composed of A trans factor and cis element complex

The presence of toxic metals in drinking water has hazardous effects on human health. This study was conducted to develop GFP-based-metal-binding biosensors for on-site assay of toxic metal ions. GFP-tagged ArsR and CadC proteins bound to a cis element, and lost the capability of binding to it in their As- and Cd-binding conformational states, respectively. Water samples containing toxic metals were incubated on a complex of GFP-tagged ArsR or CadC and cis element which was immobilized on a solid surface. Metal concentrations were quantified with fluorescence intensity of the metal-binding states released from the cis element. Fluorescence intensity obtained with the assay significantly increased with increasing concentrations of toxic metals. Detection limits of 1 μg/L for Cd(II) and 5 μg/L for As(III) in purified water and 10 µg/L for Cd(II) and As(III) in tap water and bottled mineral water were achieved by measurement with a battery-powered portable fluorometer after 15-min and 30-min incubation, respectively. A complex of freeze dried GFP-tagged ArsR or CadC binding to cis element was stable at 4 °C and responded to 5 μg/L As(III) or Cd(II). The solid phase biosensors are sensitive, less time-consuming, portable, and could offer a protocol for on-site evaluation of the toxic metals in drinking water.

Distribution of retinal cone photoreceptor oil droplets, and identification of associated carotenoids in crow (Corvus macrorhynchos)

The topography of cone oil droplets and their carotenoids were investigated in the retina of jungle crow (Corvus macrorhynchos). Fresh retina was sampled for the study of retinal cone oil droplets, and extracted retinal carotenoids were saponified using methods adapted from a recent study, then identified with reverse-phase high-performance liquid chromatography (HPLC). To assess the effects of saponification conditions on carotenoid recovery from crow retina, we varied base concentration and total time of saponification across a wide range of conditions, and again used HPLC to compare carotenoid concentrations. Based on colors, at least four types of oil droplets were recognized, i.e., red, orange, green, and translucent, across the retina. With an average of 91,202 /mm(2), density gradually declines in an eccentric manner from optic disc. In retina, the density and size of droplets are inversely related. In the peripheral zone, oil droplets were significantly larger than those of the central area. The proportion of orange oil droplets (33%) was higher in the central area, whereas green was predominant in other areas. Three types of carotenoid (astaxanthin, galloxanthin and lutein), together with one unknown carotenoid, were recovered from the crow retina; astaxanthin was the dominant carotenoid among them. The recovery of carotenoids was affected by saponification conditions. Astaxanthin was well recovered in weak alkali (0.06 M KOH), in contrast, xanthophyllic carotenoids were best recovered in strong alkali (0.6 M KOH) after 12 h of saponification at freeze temperature.

Application of fluorescent protein-tagged trans factors and immobilized cis elements to monitoring of toxic metals based on in vitro protein-DNA interactions

Environmental toxic metals cause serious global public health problems. On-site monitoring protects people from exposure to such harmful elements. In this study, the bacterial transcriptional switches were applied to monitoring of toxic metals. ArsR and CadC, trans factors of Escherichia coli and Staphylococcus aureus, were fused to GFP. The fusion proteins, ArsR-GFP and CadC-GFP, associated with cis elements, P(ars)-O(ars) and P(cad)-O(cad), respectively and dissociated from those upon recognition of As(III) or Pb/Cd. Cell lysates containing ArsR-GFP were pre-incubated with As(III) standard solutions for 15 min and loaded into P(ars)-O(ars)-immobilized microplate wells. Cell lysates containing CadC-GFP were pre-incubated with Pb or Cd solutions and loaded into P(cad)-O(cad)-immobilized wells. The cell lysates were incubated for 15 min and removed from the wells. Fluorescence intensity in the wells dose-dependently decreased in response to As(III) up to 200 μg/l or Pb/Cd up to 100 μg/l. Detection limits were 10 μg/l for As(III) 10 μg/l for Cd, and 20 μg/l for Pb with a microplate fluororeader, whereas 5.0 μg/l for As(III), 1.0 μg/l for Cd, and 10 μg/l for Pb with a handheld fluorometer. This method was available to detect Pb/Cd or As(III) in water containing soil extracts. This is the first demonstration of a simple and rapid fluorometry to detect analytes based on in vitro interaction between a cis element and a trans factor.

Increased expression levels of tensin3 mRNA in thyroid functional adenomas as compared to non-functioning adenomas

Tensin3 is a member of tensin family which is localized in focal adhesion. In our previous study, a high level of tensin3 mRNA expression was observed in the thyroid but not in other tissues, thus, tensin3 gene was regarded as a novel thyroid-specific gene. The high expression level of tensin3 mRNA in normal thyroid tissue suggests some fundamental roles in thyroid functions. In fact, the expression level of tensin3 mRNA was low in most thyroid carcinomas and non-functioning thyroid follicular adenomas which do not produce thyroid hormone. In the present study, we measured the expression levels of tensin3 mRNA in twelve functional adenomas and compared the results with those in normal thyroid tissues, adenomatous goiters and non-functioning thyroid follicular adenomas. Tensin3 mRNA was expressed abundantly in all twelve functional adenomas at almost the same level as in normal thyroid tissues and adenomatous goiters, while its expression was significantly lower in non-functioning follicular adenomas. Considering these facts, an abundant expression of tensin3 mRNA is observed in tissues that produce thyroid hormone, which suggests some fundamental roles in basic thyroid functions.

Evaluation of colors in green mutants isolated from purple bacteria as a host for colorimetric whole-cell biosensors

The change in carotenoid-based bacterial color from yellow to red can be applied to whole-cell biosensors. We generated several green mutants to emphasize the color change in such biosensors. The blue-green crtI-deleted mutant, Rhodopseudomonas palustris no.711, accumulated the colorless carotenoid precursor, phytoene. Green Rhodovulum sulfidophilum M31 accumulated neurosporene, a downstream product of phytoene. Another green mutant, Rhodobacter sphaeroides Ga, accumulated neurosporene and chloroxanthin, which are both downstream products of phytoene. All green mutants accumulated bacteriochlorophyll a. Photosynthetic membrane obtained from the green mutants all exhibited decreased absorption of wavelength range at 510-570 nm. Therefore, these indicate that the greenish bacterial colors were mainly caused by the existence of bacteriochlorophyll a and the changes in carotenoid composition in photosynthetic membrane. The colors of the green mutants and their wild-type strains were plotted in the CIE-L*a*b* color space, and the color difference (DeltaE*ab) values between a green mutant and its wild type were calculated. DeltaE*ab values were higher in the green mutants than in Rdv. sulfidophilum CDM2, the yellowish host strain of reported biosensors. These data indicate that change in bacterial color from green to red is more distinguishable than that from yellow to red as a reporter signal of carotenoid-based whole-cell biosensors.

Whole-cell arsenite biosensor using photosynthetic bacterium Rhodovulum sulfidophilum. Rhodovulum sulfidophilum as an arsenite biosensor

An arsenite biosensor plasmid was constructed in Escherichia coli by inserting the operator/promoter region of the ars operon and the arsR gene from E. coli and the crtA gene, which is responsible for carotenoid synthesis in the photosynthetic bacterium, Rhodovulum sulfidophilum, into the broad-host-range plasmid vector, pRK415. The biosensor plasmid, pSENSE-As, was introduced into a crtA-deleted mutant strain of R. sulfidophilum (CDM2), which is yellow in culture due to its content of spheroiden (SE) and demethylspheroidene (DMSE). CDM2 containing pSENSE-As changed from yellow to red by the addition of arsenite, which caused enzymatic transformation of SE and DMSE to spheroidenone (SO) and demethylspheroidenone (DMSO). Reverse transcriptase PCR analysis showed that the color change depended on transcription of the crtA gene in pSENSE-As. The color change could be clearly recognized with the naked eye at 5 microg/l arsenite. The biosensor strain did not respond to other metals except for bismuth and antimony, which caused significant accumulation of SO and DMSO in the cells at 60 and 600 microg/l, respectively. This biosensor indicates the presence of arsenite with a bacterial color change without the need to add a special reagent or substrate for color development, enabling this pollutant to be monitored in samples by the naked eye in sunlight, even where electricity is not available.

Colorimetric dimethyl sulfide sensor using Rhodovulum sulfidophilum cells based on intrinsic pigment conversion by CrtA

A colorimetric whole-cell sensor for dimethyl sulfide (DMS) was constructed based on the in vivo conversion of intrinsic pigments in response to the analyte. In a marine bacterium, Rhodovulum sulfidophilum, carotenoids are synthesized via the spheroidene pathway. In this pathway, demethylspheroidene, a yellow carotenoid, is converted to spheroidene under catalysis of O-methyltransferase. Spheroidene monooxygenase (CrtA) catalyzes the terminal step of the pathway and converts spheroidene to spheroidenone, a red carotenoid. Here, the CrtA gene in R. sulfidophilum was removed and then reintroduced downstream of the DMS dehydrogenase gene promoter. Using this whole-cell sensor, 3 muM DMS or dimethyl sulfoxide can be detected without adding any color-forming reagent. The ratio of the red spheroidenone to total carotenoids increased, as the DMS concentration was raised to 0.3 mM. Comparison of the signal to the background color indicated a shift in the color coordinate from a yellow to a red hue. An intense signal was obtained with 1-day incubation at a high cell density when sensor cells at the exponential growth phase were used. These results show that the genetically engineered R. sulfidophilum cells can be used to monitor the quality of marine aquacultural environments by the naked eye.

The peroxisomal Acyl-CoA thioesterase Pte1p from Saccharomyces cerevisiae is required for efficient degradation of short straight chain and branched chain fatty acids

The role of the Saccharomyces cerevisae peroxisomal acyl-coenzyme A (acyl-CoA) thioesterase (Pte1p) in fatty acid beta-oxidation was studied by analyzing the in vitro kinetic activity of the purified protein as well as by measuring the carbon flux through the beta-oxidation cycle in vivo using the synthesis of peroxisomal polyhydroxyalkanoate (PHA) from the polymerization of the 3-hydroxyacyl-CoAs as a marker. The amount of PHA synthesized from the degradation of 10-cis-heptadecenoic, tridecanoic, undecanoic, or nonanoic acids was equivalent or slightly reduced in the pte1Delta strain compared with wild type. In contrast, a strong reduction in PHA synthesized from heptanoic acid and 8-methyl-nonanoic acid was observed for the pte1Delta strain compared with wild type. The poor catabolism of 8-methyl-nonanoic acid via beta-oxidation in pte1Delta negatively impacted the degradation of 10-cis-heptadecenoic acid and reduced the ability of the cells to efficiently grow in medium containing such fatty acids. An increase in the proportion of the short chain 3-hydroxyacid monomers was observed in PHA synthesized in pte1Delta cells grown on a variety of fatty acids, indicating a reduction in the metabolism of short chain acyl-CoAs in these cells. A purified histidine-tagged Pte1p showed high activity toward short and medium chain length acyl-CoAs, including butyryl-CoA, decanoyl-CoA and 8-methyl-nonanoyl-CoA. The kinetic parameters measured for the purified Pte1p fit well with the implication of this enzyme in the efficient metabolism of short straight and branched chain fatty acyl-CoAs by the beta-oxidation cycle.

Simultaneous control of turbidity and dilution rate through adjustment of medium composition in semi-continuousChlamydomonas cultures

For production of starch in algal cultures, a growth rate limited by a nutrient is an important factor. Under phototrophic conditions, turbidity must be also paid attention, as the shading effect may affect its productivity. Semi-continuous cultivation methods, which enable control of turbidity and dilution rate (D) at the same time, have been developed for evaluation of those factors on starch production in Chlamydomonas sp. A specific feature of the methods is in a process of alternately feeding medium adjusted at two different nitrogen (N) concentrations. In the turbidostat-based method, a turbidostat culture was operated repeating three steps of determining D within a preset interval, alternating media by comparing the D with a preset value, and adjusting D in the next interval by feeding the selected medium. In the chemostat-based method, turbidity of a chemostat culture was controlled by repeating two steps of alternating media by comparing transmitted photon flux intensity (I) with a preset value and adjusting I by feeding the selected medium. D controlled by the turbidostat-based method reached quickly a preset value as low as 0.010/h, and then it was dispersed around but above the preset value. On the other hand, mean N concentrations of fed media formed a plateau. In the chemostat-based method, I was well controlled to a preset value while the mean N concentrations were a bit fluctuated. Starch concentration varied from 0.052 to 0.41 g/L with turbidity and D defined by these methods.

Polyethyleneimine/chitosan hexamer-mediated gene transfection into intestinal epithelial cell cultured in serum-containing medium

In search of an efficient nonviral vector, polyethyleneimine (PEI)-based vectors were examined. In general, the transfection efficiency of nonviral vectors is suppressed by serum. Here we show that PEI based vectors, particularly, the chitosan hexamer-PEI vector, could perform efficient gene transfection into intestinal epithelial cells (IEC-6) in the presence of serum. The conjugation order of the two polymers with a plasmid (first, chitosan hexamer; second, PEI) was found to be an important factor in enhancing transfection efficiency.

Unusual Accumulation of Demethylspheroidene in Anaerobic-Phototrophic Growth of crtA-Deleted Mutants of Rhodovulum sulfidophilum

Rhodovulum sulfidophilum produces carotenoids in the spheroidene pathway. Spheroidene monooxygenase, CrtA, catalyzes the conversion of spheroidene to spheroidenone. crtA-deleted mutants of R. sulfidophilum did not produce spheroidenone and demethylspheroidenone. In these mutants, the ratio of demethylspheroidene to spheroidene increased with exposure to light. One mutant exhibiting a spheroidene-predominant phenotype did not grow under anaerobic-light conditions and was devoid of bacteriochlorophyll a, even under semiaerobic-light conditions There was no difference in the growth of the mutants under aerobic-dark conditions. These data suggest that demethylspheroidene is important for photosynthesis in R. sulfidophilum.

Increasing the carbon flux toward synthesis of short-chain-length--medium-chain-length polyhydroxyalkanoate in the peroxisome of Saccharomyces cerevisiae through modification of the beta-oxidation cycle

Short-chain-length-medium-chain-length polyhydroxyalkanoates were synthesized in Saccharomyces cerevisiae from intermediates of the beta-oxidation cycle by expressing the polyhydroxyalkanoate synthases from Aeromonas caviae and Ralstonia eutropha in the peroxisomes. The quantity of polymer produced was increased by using a mutant of the beta-oxidation-associated multifunctional enzyme with low dehydrogenase activity toward R-3-hydroxybutyryl coenzyme A.

Adenoviral transfection of hepatocytes with the thioredoxin gene confers protection against apoptosis and necrosis

A recombinant adenovirus vector containing the human thioredoxin (TRX) gene was constructed using the Cre-loxP recombination system and used to transfect rat hepatocytes with very high efficiency. The TRX gene was expressed in a dose-dependent manner and significantly modulated rat cellular functions. The TRX gene conferred resistance to oxidative stress, such as hydrogen peroxide treatment, on the host hepatocytes. FACS analysis of DNA fragmentation showed that the TRX gene suppressed hepatocyte apoptosis. It also significantly extended the life span of hepatocytes cultured conventionally on polystyrene plates. Liver-specific functions were maintained in the viability-modulated hepatocytes. Moreover, TRX expression did not affect hepatocyte spheroid formation and it extensively suppressed necrosis in the internal cells. Thus, the transfection of hepatocytes with the TRX gene successfully confers global maintenance of liver functions. These findings provide important information for the development of bioartificial liver support systems and gene therapy for liver diseases.

Comparative study of the N-terminal hydrophilic region in Streptomyces lividans and E. coli FtsY

Streptomyces lividans FtsY (SlFtsY) was cloned and overexpressed in Escherichia coli. Analysis of the amino acid (aa) sequence showed a concentration of hydrophilic aa's in the N-terminal half region of SlFtsY as observed in that of E. coli FtsY (EcFtsY). However, the length of the hydrophilic region was shorter in SlFtsY than in EcFtsY. Overexpression of SlFtsY in E. coli resulted in growth suppression as in the case of the overexpression of EcFtsY, while growth suppression as a result of the overexpression of the C-terminal half region of SlFtsY was limited. This result suggests that the N-terminal hydrophilic region of SlFtsY, regardless of its short length, would behave like its counterpart region of EcFtsY in E. coli.

Maximization of hydrogen production ability in high-density suspension of Rhodovulum sulfidophilum cells using intracellular poly(3-hydroxybutyrate) as sole substrate

Growth of and hydrogen production by wild-type (WT) Rhodovulum sulfidophilum were compared with those by one of its mutants lacking the poly(3-hydroxybutyrate) (PHB) biosynthesis ability (PNM2). During phototrophic growth under aerobic conditions with fixed illumination, changes in the extinction coefficient and PHB content of WT and PNM2 cells revealed interference of light penetration by PHB. WT cells synthesized PHB at an early stage of the cultivation. PHB degradation after exhaustion of acetate during the cultivation of WT resulted in a decrease of the extinction coefficient. The hydrogen production rate under anaerobic conditions with fixed illumination was examined in WT and PNM2 cell suspensions at different densities. The hydrogen production rate was determined not by the light penetration but by the kinds of hydrogen donors and the density of suspension. The highest value of the rate of hydrogen production from PHB, 33.0 ml/l/h, was improved compared with 26.6 ml/l/h, which was the highest value in hydrogen production from succinate. Under the same illumination, conversion to hydrogen from PHB is more efficient than that from succinate, which is one of the best substrates for hydrogen production. These results suggest that the hydrogen production rate can be maximized in the hydrogen production system based on PHB degradation, which is achieved in high-density suspension under external-substrate-depleted conditions after aerobic cultivation in the presence of an excess amount of acetate.

Novel transdermal drug delivery system with polyhydroxyalkanoate and starburst polyamidoamine dendrimer

In search of an efficient transdermal drug delivery system (TDDS), a polyhydroxyalkanoate (PHA)-based system with a polyamidoamine dendrimer was examined. Tamsulosin was used as the model drug. The dendrimer was found to act as the weak enhancer. By adding the dendrimer, the dendrimer-containing PHA matrix achieved the clinically required amount of tamsulosin permeating through the skin model. This is also the first report of the application of PHA and dendrimer to the TDDS.

Mechanism of enhancement effect of dendrimer on transdermal drug permeation through polyhydroxyalkanoate matrix

The possible application of polyhydroxyalkanoate (PHA) in transdermal drug delivery systems (TDDSs) for tamsulosin was previously reported. PHAs containing the drugs, ketoprofen, clonidine and tamsulosin showed good adhesiveness to the skin model used, that is, shed snake skin, and dispersed well all model drugs tested. The model drugs hardly permeated through snake skin in solution form. However, these drugs permeated well through snake skin from the PHA matrix. It was previously reported that the addition of a dendrimer, a polymeric permeation enhancer, is effective for the TDDS for tamsulosin to establish an effective clinical TDDS. The effect of dendrimer addition was examined in TDDSs for ketoprofen and clonidine. The dendrimer added did not show an enhancement effect on the TDDSs for the two drugs. To investigate the mechanism of the enhancement effect of a dendrimer on the tamsulosin TDDS, X-ray analyses were performed. With dendrimer addition, drug crystallization in PHA was promoted. The crystal in PHA had highly ordered and changed its space group. These findings are very important for exploiting high-performance PHA-based TDDSs.

Cloning and molecular analysis of poly(3-hydroxyalkanoate) biosynthesis genes in Pseudomonas aureofaciens

Pseudomonas aureofaciens grown on octanoate or gluconate synthesized medium-chain-length polyhydroxyalkanoates (mcl-PHAs). To clone the PHA synthase gene(s) (phaC), the genomic library of P. aureofaciens was constructed using a cosmid vector. The recombinant cosmids that clone phaC were detected by the complementation with a PHA-negative mutant, P. putida GPp104. The resulting recombinant cosmid, named pVK6, contained a 13-kbp DNA insert. Genetic analysis of the pha locus in pVK6 revealed the presence of six ORFs, genes encoding two PHA synthases, 1 and 2 (phaC1 and phaC2), PHA depolymerase (phaZ), two PHA granule-associated proteins (phaF and phaI), and an unknown protein (phaD). The heterologous expression of pha genes from P. aureofaciens was confirmed. P. putida GPp104 regained the ability to accumulate PHA on introduction of pVK6. Wild-type strains P. oleovorans and P. fluorescens, which were unable to accumulate PHA when grown on gluconate, acquired the ability to accumulate PHA from gluconate when they possessed pVK6.

Homology study of two polyhydroxyalkanoate (PHA) synthases from Pseudomonas aureofaciens

Recently, we have cloned and analyzed two polyhydroxyalkanoate (PHA) synthase genes (phaC1 and phaC2 in the pha cluster) from Pseudomonas aureofaciens. In this report, the deduced amino acid (AA) sequences of PHA synthase 1 and PHA synthase 2 from P. aureofaciens are compared with those from three other bacterial strains (Pseudomonas sp. 61-3, P. oleovorans and P. aeruginosa) containing the homologous pha cluster. The level of homology of either PHA synthase 1 or PHA synthase 2 was high with each enzyme from these three bacterial strains. Furthermore, multialignment of PHA synthase AA sequences implied that both enzymes of PHA synthase 1 and PHA synthase 2 were highly conserved in the four strains including P. aureofaciens.

The RING heterodimer BRCA1-BARD1 is a ubiquitin ligase inactivated by a breast cancer-derived mutation

BRCA1-BARD1 constitutes a heterodimeric RING finger complex associated through its N-terminal regions. Here we demonstrate that the BRCA1-BARD1 heterodimeric RING finger complex contains significant ubiquitin ligase activity that can be disrupted by a breast cancer-derived RING finger mutation in BRCA1. Whereas individually BRCA1 and BARD1 have very low ubiquitin ligase activities in vitro, BRCA1 combined with BARD1 exhibits dramatically higher activity. Bacterially purified RING finger domains comprising residues 1-304 of BRCA1 and residues 25-189 of BARD1 are capable of polymerizing ubiquitin. The steady-state level of transfected BRCA1 in vivo was increased by co-transfection of BARD1, and reciprocally that of transfected BARD1 was increased by BRCA1 in a dose-dependent manner. The breast cancer-derived BARD1-interaction-deficient mutant, BRCA1(C61G), does not exhibit ubiquitin ligase activity in vitro. These results suggest that the BRCA1-BARD1 complex contains a ubiquitin ligase activity that is important in prevention of breast and ovarian cancer development.

In vitro ubiquitination of cyclin D1 by ROC1-CUL1 and ROC1-CUL3

Overexpression of cyclin D1 has been implicated in a variety of tumors, such as breast cancers, gastrointestinal cancers and lymphomas. Both gene amplification and protein degradation mediated by ubiquitin (Ub)-dependent proteolysis regulate the abundance of cyclin D1. Here we report that ROC1 interacted with all three D type cyclins in vivo but did not bind to other cyclins tested. The ROC1-CUL1 and ROC1-CUL3, but not ROC1-CUL2, -CUL3 and -CUL4, immunocomplexes promoted polyubiquitination of bacterially purified cyclin D1 in vitro. RING finger mutations of ROC1 eliminated the Ub ligase activity toward cyclin D1. In all cases the ubiquitination of cyclin D1 was accompanied by autoubiquitination of the cullins. The results suggest the involvement of ROC1-cullin ligases in cyclin D1 ubiquitination and a potential mechanism whereby the cullin subunit is ubiquitinated itself while ubiquitinating a substrate.

Repression of starch degradation under anaerobic conditions by irregularly high levels of ATP in Chlamydomonas sp. MGA161

It is generally known that in green algal species the acceleration of starch degradation upon transition from aerobic to anaerobic conditions is a result of the Pasteur effect in glycolysis. However, the acceleration of starch degradation did not occur in cells of Chlamydomonas sp. MGA161. In MGA161 cells, the anaerobic ATP level, which decreased to about half of the aerobic ATP level in cells of Chlamydomonas reinhardtii after fermentation for 2 h, was kept higher than its aerobic ATP level. Gramicidin D, a monovalent cation ionophore, markedly decreased the anaerobic and aerobic ATP levels due to the increase in ATP demand, accompanied by the acceleration of starch degradation in MGA161 cells. Although the anaerobic ATP level of C. reinhardtii cells was partially decreased by gramicidin D, starch degradation did not accelerate markedly when compared with the result in MGA161 cells. Therefore, starch was degraded at nearly the maximum rate in C. reinhardtii cells under anaerobic conditions; in contrast, the high level of ATP in MGA161 cells repressed starch degradation even under anaerobic conditions, resulting in the absence of the Pasteur effect.

[Informed consent for the use of the remaining portion of laboratory specimens for education, research, and quality control of laboratory tests]

The remaining portion of a laboratory specimen is usually used for education, research, and quality control of laboratory tests in hospitals, but informed consent has not been obtained because of the high volume of patients who undergo laboratory tests. However, patients must be informed in some manner. Therefore, we decided to inform patients that any remaining specimen would be used for various purposes by placing such a notice on walls in the central clinical laboratory and hospital lobby. We then obtained a signature on a dissent document, instead of a consent document, from any patient who dissented from such use. This indirect process for obtaining informed consent was approved by the ethics committee of Osaka University Medical School. The number of dissent documents sent in to the director was 54 of about 400,000 patients who underwent laboratory tests over the last 3 years, and there was no complaint against this "informed consent process".