Amino acid neurotransmitters: separation approaches and diagnostic value

Amino acids in the central nervous system can be divided into non-neurotransmitter or neurotransmitter depending on their function. The measurement of these small molecules in brain tissue and extracellular fluid has been used to develop effective treatment strategies for neuropsychiatric and neurodegenerative diseases and for the diagnosis of such pathologies. Here we describe the separation and detection techniques that have been used for the measurement of amino acids at trace levels in brain tissue and dialysates. An overview of the function of amino acid transmitters in the brain is given. In addition, the type of sampling techniques that are used for the determination of amino acid levels in the brain is described.     

Genetic code correlations: Differential rates of non-enzymatic activation of hydrophobic amino acids by ATP

The relative rates of non-enzymatic activation of several hydrophobic amino acids by ATP have been found to bear an interesting relationship to the ordering of these amino acids in the genetic anticode. All of these hydrophobic amino acids (phe, leu, val, ile and met) have adenylic acid, the most hydrophobic nucleotide, as the central and most important member of their anticodons, and the ordering of their relative rates of nonenzymatic activation by ATP has been found not to correlate with the ordering of the hydrophobicities of the amino acids themselves, but rather with the ordering of the average estimates of the hydrophobicities of their respective anticodonic dinucleotides. These data suggest that the genetic code is based not just on hydrophobic relationships or affinities between amino acids and nucleotides, but perhaps more importantly, on the total reaction chemistry between amino acids and nucleotides.     

Beta-adrenergic control of brain uptake of large neutral amino acids

The amino acids tyrosine and tryptophan are precursors of physiologically active amines in the central nervous system. To reach the brain they have to compete with other large neutral aminio acids (LNAA) for the normally saturated carrier by which these amino acids are transported into the brain. The beta-adrenergic agonist isoprenaline is demonstrated to cause an increase in the brain concentration of most LNAA without a concomitant decrease in any of them. This finding indicates that the transport of LNAA into the brain is regulated by a beta-adrenergic mechanism.     

Metabolic costs of amino acid and protein production in Escherichia coli

Escherichia coli is the most popular microorganism for the production of recombinant proteins and is gaining increasing importance for the production of low-molecular weight compounds such as amino acids. The metabolic cost associated with the production of amino acids and (recombinant) proteins from glucose, glycerol and acetate was determined using three different computational techniques to identify those amino acids that put the highest burden on the biosynthetic machinery of E. coli. Comparing the costs of individual amino acids, we find that methionine is the most expensive amino acid in terms of consumed mol of ATP per molecule produced, while leucine is the most expensive amino acid when taking into account the cellular abundances of amino acids. Moreover, we show that the biosynthesis of a large number of amino acids from glucose and particularly from glycerol provides a surplus of energy, which can be used to balance the high energetic cost of amino acid polymerization.     

Variation of enzyme activities and metabolite levels in 24 Arabidopsis accessions growing in carbon-limited conditions

Our understanding of the interaction of carbon (C) metabolism with nitrogen (N) metabolism and growth is based mainly on studies of responses to environmental treatments, and studies of mutants and transformants. Here, we investigate which metabolic parameters vary and which parameters change in a coordinated manner in 24 genetically diverse Arabidopsis (Arabidopsis thaliana) accessions, grown in C-limited conditions. The accessions were grown in short days, moderate light, and high nitrate, and analyzed for rosette biomass, levels of structural components (protein, chlorophyll), total phenols and major metabolic intermediates (sugars, starch, nitrate, amino acids), and the activities of seven representative enzymes from central C and N metabolism. The largest variation was found for plant weight, reducing sugars, starch at the end of the night, and several enzyme activities. High levels of one sugar correlated with high levels of other sugars and starch, and a trend to increased amino acids, slightly lower nitrate, and higher protein. The activities of enzymes at the interface of C and N metabolism correlated with each other, but were unrelated to carbohydrates, amino acid levels, and total protein. Rosette weight was unrelated or showed a weak negative trend to sugar and amino acid contents at the end of the day in most of the accessions, and was negatively correlated with starch at the end of the night. Rosette weight was positively correlated with several enzyme activities. We propose that growth is not related to the absolute levels of starch, sugars, and amino acids; instead, it is related to flux, which is indicated by the enzymatic capacity to use these central resources.     

Sequencing of the nuclear gene for the yeast cytochrome c1 precursor reveals an unusually complex amino-terminal presequence.

Cytochrome c1 is a component of the mitochondrial respiratory chain in most eukaryotes. The protein is coded by nuclear DNA, synthesized as a larger precursor outside the mitochondria and then cleaved to the mature form in two successive steps during its import into the mitochondria. We have cloned the structural gene for yeast cytochrome c1 by functional complementation of a cytochrome c1-deficient yeast mutant with a yeast genomic library in the yeast-Escherichia coli 'shuttle' vector YEp 13. The complete nucleotide sequence of the gene and of its 5'- and 3'-flanking regions was determined. The deduced amino acid sequence of the yeast cytochrome c1 precursor reveals an unusually long transient amino-terminal presequence of 61 amino acids. This presequence consists of a strongly basic amino-terminal region of 35 amino acids, a central region of 19 uncharged amino acids and an acidic carboxy-terminal region of seven amino acids. This tripartite structure of the presequence resembles that of the precursor of cytochrome c peroxidase and supports a previous suggestion on the import pathways of these two precursors.     

Amino acid cost and codon-usage biases in 6 prokaryotic genomes: a whole-genome analysis

For most prokaryotic organisms, amino acid biosynthesis represents a significant portion of their overall energy budget. The difference in the cost of synthesis between amino acids can be striking, differing by as much as 7-fold. Two prokaryotic organisms, Escherichia coli and Bacillus subtilis, have been shown to preferentially utilize less costly amino acids in highly expressed genes, indicating that parsimony in amino acid selection may confer a selective advantage for prokaryotes. This study confirms those findings and extends them to 4 additional prokaryotic organisms: Chlamydia trachomatis, Chlamydophila pneumoniae AR39, Synechocystis sp. PCC 6803, and Thermus thermophilus HB27. Adherence to codon-usage biases for each of these 6 organisms is inversely correlated with a coding region's average amino acid biosynthetic cost in a fashion that is independent of chemoheterotrophic, photoautotrophic, or thermophilic lifestyle. The obligate parasites C. trachomatis and C. pneumoniae AR39 are incapable of synthesizing many of the 20 common amino acids. Removing auxotrophic amino acids from consideration in these organisms does not alter the overall trend of preferential use of energetically inexpensive amino acids in highly expressed genes.     

Optimizing the protein nutrition of growing-finishing pigs

Growing-finishing pigs should consume each day the minimum amounts of energy and amino acids needed for maximum lean deposition. This should optimize performance traits, carcass leanness, and N excretion. These ideal conditions are difficult to achieve under experimental or farm conditions due to the factors affecting amino acid requirements and feed intake on a daily basis. Lean deposition rate and sex are two of the major factors affecting amino acid needs. If possible, maximum lean deposition rates should be determined for each herd in order to customize feeding programs, and split-sex feeding will improve N utilization.

Amino acid requirements have been determined empirically and by the factorial method. The latter is preferred if the efficiency of use of absorbed amino acids can be accurately determined. Development of computer models will likely be needed to accomplish this. Apparent ileal digestibility of amino acids is the most practical means of estimating amino acid absorption at present, although it likely overestimates amino acid availability for some amino acids.

Crystalline amino acids can be used to improve amino acid balance and reduce excessive intake of protein which should improve feed efficiency. A portion of the high-quality protein feeds in pig diets can be replaced by synthetic amino acids without sacrificing performance, but the effects of these substitutions on carcass merit is uncertain.

Excretion of N, and the concomitant reduction of N in manure that has to be disposed of, can be manipulated nutritionally by increased use of crystalline amino acids to lower dietary protein, by use of highly digestible feedstuffs and by precise matching of amino acid needs to amino acid supply. Use of these factors could lead to a reduction in total N wastes of 20–30%.     

Engineering of a novel thioether bridge and role of modified residues in the lantibiotic Pep5.

Pep5 is a 34-amino-acid antimicrobial peptide, produced by Staphylococcus epidermidis 5, that contains the thioether amino acids lanthionine and methyllanthionine, which form three intramolecular ring structures. In addition, two didehydrobutyrines are present in the central part of the lantibiotic and an oxobutyryl residue is located at the N terminus. All rare amino acids are introduced by posttranslational modifications of a ribosomally made precursor peptide. To elucidate the function of the modified residues for the antimicrobial action of Pep5, mutant peptides, in which single modified residues had been eliminated, were produced by site-directed mutagenesis. All of these peptides showed a reduced antimicrobial activity. In addition, those peptides from which the ring structures had been deleted became susceptible to proteolytic digest. This demonstrates that the ring structures serve as stabilizers of conformations essential for activity, e.g., amphiphilicity, as well as for protecting Pep5 against proteases of the producing strains. In addition, residues that could serve as precursors of new modified amino acids in lantibiotics were introduced into the Pep5 precursor peptide. This way, a novel methyllanthionine and a didehydroalanine were inserted into the flexible central part of Pep5, demonstrating that biosynthesis of modified amino acids is feasible by protein engineering and use of the lantibiotic modification system.     

Modulation of amino acid neurotransmitter actions by other neurotransmitters: some examples.

Developments in the field of central neurotransmission indicate that amino acids serve as important and widespread transmitters throughout the central nervous system. There are increasing indications from recent experimental studies that several of the other central neurotransmitters may exert potent effects on central neurons by modulating the actions of amino acids. Noradrenaline and serotonin have received particular attention as potential modulators, and a wide variety of actions has been reported for them. Modulatory actions have been reported at both pre- and post-synaptic levels, including both short- and long-term effects and facilitation or inhibition of amino acid actions. Selectivity has been found both for specific receptor subtypes of the neuromodulator and for specific effects of amino acids. Examples of such selectivity are modification of actions of an amino acid with little effect on spontaneous activity or membrane properties of the target cell, or in comparison to the actions of other neurotransmitters, or even other selective amino acid analogs. Modulatory actions on amino acids have also been reported for several other neurotransmitters including acetylcholine and various peptides. Recent studies of angiotensin II demonstrate that when iontophoretically applied, it can potently and selectively block the depolarizing action of glutamate on locus coeruleus neurons. It is possible that physiological influences of these various transmitter substances are expressed through modification of amino acid actions, rather than through direct effects on central neurons.     

Evolutionary combinatorial chemistry, a novel tool for SAR studies on peptide transport across the blood-brain barrier. Part 2. Design, synthesis and evaluation of a first generation of peptides.

The use of high-throughput methods in drug discovery allows the generation and testing of a large number of compounds, but at the price of providing redundant information. Evolutionary combinatorial chemistry combines the selection and synthesis of biologically active compounds with artificial intelligence optimization methods, such as genetic algorithms (GA). Drug candidates for the treatment of central nervous system (CNS) disorders must overcome the blood-brain barrier (BBB). This paper reports a new genetic algorithm that searches for the optimal physicochemical properties for peptide transport across the blood-brain barrier. A first generation of peptides has been generated and synthesized. Due to the high content of N-methyl amino acids present in most of these peptides, their syntheses were especially challenging due to over-incorporations, deletions and DKP formations. Distinct fragmentation patterns during peptide cleavage have been identified. The first generation of peptides has been studied by evaluation techniques such as immobilized artificial membrane chromatography (IAMC), a cell-based assay, log Poctanol/water calculations, etc. Finally, a second generation has been proposed.     

Evaluation of methods for the separation and analysis of proteins and free amino acids in phytoplankton samples

Due to their importance as not only major constituents in paniculatematter but also the metabolism of nitrogen in marine microorganisms,numerous methods have been employed to measure proteins andfree amino acids. However, two difficulties frequently complicatethese measurements. First, an initial separation of proteinsfrom free amino acids is helpful since most analytical methodsare somewhat sensitive to both compound types. Second, the choiceof detection techniques that minimize response differences betweenvarious proteins or amino acids is desirable since natural samplesof microorganisms consist of mixtures of many proteins and aminoacids. To address these problems, four protein detection techniques(modified Lowry et al., Dorsey et al., Bradford and fluorescamine)and two amino acid detection techniques (fluorescamine and o-phthaldialdehyde)were evaluated. Relative extraction efficiencies for proteinfrom phytoplankton samples were also evaluated with six homogenizationsolutions/protocols (TCA, NaOH, boiling NaOH, Triton X-100,NaOH plus Triton X-100 and distilled water). TCA homogenizationyielded the highest protein recoveries, and sufficient physicalseparations between proteins and free amino acids were obtainedwith TCA concentrations between 0.18 and 0.37 M. Results ofthese studies allowed for development of a method for extracting,separating and analyzing proteins and total free amino acidsfrom a common phytoplankton sample. The procedure involves initialhomogenization in a TCA solution, followed by centrifugationto separate protein and free amino acid fractions. Proteinsare then analyzed by a modification of the Lowry et al. procedure,and amino acids by a fluorescamine procedure. ²Present address: Science Applications International Corporation,4224Campus Point Court, San Diego, CA 92121, USA     

Predicting the subcellular localization of human proteins using machine learning and exploratory data analysis

Identifying the subcellular localization of proteins is particularly helpful in the functional annotation of gene products. In this study, we use Machine Learning and Exploratory Data Analysis （EDA） techniques to examine and characterize amino acid sequences of human proteins localized in nine cellular compartments. A dataset of 3,749 protein sequences representing human proteins was extracted from the SWISS-PROT database. Feature vectors were created to capture specific amino acid sequence characteristics. Relative to a Support Vector Machine, a Multi-layer Perceptron, and a Naive Bayes classifier, the C4.5 Decision Tree algorithm was the most consistent performer across all nine compartments in reliably predicting the subcellular localization of proteins based on their amino acid sequences （average Precision=0.88; average Sensitivity=0.86）. Furthermore, EDA graphics characterized essential features of proteins in each compartment. As examples, proteins localized to the plasma membrane had higher proportions of hydrophobic amino acids; cytoplasmic proteins had higher proportions of neutral amino acids; and mitochondrial proteins had higher proportions of neutral amino acids and lower proportions of polar amino acids. These data showed that the C4.5 classifier and EDA tools can be effective for characterizing and predicting the subcellular localization of human proteins based on their amino acid sequences.     

Incorporation of non-natural amino acids into proteins

Chemical and biological diversity of protein structures and functions can be widely expanded by position-specific incorporation of non-natural amino acids carrying a variety of specialty side groups. After the pioneering works of Schultz's group and Chamberlin's group in 1989, noticeable progress has been made in expanding types of amino acids, in finding novel methods of tRNA aminoacylation and in extending genetic codes for directing the positions. Aminoacylation of tRNA with non-natural amino acids has been achieved by directed evolution of aminoacyl-tRNA synthetases or some ribozymes. Codons have been extended to include four-base codons or non-natural base pairs. Multiple incorporation of different non-natural amino acids has been achieved by the use of a different four-base codon for each tRNA. The combination of these novel techniques has opened the possibility of synthesising non-natural mutant proteins in living cells.     

An aminotransferase from Lactococcus lactis initiates conversion of amino acids to cheese flavor compounds.

The enzymatic degradation of amino acids in cheese is believed to generate aroma compounds and therefore to be involved in the complex process of cheese flavor development. In lactococci, transamination is the first step in the degradation of aromatic and branched-chain amino acids which are precursors of aroma compounds. Here, the major aromatic amino acid aminotransferase of a Lactococcus lactis subsp. cremoris strain was purified and characterized. The enzyme transaminates the aromatic amino acids, leucine, and methionine. It uses the ketoacids corresponding to these amino acids and alpha-ketoglutarate as amino group acceptors. In contrast to most bacterial aromatic aminotransferases, it does not act on aspartate and does not use oxaloacetate as second substrate. It is essential for the transformation of aromatic amino acids to flavor compounds. It is a pyridoxal 5'-phosphate-dependent enzyme and is composed of two identical subunits of 43.5 kDa. The activity of the enzyme is optimal between pH 6.5 and 8 and between 35 and 45 degrees C, but it is still active under cheese-ripening conditions.     

Feed formulations to reduce N excretion and ammonia emission from poultry manure

This summary focuses on reducing nitrogen (N) and ammonia emissions from poultry manure through the use of improved amino acid digestibilities and enzyme supplementation. Proper feed processing techniques, phase feeding, and the minimization of feed and water waste can contribute to additional minor reductions in these emissions. Reductions in environmental pollution can be achieved through improved diet formulation based on available nutrients in the ingredients, reducing crude protein (CP) levels and adding synthetic amino acids. Use of amino acid and CP digestibilities can reduce N excretion up to 40% and a 25% increase in N digestibility can be achieved with enzyme supplementation in broiler diets. Digestibilities can be measured by two methods: the excreta and ileal amino acid digestibilities. Both methods allow amino acid levels to be reduced by 10% or more. Enzyme supplementation decreases intestinal viscosity, improves metabolizable energy levels, and increases amino acid digestibilities. Many feed manufacturers still use total amino acid content to formulate feeds. To meet amino acid requirements, crystalline amino acids are needed. The use of feather, meat and bone meal must not be overestimated or underestimated and the limiting amino acids such as cystine, tryptophan, and threonine must be carefully analyzed.     

THE CONCENTRATIONS OF FREE AMINO ACIDS AND OTHER ELECTROLYTES IN CEREBROSPINAL FLUID,IN VIVO DIALYSATE OF BRAIN,AND BLOOD PLASMA OF THE DOG*

The concentrations of free amino acids in plasma, CSF and in vivo dialysates of peripheral blood (neck sac fluid) and central nervous tissue (brain sac fluid) from each of five dogs (neck sac fluid from four of five dogs) were determined by ion-exchange chromatography. Dialysates were obtained by implanting small dialysis sacs filled with a dextran-saline solution into the subcutaneous tissue of the neck or the parenchyma of the brain at least 10 weeks before sample collection. The mean plasma concentration of most amino acids was within the range of values reported in the literature for human or dog plasma. The concentrations of most amino acids were higher in the neck sac fluid than in plasma; this discrepancy, however, was, for the most part, small and could most likely be accounted for by falling plasma free amino acid levels prior to sample taking. Previous conclusions that the CSF concentrations of most amino acids are lower than plasma concentrations are confirmed, although the present work indicates that there may be considerable individual variation in the CSF/plasma distribution ratio with respect to most amino acids. In the brain sac fluid the concentration of nearly every amino acid was consistently higher than that in CSF and lower than that in the neck sac fluid. The potassium concentration in the brain sac fluid was significantly higher than, and the total osmolality significantly lower than, those in the neck sac fluid. On the assumption that the brain sac fluid represents a dialysate of the brain extracellular fluid, these results contradict recent findings (Bito and Davson , 1965; 1966) indicating that the potassium concentration of the cortex extracellular fluid is lower than that of ventricular or cisterna magna CSF and certainly lower than that of plasma. Because of this and on the basis of consideration of the reaction of the brain to a foreign body, the possibility that the implanted brain sac lay on the‘blood side’of the bloodbrain barrier was suggested. Some implications of this possibility are discussed.     

Toxins from cone snails: properties,applications and biotechnological production

Cone snails are marine predators that use venoms to immobilize their prey. The venoms of these mollusks contain a cocktail of peptides that mainly target different voltage- and ligand-gated ion channels. Typically, conopeptides consist of ten to 30 amino acids but conopeptides with more than 60 amino acids have also been described. Due to their extraordinary pharmacological properties, conopeptides gained increasing interest in recent years. There are several conopeptides used in clinical trials and one peptide has received approval for the treatment of pain. Accordingly, there is an increasing need for the production of these peptides. So far, most individual conopeptides are synthesized using solid phase peptide synthesis. Here, we describe that at least some of these peptides can be obtained using prokaryotic or eukaryotic expression systems. This opens the possibility for biotechnological production of also larger amounts of long chain conopeptides for the use of these peptides in research and medical applications.     

AAP1 transports uncharged amino acids into roots of Arabidopsis

Amino acids are available to plants in some soils in significant amounts, and plants frequently make use of these nitrogen sources. The goal of this study was to identify transporters involved in the uptake of amino acids into root cells. Based on the fact that high concentrations of amino acids inhibit plant growth, we hypothesized that mutants tolerating toxic levels of amino acids might be deficient in the uptake of amino acids from the environment. To test this hypothesis, we employed a forward genetic screen for Arabidopsis thaliana mutants tolerating toxic concentrations of amino acids in the media. We identified an Arabidopsis mutant that is deficient in the amino acid permease 1 (AAP1, At1g58360) and resistant to 10 mm phenylalanine and a range of other amino acids. The transporter was localized to the plasma membrane of root epidermal cells, root hairs, and throughout the root tip of Arabidopsis. Feeding experiments with [(14)C]-labeled neutral, acidic and basic amino acids showed significantly reduced uptake of amino acids in the mutant, underscoring that increased tolerance of aap1 to high levels of amino acids is coupled with reduced uptake by the root. The growth and uptake studies identified glutamate, histidine and neutral amino acids, including phenylalanine, as physiological substrates for AAP1, whereas aspartate, lysine and arginine are not. We also demonstrate that AAP1 imports amino acids into root cells when these are supplied at ecologically relevant concentrations. Together, our data indicate an important role of AAP1 for efficient use of nitrogen sources present in the rhizosphere.