Conserved amino acid residues in ribosome-inactivating proteins from plants.

The amino acid sequences of eleven RIPs sequenced to date have been compared in the expectation that this would be useful in the location of functionally and/or structurally important sites of these molecules. In addition to several highly conserved hydrophobic amino acids, thirteen absolutely conserved residues have been found in ricin A-chain: Tyr21, Phe24, Arg29, Tyr80, Tyr123, Gly140, Ala165, Glu177, Ala178, Arg180, Glu208, Asn209 and Trp211. The role of these residues as well as of the C-terminal region have been discussed based on the results of chemical and enzymatic modifications, site-directed mutagenesis, and deletion studies.     

Common amino acid sequence domains among the LEA proteins of higher plants

LEA proteins are late embryogenesis abundant in the seeds of many higher plants and are probably universal in occurrence in plant seeds. LEA mRNAs and proteins can be induced to appear at other stages in the plant's life by desiccation stress and/or treatment with the plant hormone abscisic acid (ABA). A role in protecting plant structures during water loss is likely for these proteins, with ABA functioning in the stress transduction process. Presented here are conserved tracts of amino acid sequence among LEA proteins from several species that may represent domains functionally important in desiccation protection. Curiously, an 11 amino acid sequence motif is found tandemly repeated in a group of LEA proteins of vastly different sizes. Analysis of this motif suggests that it exists as an amphiphilic helix which may serve as the basis for higher order structure.     

The importance of glyoxylate in amino acid biosynthesis in plants

1. [¹⁴C₂]Glyoxylate was rapidly metabolized by carrot storage tissues, pea leaves, pea cotyledons, sunflower cotyledons, corn coleoptiles, corn roots and pea roots. In many tissues over 70% of the supplied [¹⁴C₂]glyoxylate was utilized during the 6hr. experimental periods. 2. In all tissues, the chief products of [¹⁴C₂]-glyoxylate metabolism were carbon dioxide, glycine and serine. In several of the tissues, there was also a considerable incorporation of the label into the organic acids, particularly into glycollate. 3. Degradations of the labelled serine produced during [¹⁴C₂]glyoxylate metabolism showed that glyoxylate carbon was incorporated into all three positions of the serine molecule. 4. The results are interpreted as indicating that glyoxylate is utilized by the tissues by pathways involving transamination, transmethylation, reduction and oxidative decarboxylation of the supplied glyoxylate.     

Positive selection in MAOA gene is human exclusive: determination of the putative amino acid change selected in the human lineage

Monoamine oxidase A (MAOA) is the X-linked gene responsible for deamination and subsequent degradation of several neurotransmitters and other amines. Among other activities, the gene has been shown to play a role in locomotion, circadian rhythm, and pain sensitivity and to have a critical influence on behavior and cognition. Previous studies have reported a non-neutral evolution of the gene attributable to positive selection in the human lineage. To determine whether this selection was human-exclusive or shared with other species, we performed a population genetic analysis of the pattern of nucleotide variation in non-human species, including bonobo, chimpanzee, gorilla, and orangutan. Footprints of positive selection were absent in all analyzed species, suggesting that positive selection has been recent and unique to humans. To determine which human-unique genetic changes could have been responsible for this differential evolution, the coding region of the gene was compared between human, chimpanzee, and gorilla. Only one human exclusive non-conservative change is present in the gene: Glu151Lys. This human substitution affects protein dimerization according to a three-dimensional structural model that predicts a non-negligible functional shift. This is the only candidate position at present to have been selected to fixation in humans during an episode of positive selection. Divergence analysis among species has shown that, even under positive selection in the human lineage, the MAOA gene did not experience accelerated evolution in any of the analyzed lineages, and that tools such as K_a/K_s would not have detected the selective history of the gene.     

The broken-stick model for amino acid composition in proteins

Summary The relative abundances among the amino acids, which are functionally similar to one another, were explained by random partition of a unit interval.     

Branched-chain amino acid metabolism in higher plants

Valine, leucine and isoleucine contain short branched carbohydrate residues responsible for their classification as branched-chain amino acids (BCAA). Among the proteinogenic amino acids, BCAA show the highest hydrophobicity and are accordingly the major constituents of transmembrane regions of membrane proteins. BCAA cannot be synthesized by humans and thus belong to the essential amino acids. In contrast, plants are able to synthesize these amino acids de novo and are an important source for these compounds in the human diet. However, BCAA cannot only be synthesized in plants, leucine and probably also valine and isoleucine can also be degraded. Many enzymes operating in turnover are found in mitochondria, while some catabolizing activities are located in peroxisomes. The breakdown of BCAA is physically separated from their biosynthesis in chloroplasts. Additionally, in the order of the Capparales, enzymes of the leucine metabolism seem to be evolutionary related to or may even participate in the methionine chain elongation pathway, the early part of the biosynthesis of aliphatic glucosinolates. In summary, in higher plants a complex network of pathways interferes with the homeostasis of Val, Leu and Ile.     

Hydrophobicity of amino acid subgroups in proteins

Protein folding studies often utilize areas and volumes to assess the hydrophobic contribution to conformational free energy (Richards, F.M. Annu. Rev. Biophys. Bioeng. 6:151-176, 1977). We have calculated the mean area buried upon folding for every chemical group in each residue within a set of X-ray elucidated proteins. These measurements, together with a standard state cavity size for each group, are documented in a table. It is observed that, on average, each type of group buries a constant fraction of its standard state area. The mean area buried by most, though not all, groups can be closely approximated by summing contributions from three characteristic parameters corresponding to three atom types: (1) carbon or sulfur, which turn out to be 86% buried, on average; (2) neutral oxygen or nitrogen, which are 40% buried, on average; and (3) charged oxygen or nitrogen, which are 32% buried, on average.     

Molecular regulation of amino acid biosynthesis in plants

Summary Our understanding of amino acid biosynthesis in plants has grown by leaps and bounds in the last decade. It appears that most of the amino acid biosynthesis takes place in the chloroplast. Recent demonstration of glutamine synthetase and DAHP synthase in the vascular tisuue has added a new dimension in the complexity of the nitrogen cycle in plants. Isolation of various genes and transformation of plants with the modified forms of the genes are providing tools for understanding the regulation of various pathways. Plant transformation approaches are also going to provide the food of the future with an improved amino acid composition.     

Expression and transcriptional regulation of amino acid transporters in plants

Recent studies have shown that there are more than 50 amino acid transporter genes in the Arabidopsis genome. This abundance of amino acid transporters implies that they play a multitude of fundamental roles in plant growth and development. Current research on the expression and regulation (i.e., tissue-specific expression and regulation of expression in response to nutrient and environmental changes) of these genes has provided useful information about the functional significance of plant amino acid transport systems.     

The use of mutants and transgenic plants to study amino acid metabolism

Mutants of higher plants with alterations in amino acid metabolism have now been available for 20 years. Following the realization that at least four distinct classes of herbicides (phosphinothricins, glyphosates, imidazolinones and sulphonylureas) act by the inhibition of amino acid biosynthesis, mutants resistant to the herbicides have also been obtained. More recently, transgenic plants containing altered levels of enzymes of amino acid biosynthesis have been constructed. In this article, we have attempted to review several areas of amino acid biosynthesis including ammonia assimilation, the aspartate pathway, branched chain amino acids, aromatic amino acids and proline.     

Dynamics of amino acid residues in globular proteins

The dynamic differential equation model developed and tested for bovine pancreatic trypsin inhibitor and tuna ferrocytochrome c in Ponnuswamy, P.K. & Bhaskaran, R. (Int. J. Peptide Protein Res. 24, 168-179, 1984) is extended for 17 more protein crystals in this work. Average displacements are computed for 20 amino acid residues observed in 19 proteins. Detailed information on the dynamic behaviour of the individual proteins and individual residues is presented. The effect of atomic packing on the fluctuations of the amino acid residues in alpha-chymotrypsin is illustrated. A number of general points on the dynamic characteristics of globular protein molecules are presented.