The joint evolution of defence and inducibility against natural enemies

The aminoacyl-tRNA synthetases (aaRSs) ensure the fidelity of the translation of the genetic code, covalently attaching appropriate amino acids to the corresponding nucleic acid adaptor molecules-tRNA. The fundamental role of aminoacylation reaction catalysed by aaRSs implies that representatives of the family are thought to be among the earliest proteins to appear. Based on sequence analysis and catalytic domain structure, aaRSs have been partitioned into two classes of 10 enzymes each. However, based on the structural and sequence data only, it will not be easily understood that the present partitioning is not governed by chance. Our findings suggest that organization of amino acid biosynthetic pathways and clustering of aaRSs into different classes are intimately related to one another. A plausible explanation for such a relationship is dictated by early link between aaRSs and amino acids biosynthetic proteins. The aaRSs catalytic cores are highly relevant to the ancient metabolic reactions, namely, amino acids and cofactors biosynthesis. In particular we show that class II aaRSs mostly associated with the primordial amino acids, while class I aaRSs are usually related to amino acids evolved lately. Reasoning from this we propose a possible chronology of genetic code evolution.     

中国梨木虱若虫的排蜜规律及蜜露中氨基酸成分的研究

本文研究了中国梨木虱 Psylla chinensis Yang et Li若虫期的排蜜规律及蜜露中氨基酸成分。结果表明 ,若虫随着龄期的增大 ,体重增加 ,日平均排蜜量也不断增多 ,每头夏型若虫一生排蜜量为630 3.38μg。在室内条件下 ,若虫排蜜量与昼夜节律有关 ,夜间排蜜量为一昼夜的 2 / 3。温度对若虫排蜜量有一定影响 ,在 2 5℃条件下排蜜量最大。若虫蜜露中氨基酸含量为 4 .4 5% ,其中天门冬氨酸和谷氨酸含量较高 ,分别占所测定的 17种氨基酸的 4 2 .11%和 2 7.5% ,蜜露中氨基酸的种类及含量与其所寄生的梨树叶片中氨基酸的种类及含量有密切关系     

Classification of amino acids based on comparative analysis of contacts in DNA-protein complexes and specific DNA-protein interactions

We propose a classification of amino acid residues based on the events of contact formation between particular residues and DNA nucleotides, i.e., using the most integral properties that characterize interactions organizing DNA-protein complexes. We apply the Voronoi-Delaunay tessellation to draw statistics of contacts and of contact areas for a set of 1937 DNA-protein complexes. Similarity of amino acid residues is defined upon comparison of corresponding rows and matrices of contacts and areas of contacts. Nine measures of distance have been used to estimate the closeness of rows. Residues have been grouped by three hierarchical and two nonhierarchical clustering methods. In a total tree built using nine metrics with three hierarchical methods, we show that clustering centers (pairs of amino acids) in the main groups are always constant while other relationships between objects vary. Major classes of up to six amino acids correspond to certain local structures of the polypeptide chain. These data can be taken into account when designing DNA-protein ligands.     

Manipulation of dietary methionine+cysteine and threonine in broilers significantly decreases environmental nitrogen excretion

The intensification of livestock have increased the emission of pollutants to the environment, leading to a growing interest in seeking strategies that minimise these emissions. Studies have shown that it is possible to manipulate diets by reducing CP levels and thus reducing nitrogen (N) excretion, without compromising performance. However, there is no knowledge of any study that has focused on reducing N excretion and relating this reduction to individual amino acids. This study investigated the effect of dietary methionine+cysteine (MC) and threonine (THR), the two most limiting amino acids for broiler production, on nitrogen excretion (NE) and nitrogen deposition (ND) and determined the efficiency of utilisation of both amino acids for protein deposition. Six trials were conducted to measure the NE and ND in broiler chickens during three rearing phases in response to dietary amino acid. The efficiency of utilisation of the amino acids was calculated by linear regression of body protein deposition and the amino acid intake. Despite the differences between sexes and phases, the efficiency of utilisation was the same, being 0.60 and 0.59 for MC and THR, respectively. The rate of NE behaved exponentially, increasing with amino acid intake, and can exceed 50% of N intake, being higher than ND. On average, for a reduction in intake of each unit of MC or THR (mg) there is a reduction of 0.5% of NE. Although this reduction seems low, considering that it corresponds to changes in one amino acid only, the impact on a large scale would be significant. Knowledge of how animals respond to NE and ND/protein deposition according to amino acid dietary content may represent new efforts towards reducing the impact on environment.     

高纬度地区大豆蛋白含量及氨基酸组分的表型鉴定与聚类分析

对国内外高纬度地区的240份大豆种质资源的蛋白及16个氨基酸组分进行测定,通过遗传多样性、因子和聚类分析,进行了表型鉴定及基因型分类。结果表明,供试大豆种质蛋白及氨基酸组分变异较丰富,遗传多样性程度较高。根据因子分析,将筛选到的3个公因子进行聚类分析,可将供试种质资源分为7类。蛋白含量从高到低的顺序为类群Ⅶ>类群Ⅵ>类群Ⅴ>类群Ⅱ>类群Ⅰ>类群Ⅲ>类群Ⅳ。12个氨基酸组分的变化趋势与蛋白一致。类群Ⅶ和类群Ⅵ为高蛋白遗传群体,可作为高蛋白基因聚合育种的亲本材料。通过前期分析,筛选到24份高蛋氨酸资源,包括有公野04L-141、龙品03-311、Proto、和龙油太、猫眼豆、茶色豆、紫花2号、东农48等,可为高蛋氨酸种质创新提供材料基础。     

Osmotic Homeostasis in Dictyostelium Discoideum: Excretion of Amino Acids and Ingested Solutes

ABSTRACT. The response to osmotic stress in axenically cultured Dictyostelium discoideum was examined. Hypoosmotic buffers elicited two changes in the large (-50 mM) cytosolic pool of amino acids: a) the total size of the pool diminished, while b) about half of the initial pool was excreted. Hyperosmotic stress had the opposite effect. Among the predominant amino acids in the pool were glycine, alanine and proline. Putrescine, the major diamine, was neither excreted nor modulated. Recently ingested radioactive amino acids were excreded in preference to those in the cytoplasm, suggesting that the endocytic pathway might be involved in water excretion. Furthermore, hypoosmotic stresss strimulated the selective exretion of small, membrane-impermeable fluorescent dyes which had been ingested into endocytic vacuoles. Caffeine inhibited the excretion of the fluorophores but not the amino acids. We conclude that the response of Dictyostelium to osmotic stress is complex and includes both modulation of the cytoplasmic amino acid pool and the excretion of amino acids and other small solutes from the endocytic pathway.     

Synthesis of metabolism-resistant substrates for the transport system for cationic amino acids; their stimulation of the release of insulin and glucagon, and of the urinary loss of amino acids related to cystinuria

Several amino acids have been synthesized as model transport substrates building on the piperidine and cyclohexane rings. Only when the distal N atom is part of an unambiguously cationic structure are these compounds transported predominantly by the cationic amino acid system. These amino acids in labeled form are excreted rather slowly in unmodified state, very little ¹⁴CO₂ being released. Those which are unambiguously cationic (including also homoarginine) led to a greatly increased excretion of arginine, lysine, ornithine and citrulline. Those which might be expected to act as lysine analogs had little effect on the excretion of the basic amino acids, although the excretion of citrulline and the sum of glutamine plus asparagine was accelerated. Certain of the analogs intensified the excretion of citrulline in dissociation from effects on resorption of the basic amino acids, also in dissociation from effects on cystine resorption. These results indicate citrulline resorption does not occur principally by the same agency serving for the basic amino acids, nor by the agency serving for cystine, despite the observed interactions for resorption. The injection of either of three transport analogs for arginine into the rat leads to early increases in the circulating levels of immunologically reactive insulin and glucagon.     

Changes in Nicotinamide Metabolism by One Amino Acid Deficiency. (I) Threonine-, Tryptophan-, Aspartic Acid-, Lysine-, Leucine-, or Methionine-free Diet

Effects of a threonine-, tryptophan-, aspartic acid-, lysine-, leucine-, or methionine-free diet fed to rats on the metabolism of nicotinamide were investigated. The body weights of rats and food intakes were greatly decreased by feeding of the diet excluding any of the above essential amino acids compared to the control group, however, not by feeding of an aspartic acid-free diet. The sum of the urinary excretion of nicotinamide, N¹-methylnicotinamide (MNA), N¹ -methyl-2-pyridone-5-carboxamide (2-Py), and N¹ -methyl-4-pyridone-3-carboxamide (4-Py) changed roughly in proportion to food intake. In the groups fed with the threonine- and lysine-free diets, the urinary excretion of MNA greatly increased compared with the control group during the whole experimental period and in the groups fed with the leucine- and methionine-free diets, increased excretion of MNA was observed on day o–day 1. Whenever the increase in MNA excretion was observed, a decrease in 4-Py excretion was observed. This was attributed to the activity of 4-Py-forming MNA oxidase decreasing when rats were fed with the diet excluding one of the essential amino acid except for tryptophan. Therefore, the (2-Py +4-Py)/MNA excretion was greatly decreased by feeding of the diet excluding one of the essential amino acids except for the tryptophan-free diet. These results strengthened our hypothesis that the (2-Py +4-Py)/MNA excretion reflects the adequacy of amino acid nutrition.     

Use of fuzzy clustering technique and matrices to classify amino acids and its impact to Chou's pseudo amino acid composition

In this paper we present a study of classification of the 20 amino acids via a fuzzy clustering technique. In order to calculate distances among the various elements we employ two different distance functions: the Minkowski distance function and the NTV metric. In the clustering procedure we take into account several physical properties of the amino acids. We examine the effect of the number and nature of properties taken into account to the clustering procedure as a function of the degree of similarity and the distance function used. It turns out that one should use the properties that determine in the more important way the behavior of the amino acids and that the use of the appropriate metric can help in defining the separation into groups.     

Plasma and urine amino acid pattern in preterm infants on enteral nutrition: impact of gestational age

Plasma and urine amino acids were determined by ion-exchange chromatography in 80 healthy preterm infants divided into three groups: (1) 23 0/7–28 0/7, (2) 28 1/7–32 0/7 and (3) 32 1/7–35 0/7 weeks of gestation. Samples were collected from days 5 to 57 of life, when infants were exclusively orally fed. Infants with evidence of underlying diseases were excluded. Concentrations of most plasma amino acids increased with gestational and maturational age; urinary excretion followed an opposite course. Few amino acids depended on postnatal age. Plasma amino acids did not correlate inversely to their counterparts in urine indicating that plasma amino acids do not simply reflect kidney function. Some amino acids in blood and urine were linked to nutrient intake and body weight. Our data clearly indicate the heterogeneity of the preterm cohort; therefore, gestational age-matched reference values have to be used for diagnostic purposes in preterm infants.     

Biliary amino acid excretion in rats before and after bilateral nephrectomy.

In previous studies it could be shown that after bilateral nephrectomy (NX) the excretory function of the liver is disturbed. To further clarify whether or not this "renohepatic syndrome" is caused by toxic effects of uremia or by competition phenomena between various uraemic toxins an additional aspect was investigated: the biliary excretion of endogenous amino acids. Furthermore, previously it could be shown that renal and hepatic excretory functions overlap. Therefore, the renal excretion of effectively biliary eliminated amino acids (glutamic acid, alanine, tyrosine, isoleucine) is very low and vice versa. That means, that the renal excretion of amino acids with low hepatic elimination (tryptophan, citrulline, lysine, taurine) dominates. The hepatic excretion of amino acids is hardly altered after NX. Remarkably, the removal of both kidneys is followed by a distinct reduction in amino acid plasma concentrations, especially if these concentrations are relatively high in the controls. Interestingly, there is no correlation between plasma concentrations and biliary excretion of amino acids. But the calculation of the bile to plasma concentration ratios of amino acids makes it possible to differentiate three groups of amino acids: Amino acids excreted actively into bile (ratio > or = 1), amino acids with ratios below 1, indicating effective retention, and amino acids with ratios of about 1, whose hepatic handling is passive. After NX these ratios tended to approach 1; low ratios increased and high ratios decreased. That means, active processes involved in excretion or retention are obviously disturbed. These changes could indicate uraemic liver damage as proved regarding influence of NX on hepatic excretion of other endogenous substances and xenobiotics.     

STUDIES OF THE INTER-RELATIONSHIP BETWEEN CEREBROSPINAL FLUID AND PLASMA AMINO ACID CONCENTRATIONS IN NORMAL INDIVIDUALS

Abstract— —The concentration of free amino acids has been determined in lumbar CSF in 37 fasting normal subjects. The values obtained have been compared with the concentration of the same amino acids measured in venous plasma collected simultaneously and with ventricular CSF amino acid concentrations. Twenty-three amino acids have been identified and quantitated in CSF and plasma. Trace quantities of eight other amino acids have been also detected.
The concentration of 13 amino acids in CSF has been shown to be directly related to the plasma concentration. No such relationship was noted for the other 7 amino acids. Significant variations in the concentration of individual amino acids relating to both age and sex have been noted. A large number of unidentified ninhydrin positive compounds have been found in CSF. Preliminary studies have identified one of these as ɛ-aminobutyric acid (GABA).     

Amino acids metabolism by VO 208 hybridoma cells: some aspects of the culture process and medium composition influence

In the present study an approach has been developed in order to examine the consequence of essential and non essential amino acid supplementation on VO208 hybridoma cells behaviour. The effect of amino acid enrichment has been studied taking into account the culture process, i.e., batch or continuous culture mode and the medium composition, i.e., a home made serum-free medium or a serum containing one. A group of 4 amino acids, i.e., Ser, Pro, Gly and Arg presented atypical evolution pattern of their extracellular concentration depending on the type of the medium and on the culture mode. Some amino acids were probably involved in the limitation of the cellular proliferation. Met was one of the amino acids that appears to may have been at limiting concentration in all cases. In continuous culture mode, an enrichment of amino acids resulted in a rapid improvement of the viable cell density in both media, with or without the presence of serum. For most amino acids, supplementation during continuous culture induced an increase of the amino acid uptake rate. A comparative analysis of amino acids utilisation, depending on the culture conditions studied in the present study, has been performed in order to propose an overall picture of amino acids metabolism by VO 208 Hybridoma cell line. This revised version was published online in August 2006 with corrections to the Cover Date.     

FSP27 promotes lipid droplet clustering and then fusion to regulate triglyceride accumulation

Fat Specific Protein 27 (FSP27), a lipid droplet (LD) associated protein in adipocytes, regulates triglyceride (TG) storage. In the present study we demonstrate that FSP27 plays a key role in LD morphology to accumulate TGs. We show here that FSP27 promotes clustering of the LDs which is followed by their fusion into fewer and enlarged droplets. To map the domains of FSP27 responsible for these events, we generated GFP-fusion constructs of deletion mutants of FSP27. Microscopic analysis revealed that amino acids 173-220 of FSP27 are necessary and sufficient for both the targeting of FSP27 to LDs and the initial clustering of the droplets. Amino acids 120-140 are essential but not sufficient for LD enlargement, whereas amino acids 120-210 are necessary and sufficient for both clustering and fusion of LDs to form enlarged droplets. In addition, we found that FSP27-mediated enlargement of LDs, but not their clustering, is associated with triglyceride accumulation. These results suggest a model in which FSP27 facilitates LD clustering and then promotes their fusion to form enlarged droplets in two discrete, sequential steps, and a subsequent triglyceride accumulation.     

The sypA,sypS, and sypC synthetase genes encode twenty-two modules involved in the nonribosomal peptide synthesis of syringopeptin by Pseudomonas syringae pv. syringae B301D

Syringopeptin is a necrosis-inducing phytotoxin, composed of 22 amino acids attached to a 3-hydroxy fatty acid tail. Syringopeptin, produced by Pseudomonas syringae pv. syringae, functions as a virulence determinant in the plant-pathogen interaction. A 73,800-bp DNA region was sequenced, and analysis identified three large open reading frames, sypA, sypB, and sypC, that are 16.1, 16.3, and 40.6 kb in size. Sequence analysis of the putative SypA, SypB, and SypC sequences determined that they are homologous to peptide synthetases, containing five, five, and twelve amino acid activation modules, respectively. Each module exhibited characteristic domains for condensation, aminoacyl adenylation, and thiolation. Within the aminoacyl adenylation domain is a region responsible for substrate specificity. Phylogenetic analysis of the substrate-binding pockets resulted in clustering of the 22 syringopeptin modules into nine groups. This clustering reflects the substrate amino acids predicted to be recognized by each of the respective modules based on placement of the syringopeptin NRPS (nonribosomal peptide synthetase) system in the linear (type A) group. Finally, SypC contains two C-terminal thioesterase domains predicted to catalyze the release of syringopeptin from the synthetase and peptide cyclization to form the lactone ring. The syringopeptin synthetases, which carry 22 NRPS modules, represent the largest linear NRPS system described for a prokaryote.     

Protein sequence analysis studies on the low molecular weight hydrophobic proteins associated with bovine pulmonary surfactant

Lipid extracts of bovine pulmonary surfactant, which exhibit biophysical and biological activity, contain two hydrophobic proteins which have been designated surfactant protein-B (SP-B) and SP-C. Amino terminal amino acid sequence analysis of whole lipid extracts and partially purified protein fractions gave rise to three sequences, two major and one minor. The first sequence, identified as a member of the SP-B family, extended for 60 amino acids beginning with an amino terminal phe. The second polypeptide, identified as a member of the SP-C family, sequenced for 35 amino acids and had a leu amino terminus. The third minor sequence corresponded to amino acids 2-9 of SP-C (N-leu) and was designated SP-C (N-ile). Sequence analysis of cyanogen bromide peptides derived from methyl isocyanate-blocked lipid extract material produced two peptides which extended the amino acid sequence of SP-B to residue 79, which appears to be a glycine.     

Influence of triiodothyronine and dexamethasone on renal amino acid handling in rats loaded with various amino acid mixtures

Summary In adult female rats, the influence of dexamethasone or triiodothyronine on renal amino acid handling was investigated in amino acid loaded animals. Amino acids were administered intravenously as two mixtures, each containing four amino acids to overload amino acid reabsorption capacity. Bolus injections of both mixtures were followed by temporary increase in fractional excretion of the administered amino acids as well of the amino acids which were not covered in the mixtures. The administration of the two mixtures was followed by different interactions between various amino acid carriers.After dexamethasone pretreatment (60µg/100g b.wt. for 3 days, once daily) a stimulation of the renal amino acid handling could be shown. Triiodothyronine (20µg/100g b.wt. for 3 days, once daily) did not increase tubular reabsorption capacity for amino acids. It even increased fractional amino acid excretion in amino acid loaded rats as a sign of enhanced amino acid metabolism in the kidney and/or increased amino acid uptake into the tubular cells from the luminal site.     

Chemosensory protein from the moth Mamestra brassicae. Expression and secondary structure from 1H and 15N NMR.

A group of ubiquitous small proteins (average 13 kDa) has been isolated from several sensory organs of a wide range of insect species. They are believed to be involved in chemical communication and perception (olfaction or taste) and have therefore been called chemo-sensory proteins (CSPs). Several CSPs have been identified in the antennae and proboscis of the moth Mamestra brassicae. We have expressed one of the antennal proteins (CSPMbraA6) in large quantities as a soluble recombinant protein in Escherichia coli periplasm. This 112-residue protein is a highly soluble monomer of 13 072 Da with a pI of 5.5. NMR data (1H and 15N) indicate that CSPMbraA6 is well folded and contains seven alpha helices (59 amino acids) and two short extended structures (12 amino acids) from positions 5 to 10 and from 107 to 112. Thirty-seven amino acids are involved in beta turns and coiled segments and four amino acids are not assigned in the NMR spectra (the N-terminus and the residue 52 in the loop 48-53), probably due to their mobility. This is the first report on the expression and structural characterization of a recombinant CSP.     

N tau methyl histidine excretion and [U-14C]amino acid oxidation in fully chickens from two lines selected for high and low body fat contents

Protein turnover and amino acid oxidation were examined in two lines of domestic broiler chicken selected for high (fat) and low (lean) plasma very low density lipoprotein levels. Protein turnover was assessed by comparing N tau methyl histidine excretion in two lines. No differences between the fat and lean birds were found. Oxidation of [U-14C]amino acids in vivo was measured in birds of both lines which had been fed ad lib. The lean birds oxidized significantly less of the administered [U-14C]amino acids to 14CO2 than their fat counterparts during the first 90 min following administration. Lean birds also excreted significantly less 14C than fat birds from [U-14C]amino acids.     

tRNA序列的进化网络研究

根据tRNA序列的反密码子,把3420 条tRNA 序列分成了21组,其中包括20 组氨基酸及1 组Stop。通过tRNA序列的相似度构建了1 组整体网络和21 组子网络,并计算了它们在不同相似度下的平均度、平均聚类系数以及平均最短路径。通过分析、比较和讨论网络中的三个重要参数,进一步说明点突变是tRNA序列进化的重要机制,并反映了它们的进化近似符合中性理论,且在同一组氨基酸和Stop 内的tRNA序列在进化历史上的同源关系更密切;同时表明了tRNA 序列在进化过程中具有自相似性。