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1.
The cytochrome b 6 f complex of oxygenic photosynthesis produces substantial levels of reactive oxygen species (ROS). It has been observed that the ROS production rate by b 6 f is 10–20 fold higher than that observed for the analogous respiratory cytochrome bc1 complex. The types of ROS produced (O2??, 1O2, and, possibly, H2O2) and the site(s) of ROS production within the b 6 f complex have been the subject of some debate. Proposed sources of ROS have included the heme b p , PQ p ?? (possible sources for O2??), the Rieske iron–sulfur cluster (possible source of O2?? and/or 1O2), Chl a (possible source of 1O2), and heme c n (possible source of O2?? and/or H2O2). Our working hypothesis is that amino acid residues proximal to the ROS production sites will be more susceptible to oxidative modification than distant residues. In the current study, we have identified natively oxidized amino acid residues in the subunits of the spinach cytochrome b 6 f complex. The oxidized residues were identified by tandem mass spectrometry using the MassMatrix Program. Our results indicate that numerous residues, principally localized near p-side cofactors and Chl a, were oxidatively modified. We hypothesize that these sites are sources for ROS generation in the spinach cytochrome b 6 f complex.  相似文献   

2.
Bioenergetics of the aerobic bacteriochlorophyll a-containing (BCl a) bacterium (ABC bacterium) Roseinatronobacter thiooxidans is a combination of photosynthesis, oxygen respiration, and oxidation of sulfur compounds under alkaliphilic conditions. The photosynthetic activity of Rna. thiooxidans cells was established by the photoinhibition of cell respiration and reversible photobleaching discoloration of the BCl a of reaction centers (RC), connected by the chain of electron transfer with cytochrome c 551 oxidation. The species under study, like many purple bacteria and some of the known ABC bacteria, possesses a light-harvesting pigment-protein (LHI) complex with the average number of 30 molecules of antenna BCl a per one photosynthetic RC. Under microaerobic growth conditions, the cells contained bc 1 complex and two terminal oxidases: cbb 3-cytochrome oxidase and the alternative cytochrome oxidase of the a 3 type. Besides, Rna. thiooxidans was shown to have several different soluble low- and high-potential cytochromes c, probably associated with the ability of utilizing sulfur compounds as additional electron donors.  相似文献   

3.
L-Lactate cytochrome c oxidoreductase (flavocytochrome b 2, FC b 2) from the thermotolerant methylotrophic yeast Hansenula polymorpha (Pichia angusta) is, unlike the enzyme form baker’s yeast, a thermostable enzyme potentially important for bioanalytical technologies for highly selective assays of L-lactate in biological fluids and foods. This paper describes the construction of flavocytochrome b 2 producers with over-expression of the H. polymorpha CYB2 gene, encoding FC b 2. The HpCYB2 gene under the control of the strong H. polymorpha alcohol oxidase promoter in a plasmid for multicopy integration was transformed into the recipient strain H. polymorpha C-105 (grc1 catX), impaired in glucose repression and devoid of catalase activity. A method was developed for preliminary screening of the transformants with increased FC b 2 activity in permeabilized yeast cells. The optimal cultivation conditions providing for the maximal yield of the target enzyme were found. The constructed strain is a promising FC b 2 producer characterized by a sixfold increased (to 3 μmol min?1 mg?1 protein in cell-free extract) activity of the enzyme.  相似文献   

4.
Quantitative analysis was performed for the first time for the interaction of Escherichia coli RecA, which plays the central role in homologous recombination, and ssDNA varying in length and structure. DNA recognition was shown to depend on weak additive interactions between RecA monomers of the filament and various structural elements of DNA. Orthophosphate and dNMPs acted as minimal inhibitors of RecA filamentation on d(pN)20. A stepwise increase in homooligonucleotide length by one nucleotide (from 2 to 20 nt) monotonically increased the affinity approximately twofold (factor f) due to weak additive contacts of RecA with each internucleoside phosphate (f ≈ 1.56) and specific interactions with T and C (f ≈ 1.32). In the case of d(pA) n , the RecA filament showed virtually no interaction with bases and interacted more efficiently with internucleoside phosphates of the first than of the next helix turn (n < 10, f ≈ 2.1 vs. n > 10, f ≈ 1.3). The affinity of RecA for d(pN) n and various modified bases proved to depend on the base, the DNA structure, and the conformation of the sugar-phosphate backbone. The affinity considerably increased with bases containing exocyclic proton-accepting groups. Possible causes of the preferential binding of RecA with DNAs of a particular length and composition are considered. Mechanisms are proposed for ssDNA recognition by RecA and for homologous strand exchange.  相似文献   

5.
The finding of unique Chl d- and Chl f-containing cyanobacteria in the last decade was a discovery in the area of biology of oxygenic photosynthetic organisms. Chl b, Chl c, and Chl f are considered to be accessory pigments found in antennae systems of photosynthetic organisms. They absorb energy and transfer it to the photosynthetic reaction center (RC), but do not participate in electron transport by the photosynthetic electron transport chain. However, Chl d as well as Chl a can operate not only in the light-harvesting complex, but also in the photosynthetic RC. The long-wavelength (Qy) Chl d and Chl f absorption band is shifted to longer wavelength (to 750 nm) compared to Chl a, which suggests the possibility for oxygenic photosynthesis in this spectral range. Such expansion of the photosynthetically active light range is important for the survival of cyanobacteria when the intensity of light not exceeding 700 nm is attenuated due to absorption by Chl a and other pigments. At the same time, energy storage efficiency in photosystem 2 for cyanobacteria containing Chl d and Chl f is not lower than that of cyanobacteria containing Chl a. Despite great interest in these unique chlorophylls, many questions related to functioning of such pigments in primary photosynthetic processes are still not elucidated. This review describes the latest advances in the field of Chl d and Chl f research and their role in primary photosynthetic processes of cyanobacteria.  相似文献   

6.
Yeast flavocytochrome b 2 tranfers reducing equivalents from lactate to oxygen via cytochrome c and cytochrome c oxidase. The enzyme catalytic cycle includes FMN reduction by lactate and reoxidation by intramolecular electron transfer to heme b 2. Each subunit of the soluble tetrameric enzyme consists of an N terminal b 5-like heme-binding domain and a C terminal flavodehydrogenase. In the crystal structure, FMN and heme are face to face, and appear to be in a suitable orientation and at a suitable distance for exchanging electrons. But in one subunit out of two, the heme domain is disordered and invisible. This raises a central question: is this mobility required for interaction with the physiological acceptor cytochrome c, which only receives electrons from the heme and not from the FMN? The present review summarizes the results of the variety of methods used over the years that shed light on the interactions between the flavin and heme domains and between the enzyme and cytochrome c. The conclusion is that one should consider the interaction between the flavin and heme domains as a transient one, and that the cytochrome c and the flavin domain docking areas on the heme b 2 domain must overlap at least in part. The heme domain mobility is an essential component of the flavocytochrome b 2 functioning. In this respect, the enzyme bears similarity to a variety of redox enzyme systems, in particular those in which a cytochrome b 5-like domain is fused to proteins carrying other redox functions.  相似文献   

7.
On the basis of the winter bread wheat cultivar Obryi, two independent disomic addition lines BC12F with the chromosome of the E. sibiricus St genome are created. A practical algorithm for determining the probabilities of transmission of the odd chromosome separately through male and female gametes in selfpollination of hemizygous hybrids from the equation p2–(1 + f1f4) × p + f1 = 0 is proposed, where p is the probability of the formation of viable gametes with the considered chromosome and f1 and f4 are the empirical frequencies of the corresponding homozygotes with and without the trait. The probability of transmission of an alien univalent chromosome through pollen (p) is associated with the frequency of its transmission through the egg cell (p) in backcrosses and in self-pollination (1–f4) by the equation p = 1–f4/(1–p). The calculated empirically dependent estimates of the probabilities of transmission of the added chromosome through the egg cell p = 18.7% and through pollen p = 4.3% correspond to the empirical frequencies obtained for backcrosses. The coefficients of the gamete selection V = 0.748 and V = 0.172 are calculated, and the expected segregation for the alien trait controlled by a dominant gene located in the added chromosome is determined—with the trait: without the trait is 0.222: 0.778 in F2; 0.187: 0.813 in equational and 0.043: 0.957 in certational backcrosses.  相似文献   

8.
Kinetics of the reduction of the hemes in cytochrome c oxidase in the presence of high concentration of ruthenium(III)hexaammine chloride was examined using a stopped-flow spectrophotometer. Upon mixing of the oxidized enzyme with dithionite and Ru(NH3) 6 3+ , three well-resolved phases were observed: heme a reduction reaching completion within a few milliseconds is followed by two slow phases of heme a 3 reduction. The difference spectrum of heme a 3 reduction in the visible region is characterized by a maximum at ~612 nm, rather than at 603 nm as was believed earlier. It is shown that in the case of bovine heart cytochrome c oxidase containing a special cation-binding site in which reversible binding of calcium ion occurs, heme a 3 reduction is slowed down by low concentrations of Ca2+. The effect is absent in the case of the bacterial cytochrome oxidase in which the cation-binding site contains a tightly bound Ca2+ ion. The data corroborate the inhibition of the cytochrome oxidase enzymatic activity by Ca2+ ions discovered earlier and indicate that the cation affects intramolecular electron transfer.  相似文献   

9.
Salinity is a major problem of many agricultural lands that is usually associated with drought stress in arid and semi-arid regions. In this study we examine the role of salinity stress on temperature requirements of two herbaceous species and how it could be modeled to quantify alterations. We applied four non-linear regression models (segmented, beta, beta modified, and dent-like) to describe the germination rate–temperature relationships of Silybum marinum L. and Calendua officinalis L. over six constant temperatures exposed to different levels of salinity stress. Our results revealed that salinity could affect the cardinal temperatures in both plants and, as a result, it is not possible to suggest one model for all levels of salinity stress. The best model to fit data to predict cardinal temperatures of Silybum marianum and Calendula officinalis at the no-salinity condition were dent-like (AICc?=?4.03) and beta (AICc = ??2.30), respectively. Knowing the thermal time constant (fo) value helps us predict the minimum number of hours required for completion of germination at the optimal temperature. All models in this study were estimated higher fo due to higher salinity stress in both Silybum marianum and Calendula officinalis seeds. The highest estimated fo for Silybum marianum (91.5?±?59.6) and Calendula officinalis (178.9?±?26.5) was obtained from the results of germination rate prediction using a dent-like model at 200 mM salinity.  相似文献   

10.
Results are presented from the study of the electrical and optical characteristics of a transverse RF discharge in Xe/Cl2 mixtures at pressures of p≤400 Pa. The working mixture was excited by a modulated RF discharge (f=1.76 MHz) with a transverse electrode configuration (L≤17 cm). The emission spectrum in the spectral range of 210–600 nm and the waveforms of the discharge current, discharge voltage, and plasma emission intensity were investigated. The UV emission power from the discharge was studied as a function of the pressure and composition of a Xe/Cl2 mixture. It is shown that a discharge in a xenon-chlorine mixture acts as planar excimer-halogen lamp operating in the spectral range of 220–450 nm, which contains a system of overlapping XeCl(D, B-X; B, C-A) and Cl2(D′-A′) bands. Transverse RF discharges in Xe/Cl2 mixtures can be used to create a wideband lamp with two 50-cm2 planar apertures and the low circulation rate of the working mixture.  相似文献   

11.
Plants grown in phosphorus-deprived solutions often exhibit disruption of water transport due to reduction in root hydraulic conductivity (Lpr). To uncover the relationship between root Lpr and water permeability coefficient (Pf) of plasma membrane and the role of aquaporins, we evaluated Pf of plasma membrane and also PIP-type aquaporin gene expression in tobacco (Nicotiana tabacum L.) plant roots after seven days P-deprivation. The results showed significant reduction in sap flow rate (Jv) and osmotic root hydraulic conductivity (Lpr-o) in P-deprived roots. These effects were reversed 24 h after P-resupplying. Interestingly, the Pf of root protoplasts was 57% lower in P-deprived plants compared with P-sufficient ones. The expression of NtPIP1;1 and NtPIP2;1 aquaporins did not change significantly in P-deprived plants compared with P-sufficient ones, but the copy number of NtAQP1 increased significantly in P-deprived plants. P-deprivation did not change Lpr-o significantly in antisense NtAQP1 plants. Taken together, these findings suggest that P-deprivation may play an important role in modulation of root hydraulic conductivity by affecting Pf in transcellular pathway of water flow across roots and aquaporins. Finally, we concluded that dominant water transport pathway under P-deprivation was transcellular one.  相似文献   

12.
Fluorescence of the marine alga Thalassiosira weissflogii (Grunow) Fryxell et Hasle with open (F o ) and closed (F m ) reaction centers of photosystem 2 (PS 2) and its relative variable fluorescence (F v/F m ) were measured at various levels of inorganic nitrogen. A significant heterogeneity of the population in terms of these parameters was revealed. Some cells within the population were more sensitive to nitrogen deficiency, and their photosynthetic apparatus was disrupted to a greater extent. The cells within a population also differed in terms of their ability to recover after incubation at low nitrogen levels. Enhancement of nitrogen deficiency resulted in an increase in the variability of the F o and F v/F m values of the cells. Fluorescence variability decreased at a less pronounced deficiency. Fluorescence variability should be taken into consideration in the studies concerning responses of algae to changes in nutrient contents.  相似文献   

13.
Knoevenagel cyclocondensations of α-hydroxy naphthaldehyde with β-oxodithioesters and ketene dithioacetals yielded 2H-benzo[f]chromene-2-thiones and 2H-benzo[f]chromen-2-ones, respectively, in high yields. The newly synthesized compounds were evaluated for antifungal and antibacterial activities. Among them, compounds (2-furyl)(3-thioxo-3H-benzo[f]chromen-2-yl)methanone and phenyl(3-oxo-3H-benzo[f]chromen-2-yl)methanone exhibited excellent antifungal activity against tested fungi Curvularia lunata and Fusarium moniliforme. The highest antibacterial activity against the tested bacteria Escherichia coli and Staphylococcus aureus was observed for (4-chlorophenyl)(3-oxo-3H-benzo[f]chromen-2-yl)methanone. The results of antimicrobial screening demonstrate that (2-furyl)(3-thioxo-3H-benzo[f]chromen-2-yl)methanone, phenyl(3-oxo-3H-benzo[f]chromen-2-yl)methanone, and (4-chlorophenyl)(3-oxo-3H-benzo[f]chromen-2-yl)methanone are promising as antimicrobial drugs.  相似文献   

14.
15.
Defects in autophagy and the resulting deposition of protein aggregates have been implicated in aging and neurodegenerative diseases. While gene targeting in the mouse has facilitated the characterization of these processes in different types of neurons, potential roles of autophagy and accumulation of protein substrates in neuroepithelial cells have remained elusive. Here we report that Atg7f/f Tyr-Cre mice, in which autophagy-related 7 (Atg7) is conditionally deleted under the control of the tyrosinase promoter, are a model for accumulations of the autophagy adapter and substrate sequestosome-1/p62 in both neuronal and neuroepithelial cells. In the brain of Atg7f/f Tyr-Cre but not of fully autophagy competent control mice, p62 aggregates were present in sporadic neurons in the cortex and other brain regions as well in epithelial cells of the choroid plexus and the ependyma. Western blot analysis confirmed a dramatic increase of p62 abundance and formation of high-molecular weight species of p62 in the brain of Atg7f/f Tyr-Cre mice relative to Atg7f/f controls. Immuno-electron microscopy showed that p62 formed filamentous aggregates in neurons and ependymal cells. p62 aggregates were also highly abundant in the ciliary body in the eye. Atg7f/f Tyr-Cre mice reached an age of more than 2 years although neurological defects manifesting in abnormal hindlimb clasping reflexes were evident in old mice. These results show that p62 filaments form in response to impaired autophagy in vivo and suggest that Atg7f/f Tyr-Cre mice are a model useful to study the long-term effects of autophagy deficiency on the homeostasis of different neuroectoderm-derived cells.  相似文献   

16.
In a preceding paper (Bull. Math. Biophysics,27, 175–185) the distribution function ofφ=? 1-? 2,—the difference of excitations in the two mutually inhibiting centers, has been derived in terms of the distribution functionsf 1(? 1) andf 2(? 2) of the two excitations. In the present note some properties of the distribution functionf(?) in terms of the propertiesf 1(? 1) andf 2(? 2) are derived.  相似文献   

17.

Background

NGS data contains many machine-induced errors. The most advanced methods for the error correction heavily depend on the selection of solid k-mers. A solid k-mer is a k-mer frequently occurring in NGS reads. The other k-mers are called weak k-mers. A solid k-mer does not likely contain errors, while a weak k-mer most likely contains errors. An intensively investigated problem is to find a good frequency cutoff f0 to balance the numbers of solid and weak k-mers. Once the cutoff is determined, a more challenging but less-studied problem is to: (i) remove a small subset of solid k-mers that are likely to contain errors, and (ii) add a small subset of weak k-mers, that are likely to contain no errors, into the remaining set of solid k-mers. Identification of these two subsets of k-mers can improve the correction performance.

Results

We propose to use a Gamma distribution to model the frequencies of erroneous k-mers and a mixture of Gaussian distributions to model correct k-mers, and combine them to determine f0. To identify the two special subsets of k-mers, we use the z-score of k-mers which measures the number of standard deviations a k-mer’s frequency is from the mean. Then these statistically-solid k-mers are used to construct a Bloom filter for error correction. Our method is markedly superior to the state-of-art methods, tested on both real and synthetic NGS data sets.

Conclusion

The z-score is adequate to distinguish solid k-mers from weak k-mers, particularly useful for pinpointing out solid k-mers having very low frequency. Applying z-score on k-mer can markedly improve the error correction accuracy.
  相似文献   

18.
On-line control over the plasma density in tokamaks (especially, in long-term discharges) requires reliable measurements of the averaged plasma density. For this purpose, a new method of density measurements—a pulsed time-of-flight plasma refractometry—was developed and tested in the T-11M tokamak. This method allows one to determine the averaged density from the measured time delay of nanosecond microwave pulses propagating through the plasma. For an O-wave, the measured time delay is proportional to the line-averaged density and is independent of the density profile (f?f p ) τok o \(\tfrac{1}{{f^2 }}\mathop \smallint \limits_l \) N(x dx. A similar formula is valid for an X-wave: τX = ≈ k x \(\tfrac{{f^2 + f_c^2 }}{{(f^2 - f_c^2 )^2 }}\mathop \smallint \limits_l \) N(x)dx. Here, f is the frequency of the probing wave, f p is the plasma frequency, l= 4 a is the path length for two-pass probing in the equatorial plane, a is the plasma minor radius, k O and k X are numerical factors, f c is the electron-cyclotron frequency at the axis of the plasma column, and f p ?f c , f. Measurements of the time delay provide the same information as plasma interferometry, though they do no employ the effect of interference. When the conditions f p ?f c , f are not satisfied, the measured time delay depends on the shape of the density profile. In this case, in order to determine the average density regardless of the density profile, it is necessary to perform simultaneous measurements at several probing frequencies in order to determine the average density. In ITER (Bt ~ 5T), a spectral window between the lower and upper cutoff frequencies in the range of 50–100 GHz can be used for pulsed time-of-flight X-wave refractometry. This appreciably simplifies the diagnostics and eliminates the problem of the first mirror. In this paper, the first results obtained in the FTU tokamak with a prototype of the ITER pulsed time-of-flight refractometer are presented. The geometry and layout of experiments similar to the planned ITER experiments are described. The density measured by pulsed time-of-flight refractometry is shown to agree well with the results obtained in FTU with a two-frequency scanning IR interferometer. The results obtained are analyzed, and the future experiments are discussed.  相似文献   

19.
Cytochromes c were found in the cells of the bacterium Geobacter sulfurreducens AM-1 grown on acetate and methacrylate. The periplasmic extract of G. sulfurreducens AM-1 contained about 88% of the total content of cytochromes c of intact cells. The analysis of cytochromes c from the native cells of G. sulfurreducens AM-1, from the periplasmic extract and from the cells treated by an alkaline solution showed the presence of nine proteins containing heme c. The molecular masses of cytochromes c from G. sulfurreducens AM-1 were 12.5, 15.5, 25.7, 29.5, 34.7, 41.7, 50.1, 63.1, and 67.6 kDa; localization of each cytochrome c was determined. Three heme-containing proteins (15.5 kDa, 25.7 kDa, and 29.5 kDa with the most intensive staining) were present mainly in the periplasm of the bacterium. The other two (50.1 and 67.6 kDa) were supposedly localized in the cell membrane. Cytochromes c with the molecular masses of 12.5, 15.5, and 67.6 kDa are considered as possible components of the methacrylate redox system of G. sulfurreducens AM-1.  相似文献   

20.
Escherichia coli mutants deficient in glutathione (gshA), glutaredoxin (grxA), thioredoxin (trxA), and thioredoxin reductase (trxB) synthesis were studied with respect to their resistance to far-UV (UV254) exposure. The trxA, trxB, and grxA mutants subjected to a short-term UV exposure were found to be more resistant to UV irradiation than the parent cells. Under the same conditions, the trxA and trxB mutants demonstrated a high level of induction of the sulA gene, a component of the SOS regulon. The mutagenic effect of long-term UV exposure of all the mutants with redox deficiencies was more pronounced than in the case of the parent strain, and the trxA and trxB mutants were found to be the least viable microorganisms. Pretreatment of the cells with low concentrations of the thiol-oxidizing agent diamide enhanced the sulA gene expression; however, high concentrations of diamide inhibited sulA expression. The data obtained indicate that the thiol redox systems of E. coli are involved in its response to far-UV irradiation.  相似文献   

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