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.     

Occurrence of motifs with six amino acid residues in three eukaryotic proteomes

Now it is known that 18 neurological inherited diseases connected with mutations of multiple insertion of one amino acid residue in protein sequence. Therefore, studying the functional role of such simple motifs is an important task in biology. In this work we have investigated how often homorepeats, i.e. runs of a single amino acid residue, of 6 amino acid residues long as well as simple motifs consisting from two amino acid residues of 6 residues long situated in any position occur in three eukaryotic well studied proteomes: Homo sapiens, Drosophila melanogaster, Caenorhabditis elegans. It turns out that many simple motifs occur very often. The occurrence for each motif can be found at our site: http://antares.protres.ru/motifs_six_residues.html. One can suggest that such short similar motifs are responsible for the common functions for nongomologous, unrelated proteins from different organisms.     

Evolution of the Regular Zone of Histone H1 in Fabaceae Plants

An analysis of the histone H1 subtype, H1-1, in eight legumes belonging to four genera of the tribe Vicieae (Pisum, Lathyrus, Lens, and Vicia), revealed an extended region consisting of the tandemly repeated AKPAAK motifs. We named this region the Regular zone (RZ). The AKPAAK motifs are organized into two blocks separated by a short (two or six amino acids) intervening sequence (IS). The distal block contains six AKPAAK motifs, while the number of repeats in the proximal block varies from six in V. faba to seven in the other species. In V. hirsuta, the first two repeated units of the proximal block are octapeptides AKAKPAAK. The apparent rate of synonymous substitutions in the blocks of RZ is much higher than in the rest of the gene. This can be explained by repeat shuffling within each block. In the C-domain of the orthologous H1 subtype from Medicago truncatula (tribe Trifolieae), a region corresponding to the RZ of Vicieae species was found. It also consists of two blocks of AKPAAK motifs (four and three repeats in the proximal and distal blocks, respectively). These blocks are separated by a 20-amino acid IS. The first 20 amino acids of the Medicago RZ are not part of AKPAAK repeats. We hypothesise that the RZ has most probably evolved as a result of an expansion of AKPAAK repeats from two separate sites in the C-domain. This process started tens of millions of years ago and was most likely directed by positive selection.[Reviewing Editor: Dr. Martin Kreitman]     

Asparagine transport in Lactobacillus plantarum and Streptococcus faecalis

The properties of het asparagine transport systems in Lactobacillus plantarum and Streptococcus faecalis are described. In both organisms the uptake of isotopically labeled l-asparagine was markedly stimulated by glucose. Kinetic studies yielded curvilinear Lineweaver-Burk plots in both organisms. These data were most consistently accounted for in both organisms by assuming the operation of two catalytic uptake components in addition to a diffusion component. The occasional limitation of kinetic studies in distinguishing between single or multiple catalytic components is illustrated. A large selection of structurally related amino acids and other substances were tested as competitors in initial rate studies. In L. plantarum the most effective competitors. structurally related dicarboxylic acid amide derivatives were only moderately effective competitors. In contrast, the most effective competitors of l-arparagine uptake in S. faecalis were relatively small neutral amino acids such as l-alanine, l-serine. l-αaminobutyric acid, l-cysteine and l-methionine, suggesting that asparagine enters this organism by reaction with a catalyst having relatively unspecific structural discrimination among neutral amino acids. Both organisms rapidly converted a large proportion of the transported asparagine to aspartic acid. In S. faecalis, the deamidation of l-asparagine was shown to be relatively insensitive to inhibition by those amino acids which were most effective in reducing the asparagine entry rate.     

Determination of amino acids in human serum by capillary gas chromatography

A simple and rapid method for the determination of serum amino acids by gas chromatography (GC) has been developed. Following deproteinization of serum with perchloric acid, free amino acids in the supernatant were converted into their N(O,S)-isobutoxycarbonyl methyl ester derivatives and measured by GC with flame ionization detection using a DB-17 capillary column. All the derivatives of the 22 protein amino acids were completely resolved as single peaks within 9 min by GC. The calibration curves were linear in the range 0.2–50 μg of each amino acid, and the correlation coefficients were above 0.998. By using this method, serum amino acids could be directly analysed without prior clean-up procedure such as ion-exchange column chromatography except for deproteinization of the samples, and without any interference from coexisting substances. Overall recoveries of amino acids added to serum samples were 88–108%. Analytical results for serum amino acids from normal subjects are presented.     

Amino acid utilization patterns in clostridial taxonomy

The polyamide layer technique for the chromatographic separation of dimethylaminonaphthalene sulphonyl amino acids has been adapted to the qualitative analysis of amino acids in media before and after the growth of micro-organisms. The method has been used to study the amino acids metabolized by cultures of proteolytic clostridia growing in a medium consisting of an acid hydrolysate of casein as a source of amino acids and small amounts of yeast extract and trypticase as sources of growth factors. The chromatograms of the media after growth showed which amino acids were used and which new amino acids were produced. Clostridium botulinum type F (proteolytic), C. ghoni, C. mangenoti and C. putrificum were found to reduce proline to 5-aminovaleric acid and to produce 2-aminobutyric acid, properties they shared with C. sporogenes and C. sticklandii. C. botulinum type G and C. subterminale used glycine, lysine, serine, and arginine but in contrast to C. sticklandii they neither reduced proline to 5-aminovaleric acid nor produced 2-aminobutyric acid. Both organisms oxidized phenylalanine, tyrosine and tryptophan to phenylacetic acid, p-hydroxyphenyl acetic acid and indole acetic acid respectively. C. lituseburense and C. scatologenes used serine, threonine and arginine and produced 2-amino butyric acid and ornithine. C. lentoputrescens, C. limosum and C. malenomenatum resembled C. tetanomorphum by using glutamic acid and tyrosine. The chromatograms always showed the physiological group to which an organism belonged and in some cases were characteristic of the species.Abbreviations Abu 2-aminobutyric acid - Ava 5-aminovaleric acid - DNS 1-dimethyaminonaphthalene-5-sulphonyl - DNS-Cl the sulphonyl chloride - DNS-NH₂ the sulphonamide - DNS-OH the sulphonic acid - VFA steam volatile fatty acid - u unknown     

Is the Profile of Fatty Acids,Tocopherols, and Amino Acids Suitable to Differentiate Pinus armandii Suspicious to Be Responsible for the Pine Nut Syndrome from Other Pinus Species?

Pinus armandii is suspicious to be responsible for the Pine Nut Syndrome, a long lasting bitter and metallic taste after the consumption of pine nuts. To find chemical characteristic features for the differentiation of P. armandii from other Pinus species, 41 seed samples of the genus Pinus from 22 plant species were investigated regarding the content and the composition of fatty acids, tocopherols, and amino acids. The predominant fatty acids in the seed oils were linoleic acid (35.2 – 58.2 g/100 g), oleic acid (14.6 – 48.5 g/100 g), and pinolenic acid (0.2 – 22.4 g/100 g), while the vitamin‐E‐active compounds were dominated by γ‐tocopherol. The amino acid composition was mainly characterized by arginine and glutamic acid with amounts between 0.9 and 8.9 g/100 g as well as 2.1 g/100 g and 8.3 g/100 mg. On the basis of this investigation, a Principle Component Analysis has been used to identify the most important components for the differentiation of P. armandii from other Pinus species. Using the data for glutamic acid, 20:2Δ^5,11, 18:3Δ^5,9,12, 18:1Δ⁹, and oil content, a classification of the 41 samples into four different groups by cluster analysis was possible, but the characteristic features of P. armandii were too close to some other members of the genus Pinus, making a clear differentiation of this species difficult. Nevertheless, the investigation showed the similarities of different members of the genus Pinus with regard to fatty acids, vitamin‐E‐active compounds, and amino acids.     

Role of Riboflavin and Certain Amino Acids in the Excystment of Schizopyrenus russelli*

SYNOPSIS. A simple medium, consisting of riboflavin and a mixture of L-glutamic acid, L-tryptophan, L-isoleucine, L-serine, and L-proline has been shown to induce rapid and mass scale excystment in Schizopyrenus russelli. Whereas percentage excystment was found to depend on the concentration of riboflavin and amino acids, more than 80% of cysts were found to excyst within 4 hr, when adequate amounts of these were supplied. Several individual amino acids, particularly L-glutamic acid, L-tryptophan, and L-proline, also supported considerable excystment, but riboflavin was always indispensable.     

Selection on Synthesis Cost Affects Interprotein Amino Acid Usage in All Three Domains of Life

Most investigations of the forces shaping protein evolution have focussed on protein function. However, cells are typically 50%–75% protein by dry weight, with protein expression levels distributed over five orders of magnitude. Cells may, therefore, be under considerable selection pressure to incorporate amino acids that are cheap to synthesize into proteins that are highly expressed. Such selection pressure has been demonstrated to alter amino acid usage in a few organisms, but whether “cost selection” is a general phenomenon remains unknown. One reason for this is that reliable protein expression level data is not available for most organisms. Accordingly, I have developed a new method for detecting cost selection. This method depends solely on interprotein gradients in amino acid usage. Applying it to an analysis of 43 whole genomes from all three domains of life, I show that selection on the synthesis cost of amino acids is a pervasive force in shaping the composition of proteins. Moreover, some amino acids have different price tags for different organisms—the cost of amino acids is changed for organisms living in hydrothermal vents compared with those living at the sea surface or for organisms that have difficulty acquiring elements such as nitrogen compared with those that do not—so I also investigated whether differences between organisms in amino acid usage might reflect differences in synthesis or acquisition costs. The results suggest that organisms evolve to alter amino acid usage in response to environmental conditions. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. [Reviewing Editor: Hector Musto]     

A Functional Aqp1 Gene Product Localizes on The Contractile Vacuole Complex in Paramecium multimicronucleatum

In a ciliate Paramecium, the presence of water channels on the membrane of contractile vacuole has long been predicted by both morphological and physiological data, however, to date either the biochemical or the molecular biological data have not been provided. In the present study, to examine the presence of aquaporin in Paramecium, we carried out RT-PCR with degenerated primers designed based on the ParameciumDB, and an aquaporin cDNA (aquaporin 1, aqp1) with a full-length ORF encoding 251 amino acids was obtained from Paramecium multimicronucleatum by using RACE. The deduced amino acid sequence of AQP1 had NPA-NPG motifs, and the prediction of protein secondary structure by CNR5000 and hydropathy plot showed the presence of six putative transmembrane domains and five connecting loops. Phylogenetic analysis results showed that the amino acid sequence of AQP1 was close to that of the Super-aquaporin group. The AQP1-GFP fusion protein clearly demonstrated the subcellular localization of AQP1 on the contractile vacuole complex, except for the decorated spongiome membrane. The functional analyses of aqp1 were done by RNA interference-based gene silencing, using an established feeding method. The aqp1 was found to be crucial for the total fluid output of the cell, the function of contractile vacuole membranes.     

hfAIM: A reliable bioinformatics approach for in silico genome-wide identification of autophagy-associated Atg8-interacting motifs in various organisms

Most of the proteins that are specifically turned over by selective autophagy are recognized by the presence of short Atg8 interacting motifs (AIMs) that facilitate their association with the autophagy apparatus. Such AIMs can be identified by bioinformatics methods based on their defined degenerate consensus F/W/Y-X-X-L/I/V sequences in which X represents any amino acid. Achieving reliability and/or fidelity of the prediction of such AIMs on a genome-wide scale represents a major challenge. Here, we present a bioinformatics approach, high fidelity AIM (hfAIM), which uses additional sequence requirements—the presence of acidic amino acids and the absence of positively charged amino acids in certain positions—to reliably identify AIMs in proteins. We demonstrate that the use of the hfAIM method allows for in silico high fidelity prediction of AIMs in AIM-containing proteins (ACPs) on a genome-wide scale in various organisms. Furthermore, by using hfAIM to identify putative AIMs in the Arabidopsis proteome, we illustrate a potential contribution of selective autophagy to various biological processes. More specifically, we identified 9 peroxisomal PEX proteins that contain hfAIM motifs, among which AtPEX1, AtPEX6 and AtPEX10 possess evolutionary-conserved AIMs. Bimolecular fluorescence complementation (BiFC) results verified that AtPEX6 and AtPEX10 indeed interact with Atg8 in planta. In addition, we show that mutations occurring within or nearby hfAIMs in PEX1, PEX6 and PEX10 caused defects in the growth and development of various organisms. Taken together, the above results suggest that the hfAIM tool can be used to effectively perform genome-wide in silico screens of proteins that are potentially regulated by selective autophagy. The hfAIM system is a web tool that can be accessed at link: http://bioinformatics.psb.ugent.be/hfAIM/.     

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。     

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     

Synthesis of Photolabile Caged Amino Acids for Measuring Amino Acid Transporters

Photolabile precursors (caged compounds) of amino acids such as Ala, Leu, Lys, and Ser were prepared by some simple reactions. These compounds were designed for the rapid, photochemically initiated release of amino acids. These amino acid transporters were expressed in Xenopus oocyte by injecting mRNA prepared from rat kidney. The electrical response of each transporter was examined by applying the amino acids and caged compounds before and after photolysis. Photolysis of the caged amino acids increased the electrical response of the facilitated amino acid transporters expressed in the oocyte. Consequently, these synthesized caged amino acids would be applicable to kinetic investigations on the transporters when combined with a pulsed laser or xenon arc flash lamp.     

茶树CsCBF1基因克隆和转录活性分析

采用RACE技术克隆了一个受冷诱导的茶树CBF基因全长cDNA,命名为CsCBF1(GenBank登录号为EU563238)。CsCBF1cDNA全长序列为1 211bp,开放阅读框编码259个氨基酸。氨基酸序列分析表明,CsCBF1具有CBF家族典型的保守结构域,与其他植物的CBF具有较高的相似性;与拟南芥、辣椒和橡胶树编码的CBF相似性分别为56%、63%和56%。亚细胞定位结果表明,CsCBF1位于细胞核内。分别将10个CsCBF1缺失突变体与GAL4DNA结合域融合的结果显示,CsCBF1的羧基末端酸性结构域(第137位氨基酸至259位氨基酸)在酵母中具有转录激活活性。实时定量RT-PCR分析表明,CsCBF1基因受低温的快速诱导表达。     

Methionine motifs of copper transport proteins provide general and flexible thioether-only binding sites for Cu(I) and Ag(I)

Cellular acquisition of copper in eukaryotic organisms is primarily accomplished through high-affinity copper transport proteins (Ctr). The extracellular N-terminal regions of both human and yeast Ctr1 contain multiple methionine residues organized in copper-binding Mets motifs. These motifs comprise combinations of methionine residues arranged in clusters of MXM and MXXM, where X can be one of several amino acids. Model peptides corresponding to 15 different Mets motifs were synthesized and determined to selectively bind Cu(I) and Ag(I), with no discernible affinity for divalent metal ions. These are rare examples of biological thioether-only metal binding sites. Effective dissociation constant (K _D) values for the model Mets peptides and Cu(I) were determined by an ascorbic acid oxidation assay and validated through electrospray ionization mass spectrometry and range between 2 and 11 μM. Affinity appears to be independent of pH, the arrangement of the motif, and the composition of intervening amino acids, all of which reveal the generality and flexibility of the MX_1–2MX_1–2M domain. Circular dichroism spectroscopy, ¹H-NMR spectroscopy, and X-ray absorption spectroscopy were also used to characterize the binding event. These results are intended to aid the development of the still unknown mechanism of copper transport across the cell membrane.     

The amino acid transport systems of the autotrophically grown green alga Chlorella

The kinetic analysis of l-amino acid uptake by the green alga Chlorella revealed at least seven different uptake systems to be present in cells grown autotrophically with nitrate as nitrogen source. There is a ‘general system’ which transports most neutral and acidic amino acids, a system for short-chain neutral amino acids including proline, a system for basic amino acids including histidine, a special system for acidic amino acids, and specific systems for methionine, glutamine and threonine. The ‘general system’ is possibly the same as that which can be stimulated by incubation of cells in glucose plus ammonium (Sauer, N. (1984) Planta 161, 425–431). The incubation of Chlorella in glucose induces the increased synthesis of six amino acid uptake systems, namely the above-mentioned system for short-chain neutral amino acids, a threonine system, a methionine system, and a glutamine system. These results indicate that the uptake of l-amino acids by the green alga Chlorella is as complex as in other free-living organisms such as bacteria or yeast. The small number of amino acid uptake systems found in cells of higher plants, i.e. two or three, seems therefore to be a consequence of integration of the cells in a tissue supplying a relatively constant environment, and not a consequence of autotrophic growth on mineral carbon and mineral nitrogen.