Evolutionary changes reflected by the cellular amino acid composition

Summary Comparison of the amino acid composition of cell-proteins using 17 amino acids has been used to investigate the biological evolution of organisms such as bacteria, blue-green alga, green alga, fungi, slime mold, protozoa and vertebrates. The degree of difference in the amino acid ratios between any two groups reflects the degree of divergency in biological evolution. The amino acid composition of the Gram-negative bacteria (Escherichia coli,Klebsiella,Proteus, andVibrio alginolyticus) was identical. However, the amino acid composition ofStaphylococcus aureus andBacillus subtilis, which are Gram-positive bacteria, differed from each other and from the Gram-negative bacteria. The amino acid composition of the blue-green alga (Cyanobacterium,Chroococidiopsis) was quite similar to that ofE. coli. A marked difference in the amino acid composition was observed betweenE. coli and green alga (Chlorella), and significant differences were observed betweenE. coli and other organisms, such as fungi, protozoa (Tetrahymena), slime mold (Dictyostelium discoideum) and vertebrates. In conclusion, the change in cellular amino acid composition reflects the divergence which has occurred during biological evolution, whereas a basic pattern of amino acid composition is maintained in spite of a long period of evolutional divergence among the various organisms. Thus, it is proposed that the primitive life forms established at the end of prebiotic evolution had a similar amino acid composition.     

The classification of various organisms according to the free amino acid composition change as the result of biological evolution

Summary. The free amino acid compositions in archaeobacteria, eubacteria, protozoa, blue-green alga, green alga, slime mold, plants and mammalian cells were analyzed, to investigate whether changes in their free amino acid compositions reflect biological evolution. Cell homogenates were treated with 80–90% ethanol to separate cellular proteins and free amino acids contained in the cells. Different patterns of the free amino acid compositions were observed in the various organisms. Characteristic differences were observed between plant and mammalian cells, and between archaeobacteria and eubacteria. The patterns of the free amino acid composition in blue-green alga, green alga, protozoa and slime mold differed from each other and from those of eubacteria and archaeobacteria. Rat hepatoma cells (R-Y121B) were cultured in Eagle's minimum essential medium (MEM) containing 5% serum or in a modified MEM lacking arginine, tyrosine and glutamine. No significant difference in the free amino acid composition was observed between the two cell groups cultured under two different conditions. It is suggested that the free amino acid composition reflects apparent biological changes as the result of evolution. Received July 5, 2000 Accepted July 31, 2001     

The amino acid composition of mammalian and bacterial cells

Summary High performance liquid chromatography was used to analyze the amino acid composition of cells. A total of 17 amino acids was analyzed. This method was used to compare the amino acid compositions of the following combinations: primary culture and established cells, normal and transformed cells, mammalian and bacterial cells, andEscherichia coli andStaphylococcus aureus. The amino acid compositions of mammalian cells were similar, but the amino acid compositions ofEscherichia coli andStaphylococcus aureus differed not only from mammalian cells, but also from each other. It was concluded that amino acid composition is almost independent of cell establishment and cell transformation, and that the amino acid compositions of mammalian and bacterial cells differ. Thus, it is likely that changes in amino acid composition due to cell transformation or species differences between mammalian cells are negligible compared with the differences between mammalian and bacterial cells, which are more distantly related.     

Using cellular automata images and pseudo amino acid composition to predict protein subcellular location

Summary. The avalanche of newly found protein sequences in the post-genomic era has motivated and challenged us to develop an automated method that can rapidly and accurately predict the localization of an uncharacterized protein in cells because the knowledge thus obtained can greatly speed up the process in finding its biological functions. However, it is very difficult to establish such a desired predictor by acquiring the key statistical information buried in a pile of extremely complicated and highly variable sequences. In this paper, based on the concept of the pseudo amino acid composition (Chou, K. C. PROTEINS: Structure, Function, and Genetics, 2001, 43: 246–255), the approach of cellular automata image is introduced to cope with this problem. Many important features, which are originally hidden in the long amino acid sequences, can be clearly displayed through their cellular automata images. One of the remarkable merits by doing so is that many image recognition tools can be straightforwardly applied to the target aimed here. High success rates were observed through the self-consistency, jackknife, and independent dataset tests, respectively.     

Conservation of the basic pattern of cellular amino acid composition during biological evolution in plants

The cellular amino acid composition of plant cells was analyzed. The callus of carrot (Daucus carota), leaves of Torenia fournieri and protocomb-like body of Cymbidium, s.p. were examined as examples of plant cells. The cellular amino acid compositions differed in the plant cells, but their basic patterns were quite similar. It is concluded that the basic pattern of the cellular amino acid composition is conserved in all terrestrial organisms, including plants.     

Variations in the amino acid composition of cyanophycin in the cyanobacterium Synechocystis sp. PCC 6308 as a function of growth conditions

Gas chromatography-mass spectrometry studies of the nitrogen isotopic composition of the N-trifluoroacetyl n-butyl ester derivatives of the amino acids from isolated hydrolyzed cyanophycin from ¹⁵N-enriched cells led to two major findings: (1) the amino acid composition of this granular polypeptide, isolated using procedures optimized for extracting and purifying cyanophycin from cells in the stationary growth phase, varied with the culture growth condition; (2) the rate of incorporation of exogenous nitrate differed for each nitrogen atom of the amino acid constituents of cyanophycin or cyanophycin-like polypeptide. Arginine and aspartic acid were the principle components of cyanophycin isolated from exponentially growing cells and from light-limited stationary phase cells, with glutamic acid as an additional minor component. The cyanophycin-like polypeptide from nitrogen-limited cells contained only aspartic and glutamic acids, but no arginine. The glutamic acid content decreased and arginine content increased as nitrate was provided to nitrogen-limited cells. These cells rapidly incorporated nitrate at different rates at each cyanophycin nitrogen site: guanidino nitrogens of arginine>aspartic acid >-amino nitrogen of arginine>glutamic acid. Little media-derived nitrogen was incorporated into cyanophycin of exponentially growing cells during one cellular doubling time.Abbreviations asp-TAB, glu-TAB, arg-TAB N-Trifluoroacetyl n-butyl ester derivatives of aspartic acid, glutamic acid and arginine, respectively - CAP chloramphenicol - CF correction factor - TFAA Trifluoroacetic anhydride - MBTFA N-Methyl-bis-trifluoroacetamide     

Phenotypic selection on nectar amino acid composition in the Lepidoptera pollinated orchid species Gymnadenia conopsea

Plant–pollinator interactions are potential drivers of evolution in floral traits. Because nectar chemical composition is known to mediate both plant–pollinator interactions and plant reproductive success, it can be expected that chemical composition of nectar is subjected to strong pollinator‐mediated selective forces. However, the extent of natural selection on different nectar components has not been studied so far. Using the Lepidoptera pollinated fragrant orchid Gymnadenia conopsea as a model species, we used high‐performance anion‐exchange chromatography (HPAEC) to characterize the sugar and amino acid composition of floral nectar in three calcareous grassland populations of G. conopsea. We then measured phenotypic selection on nectar composition and on other plant and floral traits through applying both linear regression and structural equation modelling. We demonstrate phenotypic selection on plant height, inflorescence height and on specific nectar amino acids, whereas spur length, total sugar and amino acid concentration were not direct targets of selection. Chemical nectar composition is thus indeed under selective pressure but nectar amino acids are much more important to fitness of G. conopsea, as compared to nectar sugars. Furthermore, as we found no evidence of selection on the total amino acid concentration, it is unlikely that amino acids increase pollinator attraction because they are a pollinator nitrogen source. To further unravel the evolutionary ecology of floral nectar, behavioural experiments with pollinators exposed to different nectar components and studies experimentally identifying the selective agents are recommended.     

A comparison between the amino acid composition of an egg parasitoid wasp and some of its hosts

Amino acid compositions of the eggs of five lepidopteran hosts for Trichogramma minutum were compared with each other and with a non-host species, Rhodnius prolixus, in which T. minutum oviposits but does not develop. Host eggs are quite homogeneous, particularly when compared according to groupings of potentially interconvertible amino acids. Combined mole percent values for glycine, serine and alanine were higher in hosts (27.5–29.2 mole%) than in R. prolixus eggs (21.5 mole%), in bovine serum albumin (14.9%), which has been used as a protein source in artificial diets for T. minutum, or in many of the mixtures used in published diets for this species. Since these three amino acids make up 26.3 mole% of the adult amino acid content of T. minutum, their deficiency in diets could require metabolic compensation detrimental to development.Adult T. minutum arising from eggs of Manduca sexta, Choristoneura fumiferana, and Sitotroga cerealella are similar in amino acid composition to each other and, in general, to their hosts. Variability appears greater in hosts than in adult wasp composition, suggesting some interconversion of host amino acids to accommodate inflexible nutritional requirements of T. minutum.In the three host species tested, free amino acids constituted 15.8–19.3% by weight of the amino acid in egg contents. In M. sexta eggs, glycine, serine and alanine together make up 28.4% by weight of the total free amino acid, a much higher proportion than in many published diets. The four free amino acids (isoleucine, leucine, phenylalanine and histidine) reported to be oviposition stimulants in experiments on encapsulated diets are present in sufficient concentrations to induce oviposition in the host species tested and in R. prolixus. S. cerealella egg contents having approximately 1.8 g amino acid, yield one or rarely two adult T. minutum (1g amino acid/insect). In contrast, M. sexta eggs with 94 g amino acid each yield an average of 10–12 adults (8.2g amino acid/insect). This suggests that small hosts are allocated few eggs which can only develop into small adults because of nutrient supply (parasitoid size in metabolically restricted), whereas much larger hosts are allocated proportionately fewer eggs than the former resulting in larger, and presumably more viable and fecund, adults (parasitoid size is established behaviourally).     

Effect of growth temperature and media composition on the fatty acid composition of Bacillus stearothermophilus AN 002

The influence of growth temperature, media composition and cell age on the chemical composition of Bacillus stearothermophilus strain AN 002 has been determined. The total cellular protein decreased and the free amino acid content increased with growth temperature, in both exponential and stationary growth phase. The protein and free amino acid contents of cells were higher in the stationary phase than in the exponential phase, irrespective of growth temperature and media composition. The RNA content was only reduced in cells grown at 55° C. No significant variations were observed in the DNA and carbohydrate contents with respect to growth temperature and cell age. The total lipid and fatty acid compositions on the other hand varied as a function of growth temperature, cell age and media composition. Differences in the relative concentrations of even, odd and branched chain fatty acids were noticed. Novariation was observed in the antiiso and unsaturated fatty acids with respect to growth temperature. The unique variations in the fatty acid composition and total lipids at the growth temperature of 50° C and their variations in the stationary growth phase seem to be characteristic for B. stearothermophilus AN 002.     

Protein subunits and amino acid composition of wild lentil

Three wild species of lentil, Lens orientalis, L. ervoides and L. nigricans were investigated for protein subunits of the albumin protein fraction (APF), globulin protein fraction (GPF) and for protein and free amino acid composition. The APF and GPF formed 12.7–16.8 % and 34.7–49.0 %, respectively, of the meal nitrogen. SDS-PAGE showed APF to contain 15 to 20 major and a similar number of minor protein subunits ranging in M_r at least from 14 400 to 94 000. The GPF was also heterogenous and contained some subunits having M_r similar to APF subunits but none < 15 000. The three wild lentil species were distinguishable by their protein subunit composition. The protein amino acid composition of the wild species was identical and similar to that of the cultivated lentil. The wild species, like the cultivated species (L. culinaris), contained major amounts of free arginine, glutamic and aspartic acids, serine and a number of unidentified amino acids. L. orientalis, L. nigricans and the cultivated lentil contained two acidic and two basic unidentified amino acids. However, L. ervoides was distinctly different in that it contained only the two acidic plus one neutral unidentified amino acid, but none of the two basic unidentified amino acids.     

Multiomics approach reveals a role of translational machinery in shaping maize kernel amino acid composition

Maize (Zea mays) seeds are a good source of protein, despite being deficient in several essential amino acids. However, eliminating the highly abundant but poorly balanced seed storage proteins has revealed that the regulation of seed amino acids is complex and does not rely on only a handful of proteins. In this study, we used two complementary omics-based approaches to shed light on the genes and biological processes that underlie the regulation of seed amino acid composition. We first conducted a genome-wide association study to identify candidate genes involved in the natural variation of seed protein-bound amino acids. We then used weighted gene correlation network analysis to associate protein expression with seed amino acid composition dynamics during kernel development and maturation. We found that almost half of the proteome was significantly reduced during kernel development and maturation, including several translational machinery components such as ribosomal proteins, which strongly suggests translational reprogramming. The reduction was significantly associated with a decrease in several amino acids, including lysine and methionine, pointing to their role in shaping the seed amino acid composition. When we compared the candidate gene lists generated from both approaches, we found a nonrandom overlap of 80 genes. A functional analysis of these genes showed a tight interconnected cluster dominated by translational machinery genes, especially ribosomal proteins, further supporting the role of translation dynamics in shaping seed amino acid composition. These findings strongly suggest that seed biofortification strategies that target the translation machinery dynamics should be considered and explored further.

An integrated approach reveals the key role of translational machinery in maize kernel amino acid natural variation and homeostasis, highlighting targets for seed amino acid biofortification.     

Changes in the amino acid composition and protein modification in phloem sap of rice

Pure phloem sap was collected from insects feeding on rice (Oryza sativa L.) leaves by a laser technique similar to the aphid stylet technique. Rapid circulation of nitrogen in the sieve tubes was demonstrated directly using ¹⁵N as a tracer. Application to the roots of the metabolic inhibitors of amino acids, aminooxyacetate and methioninesulfoximine, changed the amino acid composition in the sieve tubes. Feeding methionine to leaf tips resulted in its bulk transfer into the sieve tubes. In vitro experiments confirmed the existence of protein kinases in the pure rice phloem sap. The phosphorylation status of the sieve tube sap proteins was affected by the light regime. The possibility that changes in chemical composition or protein modification such as phosphorylation in the sieve tubes might affect plant growth are discussed.Analysis of pure phloem sap collected from rice plants by insect laser technique has shown dynamic changes in the chemical composition and the quality of proteins in the sap.     

Effect of ploidy variation on amino acid composition ofDatura innoxia (Solanaceae)

In haploid, diploid, triploid, tetraploid and hexaploid cytotypes of the scopalamine-yieldingDatura innoxia, the amino acid profiles were studied. The results suggest that the amino acid composition is influenced quantitatively by increasing ploidy levels, but in an irregular way.     

湖南道地白芷氨基酸含量与组成分析

白芷是我国常用中药材的一种,关于白芷镇痛的有效成分,主要认为是异欧前胡素、欧前胡素等香豆素类具有解痉、镇痛等作用的挥发油类化学成分,但白芷镇痛的成分及其机理尚不十分清楚,是否有其他物质也具有一定的药理作用也不得而知,比如说某些药效性氨基酸。该研究采用自动氨基酸分析仪测定了湖南道地茶陵白芷的蛋白质类氨基酸和游离氨基酸的含量,并分析其氨基酸组成。结果表明:总氨基酸检出除Asn以外的其他16种蛋白质氨基酸,含量最高的Arg占总氨基酸的31.21%,接近1/3;必需氨基酸总量达27.01%,其中含量最高的是Leu,占总必需氨基酸的24.14%;药效氨基酸比例较高,在酸水解产物总氨基酸和游离氨基酸中分别达到73.89%和85.78%,其中Arg的含量最高,达1.383g·100g-1,占比为42.24%,游离氨基酸中γ-氨基丁酸、鸟氨酸含量也较高。此外,还含有少量的高半胱氨酸和鹅肌肽等游离非蛋白质氨基酸和短肽;必需氨基酸的组成接近WHO/FAO的建议摄入值,但Met+Cys的RC值最小,为第一限制性氨基酸。这些药效性氨基酸和游离氨基酸可能是茶陵白芷具有良好药效的一个因素,而且茶陵白芷的氨基酸组成和配比较合理、符合人体需要,在强化含硫氨基酸的基础上具有开发成为新型药食同源保健性食品的潜力。研究结果可为进一步研究白芷的药理作用提供依据。     

Amino acid composition and the evolutionary rates of protein-coding genes

Summary Based on the rates of amino acid substitution for 60 mammalian genes of 50 codons or more, it is shown that the rate of amino acid substitution of a protein is correlated with its amino acid composition. In particular, the content of glycine residues is negatively correlated with the rate of amino acid substitution, and this content alone explains about 38% of the total variation in amino acid substitution rates among different protein families. The propensity of a polypeptide to evolve fast or slowly may be predicted from an index or indices of protein mutability directly derivable from the amino acid composition. The propensity of an amino acid to remain conserved during evolutionary times depends not so much on its being features prominently in active sites, but on its stability index, defined as the mean chemical distance [R. Grantham (1974) Science 185862–864] between the amino acid and its mutational derivatives produced by single-nucleotide substitutions. Functional constraints related to active and binding sites of proteins play only a minor role in determining the overall rate of amino acid substitution. The importance of amino acid composition in determining rates of substitution is illustrated with examples involving cytochrome c, cytochrome b₅,ras-related genes, the calmodulin protein family, and fibrinopeptides.     

Mito-GSAAC: mitochondria prediction using genetic ensemble classifier and split amino acid composition

Mitochondria are all-important organelles of eukaryotic cells since they are involved in processes associated with cellular mortality and human diseases. Therefore, trustworthy techniques are highly required for the identification of new mitochondrial proteins. We propose Mito-GSAAC system for prediction of mitochondrial proteins. The aim of this work is to investigate an effective feature extraction strategy and to develop an ensemble approach that can better exploit the advantages of this feature extraction strategy for mitochondria classification. We investigate four kinds of protein representations for prediction of mitochondrial proteins: amino acid composition, dipeptide composition, pseudo amino acid composition, and split amino acid composition (SAAC). Individual classifiers such as support vector machine (SVM), k-nearest neighbor, multilayer perceptron, random forest, AdaBoost, and bagging are first trained. An ensemble classifier is then built using genetic programming (GP) for evolving a complex but effective decision space from the individual decision spaces of the trained classifiers. The highest prediction performance for Jackknife test is 92.62% using GP-based ensemble classifier on SAAC features, which is the highest accuracy, reported so far on the Mitochondria dataset being used. While on the Malaria Parasite Mitochondria dataset, the highest accuracy is obtained by SVM using SAAC and it is further enhanced to 93.21% using GP-based ensemble. It is observed that SAAC has better discrimination power for mitochondria prediction over the rest of the feature extraction strategies. Thus, the improved prediction performance is largely due to the better capability of SAAC for discriminating between mitochondria and non-mitochondria proteins at the N and C terminus and the effective combination capability of GP. Mito-GSAAC can be accessed at . It is expected that the novel approach and the accompanied predictor will have a major impact to Molecular Cell Biology, Proteomics, Bioinformatics, System Biology, and Drug Development.     

Fatty acid composition of selected prosthecate bacteria

The cellular fatty acid composition of 14 strains of Caulobacter species and types, two species of Prosthecomicrobium, and two species of Asticcacaulis was determined by gas-liquid chromatography. In most of these bacteria, the major fatty acids were octadecenoic acid (C18:1), hexadecenoic acid (C16:1) and hexadecanoic acid (C16:0). Some cyclopropane and branched chain fatty acids were detected in addition to the straight chained acids. Hydroxytetradecanoic acid was an important component of P. enhydrum but significant amounts of hydroxy acids were not detected in other prosthecate bacteria examined.Abbreviations DEGS diethylene glycol succinate - A measare of association Dedicated to Prof. R. Y. Stanier on the occasion of his 60th birthday     

A precise method for the quantitation of proteins taking into account their amino acid composition.

A method for the quantitation of protein in biological material is described which gives the same response for all proteins irrespective of their amino acid composition. The method is based on the ninhydrin reaction of amino acids released after total acid hydrolysis of 5- to 20-μl solutions containing 1 to 100 μg of protein. The ammonia is released from the hydrolysate by diffusion and the amino acids are quantitated without fractionation using the continuous-flow system of an amino acid analyzer. Calibration is obtained with solutions of known amino acid content. The protein of a sample is calculated by multiplying the nanomoles of total amino acids found by a conversion factor F. F is the weight in micrograms of 1 nmol of the specific mixture of amino acid residues that the protein of the sample is composed of F has to be determined once for all further quantitations of the same material by quantitative amino acid analysis following standard procedures. By this method as little as 30 ng of protein per aliquot of hydrolysate analyzed can be determined.     

Effect of sound and Lenzites-decayed wood on the amino acid composition of Reticulitermes flavipes

In hydrolysates of the eastern subterranean termite, Reticulitermes flavipes, the most abundant protein amino acids (μmoles) were glycine, alanine, and glutamic acid; the least abundant were methionine and histidine. Sawdust from both sound and Lenzites trabea-decayed sapwood blocks of sugar maple, loblolly pine, and slash pine was force-fed to termites. A diet of decayed rather than sound wood had little effect on protein amino acid composition of the termites; glycine content varied the most. In contrast, diet affected the free amino acid composition. Except for glutamic acid, the major protein amino acids of the termites were not the predominant free amino acids. Tyrosine and histidine were relatively more abundant as free than as protein amino acids. Greatest differences in protein amino acid compositions of sound and decayed wood were in contents of glycine, leucine, lysine, and arginine.