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1.
Kyung‐Hee Rhee Ki Seog Lee Eunice Eunkyung Kim Amit Priyadarshi Kwang Yeon Hwang 《Acta Crystallographica. Section F, Structural Biology Communications》2005,61(11):1017-1019
Fatty acid‐CoA racemase plays an important role in the β‐oxidation of branched‐chain fatty acids and fatty‐acid derivatives as it catalyzes the conversion of several (2R)‐branched‐chain fatty acid‐CoAs to their (2S)‐stereoisomers. Fatty acid‐CoA racemase from Mycobacterium tuberculosis H37Rv has been purified to homogeneity and crystallized by the hanging‐drop vapour‐diffusion method with polyethylene glycol 4000 as precipitant. The crystals belong to the trigonal space group P31 or P32, with unit‐cell parameters a = b = 109.56, c = 147.97 Å. The asymmetric unit contains six monomers, corresponding to a VM value of 2.15 Å3 Da−1. A complete native data set has been collected at 2.7 Å resolution using a synchrotron‐radiation source. 相似文献
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Y. Uemoto T. Abe N. Tameoka H. Hasebe K. Inoue H. Nakajima N. Shoji M. Kobayashi E. Kobayashi 《Animal genetics》2011,42(2):141-148
Fatty acid composition, especially oleic acid (C18:1), plays an important role in the eating quality of meat in Japanese Black cattle. Therefore, the objective of this study was to identify loci associated with C18:1 in the intramuscular fat of the trapezius muscles in Japanese Black cattle using the Illumina BovineSNP50 BeadChip whole genome single nucleotide polymorphism (SNP) assay. We also evaluated the relationship between C18:1 and three fatty acid synthesis genes, fatty acid synthase (FASN), stearoyl‐CoA desaturase and sterol regulatory element‐binding protein‐1. In this experiment, we applied a mixed model and Genomic Control approach using selective genotyping to perform a genome‐wide association study. A total of 160 animals (80 animals with higher values and 80 animals with lower values), selected from 3356 animals based on corrected phenotype, were genotyped using the Illumina BovineSNP50 BeadChip and three fatty acid synthesis genes, and the quality of these SNPs was assessed. In this study, a total of 38 955 SNPs, which included SNPs in the three fatty acid synthesis genes, were used, and the estimated inflation factor was 1.06. In the studied population, a total of 32 SNPs, including the FASN gene, had significant effects, and in particular 30 SNPs of all significant SNPs were located between 49 and 55 Mbp on chromosome 19. This study is one of the first genome‐wide association studies for fatty acid composition in a cattle population using the recently released Illumina BovineSNP50 BeadChip. 相似文献
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Hui Li Adam Thrash Juliet D. Tang Linlin He Jianbing Yan Marilyn L. Warburton 《The Plant journal : for cell and molecular biology》2019,98(5):853-863
Maize (Zea mays mays) oil is a rich source of polyunsaturated fatty acids (FAs) and energy, making it a valuable resource for human food, animal feed, and bio‐energy. Although this trait has been studied via conventional genome‐wide association study (GWAS), the single nucleotide polymorphism (SNP)‐trait associations generated by GWAS may miss the underlying associations when traits are based on many genes, each with small effects that can be overshadowed by genetic background and environmental variation. Detecting these SNPs statistically is also limited by the levels set for false discovery rate. A complementary pathways analysis that emphasizes the cumulative aspects of SNP‐trait associations, rather than just the significance of single SNPs, was performed to understand the balance of lipid metabolism, conversion, and catabolism in this study. This pathway analysis indicated that acyl‐lipid pathways, including biosynthesis of wax esters, sphingolipids, phospholipids and flavonoids, along with FA and triacylglycerol (TAG) biosynthesis, were important for increasing oil and FA content. The allelic variation found among the genes involved in many degradation pathways, and many biosynthesis pathways leading from FAs and carbon partitioning pathways, was critical for determining final FA content, changing FA ratios and, ultimately, to final oil content. The pathways and pathway networks identified in this study, and especially the acyl‐lipid associated pathways identified beyond what had been found with GWAS alone, provide a real opportunity to precisely and efficiently manipulate high‐oil maize genetic improvement. 相似文献
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Yingzhi Xu Fei Sun 《Acta Crystallographica. Section F, Structural Biology Communications》2013,69(5):515-519
3‐Hydroxyacyl‐CoA dehydrogenase (HAD; EC 1.1.1.35) is the enzyme that catalyzes the third step in fatty‐acid β‐oxidation, oxidizing the hydroxyl group of 3‐hydroxyacyl‐CoA to a keto group. The 3‐hydroxyacyl‐CoA dehydrogenase from Caenorhabditis elegans (cHAD) was cloned, overexpressed in Escherichia coli and purified to homogeneity for crystallography. Initial crystals were obtained by the hanging‐drop vapour‐diffusion method. Optimization of the precipitant concentration and the pH yielded two types of well diffracting crystals with parallelepiped and cuboid shapes, respectively. Complete diffraction data sets were collected and processed from both crystal types. Preliminary crystallographic analysis indicated that the parallelepiped‐shaped crystal belonged to space group P1, while the cuboid‐shaped crystal belonged to space group P212121. Analyses of computed Matthews coefficient and self‐rotation functions suggested that there are two cHAD molecules in one asymmetric unit in both crystals, forming identical dimers but packing in distinct manners. 相似文献
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Peroxisomal fission is induced during appressorium formation and is required for full virulence of the rice blast fungus 
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下载免费PDF全文 Xiao‐Lin Chen Mi Shen Jun Yang Yunfei Xing Deng Chen Zhigang Li Wensheng Zhao Yan Zhang 《Molecular Plant Pathology》2017,18(2):222-237
Peroxisomes are involved in various metabolic processes and are important for virulence in different pathogenic fungi. How peroxisomes rapidly emerge in the appressorium during fungal infection is poorly understood. Here, we describe a gene, PEF1, which can regulate peroxisome formation in the appressorium by controlling peroxisomal fission, and is required for plant infection in the rice blast fungus Magnaporthe oryzae. Targeted deletion of PEF1 resulted in a reduction in virulence and a delay in penetration and invasive growth in host cells. PEF1 was particularly expressed during appressorial development, and its encoding protein was co‐localized with peroxisomes during appressorial development. Compared with the massive vesicle‐shaped peroxisomes formed in the wild‐type appressorium, the Δpef1 mutant could only form stringy linked immature peroxisomes, suggesting that PEF1 was involved in peroxisomal fission during appressorium formation. We also found that the Δpef1 mutant could not utilize fatty acids efficiently, which can improve significantly the expression level of PEF1 and induce peroxisomal fission. As expected, the Δpef1 mutant showed reduced intracellular production of reactive oxygen species (ROS) during appressorium formation and induced ROS accumulation in host cells during infection. Taken together, PEF1‐mediated peroxisomal fission is important for fungal infection by controlling the number of peroxisomes in the appressorium. 相似文献
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A genome‐wide association study (GWAS) was conducted on 15 milk production traits in Chinese Holstein. The experimental population consisted of 445 cattle, each genotyped by the GGP (GeneSeek genomic profiling)‐BovineLD V3 SNP chip, which had 26 151 public SNPs in its manifest file. After data cleaning, 20 326 SNPs were retained for the GWAS. The phenotypes were estimated breeding values of traits, provided by a public dairy herd improvement program center that had been collected once a month for 3 years. Two statistical models, a fixed‐effect linear regression model and a mixed‐effect linear model, were used to estimate the association effects of SNPs on each of the phenotypes. Genome‐wide significant and suggestive thresholds were set at 2.46E‐06 and 4.95E‐05 respectively. The two statistical models concurrently identified two genome‐wide significant (P < 0.05) SNPs on milk production traits in this Chinese Holstein population. The positional candidate genes, which were the ones closest to these two identified SNPs, were EEF2K (eukaryotic elongation factor 2 kinase) and KLHL1 (kelch like family member 1). These two genes could serve as new candidate genes for milk yield and lactation persistence, yet their roles need to be verified in further function studies. 相似文献
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David S. Cissel Dale L. Birkle Diana L. Whipkey J. David Blaha Geoffrey M. Graeber Philip E. Keeting 《Journal of cellular biochemistry》1995,57(4):599-609
The effects of treatment with the osteotropic steroids 1,25-dihydroxyvitamin D3 (1,25(OH)2D3), 17β-estradiol, or dexamethasone on [1-14C]arachidonic acid (AA) uptake and distribution into glycerophospholipid classes by normal adult human osteoblast-like (hOB) cells were investigated. Total uptake of [1-14C]AA was decreased in cells treated with dexamethasone when assayed after a 24-, 48-, or 96-h exposure to the hormone. Specific radiolabel incorporation into phosphatidylcholine was reduced by a 48-h treatment with dexamethasone with a concurrent increase in the radiolabeling of phosphatidylethanolamine. However, these changes were transient, and by 96 h of dexamethasone treatment the distribution of the radiolabeled fatty acid had reequilibrated to resemble the pattern found for vehicle treated samples. Total uptake of [1-14C]AA was diminished by 96-h treatment with 1,25(OH)2D3 (79 ± 3% of control, P < 0.01); at that time point, a significant decrease in the proportional radiolabeling of the phosphatidylinositol pool was identified (92 ± 2% of control, P < 0.05). The 1,25(OH)2D3-dependent decrease in total uptake and in phosphatidylinositol incorporation of [1-14C]AA were found to be hormone dose dependent. Treatment with 24,25(OH)2D3 was without effect on either total [1-14C]AA uptake or the specific [1-14C]AA radiolabeling of the phosphatidylinositol pool. 1,25(OH)2D3 treatment decreased hOB cell uptake of [1-14C]oleic acid and decreased its proportional incorporation into the phosphatidylinositol pool. Gas chromatographic analyses revealed no 1,25(OH)2D3-dependent effects on total phosphatidylinositol lipid mass or on the mole percent of arachidonic acid within the phosphatidylinositol pool, leaving the mechanism of the effects of the secosteroid on hOB cell AA metabolism unexplained. 17β-Estradiol had no effects on the parameters of AA metabolism measured. As a consequence of their modulation of arachidonic acid uptake and its distribution into hOB cellular phospholipids, steroids might alter the biological effects of other hormones whose actions include the stimulated production of bioactive AA metabolites, such as prostaglandins or the various lipoxygenase products. 相似文献
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A. Arakawa N. Okumura M. Taniguchi T. Hayashi K. Hirose K. Fukawa T. Ito T. Matsumoto H. Uenishi S. Mikawa 《Animal genetics》2015,46(5):571-575
Because of increasing litter size in Western pig breeds, additional teats are desirable to increase the capacity for nursing offspring. We applied genome‐wide SNP markers to detect QTL regions that affect teat number in a Duroc population. We phenotyped 1024 animals for total teat number. A total of 36 588 SNPs on autosomes were used in the analysis. The estimated heritability for teat number was 0.34 ± 0.05 on the basis of a genomic relationship matrix constructed from all SNP markers. Using a BayesC method, we identified a total of 18 QTL regions that affected teat number in Duroc pigs; 9 of the 18 regions were newly detected. 相似文献
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Martin Fisher Svetlana E. Sedelnikova Wayne Martindale Neil C. Thomas J. William Simon Antoni R. Slabas John B. Rafferty 《Acta Crystallographica. Section D, Structural Biology》2000,56(1):86-88
The NADP‐dependent β‐keto acyl‐carrier protein reductase (BKR) from Brassica napus has been crystallized by the hanging‐drop vapour‐diffusion method using polyethylene glycol of average molecular weight 1500 as the precipitant. The crystals belong to the hexagonal space group P6422, with unit‐cell parameters a = b = 129.9, c = 93.1 Å, α = β = 90, γ = 120°. Calculated values for Vm, the use of rotation and translation functions and consideration of the packing suggest that the asymmetric unit contains a monomer. The crystals diffract to beyond 2.8 Å resolution and are more amenable to X‐ray diffraction analysis than those reported previously for the Escherichia coli enzyme. The structure determination of B. napus BKR will provide important insights into the catalytic mechanism of the enzyme and into the evolution of the fatty‐acid elongation cycle by comparisons with the other oxidoreductase of the pathway, enoyl acyl‐carrier protein reductase (ENR). 相似文献
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Alexander Feiner Nicholi Pitra Paul Matthews Klaus Pillen Ludger A. Wessjohann David Riewe 《Plant, cell & environment》2021,44(1):323-338
Downy mildew in hop (Humulus lupulus L.) is caused by Pseudoperonospora humuli and generates significant losses in quality and yield. To identify the biochemical processes that confer natural downy mildew resistance (DMR), a metabolome‐ and genome‐wide association study was performed. Inoculation of a high density genotyped F1 hop population (n = 192) with the obligate biotrophic oomycete P. humuli led to variation in both the levels of thousands of specialized metabolites and DMR. We observed that metabolites of almost all major phytochemical classes were induced 48 hr after inoculation. But only a small number of metabolites were found to be correlated with DMR and these were enriched with phenylpropanoids. These metabolites were also correlated with DMR when measured from the non‐infected control set. A genome‐wide association study revealed co‐localization of the major DMR loci and the phenylpropanoid pathway markers indicating that the major contribution to resistance is mediated by these metabolites in a heritable manner. The application of three putative prophylactic phenylpropanoids led to a reduced degree of leaf infection in susceptible genotypes, confirming their protective activity either directly or as precursors of active compounds. 相似文献
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《Peptide Science》2017,108(3)
The conformational characteristics of protected homo‐oligomeric Boc‐[β3(R)Val]n‐OMe, n = 1, 2, 3, 4, 6, 9, and 12 have been investigated in organic solvents using nuclear magnetic resonance (NMR), Fourier transform infrared (FTIR) absorption spectroscopy and circular dichroism (CD) methods. The detailed 1H NMR analysis of Boc‐[β3(R)Val]12‐OMe reveals that the peptide aggregates extensively in CDCl3, but is disaggregated in 20%, (v/v) dimethyl sulfoxide (DMSO) in CDCl3 and in CD3OH. Limited assignment of the N‐terminus NH groups, together with solvent dependence of NH chemical shifts and temperature coefficients provides evidence for 14‐helix conformation in the 12‐residue peptide. FTIR analysis in CHCl3 establishes that the onset of folding and aggregation, as evidenced by NH stretching bands at 3375 cm−1 (intramolecular) and 3285 cm−1 (intermolecular), begins at the level of the tetrapeptide. The observed CD bands, 214 nm (negative) and 198 nm (positive), support 14‐helix formation in the 9 and 12 residue sequences. The folding and aggregation tendencies of homo‐oligomeric α‐, β‐, and γ‐ residues is compared in the model peptides Boc‐[ωVal]n‐NHMe, ω = α, β, and γ and n = 1, 2, and 3. Analysis of the FTIR spectra in CHCl3, establish that the tendency to aggregate at the di and tripeptide level follows the order β > α∼γ, while the tendency to fold follows the order γ > β > α. 相似文献
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Hong Jiao Ingrid Dahlman Per Eriksson Juha Kere Peter Arner 《Obesity (Silver Spring, Md.)》2005,13(10):1645-1650
The β2-adrenoceptor gene may be of particular importance for human obesity because catecholamines have a central role in energy expenditure both as neurotransmitters and hormones. The gene is highly polymorphic, and individual polymorphisms have previously been examined for their relationship to obesity, but results are conflicting. We performed a haplotype analysis of the β2-adrenoceptor gene in 1354 women and 421 men, all healthy and at least second generation Scandinavian and with a large interindividual variation in body fat mass. We found three common haplotypes. One of these haplotypes, identified as T, A, C, C at nucleotide positions −47, 46, 79, and 491, was in its homozygote form more common among lean (18%) than obese (13%) women (p = 0.0028), but there was no association with obesity in men (p = 0.47). Women who were homozygous for this haplotype had lower BMI (p = 0.009) and percentage body fat (p = 0.005) in comparison with those having other haplotypes or being heterozygous for TACC. The data suggest an important role of the β2-adrenoceptor gene in obesity because a common haplotype has recessive protective effects against excess body fat, at least in women. 相似文献
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Brunilda Balliu Jeanine J. Houwing‐Duistermaat Stefan Bhringer 《Biometrical journal. Biometrische Zeitschrift》2019,61(3):747-768
Marginal tests based on individual SNPs are routinely used in genetic association studies. Studies have shown that haplotype‐based methods may provide more power in disease mapping than methods based on single markers when, for example, multiple disease‐susceptibility variants occur within the same gene. A limitation of haplotype‐based methods is that the number of parameters increases exponentially with the number of SNPs, inducing a commensurate increase in the degrees of freedom and weakening the power to detect associations. To address this limitation, we introduce a hierarchical linkage disequilibrium model for disease mapping, based on a reparametrization of the multinomial haplotype distribution, where every parameter corresponds to the cumulant of each possible subset of a set of loci. This hierarchy present in the parameters enables us to employ flexible testing strategies over a range of parameter sets: from standard single SNP analyses through the full haplotype distribution tests, reducing degrees of freedom and increasing the power to detect associations. We show via extensive simulations that our approach maintains the type I error at nominal level and has increased power under many realistic scenarios, as compared to single SNP and standard haplotype‐based studies. To evaluate the performance of our proposed methodology in real data, we analyze genome‐wide data from the Wellcome Trust Case‐Control Consortium. 相似文献
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《Acta Crystallographica. Section F, Structural Biology Communications》2018,74(10):617-624
Malate dehydrogenase (MDH), a carbohydrate and energy metabolism enzyme in eukaryotes, catalyzes the interconversion of malate to oxaloacetate (OAA) in conjunction with that of nicotinamide adenine dinucleotide (NAD+) to NADH. Three isozymes of MDH have been reported in Saccharomyces cerevisiae: MDH1, MDH2 and MDH3. MDH1 is a mitochondrial enzyme and a member of the tricarboxylic acid cycle, whereas MDH2 is a cytosolic enzyme that functions in the glyoxylate cycle. MDH3 is a glyoxysomal enzyme that is involved in the reoxidation of NADH, which is produced during fatty‐acid β‐oxidation. The affinity of MDH3 for OAA is lower than those of MDH1 and MDH2. Here, the crystal structures of yeast apo MDH3, the MDH3–NAD+ complex and the MDH3–NAD+–OAA ternary complex were determined. The structure of the ternary complex suggests that the active‐site loop is in the open conformation, differing from the closed conformations in mitochondrial and cytosolic malate dehydrogenases. 相似文献
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Mathew Littlejohn Talia Grala Kathryn Sanders Caroline Walker Garry Waghorn Kevin Macdonald Richard Spelman Steve Davis Russell Snell 《Animal genetics》2012,43(6):781-784
Animal growth relative to food energy input is of key importance to agricultural production. Several recent studies highlighted genetic markers associated with food conversion efficiency in beef cattle, and there is now a requirement to validate these associations in additional populations and to assess their potential utility for selecting animals with enhanced food‐use efficiency. The current analysis tested a population of dairy cattle using 138 DNA markers previously associated with food intake and growth in a whole‐genome association analysis of beef animals. Although seven markers showed point‐wise significance at P < 0.05, none of the single‐nucleotide polymorphisms tested were significantly associated with food conversion efficiency after correction for multiple testing. These data do not support the involvement of this subset of previously implicated markers in the food conversion efficiency of the physiologically distinct New Zealand Holstein‐Friesian dairy breed. 相似文献
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The bis‐functionalized diamondoid α‐amino acid 2‐aminoadamantane‐2‐carboxylic acid (Adm) has been used as the building block of four Nα‐formyl homo‐dipeptide alkylamide sequences via a solution‐phase Ugi multicomponent reaction approach. The conformers of these peptides have been determined in the crystalline state by X‐ray diffraction to distinguish the influences of the C‐terminal substituent. One of the Adm peptides folds into an open and a hydrogen‐bonded γ‐turn geometry. Moreover, 3D‐structures have been observed featuring two consecutive γ‐turns in an incipient γ‐helical structure, a significantly distorted nonhelical β‐turn, as well as an S‐shaped conformation with opposite helical screw senses. A significant topological variety is thus exhibited by the ‐Adm‐Adm‐ sequences contingent on their C‐terminal substituents, illustrating both the broad conformational potential and the need for further characterization of this sterically bulky residue in explorations of its ϕ, ψ space. 相似文献
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