首页 | 本学科首页   官方微博 | 高级检索  
相似文献
 共查询到20条相似文献,搜索用时 15 毫秒
1.
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   

2.
RecA protein first forms filament on single-stranded (ss) DNA forming the first DNA-binding site for interaction with this ssDNA a formation of the second site for interaction with double-stranded DNA occurs in parallel. Then the formed nucleoprotein filament interacts with molecules of double-stranded (ds) DNA but can also recognize ssDNA. The formed complex realizes a search of homology and exchange of homologous strands. We have studied recently the mechanism of RecA filamentation on ssDNA. Here a study of interaction of different DNAs with the second site of RecA filament using a method of stepwise increase of the ligand complicity was performed. The second site under recognition interacts with every nucleotide units of DNA-ligand forming contact with both internucleotide phosphate groups and bases of DNA. Pyrimidinic d(pC)n [Russian character: see text d(pT)n oligonucleotides interact with the second site of the RecA filament more effectively than with d(pA)n oligonucleotides. This occurs due to a more effective interaction of the RecA filament with 5'-terminal unit of pyrimidinic DNAs and to a difference in specific conformational changes of nucleoprotein filaments in the complex with purinic and pyrimidinic DNAs. A comparison of thermodynamic characteristics of DNA recognition by the first and the second sites of DNA recognition is carried out. It was shown that at n >10 d(pC)n d(pN)n interact with the second site weaker, that with the first site. The complexation of the second site with d(pA)n at n >20 is more effective than with the first site. The difference in the affinity of d(pA)n to the fist and second sites is increased monotonically with the enhancement of their length. Possible mechanisms of RecA-dependent search of homology and strand exchange are discussed.  相似文献   

3.
Changes of 5S rDNA at the early stage of allopolyploidization were investigated in three synthetic allopolyploids: Aegilops sharonensis × Ae. umbellulata (2n = 28), Triticum urartu × Ae. tauschii (2n = 28), and T. dicoccoides × Ae. tauschii (2n = 42). Fluorescent in situ hybridization (FISH) revealed quantitative changes affecting separate loci of one of the parental genomes in S3 plants of each hybrid combination. Southern hybridization with genomic DNA of the allopolyploid T. urartu × Ae. tauschii (TMU38 × TQ27) revealed a lower intensity of signals from Ae. tauschii fragments compared with those derived from T. urartu. This confirmed the signal reduction revealed for chromosome 1D of this hybrid by FISH. Neither Southern hybridization nor PCR testing of 5–15 plants of the S2-S3 generations revealed an appearance of new 5S rDNA fragments or a complete disappearance of parental fragments from the allopolyploids under study. No changes were found by aligning nine 5S rDNA sequences of the allopolyploid TMU38 × TQ27 with corresponding sequences of the parental species. The similarity between one of the synthetic allopolyploids examined and a natural allopolyploid with the same genome composition points to an early formation of the 5S rDNA organization unique for each allopolyploid.  相似文献   

4.

Background

Deinococcus radiodurans R1 is one of the most radiation-resistant organisms known and is able to repair an unusually large amount of DNA damage without induced mutation. Single-stranded DNA-binding (SSB) protein is an essential protein in all organisms and is involved in DNA replication, recombination and repair. The published genomic sequence from Deinococcus radiodurans includes a putative single-stranded DNA-binding protein gene (ssb; DR0100) requiring a translational frameshift for synthesis of a complete SSB protein. The apparently tripartite gene has inspired considerable speculation in the literature about potentially novel frameshifting or RNA editing mechanisms. Immediately upstream of the ssb gene is another gene (DR0099) given an ssb-like annotation, but left unexplored.

Results

A segment of the Deinococcus radiodurans strain R1 genome encompassing the ssb gene has been re-sequenced, and two errors involving omitted guanine nucleotides have been documented. The corrected sequence incorporates both of the open reading frames designated DR0099 and DR0100 into one contiguous ssb open reading frame (ORF). The corrected gene requires no translational frameshifts and contains two predicted oligonucleotide/oligosaccharide-binding (OB) folds. The protein has been purified and its sequence is closely related to the Thermus thermophilus and Thermus aquaticus SSB proteins. Like the Thermus SSB proteins, the SSBDr functions as a homodimer. The Deinococcus radiodurans SSB homodimer stimulates Deinococcus radiodurans RecA protein and Escherichia coli RecA protein-promoted DNA three-strand exchange reactions with at least the same efficiency as the Escherichia coli SSB homotetramer.

Conclusions

The correct Deinococcus radiodurans ssb gene is a contiguous open reading frame that codes for the largest bacterial SSB monomer identified to date. The Deinococcus radiodurans SSB protein includes two OB folds per monomer and functions as a homodimer. The Deinococcus radiodurans SSB protein efficiently stimulates Deinococcus radiodurans RecA and also Escherichia coli RecA protein-promoted DNA strand exchange reactions. The identification and purification of Deinococcus radiodurans SSB protein not only allows for greater understanding of the SSB protein family but provides an essential yet previously missing player in the current efforts to understand the extraordinary DNA repair capacity of Deinococcus radiodurans.
  相似文献   

5.
6.
The molecular mechanisms of DNA recognition and modification by EcoRII DNA methyltransferase (M.EcoRII) were studied using 14-mer substrate analogs containing 2-aminopurine or 1′,2′-dideoxy-D-ribofuranose in the M.EcoRII recognition site. The efficiency of DNA binding and methylation depended on the position of a modified nucleoside residue in the recognition site. A structural model of M.EcoRII in complex with substrate DNA and the cofactor analog S-adenosyl-L-homocysteine (AdoHcy) was constructed using the available crystal structures of M.Hha and M.HaeIII and the recent Frankenstein’s monster approach. The amino acid residues interacting with DNA were predicted based on the model. In addition, theoretical and experimental findings made it possible to predict the groups of atoms of the heterocyclic bases of the M.EcoRII recognition site that are presumably involved in the interactions with the enzyme.  相似文献   

7.
The diversity of nitrogen-fixing microorganisms in the soil of an oligotrophic Sphagnum peat bog was studied by molecular cloning of fragments of the nifH gene encoding one of the main components of the nitrogenase complex. The fragments were amplified from the DNA isolated from the peat samples collected at the same site in January (library I) and November (library II), 2005. Analysis of the nifH sequence libraries revealed high diversity of diazotrophic bacteria in peat soil: the first library consisted of 237 clones and 55 unique sequence types, the second one included 171 clones and 52 sequence types. Comparison of the two clone libraries showed that the composition and population structure of the nitrogen-fixing community depended greatly on the sampling time; they shared only 11 phylotypes. The sequences of representatives of the class Alphaproteobacteria prevailed in both libraries (27% and 57% of clones in libraries I and II, respectively). Representatives of the classes Deltaproteobacteria and Chlorobea were minor components of library I (6% and 7% of clones, respectively), whereas they prevailed in library II (18% and 24% of clones, respectively). Members of the class Chloroflexi were present only in library I, while members of the classes Bacilli, Clostridia, and Methanomicrobia were present only in library II. Our studies demonstrated that, for complete evaluation of the diversity of natural nitrogen-fixing communities, nifH libraries should consist of at least 200–300 clones.  相似文献   

8.
A study is made of the structure of a relativistic current filament with the azimuthal magnetic field Bθ in the range 4πn e m e c2?B θ 2 n i m i c2, when the plasma quasineutrality near the filament axis is violated and a narrow peak in electron density is formed there. The ion dynamics in a strong radial electric field of the filament on time scales of about several inverse ion plasma frequencies ω pi ?1 is investigated. The initial ion pressure prevents the ion plasma component from compression to infinitely high densities under the action of the electric field and leads to the formation of a dense hot plasma core near the axis of the Z-pinch on time scales of about a dozen ω pi ?1 . The compression of the ion component in the axial region gives rise to a collisionless “unloading” shock wave that propagates away from the axis and is accompanied by the vanishing of the radial ion velocity behind the shock front, the accumulation of positive charge near the axis, and the formation of a steady-state ion density profile. It is shown theoretically that ion-ion dissipation manifests itself as the destruction of the hot core of the formed Z-pinch on picosecond time scales. This may serve to explain the explosions of “hot points” in a current-carrying plasma.  相似文献   

9.
Genetic diversity and geographic distribution of taxon-specific RAPD markers was examined in ten local populations of the house mouse Mus musculus (n = 42). The house mice were generally characterized by moderate genetic variation: polymorphism P 99 = 60%, P 95 = 32.57%; heterozygosity H = 0.12; the observed allele number n a = 1.6; the effective allele number n e = 1.18; the within-population differentiation ?s = 0.388; and Shannon index I = 0.19. The degree of genetic isolation of individual local populations was greatly variable. The genetic subdivision index G st varied from 0.162 to 0.770 at the gene flow of Nm = 2.58?0.149, while the among-population distances D N varied from 0.026 to 0.178. The largest part of the genetic diversity was found among the populations (H T = 0.125), while the within-population diversity was twice lower (H S = 0.06). The samples examined were well discriminated relative to the sets of RAPD markers. The character distribution pattern provided conditional subdivision of the mice into the “western” and the “eastern” groups with the putative boarder along the Baikal Lake. The first group was characterized by the prevalence of the markers typical of M. m. musculus and M. m. domesticus. The second group was characterized by the prevalence of the markers typical of M. m. musculus, M. m. gansuensis, M. m. castaneus, M. m. domesticus, and M. m. wagneri. The genotype of the nominative subspecies M. m. musculus was background for all populations. In the populations examined some of earlier described subspecies-specific molecular markers were found at different frequencies, pointing to the involvement of several subspecies of M. musculus in the process of hybridization.  相似文献   

10.
A major quantitative trait locus (QTL) associated with resistance to Fusarium head blight (FHB) was identified on chromosome 3BS between simple sequence repeat (SSR) markers Xgwm389 and Xgwm493 in wheat “Ning 7840”, a derivative from “Sumai 3”. However, the marker density of SSR in the QTL region was much lower than that required for marker-assisted selection (MAS) and map-based cloning. The objective of this study was to exploit new markers to increase marker density in this QTL region by using single-strand conformational polymorphism (SSCP) markers developed from wheat-expressed sequence tags (ESTs) on 3BS bin 8-0.78-1.0. Sixty-nine out of 85 SSCP primer pairs amplified PCR (polymerase chain reaction) products from the genomic DNA of “Chinese Spring”. Thirty-four primer pairs amplified PCR products that could form clear ssDNA (single strand DNA) bands through denaturation treatment. Ten SSCP markers had polymorphisms between Ning 7840 and “Clark”. Five of the ten polymorphic SSCP markers were located on chromosome 3B by nullitetrasomic analysis. Three SSCP markers (Xsscp6, Xsscp20, and Xsscp21) were mapped into the region between Xgwm493 and Xgwm533 and possessed a higher coefficient of determination (R2) than Xgwm493 and Xgwm533. The SSCP markers, Xsscp6, Xsscp20, and Xsscp21, can be used for map-based cloning of the QTL and for marker-assisted selection in FHB resistance breeding.  相似文献   

11.
European pear exhibits RNase-based gametophytic self-incompatibility controlled by the polymorphic S-locus. S-allele diversity of cultivars has been extensively investigated; however, no mutant alleles conferring self-compatibility have been reported. In this study, two European pear cultivars, ‘Abugo’ and ‘Ceremeño’, were classified as self-compatible after fruit/seed setting and pollen tube growth examination. S-genotyping through S-PCR and sequencing identified a new S-RNase allele in the two cultivars, with identical deduced amino acid sequence as S 21 , but differing at the nucleotide level. Test-pollinations and analysis of descendants suggested that the new allele is a self-compatible pistil-mutated variant of S 21 , so it was named S 21 °. S-genotypes assigned to ‘Abugo’ and ‘Ceremeño’ were S 10 S 21 ° and S 21 °S 25 respectively, of which S 25 is a new functional S-allele of European pear. Reciprocal crosses between cultivars bearing S 21 and S 21 ° indicated that both alleles exhibit the same pollen function; however, cultivars bearing S 21 ° had impaired pistil-S function as they failed to reject either S 21 or S 21 ° pollen. RT-PCR analysis showed absence of S 21 °-RNase gene expression in styles of ‘Abugo’ and ‘Ceremeño’, suggesting a possible origin for S 21 ° pistil dysfunction. Two polymorphisms found within the S-RNase genomic region (a retrotransposon insertion within the intron of S 21 ° and indels at the 3′UTR) might explain the different pattern of expression between S 21 and S 21 °. Evaluation of cultivars with unknown S-genotype identified another cultivar ‘Azucar Verde’ bearing S 21 °, and pollen tube growth examination confirmed self-compatibility for this cultivar as well. This is the first report of a mutated S-allele conferring self-compatibility in European pear.  相似文献   

12.
Extensive research has found that nighttime transpiration (E n) is positively correlated to the vapour pressure deficit (VPD), that suggested E n was highest during the night under high temperatures and low humidity along with high soil water availability, typically for the riparian forest in the extreme arid region of China. This study used the heat ratio method to measure sap velocity (V s) for mature and saplings Populus euphratica Oliv., and then E n was conservatively calculated as total nocturnal sap flow (F s, the product of V s and sapwood area A s) between 01:00 to 06:00. A gas exchange system was used to measure the leaf transpiration rate (T r) and stomatal conductance (g s) of saplings. For mature trees, nighttime V s was extensive and logarithmic correlated to VPD (similar to daytime). For saplings, g s and T r was extensive in different months, and also a strong logarithmic relationship was found between V s and VPD for both daytime and nighttime periods. Both of stem sap flow and leaf gas exchange suggusted the occurrence of E n, whether mature or sapling trees. E n contribution to daily transpiration (E d) was high just as expected for P. euphratica, which was confirmed by proportional E n to E d (E n/E d) means taken in 2012 (24.99%) and 2013 (34.08%). Compared to mature trees, E n/E d of saplings in 2013 was lower with means of 12.06%, that supported further by the shorter duration times and less T r,n (16.64%) and g s,n (26.45%) of leaf, suggesting that E n magnitude is associated to individual the tree size, that effect to stored water of individual trees, although this hypothesis requires further research.  相似文献   

13.
The formation of a peaked bell-shaped profile of the electron density n e (r) in the T-11M tokamak (B t=1 T, R/a = 0.7/0.2 m, I p = 100 kA, t shot ≤ 300 ms, Li and C limiters) was observed in Li experiments carried out in the near-plateau collisionality regime (the collisionality parameter at one-half of the minor radius was v* ≥ 0.5) under the conditions of low hydrogen recycling and intense hydrogen influx from the plasma edge. It is well known that peaked n e (r) profiles are observed in collisionless regimes at v* values as low as 10?1–10?2 or in impurity-contaminated discharges, in which this effect can be attributed to the impurity accumulation on the plasma column axis. Moreover, a bell-shaped n e (r) profile in discharges with low n e can result from the ionization of hydrogen atoms at the column axis, where they arrive from the plasma edge due to cascade charge-exchange. In quasi-steady lithium discharges in T-11M, however, peaked n e (r) profiles were observed at a relatively high central electron density n e (0) and relatively high collision frequency, such that the influence of impurities on the n e (r) profile could be ignored (Z eff = 1.1±0.1). To explain this effect, one has to assume that the pinching of hydrogen ions in T-11M is anomalous. The lower estimate of the observed pinch velocity is 4 ± 1 m/s, which is three to five times higher than the velocity of the neoclassical (Ware) pinch, characteristic of these conditions. The work is devoted to the experimental study of this effect.  相似文献   

14.
No eukaryotic species has a system for homologous DNA recombination of the mitochondrial genome. We report on an integrative genetic system based on the pQ-SRUS construct that allows the expression of the RecA recombinase from Bacillus subtilis and its transportation to mitochondria of Yarrowia lipolytica. The targeting of recombinant RecA to mitochondria is provided by leader sequences (5'-UTR and 3'-UTR) derived from the SOD2 gene mRNA, which exhibit affinity to the outer mitochondrial membrane and provides cotranslational import of RecA to the inner space of mitochondria. The accumulation of RecA in mitochondria of the Y. lipolytica recombinant strain bearing the pQ-SRUS construct has been shown by immunoblotting of purified mitochondrial preparations.  相似文献   

15.
The operon for the Bacillus stearothermophilus SE-589 nickase-modification system (NM.BstSEI, recognition site 5′-GAGTC-3′) includes two DNA methyltransferase (M.) genes, bstSEIM1 and bstSEIM2. The gene encoding M2.BstSEI was cloned in pJW and expressed in Escherichia coli cells. M2.BstSEI was purified by chromatography and displayed maximal activity at 55° C and pH 7.5. The enzyme modified adenine in the nickase recognition site 5′-GAGTC-3′ and was specific for 5′-GASTC-3′ substrates. The kinetic parameters of the methylation reaction were determined. The catalytic constant was 2.2 min?1, and the Michaelis constant was 9.8 nM on T7 DNA and 5.8 μM on SAM.  相似文献   

16.
A plasmid carrying the Deinococcus radiodurans recX gene under the control of a lactose promoter decreases the Escherichia coli cell resistance to UV irradiation and γ irradiation and also influences the conjugational recombination process. The D. radiodurans RecX protein functions in the Escherichia coli cells similarly to the E. coli RecX protein. Isolated and purified D. radiodurans RecX and E. coli RecX proteins are able to replace each other interacting with the E. coli RecA and D. radiodurans RecA proteins in vitro. Data obtained demonstrated that regulatory interaction of RecA and RecX proteins preserves a high degree of conservatism despite all the differences in the recombination reparation system between E. coli and D. radiodurans.  相似文献   

17.
The total energies, growth patterns, equilibrium geometries, relative stabilities, hardnesses, intramolecular charge transfer, and magnetic moments of HoSi n (n?=?12–20) clusters have been reexamined theoretically using two different density functional schemes in combination with relativistic small-core Stuttgart effective core potentials (ECP28MWB) for the Ho atoms. The results show that when n?=?12–15, the most stable structures are predicted to be exohedral frameworks with a quartet ground state, but when n?=?16–20, they are predicted to be endohedral frameworks with a sextuplet ground state. These trend in stability across the clusters (gauged from their dissociation energies) was found to be approximately the same regardless of the DFT scheme used in the calculations, with HoSi13, HoSi16, HoSi18, and HoSi20 calculated to be more stable than the other clusters. The results obtained for cluster hardness indicated that doping the Ho atom into Si13 and Si16 leads to the most stable HoSi n clusters, while doping Ho into the other Si n clusters increases the photochemical sensitivity of the cluster. Analyses of intracluster charge transfer and magnetic moments revealed that charge always shifts from the Ho atom to the Si n cluster during the creation of exohedral HoSi n (n?=?12–15) structures. However, the direction of charge transfer is reversed during the creation of endohedral HoSi n (n?=?16–20) structures, which implies that Ho acts as an electron acceptor when it is encapsulated in the Si n cage. Furthermore, when the most stable exohedral HoSi n (n?=?12–15) structures are generated, the 4f electrons of Ho are virtually unchanged and barely participate in intracluster bonding. However, in the most stable endohedral HoSi n (n?=?16–20) frameworks, a 4f electron does participate in bonding. It does this by transferring to the 5d orbital, which hybridizes with the 6s and 6p orbitals and then interacts with Si valence sp orbitals. Meanwhile, the total magnetic moments of the HoSi n (n?=?16–20) clusters are considerably higher than those of HoSi n (n?=?12–15). Interestingly, the endohedral HoSi16 and HoSi20 clusters can be viewed as the most suitable building blocks for novel high-density magnetic storage nanomaterials and for novel optical and optoelectronic photosensitive nanomaterials, respectively.  相似文献   

18.
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   

19.
The first cytogenetic comparisons of five snapper species from Thailand were presented here. Renal cell samples were taken from blacktail snapper (Lutjanus fulvus), five lined snapper (L. quinquelineatus), dory snapper (L. fulviflamma), brownstripe red snapper (L. vitta), and mangrove red snapper (L. argentimaculatus). The mitotic chromosome preparation was prepared directly from kidney cells. Conventional staining and Ag-NOR banding techniques were applied to stain the chromosomes. The results exhibited that all five snapper species have the diploid chromosome numbers of 2n = 48 and the fundamental numbers (NF) of 48. The presences of large, medium, and small telocentric chromosomes were 22-24-2, 24-20-4, 36-10-2, 28-16-4 and 36-10-2, respectively. The Ag- NORs banding technique provides the pair of nucleolar organizer regions (NORs) at subcentromeric region of the long arm of the respective telocentric chromosome pairs 9, 1, 3, 4 and 9. Their karyotype formulas is as follows: L. fulvus (2n = 48): L 22 t + M 24 t + S 2 t , L. quinquelineatus (2n = 48): L 24 t + M 20 t + S 4 t , L. fulviflamma (2n = 48): Lt36 + Mt10 + St2, L. vitta (2n = 48): L 28 t + M 16 t + S 4 t , and L. argentimaculatus (2n = 48): L 36 t + M 10 t + S 2 t .  相似文献   

20.
Nonquasineutral electron current filaments with the azimuthal magnetic field are considered that arise due to the generation of electron vorticity in the initial (dissipative) stage of evolution of a current-carrying plasma, when the Hall number is small (σB/en e c ? 1) because of the low values of the plasma conductivity and magnetic field strength. Equilibrium filamentary structures with both zero and nonzero net currents are considered. Structures with a zero net current type form on time scales of t < t sk = (r 0ω pe /c)2 t st, where t sk is the skin time, t st is the typical time of electron-ion collisions, and r 0 is the radius of the filament. It is shown that, in nonquasineutral filaments in which the current is carried by electrons drifting in the crossed electric (E r ) and magnetic (B θ) fields, ultrarelativistic electron beams on the typical charge-separation scale r B = B/(4πen e ) (the so-called magnetic Debye radius) can be generated. It is found that, for comparable electron currents, the characteristic electron energy in filaments with a nonzero net current is significantly lower than that in zero-net-current filaments that form on typical time scales of t < t sk. This is because, in the latter type of filaments, the oppositely directed electron currents repel one another; as a result, both the density and velocity of electrons increase near the filament axis, where the velocities of relativistic electrons are maximum. Filaments with a zero net current can emit X rays with photon energies ? ω up to 10 MeV. The electron velocity distributions in filaments, the X-ray emission spectra, and the total X-ray yield per unit filament length are calculated as functions of the current and the electron number density in the filament. Analytical estimates of the characteristic lifetime of a radiating filament and the typical size of the radiating region as functions of the plasma density are obtained. The results of calculations are compared with the available experimental data.  相似文献   

设为首页 | 免责声明 | 关于勤云 | 加入收藏

Copyright©北京勤云科技发展有限公司  京ICP备09084417号