Ring-like nucleoids and DNA repair through error-free nonhomologous end joining in Deinococcus radiodurans.
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DNA Repair↗
Biomedical subjects
Eyal Shimoni
Publications and source records attributed to Eyal Shimoni.
Three-dimensional organization of higher-plant chloroplast thylakoid membranes revealed by electron tomography.
The light-harvesting and energy-transducing functions of the chloroplast are performed within an intricate lamellar system of membranes, called thylakoid membranes, which are differentiated into granum and stroma lamellar domains. Using dual-axis electron microscope tomography, we determined the three-dimensional organization of the chloroplast thylakoid membranes within cryo-immobilized, freeze-substituted lettuce (Lactuca sativa) leaves. We found that the grana are built of repeating units that consist of paired layers formed by bifurcations of stroma lamellar sheets, which fuse within the granum body. These units are rotated relative to each other around the axis of the granum cylinder. One of the layers that makes up the pair bends upwards at its edge and fuses with the layer above it, whereas the other layer bends in the opposite direction and merges with the layer below. As a result, each unit in the granum is directly connected to its neighbors as well as to the surrounding stroma lamellae. This highly connected morphology has important consequences for the formation and function of the thylakoid membranes as well as for their stacking/unstacking response to variations in light conditions.
Chloroplasts↗
Stability and sensory shelf life of orange juice pasteurized by continuous ohmic heating.
Electrical heating of food products provides rapid and uniform heating, resulting in less thermal damage to the product. The objective of this research was to examine the effects of ohmic heating on the stability of orange juice with comparison to conventional pasteurization. During storage at 4 degrees C, degradation curves of ascorbic acid followed a linear decrease pattern in both ohmic-heated and conventionally pasteurized orange juices. For five representative flavor compounds (decanal, octana, limonene, pinene, and myrcene), higher concentrations were measured during storage in the ohmic-heated orange juice than in conventionally pasteurized juice. Although residual pectin esterase activity remained negligible in both types of juices, particle size was lower in the ohmic-heated orange juice. The sensory shelf life was determined by using the Weibull-Hazard method. Although both thermal treatments prevented the growth of microorganisms for 105 days, the sensory shelf life of ohmic-treated orange juice was >100 days and was almost 2 times longer than that of conventionally pasteurized juice.
Ascorbic Acid↗
Effect of ultrahigh-temperature continuous ohmic heating treatment on fresh orange juice.
The scope of this study is the effect of ohmic heating thermal treatment on liquid fruit juice made of oranges. Effects of ohmic heating on the quality of orange juice were examined and compared to those of heat pasteurization at 90 degrees C for 50 s. Orange juice was treated at temperatures of 90, 120, and 150 degrees C for 1.13, 0.85, and 0.68 s in an ohmic heating system. Microbial counts showed complete inactivation of bacteria, yeast, and mold during ohmic and conventional treatments. The ohmic heating treatment reduced pectin esterase activity by 98%. The reduction in vitamin C was 15%. Ohmic-heated orange juice maintained higher amounts of the five representative flavor compounds than did heat-pasteurized juice. Sensory evaluation tests showed no difference between fresh and ohmic-heated orange juice. Thus, high-temperature ohmic-heating treatment can be effectively used to pasteurize fresh orange juice with minimal sensory deterioration.
Ascorbic Acid↗
Adhesion of Vibrio cholerae to granular starches.
Cholera is a severe diarrheal disease caused by specific serogroups of Vibrio cholerae that are pathogenic to humans. Cholera can become epidemic and deadly without adequate medical care. Appropriate rehydration therapy can reduce the mortality rate from as much as 50% of the affected individuals to <1%. Thus, oral rehydration therapy (ORT) is an important measure in the treatment of this disease. To further reduce the symptoms associated with cholera, improvements in oral rehydration solution (ORS) by starch incorporation were suggested. Here, we report that V. cholerae adheres to starch granules incorporated in ORS. Adhesion of 98% of the cells was observed within 2 min when cornstarch granules were used. Other starches showed varied adhesion rates, indicating that starch source and composition play an important role in the interaction of V. cholerae and starch granules. Sugars metabolized by V. cholerae showed a repressive effect on the adhesion process. The possible mechanisms involved are discussed. Comparing V. cholerae adhesion with the adhesion of other pathogens suggests the involvement of starch degradation capabilities. This adhesion to granular starch can be used to improve ORT.
Animals↗
Nucleoid restructuring in stationary-state bacteria.
The textbook view of the bacterial cytoplasm as an unstructured environment has been overturned recently by studies that highlighted the extent to which non-random organization and coherent motion of intracellular components are central for bacterial life-sustaining activities. Because such a dynamic order critically depends on continuous consumption of energy, it cannot be perpetuated in starved, and hence energy-depleted, stationary-state bacteria. Here, we show that, at the onset of the stationary state, bacterial chromatin undergoes a massive reorganization into ordered toroidal structures through a process that is dictated by the intrinsic properties of DNA and by the ubiquitous starvation-induced DNA-binding protein Dps. As starvation proceeds, the toroidal morphology acts as a structural template that promotes the formation of DNA-Dps crystalline assemblies through epitaxial growth. Within the resulting condensed assemblies, DNA is effectively protected by means of structural sequestration. We thus conclude that the transition from bacterial active growth to stationary phase entails a co-ordinated process, in which the energy-dependent dynamic order of the chromatin is sequentially substituted with an equilibrium crystalline order.
DNA, Bacterial↗
Structure of the DNA-SspC complex: implications for DNA packaging, protection, and repair in bacterial spores.
Bacterial spores have long been recognized as the sturdiest known life forms on earth, revealing extraordinary resistance to a broad range of environmental assaults. A family of highly conserved spore-specific DNA-binding proteins, termed alpha/beta-type small, acid-soluble spore proteins (SASP), plays a major role in mediating spore resistance. The mechanism by which these proteins exert their protective activity remains poorly understood, in part due to the lack of structural data on the DNA-SASP complex. By using cryoelectron microscopy, we have determined the structure of the helical complex formed between DNA and SspC, a characteristic member of the alpha/beta-type SASP family. The protein is found to fully coat the DNA, forming distinct protruding domains, and to modify DNA structure such that it adopts a 3.2-nm pitch. The protruding SspC motifs allow for interdigitation of adjacent DNA-SspC filaments into a tightly packed assembly of nucleoprotein helices. By effectively sequestering DNA molecules, this dense assembly of filaments is proposed to enhance and complement DNA protection obtained by DNA saturation with the alpha/beta-type SASP.
Bacillus subtilis↗
Biotransformations of propenylbenzenes by an Arthrobacter sp. and its t-anethole blocked mutants.
Propenylbenzenes are often used as starting materials in the chemical synthesis of aroma compounds and fine chemicals. In the present study, we demonstrate the ability of an Arthrobacter sp. to transform various structures of propenylbenzenes derived from essential oils to flavor, fragrance, and fine chemicals. Arthrobacter strain TA13 and its t-anethole blocked mutants (incapable of growing on t-anethole) converted isoeugenol to vanillin and vanillic acid; and safrole to hydroxychavicol. High conversion efficiencies were achieved in the biotransformations of isosafrole to piperonylic acid, and eugenol to a mixture of ferulic acid and vanillic acid. In addition, anisic acid was produced in high yields from t-anethole, anisyl alcohol, or anisaldehyde. The accumulation of the corresponding aromatic acids from the tested propenylbenzenes is due to the lack of m-demethylase activity in strain TA13 that prevents further cleavage of the benzene ring. Interestingly, in the transformation of eugenol (a 2-propenylbenzene) the side chain was initially oxidized to the corresponding cinamic acid derivative (ferulic acid) while the 1-propenylbenzenes gave substituted benzoic acids, suggesting two different chain shortening mechanisms.
Allylbenzene Derivatives↗
Thermal stability of genistein and daidzein and its effect on their antioxidant activity.
Soy isoflavones, present in many processed soy foods, are known for their phytoestrogenic and antioxidant activities. The aim of this work was to study the kinetics of genistein and daidzein degradation at elevated temperatures and to follow changes in their antioxidant activity. Daidzein and genistein in model solutions (pH 7 and 9) were thermally treated at 120 degrees C or incubated at 70, 80, and 90 degrees C. Isoflavone degradation was observed at all temperatures, with apparent first-order kinetics at 70-90 degrees C, and E(a) = 8.4 and 11.6 kcal/mol at pH 9, respectively. Microcalorimetric stability tests showed a similar pattern of degradation, however, with higher E(a) (genistein, 73.7 kcal/mol; daidzein, 34.1 kcal/mol) that may be attributed to the anaerobic conditions. The antioxidant activity of incubated isoflavone solutions, followed by the ABTS test, decreased rapidly at pH 9 for genistein, whereas only moderate reduction was observed for daidzein (pH 7 and 9) or genistein at pH 7. This may indicate different degradation mechanisms for genistein and daidzein.
Antioxidants↗
Stability of isoflavones in soy milk stored at elevated and ambient temperatures.
Soy isoflavones are widely recognized for their potential health benefits. The increased use of traditional and new food products calls for the assessment of their stability during processing and storage. The present study examines the stability of genistein and daidzein derivatives in soy milk. Soy milk was stored at ambient and elevated temperatures, and the change in isoflavone concentration was monitored with time. Genistin loss in time showed typical first-order kinetics, with rate constants ranging from 0.437-3.871 to 61-109 days(-1) in the temperature ranges of 15-37 and 70-90 degrees C, respectively. The temperature dependence of genistin loss followed the Arrhenius relation with activation energies of 7.2 kcal/mol at ambient temperatures and 17.6 kcal/mol at elevated temperatures. At early stages of soy milk storage at 80 and 90 degrees C, the 6' '-O-acetyldaidzin concentration increased, followed by a slow decrease. The results obtained in this study can serve as a basis for estimating the shelf life of soy milk as related to its genistin content.
Beverages↗
Comparison of the physicochemical properties and pasting characteristics of flour and starch from red and white sweet potato cultivars.
This research characterized flour and raw starches isolated from red and white sweet potato cultivars. Their composition, determined by proximate analysis, is typical of sweet potato cultivars. These cultivars have high amylose content (32-34%) and exhibit a Ca-type X-ray diffraction pattern. Similar gelatinization characteristics were detected for both starches with onset temperature of 67 degrees C and enthalpy of 10.5-11.0 J/g. Starches of both red and white cultivars had well-correlated (r (2) = 0.982) and high solubilization and swelling temperatures, starting at 80 degrees C. Pasting properties of the white cultivar exhibit lower tendency for retrogradation. Water and oil absorption capacities were low for both red and white flours. When parboiled, both cultivars showed improved water absorption capacity and decreased least gelation concentration. It is concluded that the white cultivar should be preferred when low retrogradation tendency is required.
Adsorption↗
Ringlike structure of the Deinococcus radiodurans genome: a key to radioresistance?
The bacterium Deinococcus radiodurans survives ionizing irradiation and other DNA-damaging assaults at doses that are lethal to all other organisms. How D. radiodurans accurately reconstructs its genome from hundreds of radiation-generated fragments in the absence of an intact template is unknown. Here we show that the D. radiodurans genome assumes an unusual toroidal morphology that may contribute to its radioresistance. We propose that, because of restricted diffusion within the tightly packed and laterally ordered DNA toroids, radiation-generated free DNA ends are held together, which may facilitate template-independent yet error-free joining of DNA breaks.
Chromatin↗
Accumulation of endoplasmic membranes and novel membrane-bound ribosome-signal recognition particle receptor complexes in Escherichia coli.
In Escherichia coli, ribosomes must interact with translocons on the membrane for the proper integration of newly synthesized membrane proteins, cotranslationally. Previous in vivo studies indicated that unlike the E. coli signal recognition particle (SRP), the SRP receptor FtsY is required for membrane targeting of ribosomes. Accordingly, a putative SRP-independent, FtsY-mediated ribosomal targeting pathway has been suggested (Herskovits, A.A., E.S. Bochkareva, and E. Bibi. 2000. Mol. Microbiol. 38:927-939). However, the nature of the early contact of ribosomes with the membrane, and the involvement of FtsY in this interaction are unknown. Here we show that in cells depleted of the SRP protein, Ffh or the translocon component SecE, the ribosomal targeting pathway is blocked downstream and unprecedented, membrane-bound FtsY-ribosomal complexes are captured. Concurrently, under these conditions, novel, ribosome-loaded intracellular membrane structures are formed. We propose that in the absence of a functional SRP or translocon, ribosomes remain jammed at their primary membrane docking site, whereas FtsY-dependent ribosomal targeting to the membrane continues. The accumulation of FtsY-ribosome complexes induces the formation of intracellular membranes needed for their quantitative accommodation. Our results with E. coli, in conjunction with recent observations made with the yeast Saccharomyces cerevisiae, raise the possibility that the SRP receptor-mediated formation of intracellular membrane networks is governed by evolutionarily conserved principles.
Bacterial Proteins↗
The trans-anethole degradation pathway in an Arthrobacter sp.
A bacterial strain (TA13) capable of utilizing t-anethole as the sole carbon source was isolated from soil. The strain was identified as Arthrobacter aurescens based on its 16 S rRNA gene sequence. Key steps of the degradation pathway of t-anethole were identified by the use of t-anethole-blocked mutants and specific inducible enzymatic activities. In addition to t-anethole, strain TA13 is capable of utilizing anisic acid, anisaldehyde, and anisic alcohol as the sole carbon source. t-Anethole-blocked mutants were obtained following mutagenesis and penicillin enrichment. Some of these blocked mutants, accumulated in the presence of t-anethole quantitative amounts of t-anethole-diol, anisic acid, and 4,6-dicarboxy-2-pyrone and traces of anisic alcohol and anisaldehyde. Enzymatic activities induced by t-anethole included: 4-methoxybenzoate O-demethylase, p-hydroxybenzoate 3-hydroxylase, and protocatechuate-4,5-dioxygenase. These findings indicate that t-anethole is metabolized to protocatechuic acid through t-anethole-diol, anisaldehyde, anisic acid, and p-hydroxybenzoic acid. The protocatechuic acid is then cleaved by protocatechuate-4,5-dioxygenase to yield 2-hydroxy-4-carboxy muconate-semialdehyde. Results from inducible uptake ability and enzymatic assays indicate that at least three regulatory units are involved in the t-anethole degradation pathway. These findings provide new routes for environmental friendly production processes of valuable aromatic chemicals via bioconversion of phenylpropenoids.
Allylbenzene Derivatives↗
Stress, order and survival.
Much of the sophisticated chemistry of life is accomplished by multicomponent complexes, which act as molecular machines. Intrinsic to their accuracy and efficiency is the energy that is supplied by hydrolysis of nucleoside triphosphates. Conditions that deplete energy sources should therefore cause decay and death. But studies on organisms that are exposed to prolonged stress indicate that this fate could be circumvented through the formation of highly ordered intracellular assemblies. In these thermodynamically stable structures, vital components are protected by a physical sequestration that is independent of energy consumption.
Adaptation, Biological↗
Detection of Alternaria fungal contamination in cereal grains by a polymerase chain reaction-based assay.
Alternaria sp. are important fungal contaminants of grain products; they secrete four structural classes of compounds that are toxic or carcinogenic to plants and animals and cause considerable economic losses to growers and the food-processing industry. Alternaria toxins have been detected by high-performance liquid chromatography (HPLC), enzyme-linked immunosorbent assay, and other techniques. Here, we report the development of a polymerase chain reaction (PCR)-based method for the detection of Alternaria DNA. PCR primers were designed to anneal to the ITS1 and ITS2 regions of the 5.8S rDNA gene of Alternaria alternata or Alternaria solani but not to other microbial or plant DNA. We compared the sensitivity of PCR in detecting Alternaria DNA, that of the HPLC method in detecting Alternaria alternariol and alternariol methyl ether toxins, and that of the morphological examination of mycelia and conidia in experimentally infested corn samples. The sensitivity of toxin detection for HPLC was above the level of contamination in a set of commercially obtained grain samples, resulting in negative scores for all samples, while the PCR-based method and mold growth plating followed by morphological identification of Alternaria gave parallel, positive results for 8 of 10 samples. The PCR assay required just 8 h, enabling the rapid and simultaneous testing of many samples at a low cost. PCR-based evidence for the presence of Alternaria DNA followed by positive assay results for Alternaria toxins would support the rejection of a shipment of grain.
Alternaria↗
Small angle X-ray scattering of resistant starch type III.
Starch fraction, which is resistant to enzymatic digestion, is produced during retrogradation. This fraction, termed resistant starch type III (RSIII), has health benefits such as pre-biotic effects, improving lipid and cholesterol metabolism, and reducing the risk of colon cancer. The work presented in this paper is aimed at investigating the colloidal structure of native high amylose corn starch (HACS) and the RSIII polymorphs produced from it using small angle X-ray scattering. Experimental scattering curves were fitted with appropriate theoretical models such as the "modified lamellar model". Our results show that retrogradation at low temperature leads to formation of polymorph B with crystallinity much lower than that of the granular form, but the lamellas are arranged in long-range periodicity. Conversely, retrogradation at high temperature leads to formation of polymorphs A and V with no defined periodicity. The degree of crystallinity is very low, and the system is better described as a dilute particulate system.
Amylose↗
Utilization of amylose-lipid complexes as molecular nanocapsules for conjugated linoleic Acid.
Amylose-conjugated linoleic acid (CLA) complexes were produced by water/dimethyl sulfoxide (DMSO) and KOH/HCl complexation methods. The formation of amylose V form was confirmed by X-ray diffraction (XRD), and complexes formed at 30, 60, and 90 degrees C exhibit melting temperatures exceeding 88 degrees C. Atomic force microscopy (AFM) images showed distinct difference in complex organization, with complexes formed in water/DMSO showing spherical shape with typical diameter of 150 nm. Complexes formed by KOH/HCl showed elongated structure with typical width of 43-160 nm. Water/DMSO complexes exhibit superior protection to CLA against oxidation. All complexes showed high retention of CLA in simulated stomach conditions, and the digestion of complexes by amylases results in high hydrolysis and CLA release by pancreatin and alpha-amylase. Only moderate release was detected following hydrolysis by amyloglucosidase and beta-amylase. It is therefore suggested that amylose-CLA complexes can serve as molecular nanocapsules for protection and delivery of CLA.
Amylases↗