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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
2.
V. Grant 《Plant Systematics and Evolution》2001,230(1-2):89-96
This paper deals with the use of cladistic methods and cladograms in phylogeny reconstruction in plant groups containing
numerous taxa. How accurate are the cladograms as to details? Accuracy tests at the level of details require an independently
known phylogeny, which excludes most plant groups, but such tests can be carried out in domesticated and experimental plant
groups which have documented pedigrees. Four such tests are known and are presented here: a new case in Gilia and three previously published cases in Avena, Hordeum, and Helianthus. The four cases include domesticated and experimental plants, use of morphological and molecular evidence, and presence of
dichotomous as well as reticulate phylogenies. The cladograms of the four plant groups all differ in significant details from
the known pedigrees. These results are discussed in relation to problems of interpretation of cladograms.
Received March 21, 2000 Accepted August 16, 2001 相似文献
3.
Genes for the biosynthesis of spinosyns: applications for yield improvement in Saccharopolyspora spinosa 总被引:2,自引:0,他引:2
K Madduri C Waldron P Matsushima M C Broughton K Crawford D J Merlo R H Baltz 《Journal of industrial microbiology & biotechnology》2001,27(6):399-402
Spinosyns A and D are the active ingredients in an insect control agent produced by fermentation of Saccharopolyspora spinosa. Spinosyns are macrolides with a 21-carbon, tetracyclic lactone backbone to which the deoxysugars forosamine and tri-O-methylrhamnose are attached. The spinosyn biosynthesis genes, except for the rhamnose genes, are located in a cluster that
spans 74 kb of the S. spinosa genome. DNA sequence analysis, targeted gene disruptions and bioconversion studies identified five large genes encoding type
I polyketide synthase subunits, and 14 genes involved in sugar biosynthesis, sugar attachment to the polyketide or cross-bridging
of the polyketide. Four rhamnose biosynthetic genes, two of which are also necessary for forosamine biosynthesis, are located
outside the spinosyn gene cluster. Duplication of the spinosyn genes linked to the polyketide synthase genes stimulated the
final step in the biosynthesis — the conversion of the forosamine-less pseudoaglycones to endproducts. Duplication of genes
involved in the early steps of deoxysugar biosynthesis increased spinosyn yield significantly. Journal of Industrial Microbiology & Biotechnology (2001) 27, 399–402.
Received 31 May 2001/ Accepted in revised form 09 July 2001 相似文献
4.
Bidens cordylocarpa is a high polyploid species restricted in distribution to stream sides in the mountains of Jalisco, Mexico. The morphologically
enigmatic species was originally described as a member of the genus Coreopsis, but later transferred to Bidens, largely because the involucral bracts appear most similar to Bidens. Characters of the cypselae, often useful in generic placement, are of no value for this species because the fruits have
features not detected in either Bidens or Coreopsis. Sequences from the internal transcribed spacer region of nuclear ribosomal DNA (ITS) were used to assess the relationships
of Bidens cordylocarpa. The molecular phylogeny places B. cordylocarpa in a strongly supported clade of Mexican and South American Bidens, and provides more definitive evidence of relationships than morphology, chromosome number, or secondary chemistry. Molecular,
morphological, and chromosomal data suggest that B. cordylocarpa is an ancient polyploid, perhaps the remnant of a polyploid complex.
Received August 28, 2000 Accepted February 11, 2001 相似文献
5.
Gregory L. Dilworth 《Archives of biochemistry and biophysics》1982,219(1):30-38
The nicotinic acid hydroxylase from Clostridium barkeri is a selenoenzyme, as evidenced by the copurification of selenium with enzyme activity. This conclusion is supported by data showing a 23-fold increase in nicotinic acid hydroxylase activity when C. barkeri was cultured in media supplemented with selenium. A labile, selenium-containing compound was released from the native protein by treatment with either chaotropic agents and heat or by heating alone. A stable selenium compound was formed when the enzyme was alkylated prior to denaturation. This compound had the same chromatographic properties as dialykyl selenide in a number of systems. The formation of dialkyl selenide upon alkylation is not consistent with the selenium moiety being selenocysteine. Thus, nicotinic acid hydroxylase represents a new type of selenoenzyme. 相似文献
6.
《Journal of molecular biology》2021,433(19):167156
Na+/H+ antiporters comprise a super-family (CPA) of membrane proteins that are found in all kingdoms of life and are essential in cellular homeostasis of pH, Na+ and volume. Their activity is strictly dependent on pH, a property that underpins their role in pH homeostasis. While several human homologues have long been drug targets, NhaA of Escherichia coli has become the paradigm for this class of secondary active transporters as NhaA crystal structure provided insight into the architecture of this molecular machine. However, the mechanism of the strict pH dependence of NhaA is missing. Here, as a follow up of a recent evolutionary analysis that identified a ‘CPA motif’, we rationally designed three E. coli NhaA mutants: D133S, I134T, and the double mutant D133S-I134T. Exploring growth phenotype, transport activity and Li+-binding of the mutants, we revealed that Asp133 does not participate directly in proton binding, nor does it directly dictate the pH-dependent transport of NhaA. Strikingly, the variant I134T lost some of the pH control, and the D133S-Il134T double mutant retained Li+ binding in a pH independent fashion. Concurrent to loss of pH control, these mutants bound Li+ more strongly than the WT. Both positions are in close vicinity to the ion-binding site of the antiporter, attributing the results to electrostatic interaction between these residues and Asp164 of the ion-binding site. This is consistent with pH sensing resulting from direct coupling between cation binding and deprotonation in Asp164, which applies also to other CPA antiporters that are involved in human diseases. 相似文献
7.
Ting‐Hang Liu Chia‐Lin Chyan Feng‐Yin Li Ying‐Jie Chen Jason T. C. Tzen 《Biotechnology progress》2011,27(6):1760-1767
It has been demonstrated that caleosin alone is sufficient to stabilize artificial oil bodies. A series of recombinant caleosins, mutated with 3, 5, 8, 11, 13, 15, and 17 extra Lys residues and over‐expressed in Escherichia coli, were used as carrier proteins to render biotin as a hapten on the surface of artificial oil bodies for antibody production. Biotinylation levels of the recombinant caleosins were step‐wisely elevated as the number of extra Lys residues increased, and the biotinylated Lys residues were identified by mass spectrometric analysis. Polyclonal antibodies against biotin were successfully generated in rats injected with artificial oil bodies constituted with each of the biotinylated caleosins. Moreover, those generated via the biotinylated caleosins with eight or more extra Lys residues no longer recognized caleosin. It appears that engineered Lys‐rich caleosins are suitable carrier proteins for the production of antibodies against small molecules. © 2011 American Institute of Chemical Engineers Biotechnol. Prog., 2011 相似文献
8.
How do elevated CO2 and O3 affect the interception and utilization of radiation by a soybean canopy?
ORLA DERMODY STEPHEN P. LONG†§ KELLY McCONNAUGHAY‡ EVAN H. DeLUCIA †§ 《Global Change Biology》2008,14(3):556-564
Net productivity of vegetation is determined by the product of the efficiencies with which it intercepts light (?i) and converts that intercepted energy into biomass (?c). Elevated carbon dioxide (CO2) increases photosynthesis and leaf area index (LAI) of soybeans and thus may increase ?i and ?c; elevated O3 may have the opposite effect. Knowing if elevated CO2 and O3 differentially affect physiological more than structural components of the ecosystem may reveal how these elements of global change will ultimately alter productivity. The effects of elevated CO2 and O3 on an intact soybean ecosystem were examined with Soybean Free Air Concentration Enrichment (SoyFACE) technology where large field plots (20‐m diameter) were exposed to elevated CO2 (~550 μmol mol?1) and elevated O3 (1.2 × ambient) in a factorial design. Aboveground biomass, LAI and light interception were measured during the growing seasons of 2002, 2003 and 2004 to calculate ?i and ?c. A 15% increase in yield (averaged over 3 years) under elevated CO2 was caused primarily by a 12% stimulation in ?c , as ?i increased by only 3%. Though accelerated canopy senescence under elevated O3 caused a 3% decrease in ?i, the primary effect of O3 on biomass was through an 11% reduction in ?c. When CO2 and O3 were elevated in combination, CO2 partially reduced the negative effects of elevated O3. Knowing that changes in productivity in elevated CO2 and O3 were influenced strongly by the efficiency of conversion of light energy into energy in plant biomass will aid in optimizing soybean yields in the future. Future modeling efforts that rely on ?c for calculating regional and global plant productivity will need to accommodate the effects of global change on this important ecosystem attribute. 相似文献
9.
Formation of a Tree having a Low Lignin Content 总被引:2,自引:0,他引:2
Received 30 September 2001/ Accepted in revised form 26 October 2001 相似文献
10.
《Molecular & cellular proteomics : MCP》2022,21(12):100438
Human pancreatic stellate cells (HPSCs) are an essential stromal component and mediators of pancreatic ductal adenocarcinoma (PDAC) progression. Small extracellular vesicles (sEVs) are membrane-enclosed nanoparticles involved in cell-to-cell communications and are released from stromal cells within PDAC. A detailed comparison of sEVs from normal pancreatic stellate cells (HPaStec) and from PDAC-associated stellate cells (HPSCs) remains a gap in our current knowledge regarding stellate cells and PDAC. We hypothesized there would be differences in sEVs secretion and protein expression that might contribute to PDAC biology. To test this hypothesis, we isolated sEVs using ultracentrifugation followed by characterization by electron microscopy and Nanoparticle Tracking Analysis. We report here our initial observations. First, HPSC cells derived from PDAC tumors secrete a higher volume of sEVs when compared to normal pancreatic stellate cells (HPaStec). Although our data revealed that both normal and tumor-derived sEVs demonstrated no significant biological effect on cancer cells, we observed efficient uptake of sEVs by both normal and cancer epithelial cells. Additionally, intact membrane-associated proteins on sEVs were essential for efficient uptake. We then compared sEV proteins isolated from HPSCs and HPaStecs cells using liquid chromatography–tandem mass spectrometry. Most of the 1481 protein groups identified were shared with the exosome database, ExoCarta. Eighty-seven protein groups were differentially expressed (selected by 2-fold difference and adjusted p value ≤0.05) between HPSC and HPaStec sEVs. Of note, HPSC sEVs contained dramatically more CSE1L (chromosome segregation 1–like protein), a described marker of poor prognosis in patients with pancreatic cancer. Based on our results, we have demonstrated unique populations of sEVs originating from stromal cells with PDAC and suggest that these are significant to cancer biology. Further studies should be undertaken to gain a deeper understanding that could drive novel therapy. 相似文献