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1.
《Journal of molecular biology》2021,433(15):167097
DNA glycosylases remove damaged or modified nucleobases by cleaving the N-glycosyl bond and the correct nucleotide is restored through subsequent base excision repair. In addition to excising threatening lesions, DNA glycosylases contribute to epigenetic regulation by mediating DNA demethylation and perform other important functions. However, the catalytic mechanism remains poorly defined for many glycosylases, including MBD4 (methyl-CpG binding domain IV), a member of the helix-hairpin-helix (HhH) superfamily. MBD4 excises thymine from G·T mispairs, suppressing mutations caused by deamination of 5-methylcytosine, and it removes uracil and modified uracils (e.g., 5-hydroxymethyluracil) mispaired with guanine. To investigate the mechanism of MBD4 we solved high-resolution structures of enzyme-DNA complexes at three stages of catalysis. Using a non-cleavable substrate analog, 2′-deoxy-pseudouridine, we determined the first structure of an enzyme-substrate complex for wild-type MBD4, which confirms interactions that mediate lesion recognition and suggests that a catalytic Asp, highly conserved in HhH enzymes, binds the putative nucleophilic water molecule and stabilizes the transition state. Observation that mutating the Asp (to Gly) reduces activity by 2700-fold indicates an important role in catalysis, but probably not one as the nucleophile in a double-displacement reaction, as previously suggested. Consistent with direct-displacement hydrolysis, a structure of the enzyme-product complex indicates a reaction leading to inversion of configuration. A structure with DNA containing 1-azadeoxyribose models a potential oxacarbenium-ion intermediate and suggests the Asp could facilitate migration of the electrophile towards the nucleophilic water. Finally, the structures provide detailed snapshots of the HhH motif, informing how these ubiquitous metal-binding elements mediate DNA binding. 相似文献
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3.
Regional differences in the carbon isotopic compositions of teak from two monsoonal regimes of India
Inter and intra-annual carbon isotope compositions (δ13C) of several annual growth rings of teak trees from two monsoonal regimes from India were studied and compared with the corresponding oxygen isotopic (δ18O) variations. In teak from both the regimes, amplitudes of intra-annual δ13C were ∼2-3 times lower than that observed in δ18O. Seasonal cycle with lower δ13C values at the middle and higher at ring boundaries was observed for teak from central India, dominated by the southwest monsoon. Positive correlations of intra-annual δ13C values with the corresponding δ18O values of the same rings and with relative humidity (RH) of the concurrent period suggest a dominant role of RH in controlling δ13C values of teak from central India. Intra-annual δ13C variations of teak from southern India, receiving both the southwest and northeast monsoons, revealed an initial decreasing trend followed by an increasing trend before culminating in depleted 13C values at the end of the growing season. No correlation was observed between intra-annual δ13C and δ18O variations of teak trees from southern India. Regional differences in the climatology of δ13C of atmospheric CO2 or the lengths of growing season could be likely reasons for differing intra-annual δ13C variations of teak from the two climatic regimes. 相似文献
4.
Seed dispersal influences a wide range of ecological processes. However, measuring dispersal patterns, particularly long‐distance dispersal, has been a difficult task. Marking bird‐dispersed seeds with stable 15N isotopes has been shown to be a user‐friendly method to trace seed dispersal. In this study, we determined whether 15N urea solution could be used to enrich seeds of two common wind‐dispersed plants, Eupatorium glaucescens (Asteraceae) and Sericocarpus tortifolius (Asteraceae). We further tested if the water type (distilled versus tap) in 15N urea solutions influences the level and variability of enrichment of plant seeds, and if increasing spraying frequency per se increases enrichment. Because droughts may lower seed set or kill plants, we wanted to investigate if the additional use of an externally applied anti‐transpirant affects the intake of externally applied 15N into seeds. The results demonstrate that 15N enrichment of seeds can facilitate dispersal experiments with wind‐dispersed plants. The use of distilled water in 15N urea solutions did not increase 15N enrichment compared to tap water. Further, enrichment was more efficient at lower spray frequencies. Both the use of tap water and low frequencies could lower time, effort and project costs. The results suggest that species can be protected from drought using an anti‐transpirant without decreasing the incorporation of 15N into seeds. 相似文献
5.
C. T. DARIMONT P. C. PAQUET T. E. REIMCHEN 《Biological journal of the Linnean Society. Linnean Society of London》2007,90(1):125-137
Interindividual variation in niche presents a potentially central object on which natural selection can act. This may have important evolutionary implications because habitat use governs a suite of selective forces encountered by foragers. In a free-living native black-tailed deer, Odocoileus hemionus , population from coastal British Columbia, we used stable isotope analysis to identify individual variation in foraging niche and investigated its relationship to fitness. Using an intragenerational comparison of surviving and nonsurviving O. hemionus over 2 years of predation by wolves, Canis lupus, we detected resource-specific fitness. Individuals with isotopic signatures that suggested they foraged primarily in cedar ( Thuja plicata )-dominated and low-elevation hemlock ( Tsuga heterophylla )-dominated forest stands were more likely to be killed by C. lupus . High-quality forage in T. plicata stands, as indexed by protein content, may be involved in maintaining this foraging phenotype. Moreover, nonsurvivors diverged more than survivors from median isotopic signatures, suggesting selection against foraging specialization. Stable isotope analysis provides a novel opportunity to integrate ecological and selective landscapes in order to identify underlying ecological mechanisms of selection and provide insight into the maintenance of variability. © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 90 , 125–137. 相似文献
6.
A single locus, diallelic selection model with female and male viability differences is studied. If the variables are ratios of allele frequencies in each sex, a 2-dimensional difference equation describes the model. Because of the strong monotonicity of the resulting map, every initial genotypic structure converges to an equilibrium structure assuming that no equilibrium has eigenvalues on the unit circle.Partially supported by funds provided by a Science and Education Grant to the USDA-Forest Service, Southeastern Forest Experiment Station, Population Genetics of Forest Trees Research Unit, Raleigh, USASupported by a grant from the Max Kade Foundation, New York, USA 相似文献
7.
Water use efficiency and carbon isotope composition of plants in a cold desert environment 总被引:9,自引:0,他引:9
Summary The effects of the availabilities of water and nitrogen on water use efficiency (WUE) of plants were investigated in a sagebrush steppe. The four species studied wereArtemisia tridentata (shrub),Ceratoides lanata (suffrutescent shrub),Elymus lanceolatus (rhizomatous grass), andElymus elymoides (tussock grass). Water and nitrogen levels were manipulated in a two-by-two factorial design resulting in four treatments: control (no additions), added water, added nitrogen, and added water and nitrogen. One instantaneous and two long-term indicators of WUE were used to testa priori predictions of the ranking of WUE among treatments. The short-term indicator was the instantaneous ratio of assimilation to transpiration (A/E). The long-term measures were 1) the slope of the relationship between conductance to water vapor and maximum assimilation and 2) the carbon isotope composition (13C) of plant material. Additional water decreased WUE, whereas additional nitrogen increased WUE. For both A/E and 13C, the mean for added nitrogen alone was significantly greater than the mean for added water alone, and means for the control and added water and nitrogen fell in between. This ranking of WUE supported the hypothesis that both water and nitrogen limit plant gas exchange in this semiarid environment. The short- and long-term indicators were in agreement, providing evidence in support of theoretical models concerning the water cost of carbon assimilation. 相似文献
8.
G. Goldstein F. Rada L. Sternberg J. L. Burguera M. Burguera A. Orozco M. Montilla O. Zabala A. Azocar M. J. Canales A. Celis 《Oecologia》1989,78(2):176-183
Summary The gas exchange and water relations of the hemiparasite Pthirusa maritima and two its mangrove host species, Conocarpus erectus and Coccoloba uvifera, were studied in an intertidal zone of the Venezuelan coast. Carbon uptake and transpiration, leaf osmotic and total water potential, as well as nutrient content in the xylem sap and leaves of mistletoes and hosts were followed through the dry and wet season. In addition, carbon isotope ratios of leaf tissue were measured to further evaluate water use efficiency. Under similar light and humidity conditions, mistletoes had higher transpiration rates, lower leaf water potentials, and lower water use efficiencies than their hosts. Potassium content was much higher in mistletoes than in host leaves, but mineral nutrient content in the xylem sap of mistletoes was relatively low. The resistance of the liquid pathway from the soil to the leaf surface of mistletoes was larger than the total liquid flow resistance of host plants. Differences in the daily cycles of osmotic potential of the xylem sap also indicate the existence of a high resistance pathway along the vascular connection between the parasite pathway along the vascular connection between the parasite and its host. P. maritima mistletoes adjust to the different physiological characteristics of the host species which it parasitizes, thus ensuring an adequate water and carbon balance. 相似文献
9.
The cis/trans interconversion of Glt-Ala-Ala-Pro-Phe-4-nitroanilide and Glt-Ala-Gly-Pro-Phe-4-nitroanilide was studied both enzymatically and nonenzymatically by measuring kinetic β-deuterium isotope effects. The hydrogen atom at the α-carbon atom of the Xaa residue within the Xaa-Pro moiety was substituted by deuterium. In the nonenzymatic case the transition state of rotation is reflected by kH/kD > 1. When catalysed by 17 kDa PPIase the same bond rotation is characterized by kH/kD < 1. This suggests a covalent mechanism of catalysis which involves an approximately tetravalent carbon of the prolyl imidic bond for the transition state of reaction. 相似文献
10.
Summary We have isolated Saccharomyces cerevisiae mutants, smp, showing stable maintenance of plasmid pSRI, a Zygosaccharomyces rouxii plasmid. The smp mutants were recessive and were classified into at least three different complementation groups. The three mutants also showed increased stability of YRp plasmids and the mutations are additive for plasmid stability. One mutation, smp1, confers a respiration-deficient (rho
0) phenotype and several Rho– mutants independently isolated by ethidium bromide treatment of the same yeast strain also showed increased stabilities of pSR1 and YRp plasmids. The wild-type S. cerevisiae cells showed a strongly biased distribution of pSR1 molecules as well as YRp plasmids to the mother cells at mitosis, while the smpf mutant did not show this bias. Another mutation, smp3, at a locus linked to ade2 on chromosome XV, confers temperature-sensitive growth. The SMP3 gene encodes a 59.9 kDa hydrophobic protein and disruption of the gene is lethal. 相似文献