Impairments in pyridoxine-dependent sulphur amino acid metabolism are highly sensitive to the degree of vitamin B6 deficiency and repletion in the pig

The objectives of the current study included the characterization of the temporal changes in indices of sulphur amino acid metabolism in piglets in response to vitamin B6 deficiency and repletion with graded levels of pyridoxine hydrochloride. In Experiment 1, 12 piglets (average initial weight = 5.3 kg; n = 6 per group) were fed a semi-purified diet containing either 0 (deficiency group) or 3 mg (control group) pyridoxine·HCl/kg diet, using a pair-feeding design, for 6 weeks. Piglets consuming vitamin B6-deficient diets exhibited decreased average daily gains on the 4th week and feed conversion efficiency from the 4th week until the end of the trial (P < 0.05). Plasma pyridoxal-5'-phosphate (PLP), in pigs consuming vitamin B6-deficient diets, was significantly lower than controls throughout the experiment (P < 0.01), reaching a nadir of 14% of the control animals' value by the end of the trial. Indices of sulphur amino acid metabolism, including activities of hepatic cystathionine-β-synthase (CBS), cystathionine-γ-lyase (CGL) and serine hydroxymethyltransferase, as well as hepatic-free cysteine concentrations were markedly decreased after 6 weeks of B6 deficiency (P < 0.05). Total hepatic mRNA expressions for CBS and CGL were not affected. Concurrently, hepatic-free homocysteine concentrations increased by more than eight-fold (P < 0.01) at the end of the trial. An examination of plasma total homocysteine and cysteine concentrations revealed significant (P < 0.05) differences between treatments, with evidence of an abrupt shift in concentrations at 3 weeks post-initiation of dietary treatments (>25-fold increase in homocysteine; halving of cysteine values). At the end of Experiment 1, vitamin B6 deficiency significantly increased plasma methionine and serine levels, but decreased plasma glycine concentrations (P < 0.05). In Experiment 2, 20 pigs of 14 days old (initial BW = 5.0 kg) were subjected to a 4-week vitamin B6 depletion protocol, based on results obtained in Experiment 1. After the depletion period and assessment of baseline status (four pigs), remaining pigs were allocated to one of four dietary vitamin B6 repletion treatments: 0.75, 1.5, 2.25 and 3 mg/kg diet as pyridoxine·HCl (n = 4 per level) for 14 days. Significant dose-dependent increases in plasma PLP and cysteine, and decreases in homocysteine were observed, and these were sensitive to the duration of repletion. In conclusion, data from the current studies support the use of both plasma PLP and homocysteine as sensitive indices of vitamin B6 status in the pig. Additionally, the observed patterns of responses in vitamin B6-sensitive metabolites are supportive of an inclusion level of 2.25 mg/kg diet, as pyridoxine·HCl, in diets for young pigs.     

The amino acid composition of tissue protein is affected by the total sulfur amino acid supply in growing pigs

The factorial approach to assess the amino acid (AA) requirements of pigs is based on the assumption that the AA composition of body protein is constant. However, there are indications that this assumption may not be valid because the AA composition of body protein can be affected by the AA supply. The extent to which different tissues are affected by an AA deficiency is unknown. The objective of this study was to investigate the effect of feeding pig diets with a deficient or sufficient total sulfur AA supply (TSAA; Met+Cys) from 6 to 23 weeks of age on tissue composition and meat quality. The deficient diet (TSAA–) provided 24% Met : Lys and 51% TSAA : Lys on a standardized ileal digestible basis, which are 19% and 16% below the recommended requirements, respectively. The sufficient diet (TSAA+) provided 33% Met : Lys and 60% TSAA : Lys. Diets were offered slightly below the ad libitum feed intake capacity of the pigs. Pigs offered diet TSAA– had a lower average daily gain, lower weights of the longissimus dorsi (LM) and rhomboideus muscles (RM), and of selected skin sections (P<0.05). The weight of different sections of the small intestine and the liver was not affected by the diet. The protein content of the LM and RM decreased in pigs offered diet TSAA– (P<0.05), whereas the protein content of other tissues was not affected. The TSAA supply affected the AA composition (g/16 g N) of protein in all tissues, but the Met content was changed only in the liver (P<0.05). Pigs receiving diet TSAA– had a lower Cys content in the RM and in the distal jejunum and ileum (P<0.01). The deficient TSAA supply resulted in a lower carcass weight and higher muscle glycogen stores (P<0.05), but did not affect other meat quality traits. The results of this study indicate that the muscles, jejunum and ileum respond more to a prolonged AA deficiency than the liver. In addition, the observed changes in AA composition of tissue protein question the use of a constant AA profile of retained protein to assess AA requirements.     

基于氨基酸和二肽组成的蛋白质四级结构分类研究

基于最近邻居算法,从蛋白质一级序列出发,利用蛋白质序列氨基酸组成、二肤组成以及混合组成方法对蛋白质单聚体、二聚体、三聚体、四聚体、五聚体、六聚体和八聚体进行分类研究。结果表明:采用二肽组成编码方法的预洲效果最好,Jackknife检验和独立测试集检验的总体预测精度分别达到90.83%和95.48%,比相同数据集上基于伪氨基酸组成和组分耦合预测的方法提高了12和15个百分点;特别是对于五聚体蛋白,预测精度分别提高了90和50个百分点;说明二肽组成对于蛋白质四级结构分类研究是一种非常有效的特征提取方法。     

Synthesis of the sulfur amino acids: cysteine and methionine

This review will assess new features reported for the molecular and biochemical aspects of cysteine and methionine biosynthesis in Arabidopsis thaliana with regards to early published data from other taxa including crop plants and bacteria (Escherichia coli as a model). By contrast to bacteria and fungi, plant cells present a complex organization, in which the sulfur network takes place in multiple sites. Particularly, the impact of sulfur amino-acid biosynthesis compartmentalization will be addressed in respect to localization of sulfur reduction. To this end, the review will focus on regulation of sulfate reduction by synthesis of cysteine through the cysteine synthase complex and the synthesis of methionine and its derivatives. Finally, regulatory aspects of sulfur amino-acid biosynthesis will be explored with regards to interlacing processes such as photosynthesis, carbon and nitrogen assimilation.     

Amino acid utilization and body composition of growing pigs fed processed soybean meal or rapeseed meal with or without amino acid supplementation

Feed ingredients used in swine diets are often processed to improve nutritional value. However, (over-)processing may result in chemical reactions with amino acids (AAs) that decrease their ileal digestibility. This study aimed to determine effects of (over-)processing of soybean meal (SBM) and rapeseed meal (RSM) on post-absorptive utilization of ileal digestible AAs for retention and on body AA composition of growing pigs. Soybean meal and RSM were processed by secondary toasting in the presence of lignosulfonate to obtain processed soybean meal (pSBM) and processed rapeseed meal (pRSM). Four diets contained SBM, pSBM, RSM or pRSM as sole protein source. Two additional diets contained pSBM or pRSM and were supplemented with crystalline AA to similar standardized ileal digestible (SID) AA level as the SBM or RSM diet. These diets were used to verify that processing affected AA retention by affecting ileal AA digestibility rather than post-absorptive AA utilization. The SID AA levels of the protein sources were determined in a previous study. In total, 59 pigs were used (initial BW of 15.6±0.7 kg) of which five were used to determine initial body composition at the start of the experiment. In total, 54 pigs were fed one of six experimental diets and were slaughtered at a BW of 40 kg. The organ fraction (i.e. empty organs plus blood) and carcass were analyzed separately for N and AA content. Post-absorptive AA utilization was calculated from AA retention and SID AA intake. An interaction between diet type, comprising effects of processing and supplementing crystalline AA, and protein source was observed for CP content in the organ fraction, carcass and empty body and for nutrient retention. Processing reduced CP content and nutrient retention more for SBM than for RSM. Moreover, processing reduced (P<0.001) the lysine content in the organ fraction for both protein sources. Supplementing crystalline AA ameliorated the effect of processing on these variables. Thus, the data indicated that processing affected retention by reducing digestibility. Correcting AA retention for SID AA intake was, therefore, expected to result in similar post-absorptive AA utilization which was observed for the RSM diets. However, post-absorptive AA utilization was lower for the pSBM diet than for the SBM diet which might be related to an imbalanced post-absorptive AA supply. In conclusion, processing negatively affected nutrient retention for both protein sources and post-absorptive utilization of SID AA for retention for SBM. Effects of processing were compensated by supplementing crystalline AA.     

Unique amino acid composition of proteins in halophilic bacteria

The amino acid compositions of proteins from halophilic archaea were compared with those from non-halophilic mesophiles and thermophiles, in terms of the protein surface and interior, on a genome-wide scale. As we previously reported for proteins from thermophiles, a biased amino acid composition also exists in halophiles, in which an abundance of acidic residues was found on the protein surface as compared to the interior. This general feature did not seem to depend on the individual protein structures, but was applicable to all proteins encoded within the entire genome. Unique protein surface compositions are common in both halophiles and thermophiles. Statistical tests have shown that significant surface compositional differences exist among halophiles, non-halophiles, and thermophiles, while the interior composition within each of the three types of organisms does not significantly differ. Although thermophilic proteins have an almost equal abundance of both acidic and basic residues, a large excess of acidic residues in halophilic proteins seems to be compensated by fewer basic residues. Aspartic acid, lysine, asparagine, alanine, and threonine significantly contributed to the compositional differences of halophiles from meso- and thermophiles. Among them, however, only aspartic acid deviated largely from the expected amount estimated from the dinucleotide composition of the genomic DNA sequence of the halophile, which has an extremely high G+C content (68%). Thus, the other residues with large deviations (Lys, Ala, etc.) from their non-halophilic frequencies could have arisen merely as "dragging effects" caused by the compositional shift of the DNA, which would have changed to increase principally the fraction of aspartic acid alone.     

Cysteine restriction‐specific effects of sulfur amino acid restriction on lipid metabolism

Decreasing the dietary intake of methionine exerts robust anti‐adiposity effects in rodents but modest effects in humans. Since cysteine can be synthesized from methionine, animal diets are formulated by decreasing methionine and eliminating cysteine. Such diets exert both methionine restriction (MR) and cysteine restriction (CR), that is, sulfur amino acid restriction (SAAR). Contrarily, SAAR diets formulated for human consumption included cysteine, and thus might have exerted only MR. Epidemiological studies positively correlate body adiposity with plasma cysteine but not methionine, suggesting that CR, but not MR, is responsible for the anti‐adiposity effects of SAAR. Whether this is true, and, if so, the underlying mechanisms are unknown. Using methionine‐ and cysteine‐titrated diets, we demonstrate that the anti‐adiposity effects of SAAR are due to CR. Data indicate that CR increases serinogenesis (serine biosynthesis from non‐glucose substrates) by diverting substrates from glyceroneogenesis, which is essential for fatty acid reesterification and triglyceride synthesis. Molecular data suggest that CR depletes hepatic glutathione and induces Nrf2 and its downstream targets Phgdh (the serine biosynthetic enzyme) and Pepck‐M. In mice, the magnitude of SAAR‐induced changes in molecular markers depended on dietary fat concentration (60% fat >10% fat), sex (males > females), and age‐at‐onset (young > adult). Our findings are translationally relevant as we found negative and positive correlations of plasma serine and cysteine, respectively, with triglycerides and metabolic syndrome criteria in a cross‐sectional epidemiological study. Controlled feeding of low‐SAA, high‐polyunsaturated fatty acid diets increased plasma serine in humans. Serinogenesis might be a target for treating hypertriglyceridemia.     

Monte Carlo simulation studies on the prediction of protein folding types from amino acid composition

A number of methods to predicting the folding type of a protein based on its amino acid composition have been developed during the past few years. In order to perform an objective and fair comparison of different prediction methods, a Monte Carlo simulation method was proposed to calculate the asymptotic limit of the prediction accuracy [Zhang and Chou (1992),Biophys. J. 63, 1523–1529, referred to as simulation method I]. However, simulation method I was based on an oversimplified assumption, i.e., there are no correlations between the compositions of different amino acids. By taking into account such correlations, a new method, referred to as simulation method II, has been proposed to recalculate the objective accuracy of prediction for the least Euclidean distance method [Nakashimaet al. (1986),J. Biochem. 99, 152–162] and the least Minkowski distance method [Chou (1989),Prediction in Protein Structure and the Principles of Protein Conformation, Plenum Press, New York, pp. 549–586], respectively. The results show that the prediction accuracy of the former is still better than that of the latter, as found by simulation method I; however, after incorporating the correlative effect, the objective prediction accuracies become lower for both methods. The reason for this phenomenon is discussed in detail. The simulation method and the idea developed in this paper can be applied to examine any other statistical prediction method, including the computersimulated neural network method.     

Changes in the free and total amino acid composition of ripening chestnut seeds

The distribution of free and protein amino acids during seed development is described for three chestnut varieties. Asparagine accumulation was shown to correlate with protein biosynthesis. Accumulation of free amino acids takes place before that of proteins in ripening seeds. A temporary decrease was generally accompanied by protein biosynthesis and followed by final accumulation of both protein and free amino acids.     

Amino acid composition and protein dimension

There is indirect evidence that the amino acid composition of proteins depends on their dimension. The amino acid composition of a nonredundant set of about 550,000 proteins was determined and it was observed that, in the range of 50-200 residues, the percentage of occurrence of most of the residue types significantly depends on protein dimension. This result should prove useful in analyzing protein sequences and genomics.     

Dietary deficiencies of single amino acids: Whole-body amino acid composition of adult rats

Abstract

To ascertain whether chronic amino acid deficiency alters the amino acid composition of the body, 44 adult female rats were randomly allocated to one of 11 treatments which included one control group, ingesting an adequate diet with balanced protein, and ten deficient groups in which one group received protein-deficient diets and the other groups consumed diets each deficient in a single essential amino acid. The degree of deficiency was adjusted to achieve a gradual decline in body weight to 85% of the initial weight and was then adjusted so that this weight was maintained until the end of the experiment at 93 days, when the rats were killed. Deficient rats had lower absolute weights of liver, gastrointestinal tract and muscle than animals given the adequate diet but greater relative weights (% of body weight) of heart and kidneys. There were no significant differences amongst groups in percentages of lipid, nitrogen, protein plus lipid or dry matter. Chronic marginal amino acid deficiencies did not selectively alter amino acid composition.     

Armadillo: domain boundary prediction by amino acid composition

The identification and annotation of protein domains provides a critical step in the accurate determination of molecular function. Both computational and experimental methods of protein structure determination may be deterred by large multi-domain proteins or flexible linker regions. Knowledge of domains and their boundaries may reduce the experimental cost of protein structure determination by allowing researchers to work on a set of smaller and possibly more successful alternatives. Current domain prediction methods often rely on sequence similarity to conserved domains and as such are poorly suited to detect domain structure in poorly conserved or orphan proteins. We present here a simple computational method to identify protein domain linkers and their boundaries from sequence information alone. Our domain predictor, Armadillo (http://armadillo.blueprint.org), uses any amino acid index to convert a protein sequence to a smoothed numeric profile from which domains and domain boundaries may be predicted. We derived an amino acid index called the domain linker propensity index (DLI) from the amino acid composition of domain linkers using a non-redundant structure dataset. The index indicates that Pro and Gly show a propensity for linker residues while small hydrophobic residues do not. Armadillo predicts domain linker boundaries from Z-score distributions and obtains 35% sensitivity with DLI in a two-domain, single-linker dataset (within +/-20 residues from linker). The combination of DLI and an entropy-based amino acid index increases the overall Armadillo sensitivity to 56% for two domain proteins. Moreover, Armadillo achieves 37% sensitivity for multi-domain proteins, surpassing most other prediction methods. Armadillo provides a simple, but effective method by which prediction of domain boundaries can be obtained with reasonable sensitivity. Armadillo should prove to be a valuable tool for rapidly delineating protein domains in poorly conserved proteins or those with no sequence neighbors. As a first-line predictor, domain meta-predictors could yield improved results with Armadillo predictions.     

A universal evolutionary index for amino acid changes

Different nonsynonymous changes may be under different selective pressure during evolution. Of the 190 possible interchanges among the 20 amino acids, only 75 can be attained by a single-base substitution. An evolutionary index (EI) can be empirically computed for each of the 75 elementary changes as the likelihood of substitutions, relative to that of synonymous changes. We used 280, 1,306, 2,488, and 309 orthologous genes from primates (human versus Old World monkey), rodents (mouse versus rat), yeast (S. cerevisiae versus S. paradoxus), and Drosophila (D. melanogaster versus D. simulans), respectively, to estimate the EIs. In each data set, EI varies more than 10-fold, and the correlation coefficients of EIs from the pairwise comparisons are high (e.g., r = 0.91 between rodent and yeast). The high correlations suggest that the amino acid properties are strong determinants of protein evolution, irrespective of the identities of the proteins or the taxa of interest. However, these properties are not well captured in conventional measures of amino acid exchangeability. We, therefore, propose a universal index of exchange (U): for any large data set, its EI can be expressed as U*R, where R is the average Ka/Ks for that data set. The codon-based, empirically determined EI (i.e., U*R) makes much better predictions on protein evolution than do previous methods.     

The amino acid composition of soya lactate dehydrogenase

Lactate dehydrogenase from germinating soya plants was prepared in an electrophoretically homogeneous form by affinity chromatography on AMP-Sepharose.     

4种小檗科植物叶片的蛋白质及氨基酸组成分析

蛋白质和氨基酸是植物体内重要的营养物质,研究药用植物的蛋白质和氨基酸组成对药用植物资源的合理开发和综合利用具有重要意义,但目前对药用植物次生代谢物的研究较为广泛（如黄酮类化合物[1-2],而对其初生代谢物的研究相对较少[3-4]。     

基于分段氨基酸组成成分的蛋白质相互作用预测

蛋白质相互作用研究有助于揭示生命过程的许多本质问题,也有助于疾病预防、诊断,对药物研制具有重要的参考价值。文章首先构建出蛋白质作用数据库,提出分段氨基酸组成成分特征提取方法来预测蛋白质相互作用。10CV检验下,基于支持向量机的3段氨基酸组成成分特征提取方法的预测总精度为86.2%,比传统的氨基酸组成成分方法提高2.31个百分点;采用Guo的数据库和检验方法,3段氨基酸组成成分特征提取方法的预测总精度为90.11%,比Guo的自相关函数特征提取方法提高2.75个百分点,从而表明分段氨基酸组成成分特征提取方法可有效地应用于蛋白质相互作用预测。     

Prediction of protein secondary structure content using amino acid composition and evolutionary information

Knowing protein structure and inferring its function from the structure are one of the main issues of computational structural biology, and often the first step is studying protein secondary structure. There have been many attempts to predict protein secondary structure contents. Previous attempts assumed that the content of protein secondary structure can be predicted successfully using the information on the amino acid composition of a protein. Recent methods achieved remarkable prediction accuracy by using the expanded composition information. The overall average error of the most successful method is 3.4%. Here, we demonstrate that even if we only use the simple amino acid composition information alone, it is possible to improve the prediction accuracy significantly if the evolutionary information is included. The idea is motivated by the observation that evolutionarily related proteins share the similar structure. After calculating the homolog-averaged amino acid composition of a protein, which can be easily obtained from the multiple sequence alignment by running PSI-BLAST, those 20 numbers are learned by a multiple linear regression, an artificial neural network and a support vector regression. The overall average error of method by a support vector regression is 3.3%. It is remarkable that we obtain the comparable accuracy without utilizing the expanded composition information such as pair-coupled amino acid composition. This work again demonstrates that the amino acid composition is a fundamental characteristic of a protein. It is anticipated that our novel idea can be applied to many areas of protein bioinformatics where the amino acid composition information is utilized, such as subcellular localization prediction, enzyme subclass prediction, domain boundary prediction, signal sequence prediction, and prediction of unfolded segment in a protein sequence, to name a few.     

Molecular weight and amino acid composition of purified spinach beet phenolase

The purification of spinach beet phenolase has been modified to include equilibration of the crude macerate with 0.5% cetyl-trimethylammonium bromide a     

Conservation of the basic pattern of cellular amino acid composition of archaeobacteria during biological evolution and the putative amino acid composition of primitive life forms

Summary. Previous studies showed that the cellular amino acid composition obtained by amino acid analysis of whole cells, differs such as eubacteria, protozoa, fungi and mammalian cells. These results suggest that the difference in the cellular amino acid composition reflects biological changes as the result of evolution. However, the basic pattern of cellular amino acid composition was relatively constant in all organisms examined. In the present study, we examined archaeobacteria, because they are considered important in understanding the relationship between biological evolution and cellular amino acid composition. The cellular amino acid compositions of Archaeoglobus fulgidus, Pyrococcus horikoshii, Methanobacterium thermoautotrophicum and Methanococcus jannaschii differed slightly from each other, but were similar to those determined from codon usage data, based on the complete genomes. Thus, the cellular amino acid composition reflects biological evolution. We suggest that primitive forms of life appearing on earth at the end of prebiotic evolution had a similar-cellular amino acid composition. Received November 28, 2000 Accepted January 30, 2001