Relative availability of nitrogen in host plants of invertebrate herbivores: three possible nutritional and physiological definitions

Summary It has been postulated that free amino acids in the diet of herbivores are a more readily available source of nitrogen than are amino acids in intact proteins. When plants are subjected to any of a number of stress factors the concentration of free amino acids in their tissues may increase relative to the protein content. It has been further postulated that such changes in available nitrogen can increase the survivorship of very young herbivores feeding on the tissues of stressed plants. In this paper, the concept of readily available nitrogen is given more specific definitions in the effort to uncover an underlying nutritional or physiological mechanism responsible for such changes in larval survivorship. The first hypothesis considered is that amino acids are more readily available than proteins in the sense that, as they occur in plant tissue, they are a more nutritious source of needed nitrogenous compounds. The second hypothesis considered is that amino acids are absorbed into the insect gut free from interference by proteinase inhibitors, and thus are more chemically available than are proteins. Finally, free amino acids, because of their solubility and greater mobility, may be more available to herbivores because of physical factors restricting the movement and digestion of proteins from plant tissue into the insect gut. The applicability of each hypothesis to certain types of insects feeding on particular plant tissues is discussed.The investigation reported in this paper (No. 86-7-224) is in connection with a project of the Kentucky Agricultural Experiment Station and is published with the approval of the Director     

Comparison of the frequency of functional SH3 domains with different limited sets of amino acids using mRNA display

Although modern proteins consist of 20 different amino acids, it has been proposed that primordial proteins consisted of a small set of amino acids, and additional amino acids have gradually been recruited into the genetic code. This hypothesis has recently been supported by comparative genome sequence analysis, but no direct experimental approach has been reported. Here, we utilized a novel experimental approach to test a hypothesis that native-like globular proteins might be easily simplified by a set of putative primitive amino acids with retention of its structure and function than by a set of putative new amino acids. We performed in vitro selection of a functional SH3 domain as a model from partially randomized libraries with different sets of amino acids using mRNA display. Consequently, a library rich in putative primitive amino acids included a larger number of functional SH3 sequences than a library rich in putative new amino acids. Further, the functional SH3 sequences were enriched from the primitive library slightly earlier than from a randomized library with the full set of amino acids, while the function and structure of the selected SH3 proteins with the primitive alphabet were comparable with those from the 20 amino acid alphabet. Application of this approach to various combinations of codons in protein sequences may be useful not only for clarifying the precise order of the amino acid expansion in the early stages of protein evolution but also for efficiently creating novel functional proteins in the laboratory.     

Liquid membrane phenomena in chlorpromazine action

Chlorpromazine has been shown, in the present study, to generate a liquid membrane at an interface in accordance with Kesting's hypothesis [5]. The specific orientation of chlorpromazine molecules in a liquid membrane with hydrophobic ends facing the permeable substances has been found to reduce the permeability of catecholamines and neuroiransmitter amino acids. This observation is discussed in the light of the orientation of receptor proteins in general. The data on transport of catecholamines and neurotransmitter amino acids are discussed in the context of the mechanism of action of chlorpromazine.     

Evolution of the Genetic Code by Incorporation of Amino Acids that Improved or Changed Protein Function

Fifty years have passed since the genetic code was deciphered, but how the genetic code came into being has not been satisfactorily addressed. It is now widely accepted that the earliest genetic code did not encode all 20 amino acids found in the universal genetic code as some amino acids have complex biosynthetic pathways and likely were not available from the environment. Therefore, the genetic code evolved as pathways for synthesis of new amino acids became available. One hypothesis proposes that early in the evolution of the genetic code four amino acids—valine, alanine, aspartic acid, and glycine—were coded by GNC codons (N = any base) with the remaining codons being nonsense codons. The other sixteen amino acids were subsequently added to the genetic code by changing nonsense codons into sense codons for these amino acids. Improvement in protein function is presumed to be the driving force behind the evolution of the code, but how improved function was achieved by adding amino acids has not been examined. Based on an analysis of amino acid function in proteins, an evolutionary mechanism for expansion of the genetic code is described in which individual coded amino acids were replaced by new amino acids that used nonsense codons differing by one base change from the sense codons previously used. The improved or altered protein function afforded by the changes in amino acid function provided the selective advantage underlying the expansion of the genetic code. Analysis of amino acid properties and functions explains why amino acids are found in their respective positions in the genetic code.     

Physico-chemical basis of the genetic code origin: stereochemical analysis of interactions of amino acids and nucleotides based on the progene hypothesis

A progene hypothesis has been proposed earlier to explain the mechanism of origin of the self-reproducing genetic system. Progenes (precursors of the genetic system) are mixed anhydrides of an amino acid and deoxyribotrinucleotide at the 3'-gamma-terminal phosphate (NpNpNppp-AA); they are produced from dinucleotides (NpNp) and 3'-gamma-aminoacylnucleotidylates (Nppp-AA) as a result of specific interaction between amino acid and dinucleotide. The postulated mechanism of progene formation accounts for the selection of substances, including chirality, the origin of the genetic code as well as for the mechanisms of formation, self-reproduction and evolution of the simpliest genetic system ("gene--polypeptide"). A stereochemical analysis of the progene formation mechanism has allowed us to support the main statements of the hypothesis that relate to the origin of the genetic code and to selection of substances. Atomic groups that could be responsible for the specificity of interaction between dinucleotides and amino acids in progene formation have been revealed. Stereochemical evidence for the physicochemical basis of the origin of the existing genetic code have been produced: 1) a special role of the second nucleotide in the codon is demonstrated in amino acid coding by the progene hypothesis principle; 2) an advantage of T against U in such coding is demonstrated; 3) for 16 amino acids out of 20 an agreement has been obtained between the optimal dinucleotide as revealed by the stereochemical analysis and the codon dinucleotides; 4) an explanation for the third nucleotide selection mechanism is offered. A restoration of the prebiotic code, based on these results, has indicated that the code contains 32 codons, is statistical and group-wise. It encodes 7 groups of isofunctional amino acids: 3 overlapping groups of non-polar amino acids 1) medium-size hydrophobic amino acids (chiefly Val, n-Val and a-But), 2) small and medium-size non-polar amino acids (chiefly Ala Val, n-Val a-But and Gly), 3) small non-polar amino acids (Gly, Ala, a-But) and 4 groups of polar amino acids--1) hydroxy--+dicarbonic (Asp, Glu, Ser and Thr), 2) dicarbonic (Asp and Glu), 3) hydroxy (Ser and Thr) and 4) basic (Arg and Lys). The code includes about 20 amino acids among which are 15-17 canonical and a few common non-canonical. The prebiotic code explains many properties of the existing genetic code and is capable of evolving into the latter by way of a gradual replacement of the physicochemical coding mechanism by the enzymatic coding mechanism.     

Amino acid sequence specificities of an adhesive recognition signal

Synthetic peptides derived from the cell-binding domain of fibronectin have previously been found to inhibit fibronectin-mediated adhesion in vitro competitively and reversibly, as well as inhibiting cell migratory events in vivo. The amino acid sequence specificity required for this inhibitory activity has been examined further using variations of the originally identified active peptide sequences. The most active small peptide was found to be the pentapeptide Gly-Arg-Gly-Asp-Ser. Although the tetrapeptide Arg-Gly-Asp-Ser was found to retain substantial activity, it was approximately threefold less active. An "inverted" peptide sequence with these same four amino acids arranged in the mirror symmetrical sequence Ser-Asp-Gly-Arg was found to be nearly as active as the forward sequence. However, the same inverted tetrapeptide sequence embedded in a synthetic decapeptide derived from a sequence of histocompatibility antigens has minimal activity, suggesting the importance of adjacent sequences in modifying the activity of such peptides. Neither substitution of amino acids of the same charge nor reversal of the positions of the two charged amino acids retains biological activity. Decreasing the spacing between the charged residues also causes a loss of activity. Our results suggest the hypothesis that this adhesive recognition signal consists of a specific arrangement of one acidic and one basic charged group and additional information provided by adjacent amino acids.     

Amino acid specificity of the transfer RNA species coded for by HeLa cell mitochondrial DNA

The amino acid specificity of the tRNA species coded for by HeLa cell mitochondrial DNA has been investigated by carrying out hybridizations between amino acid-tRNA complexes labeled in the amino acid and separated mitochondrial DNA strands.The results indicate that there are in HeLa cell mitochondria at least 17 distinct tRNA species hybridizable with mitochondrial DNA, which are specific for 16 amino acids. For 14 of the 16 amino acids, amino-acyl-tRNA synthetase activities distinct from the cytoplasmic ones have been detected in mitochondria. The remaining four amino acids (asparagine, glutamine, histidine and proline) have consistently failed to charge to any detectable extent mitochondrial tRNA species hybridizable with mitochondrial DNA.No obvious relationship appears to exist between the amino acids incorporated into tRNAs hybridizable to mitochondrial DNA and the previously observed pattern of chloramphenicol-sensitive amino acid incorporation by HeLa cell mitochondria.     

Relationships Among Isoacceptor tRNAs Seems to Support the Coevolution Theory of the Origin of the Genetic Code

A new method for looking at relationships between nucleotide sequences has been used to analyze divergence both within and between the families of isoaccepting tRNA sets. A dendrogram of the relationships between 21 tRNA sets with different amino acid specificities is presented as the result of the analysis. Methionine initiator tRNAs are included as a separate set. The dendrogram has been interpreted with respect to the final stage of the evolutionary pathway with the development of highly specific tRNAs from ambiguous molecular adaptors. The location of the sets on the dendrogram was therefore analyzed in relation to hypotheses on the origin of the genetic code: the coevolution theory, the physicochemical hypothesis, and the hypothesis of ambiguity reduction of the genetic code. Pairs of 16 sets of isoacceptor tRNAs, whose amino acids are in biosynthetic relationships, occupied contiguous positions on the dendrogram, thus supporting the coevolution theory of the genetic code. Received: 4 May 1998 / Accepted: 11 July 1998     

Stress-Induced Dopamine Release in the Neostriatum: Evaluation of the Role of Action Potentials in Nigrostriatal Dopamine Neurons or Local Initiation by Endogenous Excitatory Amino Acids

Abstract: It has been hypothesized that excitatory amino acids can initiate dopamine release in neostriatum. We examined whether the increase in extracellular dopamine in neostriatum produced by acute stress reflects presynaptic initiation of dopamine release by endogenous excitatory amino acids. Thirty minutes of intermittent tail-shock stress significantly elevated extracellular concentrations of dopamine, glutamate, aspartate, and γ-aminobutyric acid in neostriatum of freely moving rats as measured with in vivo microdialysis. Local infusion of the N -methyl- d -aspartate receptor antagonist 2-amino-5-phosphonovaler-ate or the non- N -methyl- d -aspartate receptor antagonist 6-cyano-7-nitroquinoxaline-2,3-dione via the dialysis probe did not attenuate the stress-induced increase in extra cellular dopamine. In fact, the increase was prolonged in rats treated with specific excitatory amino acid receptor antagonists. Infusion of tetrodotoxin into medial forebrain bundle increased extra cellular glutamate and aspartate in neostriatum yet reduced basal dopamine in extra cellular fluid to below the limit of detection of the assay and eliminated the stress-induced increase in extra cellular dopamine. These findings fail to support the hypothesis that the stress-induced increase in extra cellular dopamine in neostriatum is initiated locally by excitatory amino acids. Rather, the effects of stress on extra cellular dopamine seem to be determined by impulse propagation in dopamine neurons.     

The two AGPase subunits evolve at different rates in angiosperms, yet they are equally sensitive to activity-altering amino acid changes when expressed in bacteria

The rate of protein evolution is generally thought to reflect, at least in part, the proportion of amino acids within the protein that are needed for proper function. In the case of ADP-glucose pyrophosphorylase (AGPase), this premise led to the hypothesis that, because the AGPase small subunit is more conserved compared with the large subunit, a higher proportion of the amino acids of the small subunit are required for enzyme activity compared with the large subunit. Evolutionary analysis indicates that the AGPase small subunit has been subject to more intense purifying selection than the large subunit in the angiosperms. However, random mutagenesis and expression of the maize (Zea mays) endosperm AGPase in bacteria show that the two AGPase subunits are equally predisposed to enzyme activity-altering amino acid changes when expressed in one environment with a single complementary subunit. As an alternative hypothesis, we suggest that the small subunit exhibits more evolutionary constraints in planta than does the large subunit because it is less tissue specific and thus must form functional enzyme complexes with different large subunits. Independent approaches provide data consistent with this alternative hypothesis.     

药效假说在配体从头设计中的适用性探讨

在基于靶蛋白结构的多肽分子设计中,药效假说是从头设计方法的基本前提。虽然该假说是否成立已有不少议论,但尚未见到系统分析的报道。通过对８个蛋白质复物界面做了氨基酸模拟图谱,并从模拟图谱的结构偏差与能量分量的关系,对药效假说的适用条件进行了讨论。同时也给出一个ＨＩＶ－１蛋白酶及抑制剂复合物的功能图谱。从所得结果来看,药效假说在以氨基酸为药效基团时,尽管不少情况下仍然有效,但不是谱遍成立的。     

药效假说在配体从头设计中的适用性探讨

在基于靶蛋白结构的多肽分子设计中,药效假说是从头设计方法的基本前提。虽然该假说是否成立已有不少议论,但尚未见到系统分析的报道。通过对８ 个蛋白质复合物界面做了氨基酸模拟图谱,并从模拟图谱的结构偏差与能量分量的关系,对药效假说的适用条件进行了讨论。同时也给出一个ＨＩＶ－ １ 蛋白酶及抑制剂复合物的功能图谱。从所得结果来看,药效假说在以氨基酸为药效基团时,尽管不少情况下仍然有效,但不是普遍成立的。     

Multi-exponential analysis of plasma free amino acid kinetics in the rat

A multi-exponential analysis has been made of the curve of decreasing specific radioactivity with time after intravenous injection of a mixture of (U-^{1 4}-C)-labelled amino acids in rats. The data were shown to accord well with a linear model which was tested using an approximate linear regression method. This confirmed the satisfactory fit of the data to the model. Values for total entry into and of irreversible disposal from plasma were calculated and the extent of external recycling of amino acids obtained by difference.     

Patterns of amino acids near signal-sequence cleavage sites

According to the signal hypothesis, a signal sequence, once having initiated export of a growing protein chain across the rough endoplasmic reticulum, is cleaved from the mature protein at a specific site. It has long been known that some part of the cleavage specificity resides in the last residue of the signal sequence, which invariably is one with a small, uncharged side-chain, but no further specific patterns of amino acids near the point of cleavage have been discovered so far. In this paper, some such patterns, based on a sample of 78 eukaryotic signal sequences, are presented and discussed, and a first attempt at formulating rules for the prediction of cleavage sites is made.     

Purification of gamma-glutamyltransferase by phenyl boronate affinity chromatography. Studies on the acceptor specificity of transpeptidation by rat kidney gamma-glutamyltransferase

gamma-Glutamyltransferase has been purified from rat kidney by a novel procedure using phenyl boronate affinity chromatography. The highly purified enzyme has been studied with respect to acceptor specificity for a number of amino acids, amino acid analogues, dipeptides and tripeptides. The acceptor activity is specific for L-amino acids. The amino acids and the majority of the essential amino acids are poor acceptors while the sulphur-containing amino acids are the best acceptors. The acceptor activity is modulated by the substitution of the amino acid side chain. Substitution of the side chain at the delta, gamma or beta positions results in a proportionally decreasing ability to act as acceptor. The carbonyl moiety of the gamma-carboxy group of the acceptor appears to be essential for acceptor activity, absence of an alpha-carboxy carbonyl group increases the Kappm of the acceptor approximately 100-fold.     

The simultaneous quantitation of ten amino acids in soil extracts by mass fragmentography

A specific and sensitive method for the identification and simultaneous quantitation by mass fragmentography of 10 of the amino acids present in soil has been developed. The technique uses a computer-driven quadrupole mass spectrometer, and a commercial preparation of deuterated amino acids is used as internal standard for purposes of quantitation. The results obtained are comparable with those from an amino acid analyser. In the quadrupole mass spectrometer-computer system used, up to 25 preselected ions may be monitored sequentially. This allows a maximum of 12 different amino acids (one specific ion in each of the undeuterated and deuterated amino acid spectra) to be quantitated. The method is relatively rapid (analysis time of approximately 1 hr) and is capable of the quantitation of nanogram quantities of amino acids.     

Non-protein amino acids in plant defense against insect herbivores: representative cases and opportunities for further functional analysis

Chemical defense against herbivores is of utmost importance for plants. Primary and secondary metabolites, including non-protein amino acids, have been implicated in plant defense against insect pests. High levels of non-protein amino acids have been identified in certain plant families, including legumes and grasses, where they have been associated with resistance to insect herbivory. Non-protein amino acids can have direct toxic effects via several mechanisms, including misincorporation into proteins, obstruction of primary metabolism, and mimicking and interfering with insect neurological processes. Additionally, certain non-protein amino acids allow nitrogen to be stored in a form that is metabolically inaccessible to herbivores and, in some cases, may act as signals for further plant defense responses. Specialized insect herbivores often possess specific mechanisms to avoid or detoxify non-protein amino acids from their host plants. Although hundreds of non-protein amino acids have been found in nature, biosynthetic pathways and defensive functions have been elucidated in only a few cases. Next-generation sequencing technologies and the development of additional plant and insect model species will facilitate further research on the production of non-protein amino acids, a widespread but relatively uninvestigated plant defense mechanism.     

Construction of modified ribosomes for incorporation of D-amino acids into proteins

While numerous biologically active peptides contain D-amino acids, the elaboration of such species is not carried out by ribosomal synthesis. In fact, the bacterial ribosome discriminates strongly against the incorporation of D-amino acids from D-aminoacyl-tRNAs. To permit the incorporation of D-amino acids into proteins using in vitro protein-synthesizing systems, a strategy has been developed to prepare modified ribosomes containing alterations within the peptidyltransferase center and helix 89 of 23S rRNA. S-30 preparations derived from colonies shown to contain ribosomes with altered 23S rRNAs were found to exhibit enhanced tolerance for D-amino acids and to permit the elaboration of proteins containing D-amino acids at predetermined sites. Five specific amino acids in Escherichia coli dihydrofolate reductase and Photinus pyralis luciferase were replaced with D-phenylalanine and D-methionine, and the specific activities of the resulting enzymes were determined.